[ { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private String extractLibrary(String sharedLibName) throws IOException {\n\n\t\tFile nativesPath = new File(System.getProperty(\"java.io.tmpdir\") + \"/steamworks4j/\" + libraryCrc);\n\t\tFile nativeFile = new File(nativesPath, sharedLibName);\n\n\t\tif (!nativesPath.exists()) {\n\t\t\tif (!nativesPath.mkdirs()) {\n\t\t\t\tthrow new IOException(\"Error creating temp folder: \" + nativesPath.getCanonicalPath());\n\t\t\t}\n\t\t}\n\n\t\tZipFile zip = new ZipFile(libraryPath);\n\t\tZipEntry entry = zip.getEntry(sharedLibName);\n\t\tInputStream input = zip.getInputStream(entry);\n\n\t\tif (input == null) {\n\t\t\tthrow new IOException(\"Error extracting \" + sharedLibName + \" from \" + libraryPath);\n\t\t}\n\n\t\tFileOutputStream output = new FileOutputStream(nativeFile);\n\t\tbyte[] buffer = new byte[4096];\n\t\twhile (true) {\n\t\t\tint length = input.read(buffer);\n\t\t\tif (length == -1) break;\n\t\t\toutput.write(buffer, 0, length);\n\t\t}\n\t\tinput.close();\n\t\toutput.close();\n\n\t\treturn nativeFile.getAbsolutePath();\n\t} \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private String extractLibrary(String sharedLibName) throws IOException {\n\n\t\tFile nativesPath = new File(System.getProperty(\"java.io.tmpdir\") + \"/steamworks4j/\" + libraryCrc);\n\t\tFile nativeFile = new File(nativesPath, sharedLibName);\n\n\t\tif (!nativesPath.exists()) {\n\t\t\tif (!nativesPath.mkdirs()) {\n\t\t\t\tthrow new IOException(\"Error creating temp folder: \" + nativesPath.getCanonicalPath());\n\t\t\t}\n\t\t}\n\n\t\tZipFile zip = new ZipFile(libraryPath);\n\t\tZipEntry entry = zip.getEntry(sharedLibName);\n\t\tInputStream input = zip.getInputStream(entry);\n\n\t\tif (input == null) {\n\t\t\tthrow new IOException(\"Error extracting \" + sharedLibName + \" from \" + libraryPath);\n\t\t}\n\n\t\tFileOutputStream output = new FileOutputStream(nativeFile);\n\t\tbyte[] buffer = new byte[4096];\n\t\twhile (true) {\n\t\t\tint length = input.read(buffer);\n\t\t\tif (length == -1) break;\n\t\t\toutput.write(buffer, 0, length);\n\t\t}\n\n\t\toutput.close();\n\t\tzip.close();\n\n\t\treturn nativeFile.getAbsolutePath();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void processInput(String input) throws SteamException {\n\n\t\tif (input.equals(\"stats request\")) {\n\t\t\tuserStats.requestCurrentStats();\n\t\t} else if (input.equals(\"stats store\")) {\n\t\t\tuserStats.storeStats();\n\t\t} else if (input.equals(\"file list\")) {\n\t\t\tint numFiles = remoteStorage.getFileCount();\n\t\t\tSystem.out.println(\"Num of files: \" + numFiles);\n\n\t\t\tfor (int i = 0; i < numFiles; i++) {\n\t\t\t\tint[] sizes = new int[1];\n\t\t\t\tString name = remoteStorage.getFileNameAndSize(i, sizes);\n\t\t\t\tboolean exists = remoteStorage.fileExists(name);\n\t\t\t\tSystem.out.println(\"# \" + i + \" : name=\" + name + \", size=\" + sizes[0] + \", exists=\" + (exists ? \"yes\" : \"no\"));\n\t\t\t}\n\t\t} else if (input.startsWith(\"file write \")) {\n\t\t\tString path = input.substring(\"file write \".length());\n\t\t\tFile file = new File(path);\n\t\t\ttry {\n\t\t\t\tFileInputStream in = new FileInputStream(file);\n\t\t\t\tSteamUGCFileWriteStreamHandle remoteFile = remoteStorage.fileWriteStreamOpen(path);\n\t\t\t\tif (remoteFile != null) {\n\t\t\t\t\tbyte[] bytes = new byte[1024];\n\t\t\t\t\tint bytesRead;\n\t\t\t\t\twhile((bytesRead = in.read(bytes, 0, bytes.length)) > 0) {\n\t\t\t\t\t\tByteBuffer buffer = ByteBuffer.allocateDirect(bytesRead);\n\t\t\t\t\t\tbuffer.put(bytes, 0, bytesRead);\n\t\t\t\t\t\tremoteStorage.fileWriteStreamWriteChunk(remoteFile, buffer, buffer.limit());\n\t\t\t\t\t}\n\t\t\t\t\tremoteStorage.fileWriteStreamClose(remoteFile);\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t} else if (input.startsWith(\"file delete \")) {\n\t\t\tString path = input.substring(\"file delete \".length());\n\t\t\tif (remoteStorage.fileDelete(path)) {\n\t\t\t\tSystem.out.println(\"deleted file '\" + path + \"'\");\n\t\t\t}\n\t\t} else if (input.startsWith(\"file share \")) {\n\t\t\tremoteStorage.fileShare(input.substring(\"file share \".length()));\n\t\t} else if (input.startsWith(\"file publish \")) {\n\t\t\tString[] paths = input.substring(\"file publish \".length()).split(\" \");\n\t\t\tif (paths.length >= 2) {\n\t\t\t\tSystem.out.println(\"publishing file: \" + paths[0] + \", preview file: \" + paths[1]);\n\t\t\t\tremoteStorage.publishWorkshopFile(paths[0], paths[1], utils.getAppID(),\n\t\t\t\t\t\t\"Test UGC!\", \"Dummy UGC file published by test application.\",\n\t\t\t\t\t\tSteamRemoteStorage.PublishedFileVisibility.Private, null,\n\t\t\t\t\t\tSteamRemoteStorage.WorkshopFileType.Community);\n\t\t\t}\n\t\t} else if (input.startsWith(\"file republish \")) {\n\t\t\tString[] paths = input.substring(\"file republish \".length()).split(\" \");\n\t\t\tif (paths.length >= 3) {\n\t\t\t\tSystem.out.println(\"republishing id: \" + paths[0] + \", file: \" + paths[1] + \", preview file: \" + paths[2]);\n\n\t\t\t\tSteamPublishedFileID fileID = new SteamPublishedFileID(Long.parseLong(paths[0]));\n\n\t\t\t\tSteamPublishedFileUpdateHandle updateHandle = remoteStorage.createPublishedFileUpdateRequest(fileID);\n\t\t\t\tif (updateHandle != null) {\n\t\t\t\t\tremoteStorage.updatePublishedFileFile(updateHandle, paths[1]);\n\t\t\t\t\tremoteStorage.updatePublishedFilePreviewFile(updateHandle, paths[2]);\n\t\t\t\t\tremoteStorage.updatePublishedFileTitle(updateHandle, \"Updated Test UGC!\");\n\t\t\t\t\tremoteStorage.updatePublishedFileDescription(updateHandle, \"Dummy UGC file *updated* by test application.\");\n\t\t\t\t\tremoteStorage.commitPublishedFileUpdate(updateHandle);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (input.equals(\"ugc query\")) {\n\t\t\tSteamUGCQuery query = ugc.createQueryUserUGCRequest(user.getSteamID().getAccountID(), SteamUGC.UserUGCList.Subscribed,\n\t\t\t\t\tSteamUGC.MatchingUGCType.UsableInGame, SteamUGC.UserUGCListSortOrder.TitleAsc,\n\t\t\t\t\tutils.getAppID(), utils.getAppID(), 1);\n\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC query: \" + query.toString());\n\t\t\t\t//ugc.setReturnTotalOnly(query, true);\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc download \")) {\n\t\t\tString name = input.substring(\"ugc download \".length());\n\t\t\tSteamUGCHandle handle = new SteamUGCHandle(Long.parseLong(name, 16));\n\t\t\tremoteStorage.ugcDownload(handle, 0);\n\t\t} else if (input.startsWith(\"ugc subscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc subscribe \".length()), 16);\n\t\t\tugc.subscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc unsubscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc unsubscribe \".length()), 16);\n\t\t\tugc.unsubscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc state \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc state \".length()), 16);\n\t\t\tCollection itemStates = ugc.getItemState(new SteamPublishedFileID(id));\n\t\t\tSystem.out.println(\"UGC item states: \" + itemStates.size());\n\t\t\tfor (SteamUGC.ItemState itemState : itemStates) {\n\t\t\t\tSystem.out.println(\" \" + itemState.name());\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc details \")) {\n\t\t\tSystem.out.println(\"requesting UGC details (deprecated API call)\");\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc details \".length()), 16);\n\t\t\tugc.requestUGCDetails(new SteamPublishedFileID(id), 0);\n\n\t\t\tSteamUGCQuery query = ugc.createQueryUGCDetailsRequest(new SteamPublishedFileID(id));\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC details query: \" + query.toString());\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc info \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc info \".length()), 16);\n\t\t\tSteamUGC.ItemInstallInfo installInfo = new SteamUGC.ItemInstallInfo();\n\t\t\tif (ugc.getItemInstallInfo(new SteamPublishedFileID(id), installInfo)) {\n\t\t\t\tSystem.out.println(\" folder: \" + installInfo.getFolder());\n\t\t\t\tSystem.out.println(\" size on disk: \" + installInfo.getSizeOnDisk());\n\t\t\t}\n\t\t\tSteamUGC.ItemDownloadInfo downloadInfo = new SteamUGC.ItemDownloadInfo();\n\t\t\tif (ugc.getItemDownloadInfo(new SteamPublishedFileID(id), downloadInfo)) {\n\t\t\t\tSystem.out.println(\" bytes downloaded: \" + downloadInfo.getBytesDownloaded());\n\t\t\t\tSystem.out.println(\" bytes total: \" + downloadInfo.getBytesTotal());\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard find \")) {\n\t\t\tString name = input.substring(\"leaderboard find \".length());\n\t\t\tuserStats.findLeaderboard(name);\n\t\t} else if (input.startsWith(\"leaderboard list \")) {\n\t\t\tString[] params = input.substring(\"leaderboard list \".length()).split(\" \");\n\t\t\tif (currentLeaderboard != null && params.length >= 2) {\n\t\t\t\tuserStats.downloadLeaderboardEntries(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardDataRequest.Global,\n\t\t\t\t\t\tInteger.valueOf(params[0]), Integer.valueOf(params[1]));\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard score \")) {\n\t\t\tString score = input.substring(\"leaderboard score \".length());\n\t\t\tif (currentLeaderboard != null) {\n\t\t\t\tSystem.out.println(\"uploading score \" + score + \" to leaderboard \" + currentLeaderboard.toString());\n\t\t\t\tuserStats.uploadLeaderboardScore(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardUploadScoreMethod.KeepBest, Integer.valueOf(score));\n\t\t\t}\n\t\t} else if (input.startsWith(\"apps subscribed \")) {\n\t\t\tString appId = input.substring(\"apps subscribed \".length());\n\t\t\tboolean subscribed = apps.isSubscribedApp(Long.parseLong(appId));\n\t\t\tSystem.out.println(\"user described to app #\" + appId + \": \" + (subscribed ? \"yes\" : \"no\"));\n\t\t}\n\n\t} \n #location 32 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tprotected void processInput(String input) throws SteamException {\n\n\t\tif (input.equals(\"stats request\")) {\n\t\t\tuserStats.requestCurrentStats();\n\t\t} else if (input.equals(\"stats store\")) {\n\t\t\tuserStats.storeStats();\n\t\t} else if (input.startsWith(\"achievement set \")) {\n\t\t\tString achievementName = input.substring(\"achievement set \".length());\n\t\t\tSystem.out.println(\"- setting \" + achievementName + \" to 'achieved'\");\n\t\t\tuserStats.setAchievement(achievementName);\n\t\t} else if (input.startsWith(\"achievement clear \")) {\n\t\t\tString achievementName = input.substring(\"achievement clear \".length());\n\t\t\tSystem.out.println(\"- clearing \" + achievementName);\n\t\t\tuserStats.clearAchievement(achievementName);\n\t\t} else if (input.equals(\"file list\")) {\n\t\t\tint numFiles = remoteStorage.getFileCount();\n\t\t\tSystem.out.println(\"Num of files: \" + numFiles);\n\n\t\t\tfor (int i = 0; i < numFiles; i++) {\n\t\t\t\tint[] sizes = new int[1];\n\t\t\t\tString name = remoteStorage.getFileNameAndSize(i, sizes);\n\t\t\t\tboolean exists = remoteStorage.fileExists(name);\n\t\t\t\tSystem.out.println(\"# \" + i + \" : name=\" + name + \", size=\" + sizes[0] + \", exists=\" + (exists ? \"yes\" : \"no\"));\n\t\t\t}\n\t\t} else if (input.startsWith(\"file write \")) {\n\t\t\tString path = input.substring(\"file write \".length());\n\t\t\tFile file = new File(path);\n\t\t\ttry {\n\t\t\t\tFileInputStream in = new FileInputStream(file);\n\t\t\t\tSteamUGCFileWriteStreamHandle remoteFile = remoteStorage.fileWriteStreamOpen(path);\n\t\t\t\tif (remoteFile != null) {\n\t\t\t\t\tbyte[] bytes = new byte[1024];\n\t\t\t\t\tint bytesRead;\n\t\t\t\t\twhile((bytesRead = in.read(bytes, 0, bytes.length)) > 0) {\n\t\t\t\t\t\tByteBuffer buffer = ByteBuffer.allocateDirect(bytesRead);\n\t\t\t\t\t\tbuffer.put(bytes, 0, bytesRead);\n\t\t\t\t\t\tremoteStorage.fileWriteStreamWriteChunk(remoteFile, buffer, buffer.limit());\n\t\t\t\t\t}\n\t\t\t\t\tremoteStorage.fileWriteStreamClose(remoteFile);\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t} else if (input.startsWith(\"file delete \")) {\n\t\t\tString path = input.substring(\"file delete \".length());\n\t\t\tif (remoteStorage.fileDelete(path)) {\n\t\t\t\tSystem.out.println(\"deleted file '\" + path + \"'\");\n\t\t\t}\n\t\t} else if (input.startsWith(\"file share \")) {\n\t\t\tremoteStorage.fileShare(input.substring(\"file share \".length()));\n\t\t} else if (input.startsWith(\"file publish \")) {\n\t\t\tString[] paths = input.substring(\"file publish \".length()).split(\" \");\n\t\t\tif (paths.length >= 2) {\n\t\t\t\tSystem.out.println(\"publishing file: \" + paths[0] + \", preview file: \" + paths[1]);\n\t\t\t\tremoteStorage.publishWorkshopFile(paths[0], paths[1], utils.getAppID(),\n\t\t\t\t\t\t\"Test UGC!\", \"Dummy UGC file published by test application.\",\n\t\t\t\t\t\tSteamRemoteStorage.PublishedFileVisibility.Private, null,\n\t\t\t\t\t\tSteamRemoteStorage.WorkshopFileType.Community);\n\t\t\t}\n\t\t} else if (input.startsWith(\"file republish \")) {\n\t\t\tString[] paths = input.substring(\"file republish \".length()).split(\" \");\n\t\t\tif (paths.length >= 3) {\n\t\t\t\tSystem.out.println(\"republishing id: \" + paths[0] + \", file: \" + paths[1] + \", preview file: \" + paths[2]);\n\n\t\t\t\tSteamPublishedFileID fileID = new SteamPublishedFileID(Long.parseLong(paths[0]));\n\n\t\t\t\tSteamPublishedFileUpdateHandle updateHandle = remoteStorage.createPublishedFileUpdateRequest(fileID);\n\t\t\t\tif (updateHandle != null) {\n\t\t\t\t\tremoteStorage.updatePublishedFileFile(updateHandle, paths[1]);\n\t\t\t\t\tremoteStorage.updatePublishedFilePreviewFile(updateHandle, paths[2]);\n\t\t\t\t\tremoteStorage.updatePublishedFileTitle(updateHandle, \"Updated Test UGC!\");\n\t\t\t\t\tremoteStorage.updatePublishedFileDescription(updateHandle, \"Dummy UGC file *updated* by test application.\");\n\t\t\t\t\tremoteStorage.commitPublishedFileUpdate(updateHandle);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (input.equals(\"ugc query\")) {\n\t\t\tSteamUGCQuery query = ugc.createQueryUserUGCRequest(user.getSteamID().getAccountID(), SteamUGC.UserUGCList.Subscribed,\n\t\t\t\t\tSteamUGC.MatchingUGCType.UsableInGame, SteamUGC.UserUGCListSortOrder.TitleAsc,\n\t\t\t\t\tutils.getAppID(), utils.getAppID(), 1);\n\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC query: \" + query.toString());\n\t\t\t\t//ugc.setReturnTotalOnly(query, true);\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc download \")) {\n\t\t\tString name = input.substring(\"ugc download \".length());\n\t\t\tSteamUGCHandle handle = new SteamUGCHandle(Long.parseLong(name, 16));\n\t\t\tremoteStorage.ugcDownload(handle, 0);\n\t\t} else if (input.startsWith(\"ugc subscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc subscribe \".length()), 16);\n\t\t\tugc.subscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc unsubscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc unsubscribe \".length()), 16);\n\t\t\tugc.unsubscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc state \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc state \".length()), 16);\n\t\t\tCollection itemStates = ugc.getItemState(new SteamPublishedFileID(id));\n\t\t\tSystem.out.println(\"UGC item states: \" + itemStates.size());\n\t\t\tfor (SteamUGC.ItemState itemState : itemStates) {\n\t\t\t\tSystem.out.println(\" \" + itemState.name());\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc details \")) {\n\t\t\tSystem.out.println(\"requesting UGC details (deprecated API call)\");\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc details \".length()), 16);\n\t\t\tugc.requestUGCDetails(new SteamPublishedFileID(id), 0);\n\n\t\t\tSteamUGCQuery query = ugc.createQueryUGCDetailsRequest(new SteamPublishedFileID(id));\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC details query: \" + query.toString());\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc info \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc info \".length()), 16);\n\t\t\tSteamUGC.ItemInstallInfo installInfo = new SteamUGC.ItemInstallInfo();\n\t\t\tif (ugc.getItemInstallInfo(new SteamPublishedFileID(id), installInfo)) {\n\t\t\t\tSystem.out.println(\" folder: \" + installInfo.getFolder());\n\t\t\t\tSystem.out.println(\" size on disk: \" + installInfo.getSizeOnDisk());\n\t\t\t}\n\t\t\tSteamUGC.ItemDownloadInfo downloadInfo = new SteamUGC.ItemDownloadInfo();\n\t\t\tif (ugc.getItemDownloadInfo(new SteamPublishedFileID(id), downloadInfo)) {\n\t\t\t\tSystem.out.println(\" bytes downloaded: \" + downloadInfo.getBytesDownloaded());\n\t\t\t\tSystem.out.println(\" bytes total: \" + downloadInfo.getBytesTotal());\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard find \")) {\n\t\t\tString name = input.substring(\"leaderboard find \".length());\n\t\t\tuserStats.findLeaderboard(name);\n\t\t} else if (input.startsWith(\"leaderboard list \")) {\n\t\t\tString[] params = input.substring(\"leaderboard list \".length()).split(\" \");\n\t\t\tif (currentLeaderboard != null && params.length >= 2) {\n\t\t\t\tuserStats.downloadLeaderboardEntries(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardDataRequest.Global,\n\t\t\t\t\t\tInteger.valueOf(params[0]), Integer.valueOf(params[1]));\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard score \")) {\n\t\t\tString score = input.substring(\"leaderboard score \".length());\n\t\t\tif (currentLeaderboard != null) {\n\t\t\t\tSystem.out.println(\"uploading score \" + score + \" to leaderboard \" + currentLeaderboard.toString());\n\t\t\t\tuserStats.uploadLeaderboardScore(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardUploadScoreMethod.KeepBest, Integer.valueOf(score));\n\t\t\t}\n\t\t} else if (input.startsWith(\"apps subscribed \")) {\n\t\t\tString appId = input.substring(\"apps subscribed \".length());\n\t\t\tboolean subscribed = apps.isSubscribedApp(Long.parseLong(appId));\n\t\t\tSystem.out.println(\"user described to app #\" + appId + \": \" + (subscribed ? \"yes\" : \"no\"));\n\t\t}\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static void extractLibrary(File librarySystemPath, InputStream input) throws IOException {\n\t\tif (input != null) {\n\t\t\ttry {\n\t\t\t\tFileOutputStream output = new FileOutputStream(librarySystemPath);\n\t\t\t\tbyte[] buffer = new byte[4096];\n\t\t\t\twhile (true) {\n\t\t\t\t\tint length = input.read(buffer);\n\t\t\t\t\tif (length == -1) break;\n\t\t\t\t\toutput.write(buffer, 0, length);\n\t\t\t\t}\n\t\t\t\toutput.close();\n\t\t\t} catch (IOException e) {\n\t\t\t\t/*\n\t\t\t\t\tExtracting the library may fail, for example because 'nativeFile' already exists and is in\n\t\t\t\t\tuse by another process. In this case, we fail silently and just try to load the existing file.\n\t\t\t\t */\n\t\t\t\tif (!librarySystemPath.exists()) {\n\t\t\t\t\tthrow e;\n\t\t\t\t}\n\t\t\t} finally {\n\t\t\t\tinput.close();\n\t\t\t}\n\t\t} else {\n\t\t\tthrow new IOException(\"Failed to read input stream for \" + librarySystemPath.getCanonicalPath());\n\t\t}\n\t} \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static void extractLibrary(File librarySystemPath, InputStream input) throws IOException {\n\t\tif (input != null) {\n\t\t\ttry (FileOutputStream output = new FileOutputStream(librarySystemPath)) {\n\t\t\t\tbyte[] buffer = new byte[4096];\n\t\t\t\twhile (true) {\n\t\t\t\t\tint length = input.read(buffer);\n\t\t\t\t\tif (length == -1) break;\n\t\t\t\t\toutput.write(buffer, 0, length);\n\t\t\t\t}\n\t\t\t\toutput.close();\n\t\t\t} catch (IOException e) {\n\t\t\t\t/*\n\t\t\t\t\tExtracting the library may fail, for example because 'nativeFile' already exists and is in\n\t\t\t\t\tuse by another process. In this case, we fail silently and just try to load the existing file.\n\t\t\t\t */\n\t\t\t\tif (!librarySystemPath.exists()) {\n\t\t\t\t\tthrow e;\n\t\t\t\t}\n\t\t\t} finally {\n\t\t\t\tinput.close();\n\t\t\t}\n\t\t} else {\n\t\t\tthrow new IOException(\"Failed to read input stream for \" + librarySystemPath.getCanonicalPath());\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void processInput(String input) throws SteamException {\n\n\t\tif (input.equals(\"stats request\")) {\n\t\t\tuserStats.requestCurrentStats();\n\t\t} else if (input.equals(\"stats store\")) {\n\t\t\tuserStats.storeStats();\n\t\t} else if (input.equals(\"file list\")) {\n\t\t\tint numFiles = remoteStorage.getFileCount();\n\t\t\tSystem.out.println(\"Num of files: \" + numFiles);\n\n\t\t\tfor (int i = 0; i < numFiles; i++) {\n\t\t\t\tint[] sizes = new int[1];\n\t\t\t\tString name = remoteStorage.getFileNameAndSize(i, sizes);\n\t\t\t\tboolean exists = remoteStorage.fileExists(name);\n\t\t\t\tSystem.out.println(\"# \" + i + \" : name=\" + name + \", size=\" + sizes[0] + \", exists=\" + (exists ? \"yes\" : \"no\"));\n\t\t\t}\n\t\t} else if (input.startsWith(\"file write \")) {\n\t\t\tString path = input.substring(\"file write \".length());\n\t\t\tFile file = new File(path);\n\t\t\ttry {\n\t\t\t\tFileInputStream in = new FileInputStream(file);\n\t\t\t\tSteamUGCFileWriteStreamHandle remoteFile = remoteStorage.fileWriteStreamOpen(path);\n\t\t\t\tif (remoteFile != null) {\n\t\t\t\t\tbyte[] bytes = new byte[1024];\n\t\t\t\t\tint bytesRead;\n\t\t\t\t\twhile((bytesRead = in.read(bytes, 0, bytes.length)) > 0) {\n\t\t\t\t\t\tByteBuffer buffer = ByteBuffer.allocateDirect(bytesRead);\n\t\t\t\t\t\tbuffer.put(bytes, 0, bytesRead);\n\t\t\t\t\t\tremoteStorage.fileWriteStreamWriteChunk(remoteFile, buffer, buffer.limit());\n\t\t\t\t\t}\n\t\t\t\t\tremoteStorage.fileWriteStreamClose(remoteFile);\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t} else if (input.startsWith(\"file delete \")) {\n\t\t\tString path = input.substring(\"file delete \".length());\n\t\t\tif (remoteStorage.fileDelete(path)) {\n\t\t\t\tSystem.out.println(\"deleted file '\" + path + \"'\");\n\t\t\t}\n\t\t} else if (input.startsWith(\"file share \")) {\n\t\t\tremoteStorage.fileShare(input.substring(\"file share \".length()));\n\t\t} else if (input.startsWith(\"file publish \")) {\n\t\t\tString[] paths = input.substring(\"file publish \".length()).split(\" \");\n\t\t\tif (paths.length >= 2) {\n\t\t\t\tSystem.out.println(\"publishing file: \" + paths[0] + \", preview file: \" + paths[1]);\n\t\t\t\tremoteStorage.publishWorkshopFile(paths[0], paths[1], utils.getAppID(),\n\t\t\t\t\t\t\"Test UGC!\", \"Dummy UGC file published by test application.\",\n\t\t\t\t\t\tSteamRemoteStorage.PublishedFileVisibility.Private, null,\n\t\t\t\t\t\tSteamRemoteStorage.WorkshopFileType.Community);\n\t\t\t}\n\t\t} else if (input.startsWith(\"file republish \")) {\n\t\t\tString[] paths = input.substring(\"file republish \".length()).split(\" \");\n\t\t\tif (paths.length >= 3) {\n\t\t\t\tSystem.out.println(\"republishing id: \" + paths[0] + \", file: \" + paths[1] + \", preview file: \" + paths[2]);\n\n\t\t\t\tSteamPublishedFileID fileID = new SteamPublishedFileID(Long.parseLong(paths[0]));\n\n\t\t\t\tSteamPublishedFileUpdateHandle updateHandle = remoteStorage.createPublishedFileUpdateRequest(fileID);\n\t\t\t\tif (updateHandle != null) {\n\t\t\t\t\tremoteStorage.updatePublishedFileFile(updateHandle, paths[1]);\n\t\t\t\t\tremoteStorage.updatePublishedFilePreviewFile(updateHandle, paths[2]);\n\t\t\t\t\tremoteStorage.updatePublishedFileTitle(updateHandle, \"Updated Test UGC!\");\n\t\t\t\t\tremoteStorage.updatePublishedFileDescription(updateHandle, \"Dummy UGC file *updated* by test application.\");\n\t\t\t\t\tremoteStorage.commitPublishedFileUpdate(updateHandle);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (input.equals(\"ugc query\")) {\n\t\t\tSteamUGCQuery query = ugc.createQueryUserUGCRequest(user.getSteamID().getAccountID(), SteamUGC.UserUGCList.Subscribed,\n\t\t\t\t\tSteamUGC.MatchingUGCType.UsableInGame, SteamUGC.UserUGCListSortOrder.TitleAsc,\n\t\t\t\t\tutils.getAppID(), utils.getAppID(), 1);\n\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC query: \" + query.toString());\n\t\t\t\t//ugc.setReturnTotalOnly(query, true);\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc download \")) {\n\t\t\tString name = input.substring(\"ugc download \".length());\n\t\t\tSteamUGCHandle handle = new SteamUGCHandle(Long.parseLong(name, 16));\n\t\t\tremoteStorage.ugcDownload(handle, 0);\n\t\t} else if (input.startsWith(\"ugc subscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc subscribe \".length()), 16);\n\t\t\tugc.subscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc unsubscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc unsubscribe \".length()), 16);\n\t\t\tugc.unsubscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc state \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc state \".length()), 16);\n\t\t\tCollection itemStates = ugc.getItemState(new SteamPublishedFileID(id));\n\t\t\tSystem.out.println(\"UGC item states: \" + itemStates.size());\n\t\t\tfor (SteamUGC.ItemState itemState : itemStates) {\n\t\t\t\tSystem.out.println(\" \" + itemState.name());\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc details \")) {\n\t\t\tSystem.out.println(\"requesting UGC details (deprecated API call)\");\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc details \".length()), 16);\n\t\t\tugc.requestUGCDetails(new SteamPublishedFileID(id), 0);\n\n\t\t\tSteamUGCQuery query = ugc.createQueryUGCDetailsRequest(new SteamPublishedFileID(id));\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC details query: \" + query.toString());\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc info \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc info \".length()), 16);\n\t\t\tSteamUGC.ItemInstallInfo installInfo = new SteamUGC.ItemInstallInfo();\n\t\t\tif (ugc.getItemInstallInfo(new SteamPublishedFileID(id), installInfo)) {\n\t\t\t\tSystem.out.println(\" folder: \" + installInfo.getFolder());\n\t\t\t\tSystem.out.println(\" size on disk: \" + installInfo.getSizeOnDisk());\n\t\t\t}\n\t\t\tSteamUGC.ItemDownloadInfo downloadInfo = new SteamUGC.ItemDownloadInfo();\n\t\t\tif (ugc.getItemDownloadInfo(new SteamPublishedFileID(id), downloadInfo)) {\n\t\t\t\tSystem.out.println(\" bytes downloaded: \" + downloadInfo.getBytesDownloaded());\n\t\t\t\tSystem.out.println(\" bytes total: \" + downloadInfo.getBytesTotal());\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard find \")) {\n\t\t\tString name = input.substring(\"leaderboard find \".length());\n\t\t\tuserStats.findLeaderboard(name);\n\t\t} else if (input.startsWith(\"leaderboard list \")) {\n\t\t\tString[] params = input.substring(\"leaderboard list \".length()).split(\" \");\n\t\t\tif (currentLeaderboard != null && params.length >= 2) {\n\t\t\t\tuserStats.downloadLeaderboardEntries(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardDataRequest.Global,\n\t\t\t\t\t\tInteger.valueOf(params[0]), Integer.valueOf(params[1]));\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard score \")) {\n\t\t\tString score = input.substring(\"leaderboard score \".length());\n\t\t\tif (currentLeaderboard != null) {\n\t\t\t\tSystem.out.println(\"uploading score \" + score + \" to leaderboard \" + currentLeaderboard.toString());\n\t\t\t\tuserStats.uploadLeaderboardScore(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardUploadScoreMethod.KeepBest, Integer.valueOf(score));\n\t\t\t}\n\t\t} else if (input.startsWith(\"apps subscribed \")) {\n\t\t\tString appId = input.substring(\"apps subscribed \".length());\n\t\t\tboolean subscribed = apps.isSubscribedApp(Long.parseLong(appId));\n\t\t\tSystem.out.println(\"user described to app #\" + appId + \": \" + (subscribed ? \"yes\" : \"no\"));\n\t\t}\n\n\t} \n #location 34 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tprotected void processInput(String input) throws SteamException {\n\n\t\tif (input.equals(\"stats request\")) {\n\t\t\tuserStats.requestCurrentStats();\n\t\t} else if (input.equals(\"stats store\")) {\n\t\t\tuserStats.storeStats();\n\t\t} else if (input.startsWith(\"achievement set \")) {\n\t\t\tString achievementName = input.substring(\"achievement set \".length());\n\t\t\tSystem.out.println(\"- setting \" + achievementName + \" to 'achieved'\");\n\t\t\tuserStats.setAchievement(achievementName);\n\t\t} else if (input.startsWith(\"achievement clear \")) {\n\t\t\tString achievementName = input.substring(\"achievement clear \".length());\n\t\t\tSystem.out.println(\"- clearing \" + achievementName);\n\t\t\tuserStats.clearAchievement(achievementName);\n\t\t} else if (input.equals(\"file list\")) {\n\t\t\tint numFiles = remoteStorage.getFileCount();\n\t\t\tSystem.out.println(\"Num of files: \" + numFiles);\n\n\t\t\tfor (int i = 0; i < numFiles; i++) {\n\t\t\t\tint[] sizes = new int[1];\n\t\t\t\tString name = remoteStorage.getFileNameAndSize(i, sizes);\n\t\t\t\tboolean exists = remoteStorage.fileExists(name);\n\t\t\t\tSystem.out.println(\"# \" + i + \" : name=\" + name + \", size=\" + sizes[0] + \", exists=\" + (exists ? \"yes\" : \"no\"));\n\t\t\t}\n\t\t} else if (input.startsWith(\"file write \")) {\n\t\t\tString path = input.substring(\"file write \".length());\n\t\t\tFile file = new File(path);\n\t\t\ttry {\n\t\t\t\tFileInputStream in = new FileInputStream(file);\n\t\t\t\tSteamUGCFileWriteStreamHandle remoteFile = remoteStorage.fileWriteStreamOpen(path);\n\t\t\t\tif (remoteFile != null) {\n\t\t\t\t\tbyte[] bytes = new byte[1024];\n\t\t\t\t\tint bytesRead;\n\t\t\t\t\twhile((bytesRead = in.read(bytes, 0, bytes.length)) > 0) {\n\t\t\t\t\t\tByteBuffer buffer = ByteBuffer.allocateDirect(bytesRead);\n\t\t\t\t\t\tbuffer.put(bytes, 0, bytesRead);\n\t\t\t\t\t\tremoteStorage.fileWriteStreamWriteChunk(remoteFile, buffer, buffer.limit());\n\t\t\t\t\t}\n\t\t\t\t\tremoteStorage.fileWriteStreamClose(remoteFile);\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t} else if (input.startsWith(\"file delete \")) {\n\t\t\tString path = input.substring(\"file delete \".length());\n\t\t\tif (remoteStorage.fileDelete(path)) {\n\t\t\t\tSystem.out.println(\"deleted file '\" + path + \"'\");\n\t\t\t}\n\t\t} else if (input.startsWith(\"file share \")) {\n\t\t\tremoteStorage.fileShare(input.substring(\"file share \".length()));\n\t\t} else if (input.startsWith(\"file publish \")) {\n\t\t\tString[] paths = input.substring(\"file publish \".length()).split(\" \");\n\t\t\tif (paths.length >= 2) {\n\t\t\t\tSystem.out.println(\"publishing file: \" + paths[0] + \", preview file: \" + paths[1]);\n\t\t\t\tremoteStorage.publishWorkshopFile(paths[0], paths[1], utils.getAppID(),\n\t\t\t\t\t\t\"Test UGC!\", \"Dummy UGC file published by test application.\",\n\t\t\t\t\t\tSteamRemoteStorage.PublishedFileVisibility.Private, null,\n\t\t\t\t\t\tSteamRemoteStorage.WorkshopFileType.Community);\n\t\t\t}\n\t\t} else if (input.startsWith(\"file republish \")) {\n\t\t\tString[] paths = input.substring(\"file republish \".length()).split(\" \");\n\t\t\tif (paths.length >= 3) {\n\t\t\t\tSystem.out.println(\"republishing id: \" + paths[0] + \", file: \" + paths[1] + \", preview file: \" + paths[2]);\n\n\t\t\t\tSteamPublishedFileID fileID = new SteamPublishedFileID(Long.parseLong(paths[0]));\n\n\t\t\t\tSteamPublishedFileUpdateHandle updateHandle = remoteStorage.createPublishedFileUpdateRequest(fileID);\n\t\t\t\tif (updateHandle != null) {\n\t\t\t\t\tremoteStorage.updatePublishedFileFile(updateHandle, paths[1]);\n\t\t\t\t\tremoteStorage.updatePublishedFilePreviewFile(updateHandle, paths[2]);\n\t\t\t\t\tremoteStorage.updatePublishedFileTitle(updateHandle, \"Updated Test UGC!\");\n\t\t\t\t\tremoteStorage.updatePublishedFileDescription(updateHandle, \"Dummy UGC file *updated* by test application.\");\n\t\t\t\t\tremoteStorage.commitPublishedFileUpdate(updateHandle);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (input.equals(\"ugc query\")) {\n\t\t\tSteamUGCQuery query = ugc.createQueryUserUGCRequest(user.getSteamID().getAccountID(), SteamUGC.UserUGCList.Subscribed,\n\t\t\t\t\tSteamUGC.MatchingUGCType.UsableInGame, SteamUGC.UserUGCListSortOrder.TitleAsc,\n\t\t\t\t\tutils.getAppID(), utils.getAppID(), 1);\n\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC query: \" + query.toString());\n\t\t\t\t//ugc.setReturnTotalOnly(query, true);\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc download \")) {\n\t\t\tString name = input.substring(\"ugc download \".length());\n\t\t\tSteamUGCHandle handle = new SteamUGCHandle(Long.parseLong(name, 16));\n\t\t\tremoteStorage.ugcDownload(handle, 0);\n\t\t} else if (input.startsWith(\"ugc subscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc subscribe \".length()), 16);\n\t\t\tugc.subscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc unsubscribe \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc unsubscribe \".length()), 16);\n\t\t\tugc.unsubscribeItem(new SteamPublishedFileID(id));\n\t\t} else if (input.startsWith(\"ugc state \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc state \".length()), 16);\n\t\t\tCollection itemStates = ugc.getItemState(new SteamPublishedFileID(id));\n\t\t\tSystem.out.println(\"UGC item states: \" + itemStates.size());\n\t\t\tfor (SteamUGC.ItemState itemState : itemStates) {\n\t\t\t\tSystem.out.println(\" \" + itemState.name());\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc details \")) {\n\t\t\tSystem.out.println(\"requesting UGC details (deprecated API call)\");\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc details \".length()), 16);\n\t\t\tugc.requestUGCDetails(new SteamPublishedFileID(id), 0);\n\n\t\t\tSteamUGCQuery query = ugc.createQueryUGCDetailsRequest(new SteamPublishedFileID(id));\n\t\t\tif (query.isValid()) {\n\t\t\t\tSystem.out.println(\"sending UGC details query: \" + query.toString());\n\t\t\t\tugc.sendQueryUGCRequest(query);\n\t\t\t}\n\t\t} else if (input.startsWith(\"ugc info \")) {\n\t\t\tLong id = Long.parseLong(input.substring(\"ugc info \".length()), 16);\n\t\t\tSteamUGC.ItemInstallInfo installInfo = new SteamUGC.ItemInstallInfo();\n\t\t\tif (ugc.getItemInstallInfo(new SteamPublishedFileID(id), installInfo)) {\n\t\t\t\tSystem.out.println(\" folder: \" + installInfo.getFolder());\n\t\t\t\tSystem.out.println(\" size on disk: \" + installInfo.getSizeOnDisk());\n\t\t\t}\n\t\t\tSteamUGC.ItemDownloadInfo downloadInfo = new SteamUGC.ItemDownloadInfo();\n\t\t\tif (ugc.getItemDownloadInfo(new SteamPublishedFileID(id), downloadInfo)) {\n\t\t\t\tSystem.out.println(\" bytes downloaded: \" + downloadInfo.getBytesDownloaded());\n\t\t\t\tSystem.out.println(\" bytes total: \" + downloadInfo.getBytesTotal());\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard find \")) {\n\t\t\tString name = input.substring(\"leaderboard find \".length());\n\t\t\tuserStats.findLeaderboard(name);\n\t\t} else if (input.startsWith(\"leaderboard list \")) {\n\t\t\tString[] params = input.substring(\"leaderboard list \".length()).split(\" \");\n\t\t\tif (currentLeaderboard != null && params.length >= 2) {\n\t\t\t\tuserStats.downloadLeaderboardEntries(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardDataRequest.Global,\n\t\t\t\t\t\tInteger.valueOf(params[0]), Integer.valueOf(params[1]));\n\t\t\t}\n\t\t} else if (input.startsWith(\"leaderboard score \")) {\n\t\t\tString score = input.substring(\"leaderboard score \".length());\n\t\t\tif (currentLeaderboard != null) {\n\t\t\t\tSystem.out.println(\"uploading score \" + score + \" to leaderboard \" + currentLeaderboard.toString());\n\t\t\t\tuserStats.uploadLeaderboardScore(currentLeaderboard,\n\t\t\t\t\t\tSteamUserStats.LeaderboardUploadScoreMethod.KeepBest, Integer.valueOf(score));\n\t\t\t}\n\t\t} else if (input.startsWith(\"apps subscribed \")) {\n\t\t\tString appId = input.substring(\"apps subscribed \".length());\n\t\t\tboolean subscribed = apps.isSubscribedApp(Long.parseLong(appId));\n\t\t\tSystem.out.println(\"user described to app #\" + appId + \": \" + (subscribed ? \"yes\" : \"no\"));\n\t\t}\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void precompile( Map> typeNames )\n {\n for( ITypeManifold tm: ManifoldHost.instance().getCurrentModule().getTypeManifolds() )\n {\n for( Map.Entry> entry: typeNames.entrySet() )\n {\n String typeManifoldClassName = entry.getKey();\n if( tm.getClass().getName().equals( typeManifoldClassName ) )\n {\n Collection namesToPrecompile = computeNamesToPrecompile( tm.getAllTypeNames(), entry.getValue() );\n for( String fqn : namesToPrecompile )\n {\n JavacElements elementUtils = JavacElements.instance( _tp.getContext() );\n // This call surfaces the type in the compiler. If compiling in \"static\" mode, this means\n // the type will be compiled to disk.\n elementUtils.getTypeElement( fqn );\n }\n }\n }\n }\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void precompile( Map> typeNames )\n {\n for( ITypeManifold tm: ManifoldHost.instance().getCurrentModule().getTypeManifolds() )\n {\n for( Map.Entry> entry: typeNames.entrySet() )\n {\n String typeManifoldClassName = entry.getKey();\n if( tm.getClass().getName().equals( typeManifoldClassName ) )\n {\n Collection namesToPrecompile = computeNamesToPrecompile( tm.getAllTypeNames(), entry.getValue() );\n for( String fqn : namesToPrecompile )\n {\n // This call surfaces the type in the compiler. If compiling in \"static\" mode, this means\n // the type will be compiled to disk.\n IDynamicJdk.instance().getTypeElement( _tp.getContext(), (JCTree.JCCompilationUnit)_tp.getCompilationUnit(), fqn );\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private Pair getClassSymbolForProducedClass( String fqn, BasicJavacTask[] task )\n {\n init();\n\n Pair fileObj = JavaParser.instance().findJavaSource( fqn, null );\n if( fileObj == null )\n {\n return null;\n }\n\n StringWriter errors = new StringWriter();\n if( _wfm == null )\n {\n _wfm = new ManifoldJavaFileManager( _fm, null, false );\n }\n task[0] = (BasicJavacTask)_javacTool.getTask( errors, _wfm, null, Arrays.asList( \"-proc:none\", \"-source\", \"1.8\", \"-Xprefer:source\" ), null, Collections.singleton( fileObj.getFirst() ) );\n\n // note, ok to call getTypeElement() directly here and not via IDynamicJdk because always in context of 1.8 (no module)\n JavacElements elementUtils = JavacElements.instance( task[0].getContext() );\n Symbol.ClassSymbol e = elementUtils.getTypeElement( fqn );\n\n if( e != null && e.getSimpleName().contentEquals( ManClassUtil.getShortClassName( fqn ) ) )\n {\n JavacTrees trees = JavacTrees.instance( task[0].getContext() );\n TreePath path = trees.getPath( e );\n if( path != null )\n {\n return new Pair<>( e, (JCTree.JCCompilationUnit)path.getCompilationUnit() );\n }\n else\n {\n // TreePath is only applicable to a source file;\n // if fqn is not a source file, there is no compilation unit available\n return new Pair<>( e, null );\n }\n }\n\n StringBuffer errorText = errors.getBuffer();\n if( errorText.length() > 0 )\n {\n throw new RuntimeException( \"Compile errors:\\n\" + errorText );\n }\n\n return null;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private Pair getClassSymbolForProducedClass( String fqn, BasicJavacTask[] task )\n {\n StringWriter errors = new StringWriter();\n\n // need javac with ManifoldJavaFileManager because the produced class must come from manifold\n task[0] = getJavacTask_ManFileMgr();\n\n Symbol.ClassSymbol e = IDynamicJdk.instance().getTypeElement( task[0].getContext(), null, fqn );\n\n if( e != null && e.getSimpleName().contentEquals( ManClassUtil.getShortClassName( fqn ) ) )\n {\n JavacTrees trees = JavacTrees.instance( task[0].getContext() );\n TreePath path = trees.getPath( e );\n if( path != null )\n {\n return new Pair<>( e, (JCTree.JCCompilationUnit)path.getCompilationUnit() );\n }\n else\n {\n // TreePath is only applicable to a source file;\n // if fqn is not a source file, there is no compilation unit available\n return new Pair<>( e, null );\n }\n }\n\n StringBuffer errorText = errors.getBuffer();\n if( errorText.length() > 0 )\n {\n throw new RuntimeException( \"Compile errors:\\n\" + errorText );\n }\n\n return null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static SrcClass genClass(String fqn, ProgramNode programNode) {\n\n ClassNode classNode = programNode.getFirstChild(ClassNode.class);\n\n SrcClass clazz = new SrcClass(fqn, SrcClass.Kind.Class);\n\n String superClass = classNode.getSuperClass();\n if (superClass != null) {\n clazz.superClass(superClass);\n }\n clazz.imports(JavascriptClass.class)\n .imports( SourcePosition.class );\n\n clazz.addField(new SrcField(\"ENGINE\", ScriptEngine.class)\n .modifiers(Modifier.STATIC)\n .initializer(new SrcRawExpression((\"JavascriptClass.init(\\\"\" + fqn + \"\\\")\"))));\n\n\n clazz.addField(new SrcField(\"_context\", ScriptObjectMirror.class));\n\n addConstructor(clazz, classNode);\n addMethods(fqn, clazz, classNode);\n addProperties(fqn, clazz, classNode);\n\n return clazz;\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n static SrcClass genClass(String fqn, ProgramNode programNode) {\n\n ClassNode classNode = programNode.getFirstChild(ClassNode.class);\n\n SrcClass clazz = new SrcClass(fqn, SrcClass.Kind.Class);\n clazz.addAnnotation(\n new SrcAnnotationExpression( SourcePosition.class )\n .addArgument( \"url\", String.class, programNode.getUrl().toString() )\n .addArgument( \"feature\", String.class, ManClassUtil.getShortClassName( fqn ) )\n .addArgument( \"offset\", int.class, classNode.getStart().getOffset() )\n .addArgument( \"length\", int.class, classNode.getEnd().getOffset() - classNode.getStart().getOffset() ) );\n\n String superClass = classNode.getSuperClass();\n if (superClass != null) {\n clazz.superClass(superClass);\n }\n clazz.imports(JavascriptClass.class)\n .imports( SourcePosition.class );\n\n clazz.addField(new SrcField(\"ENGINE\", ScriptEngine.class)\n .modifiers(Modifier.STATIC)\n .initializer(new SrcRawExpression((\"JavascriptClass.init(\\\"\" + fqn + \"\\\")\"))));\n\n\n clazz.addField(new SrcField(\"_context\", ScriptObjectMirror.class));\n\n addConstructor(clazz, classNode);\n addMethods(fqn, clazz, classNode);\n addProperties(fqn, clazz, classNode);\n\n return clazz;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void incrementalCompile( Set drivers )\n {\n JavacElements elementUtils = JavacElements.instance( _tp.getContext() );\n for( Object driver: drivers )\n {\n //noinspection unchecked\n Set files = ((Collection)ReflectUtil.method( driver, \"getResourceFiles\" ).invoke() ).stream().map( (File f) -> ManifoldHost.getFileSystem().getIFile( f ) )\n .collect( Collectors.toSet() );\n for( ITypeManifold tm : ManifoldHost.instance().getCurrentModule().getTypeManifolds() )\n {\n for( IFile file: files )\n {\n Set types = Arrays.stream( tm.getTypesForFile( file ) ).collect( Collectors.toSet() );\n if( types.size() > 0 )\n {\n ReflectUtil.method( driver, \"mapTypesToFile\", Set.class, File.class ).invoke( types, file.toJavaFile() );\n for( String fqn : types )\n {\n // This call surfaces the type in the compiler. If compiling in \"static\" mode, this means\n // the type will be compiled to disk.\n elementUtils.getTypeElement( fqn );\n }\n }\n }\n }\n }\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void incrementalCompile( Set drivers )\n {\n for( Object driver: drivers )\n {\n //noinspection unchecked\n Set files = ((Collection)ReflectUtil.method( driver, \"getResourceFiles\" ).invoke() ).stream().map( (File f) -> ManifoldHost.getFileSystem().getIFile( f ) )\n .collect( Collectors.toSet() );\n for( ITypeManifold tm : ManifoldHost.instance().getCurrentModule().getTypeManifolds() )\n {\n for( IFile file: files )\n {\n Set types = Arrays.stream( tm.getTypesForFile( file ) ).collect( Collectors.toSet() );\n if( types.size() > 0 )\n {\n ReflectUtil.method( driver, \"mapTypesToFile\", Set.class, File.class ).invoke( types, file.toJavaFile() );\n for( String fqn : types )\n {\n // This call surfaces the type in the compiler. If compiling in \"static\" mode, this means\n // the type will be compiled to disk.\n IDynamicJdk.instance().getTypeElement( _tp.getContext(), (JCTree.JCCompilationUnit)_tp.getCompilationUnit(), fqn );\n }\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @SuppressWarnings(\"WeakerAccess\")\n public String findTopLevelFqn( String fqn )\n {\n while( true )\n {\n LocklessLazyVar lazyModel = _fqnToModel.get().get( fqn );\n if( lazyModel != null )\n {\n return fqn;\n }\n int iDot = fqn.lastIndexOf( '.' );\n if( iDot <= 0 )\n {\n return null;\n }\n fqn = fqn.substring( 0, iDot );\n }\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @SuppressWarnings(\"WeakerAccess\")\n public String findTopLevelFqn( String fqn )\n {\n FqnCache> fqnCache = _fqnToModel.get();\n if( fqnCache.isEmpty() )\n {\n return null;\n }\n\n while( true )\n {\n LocklessLazyVar lazyModel = fqnCache.get( fqn );\n if( lazyModel != null )\n {\n return fqn;\n }\n int iDot = fqn.lastIndexOf( '.' );\n if( iDot <= 0 )\n {\n return null;\n }\n fqn = fqn.substring( 0, iDot );\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public Collection getAllTypeNames()\n {\n return _fqnToModel.get().getFqns();\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public Collection getAllTypeNames()\n {\n FqnCache> fqnCache = _fqnToModel.get();\n if( fqnCache.isEmpty() )\n {\n return Collections.emptySet();\n }\n\n return fqnCache.getFqns();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static boolean hasCallHandlerMethod( Class rootClass )\n {\n String fqn = rootClass.getCanonicalName();\n BasicJavacTask javacTask = RuntimeManifoldHost.get().getJavaParser().getJavacTask();\n Pair classSymbol = ClassSymbols.instance( RuntimeManifoldHost.get().getSingleModule() ).getClassSymbol( javacTask, fqn );\n Pair callHandlerSymbol = ClassSymbols.instance( RuntimeManifoldHost.get().getSingleModule() ).getClassSymbol( javacTask, ICallHandler.class.getCanonicalName() );\n if( Types.instance( javacTask.getContext() ).isAssignable( classSymbol.getFirst().asType(), callHandlerSymbol.getFirst().asType() ) )\n {\n // Nominally implements ICallHandler\n return true;\n }\n\n return hasCallMethod( javacTask, classSymbol.getFirst() );\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private static boolean hasCallHandlerMethod( Class rootClass )\n {\n if( ICallHandler.class.isAssignableFrom( rootClass ) )\n {\n // Nominally implements ICallHandler\n return true;\n }\n if( ReflectUtil.method( rootClass, \"call\", Class.class, String.class, String.class, Class.class, Class[].class, Object[].class ) != null )\n {\n // Structurally implements ICallHandler\n return true;\n }\n\n // maybe has an extension satisfying ICallHandler\n return hasCallHandlerFromExtension( rootClass );\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public boolean isTopLevelType( String fqn )\n {\n return _fqnToModel.get().get( fqn ) != null;\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public boolean isTopLevelType( String fqn )\n {\n FqnCache> fqnCache = _fqnToModel.get();\n if( fqnCache.isEmpty() )\n {\n return false;\n }\n\n return fqnCache.get( fqn ) != null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Tree getParent( Tree node )\n {\n TreePath2 path = TreePath2.getPath( getCompilationUnit(), node );\n if( path == null )\n {\n // null is indiciative of Generation phase where trees are no longer attached to symobls so the comp unit is detached\n // use the root tree instead, which is mostly ok, mostly\n path = TreePath2.getPath( _tree, node );\n }\n TreePath2 parentPath = path.getParentPath();\n return parentPath == null ? null : parentPath.getLeaf();\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Tree getParent( Tree node )\n {\n return _parents.getParent( node );\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String getResponseBody() {\n\t\tif (response == null) {\n\t\t\tthrow new IllegalStateException(\"The request must first be executed\");\n\t\t}\n\t\tif (!response.isSuccessful()) {\n\t\t\tthrow new IllegalStateException(\"The request threw an exception\");\n\t\t}\n\t\treturn response.getBody();\n\t} \n #location 8 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public String getResponseBody() {\n\t\trequireSucceededRequestState();\n\t\treturn responseBody;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Rune getDataRune(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataRune(getRegion(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Rune getDataRune(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataRune(getRegion(), getKey(), id, null, null, (RuneData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public dto.Static.Champion getDataChampion(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataChampion(region.getName(), getKey(), id, null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public dto.Static.Champion getDataChampion(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataChampion(region.getName(), getKey(), id, null, null, false, (ChampData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ItemList getDataItemList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataItemList(region.getName(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ItemList getDataItemList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataItemList(region.getName(), getKey(), null, null, (ItemListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ChampionList getDataChampionList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataChampionList(region.getName(), getKey(), null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ChampionList getDataChampionList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataChampionList(region.getName(), getKey(), null, null, false, (ChampData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Rune getDataRune(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataRune(region.getName(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Rune getDataRune(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataRune(region.getName(), getKey(), id, null, null, (RuneData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic boolean cancel() {\n\t\tboolean cancelled = super.cancel();\n\t\tif (!cancelled) {\n\t\t\treturn false;\n\t\t}\n\t\tsynchronized (signal) {\n\t\t\tsignal.notifyAll();\n\t\t}\n\t\t// Try to force-quit the connection\n\t\tif (connection != null) {\n\t\t\tsetTimeout(1);\n\t\t\tconnection.disconnect();\n\t\t}\n\t\treturn true;\n\t} \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tpublic boolean cancel() {\n\t\tsynchronized (signal) {\n\t\t\tboolean cancelled = super.cancel();\n\t\t\tif (!cancelled) {\n\t\t\t\treturn false;\n\t\t\t}\n\t\t\tsignal.notifyAll();\n\t\t\t// Try to force-quit the connection\n\t\t\tif (connection != null) {\n\t\t\t\tsetTimeout(1);\n\t\t\t\tconnection.disconnect();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void await(long timeout, TimeUnit unit, boolean cancelOnTimeout) throws InterruptedException, TimeoutException {\n\t\tfinal long end = System.currentTimeMillis() + unit.toMillis(timeout);\n\t\twhile (!isDone() && System.currentTimeMillis() < end) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.wait(end - System.currentTimeMillis());\n\t\t\t}\n\t\t}\n\t\tif (!isDone()) {\n\t\t\tif (cancelOnTimeout) {\n\t\t\t\tcancel();\n\t\t\t}\n\t\t\tthrow new TimeoutException();\n\t\t}\n\t} \n #location 8 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void await(long timeout, TimeUnit unit, boolean cancelOnTimeout) throws InterruptedException, TimeoutException {\n\t\tfinal long end = System.currentTimeMillis() + unit.toMillis(timeout);\n\t\tif (!isDone() && System.currentTimeMillis() < end) {\n\t\t\tsynchronized (signal) {\n\t\t\t\twhile (!isDone() && System.currentTimeMillis() < end) {\n\t\t\t\t\tsignal.wait(end - System.currentTimeMillis());\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (!isDone()) {\n\t\t\tif (cancelOnTimeout) {\n\t\t\t\tcancel();\n\t\t\t}\n\t\t\tthrow new TimeoutException();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public dto.Static.Champion getDataChampion(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataChampion(getRegion(), getKey(), id, null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public dto.Static.Champion getDataChampion(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataChampion(getRegion(), getKey(), id, null, null, false, (ChampData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public RuneList getDataRuneList() throws RiotApiException {\n\n return StaticDataMethod.getDataRuneList(getRegion(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public RuneList getDataRuneList() throws RiotApiException {\n\n return StaticDataMethod.getDataRuneList(getRegion(), getKey(), null, null, (RuneListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public SummonerSpellList getDataSummonerSpellList() throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpellList(getRegion(), getKey(), null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public SummonerSpellList getDataSummonerSpellList() throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpellList(getRegion(), getKey(), null, null, false, (SpellData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic boolean cancel() {\n\t\tboolean cancelled = super.cancel();\n\t\tif (!cancelled) {\n\t\t\treturn false;\n\t\t}\n\t\tsynchronized (signal) {\n\t\t\tsignal.notifyAll();\n\t\t}\n\t\t// Try to force-quit the connection\n\t\tif (connection != null) {\n\t\t\tsetTimeout(1);\n\t\t\tconnection.disconnect();\n\t\t}\n\t\treturn true;\n\t} \n #location 13 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tpublic boolean cancel() {\n\t\tsynchronized (signal) {\n\t\t\tboolean cancelled = super.cancel();\n\t\t\tif (!cancelled) {\n\t\t\t\treturn false;\n\t\t\t}\n\t\t\tsignal.notifyAll();\n\t\t\t// Try to force-quit the connection\n\t\t\tif (connection != null) {\n\t\t\t\tsetTimeout(1);\n\t\t\t\tconnection.disconnect();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MasteryList getDataMasteryList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataMasteryList(region.getName(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public MasteryList getDataMasteryList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataMasteryList(region.getName(), getKey(), null, null, (MasteryListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void init(ApiConfig config, ApiMethod method) {\n\t\tthis.config = config;\n\t\tthis.method = method;\n\t\tsetTimeout();\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void init(ApiConfig config, ApiMethod method) {\n\t\tthis.config = config;\n\t\tthis.method = method;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public T getDto(Class desiredDto) throws RiotApiException, RateLimitException {\n\t\tif (!response.isSuccessful()) {\n\t\t\t// I think we can never get here. Let's make sure though\n\t\t\tthrow new RiotApiException(RiotApiException.IOEXCEPTION);\n\t\t}\n\t\tif (response.getCode() == RequestResponse.CODE_SUCCESS_NOCONTENT) {\n\t\t\t// The Riot Api is fine with the request, and explicitly sends no content\n\t\t\treturn null;\n\t\t}\n\t\tT dto = null;\n\t\ttry {\n\t\t\tdto = new Gson().fromJson(response.getBody(), desiredDto);\n\t\t} catch (JsonSyntaxException e) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\tif (dto == null) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\treturn dto;\n\t} \n #location 12 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public T getDto(Class desiredDto) throws RiotApiException, RateLimitException {\n\t\trequireSucceededRequestState();\n\t\tif (responseCode == CODE_SUCCESS_NOCONTENT) {\n\t\t\t// The Riot Api is fine with the request, and explicitly sends no content\n\t\t\treturn null;\n\t\t}\n\t\tT dto = null;\n\t\ttry {\n\t\t\tdto = new Gson().fromJson(responseBody, desiredDto);\n\t\t} catch (JsonSyntaxException e) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\tif (dto == null) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\treturn dto;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Mastery getDataMastery(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataMastery(getRegion(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Mastery getDataMastery(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataMastery(getRegion(), getKey(), id, null, null, (MasteryData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Item getDataItem(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataItem(region.getName(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Item getDataItem(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataItem(region.getName(), getKey(), id, null, null, (ItemData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected boolean setState(RequestState state) {\n\t\tif (isDone()) {\n\t\t\treturn false;\n\t\t}\n\t\tfor (RequestListener listener : listeners) {\n\t\t\tif (state == RequestState.Succeeded) {\n\t\t\t\tlistener.onRequestSucceeded(this);\n\t\t\t} else if (state == RequestState.Failed) {\n\t\t\t\tlistener.onRequestFailed(getException());\n\t\t\t} else if (state == RequestState.TimeOut) {\n\t\t\t\tlistener.onRequestTimeout(this);\n\t\t\t}\n\t\t}\n\t\tsuper.setState(state);\n\t\tif (state == RequestState.Cancelled || state == RequestState.Succeeded || state == RequestState.Failed || state == RequestState.TimeOut) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.notifyAll();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t} \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected boolean setState(RequestState state) {\n\t\tif (isDone()) {\n\t\t\treturn false;\n\t\t}\n\t\tnotifyListeners(state);\n\t\tsuper.setState(state);\n\t\tif (isDone()) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.notifyAll();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public int getResponseCode() {\n\t\tif (response == null) {\n\t\t\tthrow new IllegalStateException(\"The request must first be executed\");\n\t\t}\n\t\treturn response.getCode();\n\t} \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public int getResponseCode() {\n\t\trequireSucceededRequestState();\n\t\treturn responseCode;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MasteryList getDataMasteryList() throws RiotApiException {\n\n return StaticDataMethod.getDataMasteryList(getRegion(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public MasteryList getDataMasteryList() throws RiotApiException {\n\n return StaticDataMethod.getDataMasteryList(getRegion(), getKey(), null, null, (MasteryListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testJoinString() throws RiotApiException {\n\t\t// Valid Usage\n\t\tassertEquals(\"abc\", Convert.joinString(\",\", \"abc\"));\n\t\tassertEquals(\"abc,def,ghi\", Convert.joinString(\",\", \"abc\", \"def\", \"ghi\"));\n\t\t// NullPointerException\n\t\tthrown.expect(NullPointerException.class);\n\t\tConvert.joinString(null, (CharSequence[]) null);\n\t} \n #location 8 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n\tpublic void testJoinString() throws RiotApiException {\n\t\t// Valid Usage for Strings\n\t\tassertEquals(\"abc\", Convert.joinString(\",\", \"abc\"));\n\t\tassertEquals(\"abc,def,ghi\", Convert.joinString(\",\", \"abc\", \"def\", \"ghi\"));\n\t\t// Valid Usage for other objects\n\t\tassertEquals(\"RANKED_SOLO_5x5,TEAM_BUILDER_DRAFT_RANKED_5x5\",\n\t\t\t\tConvert.joinString(\",\", QueueType.RANKED_SOLO_5x5, QueueType.TEAM_BUILDER_DRAFT_RANKED_5x5));\n\t\tassertEquals(\"info,lore\", Convert.joinString(\",\", ChampData.INFO, ChampData.LORE));\n\t\t// NullPointerException\n\t\tthrown.expect(NullPointerException.class);\n\t\tConvert.joinString(null, (CharSequence[]) null);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public SummonerSpellList getDataSummonerSpellList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpellList(region.getName(), getKey(), null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public SummonerSpellList getDataSummonerSpellList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpellList(region.getName(), getKey(), null, null, false, (SpellData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public RuneList getDataRuneList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataRuneList(region.getName(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public RuneList getDataRuneList(Region region) throws RiotApiException {\n\n return StaticDataMethod.getDataRuneList(region.getName(), getKey(), null, null, (RuneListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void await() throws InterruptedException {\n\t\twhile (!isDone()) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.wait();\n\t\t\t}\n\t\t}\n\t} \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void await() throws InterruptedException {\n\t\tif (!isDone()) {\n\t\t\tsynchronized (signal) {\n\t\t\t\twhile (!isDone()) {\n\t\t\t\t\tsignal.wait();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected boolean setState(RequestState state) {\n\t\tboolean success = super.setState(state);\n\t\tif (!success) {\n\t\t\treturn false;\n\t\t}\n\t\tif (listener != null) {\n\t\t\tif (state == RequestState.Succeeded) {\n\t\t\t\tlistener.onRequestSucceeded(this);\n\t\t\t} else if (state == RequestState.Failed) {\n\t\t\t\tlistener.onRequestFailed(getException());\n\t\t\t} else if (state == RequestState.TimeOut) {\n\t\t\t\tlistener.onRequestTimeout(this);\n\t\t\t}\n\t\t}\n\t\tif (state == RequestState.Succeeded || state == RequestState.Failed || state == RequestState.TimeOut) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.notifyAll();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t} \n #location 13 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected boolean setState(RequestState state) {\n\t\tboolean success = super.setState(state);\n\t\tif (!success) {\n\t\t\treturn false;\n\t\t}\n\t\tif (!listeners.isEmpty()) {\n\t\t\tif (state == RequestState.Succeeded) {\n\t\t\t\tfor (RequestListener listener : listeners) {\n\t\t\t\t\tlistener.onRequestSucceeded(this);\n\t\t\t\t}\n\t\t\t} else if (state == RequestState.Failed) {\n\t\t\t\tfor (RequestListener listener : listeners) {\n\t\t\t\t\tlistener.onRequestFailed(getException());\n\t\t\t\t}\n\t\t\t} else if (state == RequestState.TimeOut) {\n\t\t\t\tfor (RequestListener listener : listeners) {\n\t\t\t\t\tlistener.onRequestTimeout(this);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (state == RequestState.Succeeded || state == RequestState.Failed || state == RequestState.TimeOut) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.notifyAll();\n\t\t\t}\n\t\t}\n\t\treturn true;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ItemList getDataItemList() throws RiotApiException {\n\n return StaticDataMethod.getDataItemList(getRegion(), getKey(), null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ItemList getDataItemList() throws RiotApiException {\n\n return StaticDataMethod.getDataItemList(getRegion(), getKey(), null, null, (ItemListData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public SummonerSpell getDataSummonerSpell(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpell(getRegion(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public SummonerSpell getDataSummonerSpell(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpell(getRegion(), getKey(), id, null, null, (SpellData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Mastery getDataMastery(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataMastery(region.getName(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Mastery getDataMastery(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataMastery(region.getName(), getKey(), id, null, null, (MasteryData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Item getDataItem(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataItem(getRegion(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Item getDataItem(int id) throws RiotApiException {\n\n return StaticDataMethod.getDataItem(getRegion(), getKey(), id, null, null, (ItemData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void await() throws InterruptedException {\n\t\tif (!isDone()) {\n\t\t\tsynchronized (signal) {\n\t\t\t\twhile (!isDone()) {\n\t\t\t\t\tsignal.wait();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void await() throws InterruptedException {\n\t\twhile (!isDone()) {\n\t\t\tsynchronized (signal) {\n\t\t\t\tsignal.wait();\n\t\t\t}\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public SummonerSpell getDataSummonerSpell(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpell(region.getName(), getKey(), id, null, null, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public SummonerSpell getDataSummonerSpell(Region region, int id) throws RiotApiException {\n\n return StaticDataMethod.getDataSummonerSpell(region.getName(), getKey(), id, null, null, (SpellData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public T getDto(Type desiredDto) throws RiotApiException, RateLimitException {\n\t\tif (!response.isSuccessful()) {\n\t\t\t// I think we can never get here. Let's make sure though\n\t\t\tthrow new RiotApiException(RiotApiException.IOEXCEPTION);\n\t\t}\n\t\tif (response.getCode() == RequestResponse.CODE_SUCCESS_NOCONTENT) {\n\t\t\t// The Riot Api is fine with the request, and explicitly sends no content\n\t\t\treturn null;\n\t\t}\n\t\tT dto = null;\n\t\ttry {\n\t\t\tdto = new Gson().fromJson(response.getBody(), desiredDto);\n\t\t} catch (JsonSyntaxException e) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\tif (dto == null) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\treturn dto;\n\t} \n #location 12 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public T getDto(Type desiredDto) throws RiotApiException, RateLimitException {\n\t\trequireSucceededRequestState();\n\t\tif (responseCode == CODE_SUCCESS_NOCONTENT) {\n\t\t\t// The Riot Api is fine with the request, and explicitly sends no content\n\t\t\treturn null;\n\t\t}\n\t\tT dto = null;\n\t\ttry {\n\t\t\tdto = new Gson().fromJson(responseBody, desiredDto);\n\t\t} catch (JsonSyntaxException e) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\tif (dto == null) {\n\t\t\tthrow new RiotApiException(RiotApiException.PARSE_FAILURE);\n\t\t}\n\t\treturn dto;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ChampionList getDataChampionList() throws RiotApiException {\n\n return StaticDataMethod.getDataChampionList(getRegion(), getKey(), null, null, false, null);\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ChampionList getDataChampionList() throws RiotApiException {\n\n return StaticDataMethod.getDataChampionList(getRegion(), getKey(), null, null, false, (ChampData) null);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public RiotApiException getException() {\n\t\tif (!isFailed()) {\n\t\t\treturn null;\n\t\t}\n\t\treturn exception;\n\t} \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public RiotApiException getException() {\n\t\treturn exception;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected static CharSequence encodeUriQuery(CharSequence in) {\n //Note that I can't simply use URI.java to encode because it will escape pre-existing escaped things.\n StringBuilder outBuf = null;\n Formatter formatter = null;\n for(int i = 0; i < in.length(); i++) {\n char c = in.charAt(i);\n boolean escape = true;\n if (c < 128) {\n if (asciiQueryChars.get((int)c)) {\n escape = false;\n }\n } else if (!Character.isISOControl(c) && !Character.isSpaceChar(c)) {//not-ascii\n escape = false;\n }\n if (!escape) {\n if (outBuf != null)\n outBuf.append(c);\n } else {\n //escape\n if (outBuf == null) {\n outBuf = new StringBuilder(in.length() + 5*3);\n outBuf.append(in,0,i);\n formatter = new Formatter(outBuf);\n }\n //leading %, 0 padded, width 2, capital hex\n formatter.format(\"%%%02X\",(int)c);//TODO\n }\n }\n return outBuf != null ? outBuf : in;\n } \n #location 29 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected static CharSequence encodeUriQuery(CharSequence in) {\n //Note that I can't simply use URI.java to encode because it will escape pre-existing escaped things.\n StringBuilder outBuf = null;\n Formatter formatter = null;\n for(int i = 0; i < in.length(); i++) {\n char c = in.charAt(i);\n boolean escape = true;\n if (c < 128) {\n if (asciiQueryChars.get((int)c)) {\n escape = false;\n }\n } else if (!Character.isISOControl(c) && !Character.isSpaceChar(c)) {//not-ascii\n escape = false;\n }\n if (!escape) {\n if (outBuf != null)\n outBuf.append(c);\n } else {\n //escape\n if (outBuf == null) {\n outBuf = new StringBuilder(in.length() + 5*3);\n outBuf.append(in,0,i);\n try {\n formatter = new Formatter(outBuf);\n } finally {\n if (formatter != null) {\n formatter.flush();\n formatter.close();\n } \n }\n }\n //leading %, 0 padded, width 2, capital hex\n formatter.format(\"%%%02X\",(int)c);//TODO\n }\n }\n return outBuf != null ? outBuf : in;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void initCommitAndTermFromLog() {\n DBIterator iterator = db.iterator();\n try {\n iterator.seekToLast();\n byte[] keyBytes = iterator.peekNext().getKey();\n commitIndex = new Integer(asString(keyBytes));\n\n //get the term from the serialized logentry\n byte[] entryBytes = iterator.peekNext().getValue();\n LogEntry entry = asLogEntry(entryBytes);\n this.currentTerm = entry.term;\n\n } finally {\n try {\n iterator.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void initCommitAndTermFromLog() throws Exception {\n DBIterator iterator = db.iterator();\n try {\n iterator.seekToLast();\n byte[] keyBytes = iterator.peekNext().getKey();\n commitIndex = new Integer(asString(keyBytes));\n\n //get the term from the serialized logentry\n byte[] entryBytes = iterator.peekNext().getValue();\n LogEntry entry =(LogEntry)Util.streamableFromByteBuffer(LogEntry.class, entryBytes);\n this.currentTerm = entry.term;\n\n } finally {\n try {\n iterator.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void changeRole(Role new_role) {\n RaftImpl new_impl=null;\n switch(new_role) {\n case Follower:\n new_impl=new Follower(this);\n break;\n case Candidate:\n new_impl=new Follower(this);\n break;\n case Leader:\n new_impl=new Leader(this);\n break;\n }\n impl_lock.lock();\n try {\n if(!impl.getClass().equals(new_impl.getClass())) {\n impl.destroy();\n new_impl.init();\n impl=new_impl;\n }\n }\n finally {\n impl_lock.unlock();\n }\n } \n #location 16 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected void changeRole(Role new_role) {\n final RaftImpl new_impl=new_role == Role.Follower? new Follower(this) : new_role == Role.Candidate? new Candidate(this) : new Leader(this);\n withLockDo(impl_lock, new Callable() {\n public Void call() throws Exception {\n if(!impl.getClass().equals(new_impl.getClass())) {\n impl.destroy();\n new_impl.init();\n impl=new_impl;\n }\n return null;\n }\n });\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void handleEvent(Message msg, RaftHeader hdr) {\n log.trace(\"%s: received %s from %s\", local_addr, hdr, msg.src());\n impl_lock.lock();\n try {\n if(hdr instanceof AppendEntriesRequest) {\n AppendEntriesRequest req=(AppendEntriesRequest)hdr;\n impl.handleAppendEntriesRequest(msg.src(),req.term());\n }\n else if(hdr instanceof AppendEntriesResponse) {\n AppendEntriesResponse rsp=(AppendEntriesResponse)hdr;\n impl.handleAppendEntriesResponse(msg.src(),rsp.term());\n }\n else if(hdr instanceof VoteRequest) {\n VoteRequest header=(VoteRequest)hdr;\n impl.handleVoteRequest(msg.src(),header.term());\n }\n else if(hdr instanceof VoteResponse) {\n VoteResponse rsp=(VoteResponse)hdr;\n impl.handleVoteResponse(msg.src(),rsp.term());\n }\n else if(hdr instanceof InstallSnapshotRequest) {\n InstallSnapshotRequest req=(InstallSnapshotRequest)hdr;\n impl.handleInstallSnapshotRequest(msg.src(),req.term());\n }\n else if(hdr instanceof InstallSnapshotResponse) {\n InstallSnapshotResponse rsp=(InstallSnapshotResponse)hdr;\n impl.handleInstallSnapshotResponse(msg.src(),rsp.term());\n }\n else\n log.warn(\"%s: invalid header %s\",local_addr,hdr.getClass().getCanonicalName());\n }\n finally {\n impl_lock.unlock();\n }\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void handleEvent(Message msg, RaftHeader hdr) {\n // log.trace(\"%s: received %s from %s\", local_addr, hdr, msg.src());\n impl_lock.lock();\n try {\n if(hdr instanceof AppendEntriesRequest) {\n AppendEntriesRequest req=(AppendEntriesRequest)hdr;\n impl.handleAppendEntriesRequest(msg.src(),req.term());\n }\n else if(hdr instanceof AppendEntriesResponse) {\n AppendEntriesResponse rsp=(AppendEntriesResponse)hdr;\n impl.handleAppendEntriesResponse(msg.src(),rsp.term());\n }\n else if(hdr instanceof VoteRequest) {\n VoteRequest header=(VoteRequest)hdr;\n impl.handleVoteRequest(msg.src(),header.term());\n }\n else if(hdr instanceof VoteResponse) {\n VoteResponse rsp=(VoteResponse)hdr;\n impl.handleVoteResponse(msg.src(),rsp.term());\n }\n else if(hdr instanceof InstallSnapshotRequest) {\n InstallSnapshotRequest req=(InstallSnapshotRequest)hdr;\n impl.handleInstallSnapshotRequest(msg.src(),req.term());\n }\n else if(hdr instanceof InstallSnapshotResponse) {\n InstallSnapshotResponse rsp=(InstallSnapshotResponse)hdr;\n impl.handleInstallSnapshotResponse(msg.src(),rsp.term());\n }\n else\n log.warn(\"%s: invalid header %s\",local_addr,hdr.getClass().getCanonicalName());\n }\n finally {\n impl_lock.unlock();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static String readResource(final String name) {\n final StringBuilder ret = new StringBuilder();\n InputStream is = null;\n try {\n is = UrlRegularExpressions.class.getClassLoader().getResourceAsStream(name);\n final InputStreamReader reader = new InputStreamReader(is, ASCII);\n int read = 0;\n final char[] buf = new char[1024];\n do {\n read = reader.read(buf, 0, buf.length);\n if (read > 0) {\n ret.append(buf, 0, read);\n }\n } while (read >= 0);\n } catch (final IOException ex) {\n throw new RuntimeException(ex);\n } finally {\n closeQuietly(is);\n }\n return ret.toString();\n } \n #location 18 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static String readResource(final String name) {\n final StringBuilder ret = new StringBuilder();\n InputStream is = null;\n InputStreamReader reader = null;\n try {\n is = UrlRegularExpressions.class.getClassLoader().getResourceAsStream(name);\n reader = new InputStreamReader(is, ASCII);\n int read = 0;\n final char[] buf = new char[1024];\n do {\n read = reader.read(buf, 0, buf.length);\n if (read > 0) {\n ret.append(buf, 0, read);\n }\n } while (read >= 0);\n } catch (final IOException ex) {\n throw new RuntimeException(ex);\n } finally {\n closeQuietly(is);\n closeQuietly(reader);\n }\n return ret.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static UrlBuilder fromString(final String url, final Charset inputEncoding) {\n if (url.isEmpty()) {\n return new UrlBuilder();\n }\n final Matcher m = URI_PATTERN.matcher(url);\n String protocol = null, hostName = null, path = null, anchor = null;\n Integer port = null;\n Map> queryParameters = null;\n if (m.find()) {\n protocol = m.group(2);\n if (m.group(4) != null) {\n final Matcher n = AUTHORITY_PATTERN.matcher(m.group(4));\n if (n.find()) {\n hostName = IDN.toUnicode(n.group(1));\n if (n.group(3) != null) {\n port = Integer.parseInt(n.group(3));\n }\n }\n }\n path = decodePath(m.group(5), inputEncoding);\n queryParameters = decodeQueryParameters(m.group(7), inputEncoding);\n anchor = m.group(9);\n }\n return of(inputEncoding, DEFAULT_ENCODING, protocol, hostName, port, path, queryParameters, anchor);\n } \n #location 24 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static UrlBuilder fromString(final String url, final Charset inputEncoding) {\n if (url.isEmpty()) {\n return new UrlBuilder();\n }\n final Matcher m = URI_PATTERN.matcher(url);\n String protocol = null, hostName = null, path = null, anchor = null;\n Integer port = null;\n final Map> queryParameters;\n if (m.find()) {\n protocol = m.group(2);\n if (m.group(4) != null) {\n final Matcher n = AUTHORITY_PATTERN.matcher(m.group(4));\n if (n.find()) {\n hostName = IDN.toUnicode(n.group(1));\n if (n.group(3) != null) {\n port = Integer.parseInt(n.group(3));\n }\n }\n }\n path = decodePath(m.group(5), inputEncoding);\n queryParameters = decodeQueryParameters(m.group(7), inputEncoding);\n anchor = m.group(9);\n } else {\n queryParameters = emptyMap();\n }\n return of(inputEncoding, DEFAULT_ENCODING, protocol, hostName, port, path, queryParameters, anchor);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static String readResource(final String name) {\n final StringBuilder ret = new StringBuilder();\n InputStream is = null;\n try {\n is = UrlRegularExpressions.class.getClassLoader().getResourceAsStream(name);\n final InputStreamReader reader = new InputStreamReader(is, ASCII);\n int read = 0;\n final char[] buf = new char[1024];\n do {\n read = reader.read(buf, 0, buf.length);\n if (read > 0) {\n ret.append(buf, 0, read);\n }\n } while (read >= 0);\n } catch (final IOException ex) {\n throw new RuntimeException(ex);\n } finally {\n closeQuietly(is);\n }\n return ret.toString();\n } \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static String readResource(final String name) {\n final StringBuilder ret = new StringBuilder();\n InputStream is = null;\n InputStreamReader reader = null;\n try {\n is = UrlRegularExpressions.class.getClassLoader().getResourceAsStream(name);\n reader = new InputStreamReader(is, ASCII);\n int read = 0;\n final char[] buf = new char[1024];\n do {\n read = reader.read(buf, 0, buf.length);\n if (read > 0) {\n ret.append(buf, 0, read);\n }\n } while (read >= 0);\n } catch (final IOException ex) {\n throw new RuntimeException(ex);\n } finally {\n closeQuietly(is);\n closeQuietly(reader);\n }\n return ret.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static ClassName get(Class clazz) {\n checkNotNull(clazz, \"clazz == null\");\n checkArgument(!clazz.isPrimitive(), \"primitive types cannot be represented as a ClassName\");\n checkArgument(!void.class.equals(clazz), \"'void' type cannot be represented as a ClassName\");\n checkArgument(!clazz.isArray(), \"array types cannot be represented as a ClassName\");\n\n String anonymousSuffix = \"\";\n while (clazz.isAnonymousClass()) {\n int lastDollar = clazz.getName().lastIndexOf('$');\n anonymousSuffix = clazz.getName().substring(lastDollar) + anonymousSuffix;\n clazz = clazz.getEnclosingClass();\n }\n String name = clazz.getSimpleName() + anonymousSuffix;\n\n if (clazz.getEnclosingClass() == null) {\n // Avoid unreliable Class.getPackage(). https://github.com/square/javapoet/issues/295\n int lastDot = clazz.getName().lastIndexOf('.');\n String packageName = (lastDot != -1) ? clazz.getName().substring(0, lastDot) : null;\n return new ClassName(packageName, null, name);\n }\n\n return ClassName.get(clazz.getEnclosingClass()).nestedClass(name);\n } \n #location 19 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static ClassName get(Class clazz) {\n checkNotNull(clazz, \"clazz == null\");\n checkArgument(!clazz.isPrimitive(), \"primitive types cannot be represented as a ClassName\");\n checkArgument(!void.class.equals(clazz), \"'void' type cannot be represented as a ClassName\");\n checkArgument(!clazz.isArray(), \"array types cannot be represented as a ClassName\");\n\n String anonymousSuffix = \"\";\n while (clazz.isAnonymousClass()) {\n int lastDollar = clazz.getName().lastIndexOf('$');\n anonymousSuffix = clazz.getName().substring(lastDollar) + anonymousSuffix;\n clazz = clazz.getEnclosingClass();\n }\n String name = clazz.getSimpleName() + anonymousSuffix;\n\n if (clazz.getEnclosingClass() == null) {\n // Avoid unreliable Class.getPackage(). https://github.com/square/javapoet/issues/295\n int lastDot = clazz.getName().lastIndexOf('.');\n String packageName = (lastDot != -1) ? clazz.getName().substring(0, lastDot) : NO_PACKAGE;\n return new ClassName(packageName, null, name);\n }\n\n return ClassName.get(clazz.getEnclosingClass()).nestedClass(name);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void populateJMeterDirectoryTree() throws MojoExecutionException {\n\t\tfor (Artifact artifact : pluginArtifacts) {\n\t\t\ttry {\n\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_\")) {\n\t\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_config\")) {\n\t\t\t\t\t\tJarFile configSettings = new JarFile(artifact.getFile());\n\t\t\t\t\t\tEnumeration entries = configSettings.entries();\n\t\t\t\t\t\twhile (entries.hasMoreElements()) {\n\t\t\t\t\t\t\tJarEntry jarFileEntry = entries.nextElement();\n\t\t\t\t\t\t\t// Only interested in files in the /bin directory that are not properties files\n\t\t\t\t\t\t\tif (jarFileEntry.getName().startsWith(\"bin\") && !jarFileEntry.getName().endsWith(\".properties\")) {\n\t\t\t\t\t\t\t\tif (!jarFileEntry.isDirectory()) {\n\t\t\t\t\t\t\t\t\tInputStream is = configSettings.getInputStream(jarFileEntry); // get the input stream\n\t\t\t\t\t\t\t\t\tOutputStream os = new FileOutputStream(new File(workDir.getCanonicalPath() + File.separator + jarFileEntry.getName()));\n\t\t\t\t\t\t\t\t\twhile (is.available() > 0) {\n\t\t\t\t\t\t\t\t\t\tos.write(is.read());\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tos.close();\n\t\t\t\t\t\t\t\t\tis.close();\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconfigSettings.close();\n\t\t\t\t\t} else {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t/**\n\t\t\t\t\t * TODO: exclude jars that maven put in #pluginArtifacts for maven run? (e.g. plexus jars, the plugin artifact itself)\n\t\t\t\t\t * Need more info on above, how do we know which ones to exclude??\n\t\t\t\t\t * Most of the files pulled down by maven are required in /lib to match standard JMeter install\n\t\t\t\t\t */\n\t\t\t\t\tif (Artifact.SCOPE_RUNTIME.equals(artifact.getScope())) {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t} else {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\tthrow new MojoExecutionException(\"Unable to populate the JMeter directory tree: \" + e);\n\t\t\t}\n\t\t}\n\t\t//TODO Check if we really need to do this\n\t\t//empty classpath, JMeter will automatically assemble and add all JARs in #libDir and #libExtDir and add them to the classpath. Otherwise all jars will be in the classpath twice.\n\t\tSystem.setProperty(\"java.class.path\", \"\");\n\t} \n #location 39 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void populateJMeterDirectoryTree() throws MojoExecutionException {\n\t\tfor (Artifact artifact : pluginArtifacts) {\n\t\t\ttry {\n\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_\")) {\n\t\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_config\")) {\n\t\t\t\t\t\tJarFile configSettings = new JarFile(artifact.getFile());\n\t\t\t\t\t\tEnumeration entries = configSettings.entries();\n\t\t\t\t\t\twhile (entries.hasMoreElements()) {\n\t\t\t\t\t\t\tJarEntry jarFileEntry = entries.nextElement();\n\t\t\t\t\t\t\t// Only interested in files in the /bin directory that are not properties files\n\t\t\t\t\t\t\tif (jarFileEntry.getName().startsWith(\"bin\") && !jarFileEntry.getName().endsWith(\".properties\")) {\n\t\t\t\t\t\t\t\tif (!jarFileEntry.isDirectory()) {\n\t\t\t\t\t\t\t\t\tcopyInputStreamToFile(configSettings.getInputStream(jarFileEntry), new File(workDir.getCanonicalPath() + File.separator + jarFileEntry.getName()));\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconfigSettings.close();\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t/**\n\t\t\t\t\t * TODO: exclude jars that maven put in #pluginArtifacts for maven run? (e.g. plexus jars, the plugin artifact itself)\n\t\t\t\t\t * Need more info on above, how do we know which ones to exclude??\n\t\t\t\t\t * Most of the files pulled down by maven are required in /lib to match standard JMeter install\n\t\t\t\t\t */\n\t\t\t\t\tif (Artifact.SCOPE_RUNTIME.equals(artifact.getScope())) {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\tthrow new MojoExecutionException(\"Unable to populate the JMeter directory tree: \" + e);\n\t\t\t}\n\t\t}\n\t\t//TODO Check if we really need to do this\n\t\t//empty classpath, JMeter will automatically assemble and add all JARs in #libDir and #libExtDir and add them to the classpath. Otherwise all jars will be in the classpath twice.\n\t\tSystem.setProperty(\"java.class.path\", \"\");\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void populateJMeterDirectoryTree() throws MojoExecutionException {\n\t\tfor (Artifact artifact : pluginArtifacts) {\n\t\t\ttry {\n\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_\")) {\n\t\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_config\")) {\n\t\t\t\t\t\tJarFile configSettings = new JarFile(artifact.getFile());\n\t\t\t\t\t\tEnumeration entries = configSettings.entries();\n\t\t\t\t\t\twhile (entries.hasMoreElements()) {\n\t\t\t\t\t\t\tJarEntry jarFileEntry = entries.nextElement();\n\t\t\t\t\t\t\t// Only interested in files in the /bin directory that are not properties files\n\t\t\t\t\t\t\tif (jarFileEntry.getName().startsWith(\"bin\") && !jarFileEntry.getName().endsWith(\".properties\")) {\n\t\t\t\t\t\t\t\tif (!jarFileEntry.isDirectory()) {\n\t\t\t\t\t\t\t\t\tInputStream is = configSettings.getInputStream(jarFileEntry); // get the input stream\n\t\t\t\t\t\t\t\t\tOutputStream os = new FileOutputStream(new File(workDir.getCanonicalPath() + File.separator + jarFileEntry.getName()));\n\t\t\t\t\t\t\t\t\twhile (is.available() > 0) {\n\t\t\t\t\t\t\t\t\t\tos.write(is.read());\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tos.close();\n\t\t\t\t\t\t\t\t\tis.close();\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconfigSettings.close();\n\t\t\t\t\t} else {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t/**\n\t\t\t\t\t * TODO: exclude jars that maven put in #pluginArtifacts for maven run? (e.g. plexus jars, the plugin artifact itself)\n\t\t\t\t\t * Need more info on above, how do we know which ones to exclude??\n\t\t\t\t\t * Most of the files pulled down by maven are required in /lib to match standard JMeter install\n\t\t\t\t\t */\n\t\t\t\t\tif (Artifact.SCOPE_RUNTIME.equals(artifact.getScope())) {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t} else {\n\t\t\t\t\t\tFileUtils.copyFile(artifact.getFile(), new File(libDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\tthrow new MojoExecutionException(\"Unable to populate the JMeter directory tree: \" + e);\n\t\t\t}\n\t\t}\n\t\t//TODO Check if we really need to do this\n\t\t//empty classpath, JMeter will automatically assemble and add all JARs in #libDir and #libExtDir and add them to the classpath. Otherwise all jars will be in the classpath twice.\n\t\tSystem.setProperty(\"java.class.path\", \"\");\n\t} \n #location 39 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void populateJMeterDirectoryTree() throws MojoExecutionException {\n\t\tfor (Artifact artifact : pluginArtifacts) {\n\t\t\ttry {\n\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_\")) {\n\t\t\t\t\tif (artifact.getArtifactId().startsWith(\"ApacheJMeter_config\")) {\n\t\t\t\t\t\tJarFile configSettings = new JarFile(artifact.getFile());\n\t\t\t\t\t\tEnumeration entries = configSettings.entries();\n\t\t\t\t\t\twhile (entries.hasMoreElements()) {\n\t\t\t\t\t\t\tJarEntry jarFileEntry = entries.nextElement();\n\t\t\t\t\t\t\t// Only interested in files in the /bin directory that are not properties files\n\t\t\t\t\t\t\tif (jarFileEntry.getName().startsWith(\"bin\") && !jarFileEntry.getName().endsWith(\".properties\")) {\n\t\t\t\t\t\t\t\tif (!jarFileEntry.isDirectory()) {\n\t\t\t\t\t\t\t\t\tcopyInputStreamToFile(configSettings.getInputStream(jarFileEntry), new File(workDir.getCanonicalPath() + File.separator + jarFileEntry.getName()));\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconfigSettings.close();\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t/**\n\t\t\t\t\t * TODO: exclude jars that maven put in #pluginArtifacts for maven run? (e.g. plexus jars, the plugin artifact itself)\n\t\t\t\t\t * Need more info on above, how do we know which ones to exclude??\n\t\t\t\t\t * Most of the files pulled down by maven are required in /lib to match standard JMeter install\n\t\t\t\t\t */\n\t\t\t\t\tif (Artifact.SCOPE_RUNTIME.equals(artifact.getScope())) {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libExtDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcopyFile(artifact.getFile(), new File(libDir + File.separator + artifact.getFile().getName()));\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (IOException e) {\n\t\t\t\tthrow new MojoExecutionException(\"Unable to populate the JMeter directory tree: \" + e);\n\t\t\t}\n\t\t}\n\t\t//TODO Check if we really need to do this\n\t\t//empty classpath, JMeter will automatically assemble and add all JARs in #libDir and #libExtDir and add them to the classpath. Otherwise all jars will be in the classpath twice.\n\t\tSystem.setProperty(\"java.class.path\", \"\");\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public int blockSize() {\n return BLOCK_SIZE;\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public int blockSize() {\n return blockSize;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void releaseValue(long newValueReference) {\n memoryManager.releaseSlice(buildValueSlice(newValueReference));\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n Chunk(ByteBuffer minKey, Chunk creator, OakComparator comparator, MemoryManager memoryManager,\n int maxItems, AtomicInteger externalSize,\n OakSerializer keySerializer, OakSerializer valueSerializer) {\n this.memoryManager = memoryManager;\n this.maxItems = maxItems;\n this.entries = new int[maxItems * FIELDS + FIRST_ITEM];\n this.entryIndex = new AtomicInteger(FIRST_ITEM);\n\n this.sortedCount = new AtomicInteger(0);\n this.minKey = minKey;\n this.creator = new AtomicReference<>(creator);\n if (creator == null) {\n this.state = new AtomicReference<>(State.NORMAL);\n } else {\n this.state = new AtomicReference<>(State.INFANT);\n }\n this.next = new AtomicMarkableReference<>(null, false);\n this.pendingOps = new AtomicInteger();\n this.rebalancer = new AtomicReference<>(null); // to be updated on rebalance\n this.statistics = new Statistics();\n this.comparator = comparator;\n this.externalSize = externalSize;\n\n this.keySerializer = keySerializer;\n this.valueSerializer = valueSerializer;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static void setBlockSize(int blockSize) {\n BLOCK_SIZE = blockSize;\n synchronized (BlocksPool.class) { // can be easily changed to lock-free\n instance = new BlocksPool();\n }\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n static void setBlockSize(int blockSize) {\n synchronized (BlocksPool.class) { // can be easily changed to lock-free\n instance = new BlocksPool(blockSize);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Result putIfAbsent(K key, V value, Function transformer) {\n if (key == null || value == null) {\n throw new NullPointerException();\n }\n\n Chunk c = findChunk(key); // find chunk matching key\n Chunk.LookUp lookUp = c.lookUp(key);\n if (lookUp != null && lookUp.valueSlice != null) {\n if (transformer == null) {\n return Result.withFlag(false);\n }\n AbstractMap.SimpleEntry res = ValueUtils.transform(lookUp.valueSlice,\n transformer);\n if (res.getKey() == SUCCESS) {\n return Result.withValue(res.getValue());\n }\n return putIfAbsent(key, value, transformer);\n }\n\n // if chunk is frozen or infant, we can't add to it\n // we need to help rebalancer first, then proceed\n Chunk.State state = c.state();\n if (state == Chunk.State.INFANT) {\n // the infant is already connected so rebalancer won't add this put\n rebalance(c.creator());\n return putIfAbsent(key, value, transformer);\n }\n if (state == Chunk.State.FROZEN || state == Chunk.State.RELEASED) {\n rebalance(c);\n return putIfAbsent(key, value, transformer);\n }\n\n\n int ei;\n long oldReference = DELETED_VALUE;\n\n // Is there already an entry associated with this key?\n if (lookUp != null) {\n // There's an entry for this key, but it isn't linked to any value (in which case valueReference is\n // DELETED_VALUE)\n // or it's linked to a deleted value that is referenced by valueReference (a valid one)\n ei = lookUp.entryIndex;\n assert ei > 0;\n oldReference = lookUp.valueReference;\n } else {\n ei = c.allocateEntryAndKey(key);\n if (ei == -1) {\n rebalance(c);\n return putIfAbsent(key, value, transformer);\n }\n int prevEi = c.linkEntry(ei, key);\n if (prevEi != ei) {\n // some other thread linked its entry with the same key.\n oldReference = c.getValueReference(prevEi);\n if (oldReference != DELETED_VALUE) {\n if (transformer == null) {\n return Result.withFlag(false);\n }\n AbstractMap.SimpleEntry res =\n ValueUtils.transform(c.buildValueSlice(oldReference), transformer);\n if (res.getKey() == SUCCESS) {\n return Result.withValue(res.getValue());\n }\n return putIfAbsent(key, value, transformer);\n } else {\n // both threads compete for the put\n ei = prevEi;\n }\n }\n }\n\n long newValueReference = c.writeValue(value); // write value in place\n\n Chunk.OpData opData = new Chunk.OpData(Operation.PUT_IF_ABSENT, ei, newValueReference, oldReference, null);\n\n // publish put\n if (!c.publish()) {\n c.releaseValue(newValueReference);\n rebalance(c);\n return putIfAbsent(key, value, transformer);\n }\n\n if (!finishAfterPublishing(opData, c)) {\n c.releaseValue(newValueReference);\n return putIfAbsent(key, value, transformer);\n }\n\n return transformer != null ? Result.withValue(null) : Result.withFlag(true);\n } \n #location 83 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n InternalOakMap(K minKey,\n OakSerializer keySerializer,\n OakSerializer valueSerializer,\n OakComparator oakComparator,\n MemoryManager memoryManager,\n int chunkMaxItems) {\n\n this.size = new AtomicInteger(0);\n this.memoryManager = memoryManager;\n\n this.keySerializer = keySerializer;\n this.valueSerializer = valueSerializer;\n\n this.comparator = oakComparator;\n\n this.minKey = ByteBuffer.allocate(this.keySerializer.calculateSize(minKey));\n this.minKey.position(0);\n this.keySerializer.serialize(minKey, this.minKey);\n\n // This is a trick for letting us search through the skiplist using both serialized and unserialized keys.\n // Might be nicer to replace it with a proper visitor\n Comparator mixedKeyComparator = (o1, o2) -> {\n if (o1 instanceof ByteBuffer) {\n if (o2 instanceof ByteBuffer) {\n return oakComparator.compareSerializedKeys((ByteBuffer) o1, (ByteBuffer) o2);\n } else {\n // Note the inversion of arguments, hence sign flip\n return (-1) * oakComparator.compareKeyAndSerializedKey((K) o2, (ByteBuffer) o1);\n }\n } else {\n if (o2 instanceof ByteBuffer) {\n return oakComparator.compareKeyAndSerializedKey((K) o1, (ByteBuffer) o2);\n } else {\n return oakComparator.compareKeys((K) o1, (K) o2);\n }\n }\n };\n this.skiplist = new ConcurrentSkipListMap<>(mixedKeyComparator);\n\n Chunk head = new Chunk<>(this.minKey, null, this.comparator, memoryManager, chunkMaxItems,\n this.size, keySerializer, valueSerializer);\n this.skiplist.put(head.minKey, head); // add first chunk (head) into skiplist\n this.head = new AtomicReference<>(head);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testResizeWithZCGetNewBuffer() {\n String smallValue = \"\";\n StringBuilder stringBuilder = new StringBuilder();\n stringBuilder.setLength((BLOCK_SIZE / Character.BYTES) / 2);\n String longValue = stringBuilder.toString();\n\n oak.zc().put(\"A\", \"\");\n oak.zc().put(\"B\", longValue);\n OakRBuffer buffer = oak.zc().get(\"A\");\n assertEquals(0, buffer.getInt(0));\n\n oak.zc().put(\"A\", longValue);\n assertEquals(longValue.length(), buffer.getInt(0));\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testResizeWithZCGetNewBuffer() {\n final int blockSize = BlocksPool.getInstance().blockSize();\n\n StringBuilder stringBuilder = new StringBuilder();\n stringBuilder.setLength((blockSize / Character.BYTES) / 2);\n String longValue = stringBuilder.toString();\n String smallValue = \"\";\n\n oak.zc().put(\"A\", smallValue);\n oak.zc().put(\"B\", longValue);\n OakRBuffer buffer = oak.zc().get(\"A\");\n assertEquals(0, buffer.getInt(0));\n\n oak.zc().put(\"A\", longValue);\n assertEquals(longValue.length(), buffer.getInt(0));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testUnsafeCopy() {\n\n IntHolder minKey = new IntHolder(0, new int[0]);\n\n OakMapBuilder builder =\n new OakMapBuilder(\n new UnsafeTestComparator(),new UnsafeTestSerializer(),new UnsafeTestSerializer())\n .setMinKey(minKey)\n ;\n\n OakMap oak = builder.build();\n\n IntHolder key1 = new IntHolder(5, new int[]{1, 2, 3, 4, 5});\n IntHolder value1 = new IntHolder(5, new int[]{1, 2, 3, 4, 5});\n\n IntHolder key2 = new IntHolder(6, new int[]{10, 20, 30, 40, 50, 60});\n IntHolder value2 = new IntHolder(6, new int[]{10, 20, 30, 40, 50, 60});\n\n oak.put(key1, value1);\n oak.put(key2, value2);\n\n\n IntHolder resValue1 = oak.get(key1);\n assertEquals(value1.size, resValue1.size);\n\n for (int i = 0; i < value1.size; ++i) {\n assertEquals(value1.array[i], resValue1.array[i]);\n }\n IntHolder resValue2 = oak.get(key2);\n assertEquals(value2.size, resValue2.size);\n for (int i = 0; i < value2.size; ++i) {\n assertEquals(value2.array[i], resValue2.array[i]);\n }\n\n Iterator> iter = oak.zc().entrySet().iterator();\n while (iter.hasNext()) {\n Map.Entry entry = iter.next();\n int size = entry.getKey().getInt(0);\n int[] dstArrayValue = new int[size];\n int[] dstArrayKey = new int[size];\n entry.getKey().unsafeCopyBufferToIntArray(Integer.BYTES, dstArrayKey, size);\n entry.getValue().unsafeCopyBufferToIntArray(Integer.BYTES, dstArrayValue, size);\n if (size == 5) {\n //value1\n assertArrayEquals(value1.array, dstArrayKey);\n assertArrayEquals(value1.array, dstArrayValue);\n } else if (size == 6) {\n //value2\n assertArrayEquals(value2.array, dstArrayKey);\n assertArrayEquals(value2.array, dstArrayValue);\n } else {\n fail();\n }\n }\n\n } \n #location 25 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testUnsafeCopy() {\n\n IntHolder minKey = new IntHolder(0, new int[0]);\n\n OakMapBuilder builder =\n new OakMapBuilder(\n new UnsafeTestComparator(),\n new UnsafeTestSerializer(),new UnsafeTestSerializer(), minKey);\n\n OakMap oak = builder.build();\n\n IntHolder key1 = new IntHolder(5, new int[]{1, 2, 3, 4, 5});\n IntHolder value1 = new IntHolder(5, new int[]{1, 2, 3, 4, 5});\n\n IntHolder key2 = new IntHolder(6, new int[]{10, 20, 30, 40, 50, 60});\n IntHolder value2 = new IntHolder(6, new int[]{10, 20, 30, 40, 50, 60});\n\n oak.put(key1, value1);\n oak.put(key2, value2);\n\n\n IntHolder resValue1 = oak.get(key1);\n assertEquals(value1.size, resValue1.size);\n\n for (int i = 0; i < value1.size; ++i) {\n assertEquals(value1.array[i], resValue1.array[i]);\n }\n IntHolder resValue2 = oak.get(key2);\n assertEquals(value2.size, resValue2.size);\n for (int i = 0; i < value2.size; ++i) {\n assertEquals(value2.array[i], resValue2.array[i]);\n }\n\n Iterator> iter = oak.zc().entrySet().iterator();\n while (iter.hasNext()) {\n Map.Entry entry = iter.next();\n int size = entry.getKey().getInt(0);\n int[] dstArrayValue = new int[size];\n int[] dstArrayKey = new int[size];\n entry.getKey().unsafeCopyBufferToIntArray(Integer.BYTES, dstArrayKey, size);\n entry.getValue().unsafeCopyBufferToIntArray(Integer.BYTES, dstArrayValue, size);\n if (size == 5) {\n //value1\n assertArrayEquals(value1.array, dstArrayKey);\n assertArrayEquals(value1.array, dstArrayValue);\n } else if (size == 6) {\n //value2\n assertArrayEquals(value2.array, dstArrayKey);\n assertArrayEquals(value2.array, dstArrayValue);\n } else {\n fail();\n }\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static void setBlockSize(int blockSize) {\n BLOCK_SIZE = blockSize;\n synchronized (BlocksPool.class) { // can be easily changed to lock-free\n instance = new BlocksPool();\n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n static void setBlockSize(int blockSize) {\n synchronized (BlocksPool.class) { // can be easily changed to lock-free\n instance = new BlocksPool(blockSize);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void unmarshal0(Class type, Consumer consumer, OPCPackage open) throws IOException, SAXException, OpenXML4JException {\n\n //ISSUE #55\n XSSFWorkbook wb = new XSSFWorkbook(open);\n Workbook workbook = new SXSSFWorkbook(wb);\n //work out which sheet must process\n int processIndex = PoijiOptions.getSheetIndexToProcess(workbook, options);\n\n ReadOnlySharedStringsTable readOnlySharedStringsTable = new ReadOnlySharedStringsTable(open);\n XSSFReader xssfReader = new XSSFReader(open);\n StylesTable styles = xssfReader.getStylesTable();\n\n SheetIterator iter = (SheetIterator) xssfReader.getSheetsData();\n int index = 0;\n\n while (iter.hasNext()) {\n try (InputStream stream = iter.next()) {\n //if (index == options.sheetIndex()) {\n if (index == processIndex) {\n processSheet(styles, readOnlySharedStringsTable, type, stream, consumer);\n return;\n }\n }\n ++index;\n }\n } \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n XSSFUnmarshaller(PoijiOptions options) {\n this.options = options;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @SuppressWarnings(\"unchecked\")\n private static Deserializer deserializer(File file) throws FileNotFoundException {\n final PoijiStream poiParser = new PoijiStream(fileInputStream(file));\n final PoiWorkbook workbook = PoiWorkbook.workbook(Files.getExtension(file.getName()), poiParser);\n return Unmarshaller.instance(workbook);\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @SuppressWarnings(\"unchecked\")\n private static Deserializer deserializer(File file) throws FileNotFoundException {\n final PoijiStream poiParser = new PoijiStream(fileInputStream(file));\n final PoiWorkbook workbook = PoiWorkbook.workbook(Files.getExtension(file.getName()), poiParser);\n return Deserializer.instance(workbook);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void unmarshal(Class type, Consumer consumer) {\n HSSFWorkbook workbook = (HSSFWorkbook) workbook();\n Optional maybeSheetName = this.getSheetName(type, options);\n\n hssfFormulaEvaluator = HSSFFormulaEvaluator.create(workbook, null, null);\n Sheet sheet = this.getSheetToProcess(workbook, options, maybeSheetName.orElse(null));\n\n int skip = options.skip();\n int maxPhysicalNumberOfRows = sheet.getPhysicalNumberOfRows() + 1 - skip;\n\n loadColumnTitles(sheet, maxPhysicalNumberOfRows);\n AnnotationUtil.validateMandatoryNameColumns(options, type, columnIndexPerTitle.keySet());\n\n for (Row currentRow : sheet) {\n if (!skip(currentRow, skip) && !isRowEmpty(currentRow)) {\n internalCount += 1;\n\n if (limit != 0 && internalCount > limit)\n return;\n\n T instance = deserializeRowToInstance(currentRow, type);\n consumer.accept(instance);\n }\n }\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void unmarshal(Class type, Consumer consumer) {\n HSSFWorkbook workbook = (HSSFWorkbook) workbook();\n Optional maybeSheetName = this.getSheetName(type, options);\n\n baseFormulaEvaluator = HSSFFormulaEvaluator.create(workbook, null, null);\n Sheet sheet = this.getSheetToProcess(workbook, options, maybeSheetName.orElse(null));\n\n processRowsToObjects(sheet, type, consumer);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @SuppressWarnings(\"unchecked\")\n private static Deserializer deserializer(File file, PoijiOptions options) throws FileNotFoundException {\n final PoijiStream poiParser = new PoijiStream(fileInputStream(file));\n final PoiWorkbook workbook = PoiWorkbook.workbook(Files.getExtension(file.getName()), poiParser);\n return Deserializer.instance(workbook, options);\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @SuppressWarnings(\"unchecked\")\n private static Deserializer deserializer(File file, PoijiOptions options) {\n final PoijiStream poiParser = new PoijiStream(file);\n final PoiWorkbook workbook = PoiWorkbook.workbook(Files.getExtension(file.getName()), poiParser);\n return Deserializer.instance(workbook, options);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws IOException {\n\n SplitInputStream splitInputStream = null;\n try {\n splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n if (splitInputStream != null) {\n splitInputStream.close();\n }\n throw e;\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws IOException {\n\n SplitInputStream splitInputStream = null;\n try {\n splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n if (splitInputStream != null) {\n splitInputStream.close();\n }\n throw e;\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static ZipInputStream createZipInputStream(ZipModel zipModel, FileHeader fileHeader, char[] password)\n throws IOException {\n\n SplitInputStream splitInputStream = null;\n try {\n splitInputStream = new SplitInputStream(zipModel.getZipFile(), zipModel.isSplitArchive(),\n zipModel.getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n\n ZipInputStream zipInputStream = new ZipInputStream(splitInputStream, password);\n if (zipInputStream.getNextEntry(fileHeader) == null) {\n throw new ZipException(\"Could not locate local file header for corresponding file header\");\n }\n\n return zipInputStream;\n } catch (IOException e) {\n if (splitInputStream != null) {\n splitInputStream.close();\n }\n throw e;\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n protected void executeTask(RenameFilesTaskParameters taskParameters, ProgressMonitor progressMonitor) throws IOException {\n Map fileNamesMap = filterNonExistingEntriesAndAddSeparatorIfNeeded(taskParameters.fileNamesMap);\n if (fileNamesMap.size() == 0) {\n return;\n }\n\n File temporaryFile = getTemporaryFile(zipModel.getZipFile().getPath());\n boolean successFlag = false;\n try(RandomAccessFile inputStream = new RandomAccessFile(zipModel.getZipFile(), RandomAccessFileMode.WRITE.getValue());\n OutputStream outputStream = new CountingOutputStream(new SplitOutputStream(temporaryFile))) {\n\n long currentFileCopyPointer = 0;\n\n // Maintain a different list to iterate, so that when the file name is changed in the central directory\n // we still have access to the original file names. If iterating on the original list from central directory,\n // it might be that a file name has changed because of other file name, ex: if a directory name has to be changed\n // and the file is part of that directory, by the time the file has to be changed, its name might have changed\n // when changing the name of the directory. There is some overhead with this approach, but is safer.\n List allUnchangedFileHeaders = new ArrayList<>(zipModel.getCentralDirectory().getFileHeaders());\n\n for (FileHeader fileHeader : allUnchangedFileHeaders) {\n Map.Entry fileNameMapForThisEntry = getCorrespondingEntryFromMap(fileHeader, fileNamesMap);\n progressMonitor.setFileName(fileHeader.getFileName());\n\n if (fileNameMapForThisEntry == null) {\n // copy complete entry without any changes\n long lengthToCopy = getLocalFileHeaderSize(fileHeader) + fileHeader.getCompressedSize() + getDataDescriptorSize(zipModel, fileHeader);\n currentFileCopyPointer += copyFile(inputStream, outputStream, currentFileCopyPointer, lengthToCopy, progressMonitor);\n } else {\n String newFileName = getNewFileName(fileNameMapForThisEntry.getValue(), fileNameMapForThisEntry.getKey(), fileHeader.getFileName());\n byte[] newFileNameBytes = newFileName.getBytes(charset);\n int headersOffset = newFileNameBytes.length - fileHeader.getFileNameLength();\n\n currentFileCopyPointer = copyEntryAndChangeFileName(newFileNameBytes, fileHeader, currentFileCopyPointer,\n inputStream, outputStream, progressMonitor);\n\n updateHeadersInZipModel(fileHeader, newFileName, newFileNameBytes, headersOffset);\n }\n\n verifyIfTaskIsCancelled();\n }\n\n headerWriter.finalizeZipFile(zipModel, outputStream, charset);\n successFlag = true;\n } finally {\n cleanupFile(successFlag, zipModel.getZipFile(), temporaryFile);\n }\n\n } \n #location 46 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n protected void executeTask(RenameFilesTaskParameters taskParameters, ProgressMonitor progressMonitor) throws IOException {\n Map fileNamesMap = filterNonExistingEntriesAndAddSeparatorIfNeeded(taskParameters.fileNamesMap);\n if (fileNamesMap.size() == 0) {\n return;\n }\n\n File temporaryFile = getTemporaryFile(zipModel.getZipFile().getPath());\n boolean successFlag = false;\n try(RandomAccessFile inputStream = new RandomAccessFile(zipModel.getZipFile(), RandomAccessFileMode.WRITE.getValue());\n SplitOutputStream outputStream = new SplitOutputStream(temporaryFile)) {\n\n long currentFileCopyPointer = 0;\n\n // Maintain a different list to iterate, so that when the file name is changed in the central directory\n // we still have access to the original file names. If iterating on the original list from central directory,\n // it might be that a file name has changed because of other file name, ex: if a directory name has to be changed\n // and the file is part of that directory, by the time the file has to be changed, its name might have changed\n // when changing the name of the directory. There is some overhead with this approach, but is safer.\n List allUnchangedFileHeaders = new ArrayList<>(zipModel.getCentralDirectory().getFileHeaders());\n\n for (FileHeader fileHeader : allUnchangedFileHeaders) {\n Map.Entry fileNameMapForThisEntry = getCorrespondingEntryFromMap(fileHeader, fileNamesMap);\n progressMonitor.setFileName(fileHeader.getFileName());\n\n long lengthToCopy = HeaderUtil.getOffsetOfNextEntry(zipModel, fileHeader) - outputStream.getFilePointer();\n if (fileNameMapForThisEntry == null) {\n // copy complete entry without any changes\n currentFileCopyPointer += copyFile(inputStream, outputStream, currentFileCopyPointer, lengthToCopy, progressMonitor);\n } else {\n String newFileName = getNewFileName(fileNameMapForThisEntry.getValue(), fileNameMapForThisEntry.getKey(), fileHeader.getFileName());\n byte[] newFileNameBytes = newFileName.getBytes(charset);\n int headersOffset = newFileNameBytes.length - fileHeader.getFileNameLength();\n\n currentFileCopyPointer = copyEntryAndChangeFileName(newFileNameBytes, fileHeader, currentFileCopyPointer, lengthToCopy,\n inputStream, outputStream, progressMonitor);\n\n updateHeadersInZipModel(fileHeader, newFileName, newFileNameBytes, headersOffset);\n }\n\n verifyIfTaskIsCancelled();\n }\n\n headerWriter.finalizeZipFile(zipModel, outputStream, charset);\n successFlag = true;\n } finally {\n cleanupFile(successFlag, zipModel.getZipFile(), temporaryFile);\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static byte[] getFileAttributes(File file) {\n try {\n if (file == null || (!Files.isSymbolicLink(file.toPath()) && !file.exists())) {\n return new byte[4];\n }\n\n Path path = file.toPath();\n\n String os = System.getProperty(\"os.name\").toLowerCase();\n if (isWindows(os)) {\n return getWindowsFileAttributes(path);\n } else if (isMac(os) || isUnix(os)) {\n return getPosixFileAttributes(path);\n } else {\n return new byte[4];\n }\n } catch (NoSuchMethodError e) {\n return new byte[4];\n }\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static byte[] getFileAttributes(File file) {\n try {\n if (file == null || (!Files.isSymbolicLink(file.toPath()) && !file.exists())) {\n return new byte[4];\n }\n\n Path path = file.toPath();\n\n if (isWindows()) {\n return getWindowsFileAttributes(path);\n } else if (isMac() || isUnix()) {\n return getPosixFileAttributes(path);\n } else {\n return new byte[4];\n }\n } catch (NoSuchMethodError e) {\n return new byte[4];\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n protected void executeTask(RenameFilesTaskParameters taskParameters, ProgressMonitor progressMonitor) throws IOException {\n Map fileNamesMap = filterNonExistingEntriesAndAddSeparatorIfNeeded(taskParameters.fileNamesMap);\n if (fileNamesMap.size() == 0) {\n return;\n }\n\n File temporaryFile = getTemporaryFile(zipModel.getZipFile().getPath());\n boolean successFlag = false;\n try(RandomAccessFile inputStream = new RandomAccessFile(zipModel.getZipFile(), RandomAccessFileMode.WRITE.getValue());\n CountingOutputStream outputStream = new CountingOutputStream(new SplitOutputStream(temporaryFile))) {\n\n long currentFileCopyPointer = 0;\n\n // Maintain a different list to iterate, so that when the file name is changed in the central directory\n // we still have access to the original file names. If iterating on the original list from central directory,\n // it might be that a file name has changed because of other file name, ex: if a directory name has to be changed\n // and the file is part of that directory, by the time the file has to be changed, its name might have changed\n // when changing the name of the directory. There is some overhead with this approach, but is safer.\n List allUnchangedFileHeaders = new ArrayList<>(zipModel.getCentralDirectory().getFileHeaders());\n\n for (FileHeader fileHeader : allUnchangedFileHeaders) {\n Map.Entry fileNameMapForThisEntry = getCorrespondingEntryFromMap(fileHeader, fileNamesMap);\n progressMonitor.setFileName(fileHeader.getFileName());\n\n long lengthToCopy = HeaderUtil.getOffsetOfNextEntry(zipModel, fileHeader) - outputStream.getFilePointer();\n if (fileNameMapForThisEntry == null) {\n // copy complete entry without any changes\n currentFileCopyPointer += copyFile(inputStream, outputStream, currentFileCopyPointer, lengthToCopy, progressMonitor);\n } else {\n String newFileName = getNewFileName(fileNameMapForThisEntry.getValue(), fileNameMapForThisEntry.getKey(), fileHeader.getFileName());\n byte[] newFileNameBytes = newFileName.getBytes(charset);\n int headersOffset = newFileNameBytes.length - fileHeader.getFileNameLength();\n\n currentFileCopyPointer = copyEntryAndChangeFileName(newFileNameBytes, fileHeader, currentFileCopyPointer, lengthToCopy,\n inputStream, outputStream, progressMonitor);\n\n updateHeadersInZipModel(fileHeader, newFileName, newFileNameBytes, headersOffset);\n }\n\n verifyIfTaskIsCancelled();\n }\n\n headerWriter.finalizeZipFile(zipModel, outputStream, charset);\n successFlag = true;\n } finally {\n cleanupFile(successFlag, zipModel.getZipFile(), temporaryFile);\n }\n\n } \n #location 46 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n protected void executeTask(RenameFilesTaskParameters taskParameters, ProgressMonitor progressMonitor) throws IOException {\n Map fileNamesMap = filterNonExistingEntriesAndAddSeparatorIfNeeded(taskParameters.fileNamesMap);\n if (fileNamesMap.size() == 0) {\n return;\n }\n\n File temporaryFile = getTemporaryFile(zipModel.getZipFile().getPath());\n boolean successFlag = false;\n try(RandomAccessFile inputStream = new RandomAccessFile(zipModel.getZipFile(), RandomAccessFileMode.WRITE.getValue());\n SplitOutputStream outputStream = new SplitOutputStream(temporaryFile)) {\n\n long currentFileCopyPointer = 0;\n\n // Maintain a different list to iterate, so that when the file name is changed in the central directory\n // we still have access to the original file names. If iterating on the original list from central directory,\n // it might be that a file name has changed because of other file name, ex: if a directory name has to be changed\n // and the file is part of that directory, by the time the file has to be changed, its name might have changed\n // when changing the name of the directory. There is some overhead with this approach, but is safer.\n List allUnchangedFileHeaders = new ArrayList<>(zipModel.getCentralDirectory().getFileHeaders());\n\n for (FileHeader fileHeader : allUnchangedFileHeaders) {\n Map.Entry fileNameMapForThisEntry = getCorrespondingEntryFromMap(fileHeader, fileNamesMap);\n progressMonitor.setFileName(fileHeader.getFileName());\n\n long lengthToCopy = HeaderUtil.getOffsetOfNextEntry(zipModel, fileHeader) - outputStream.getFilePointer();\n if (fileNameMapForThisEntry == null) {\n // copy complete entry without any changes\n currentFileCopyPointer += copyFile(inputStream, outputStream, currentFileCopyPointer, lengthToCopy, progressMonitor);\n } else {\n String newFileName = getNewFileName(fileNameMapForThisEntry.getValue(), fileNameMapForThisEntry.getKey(), fileHeader.getFileName());\n byte[] newFileNameBytes = newFileName.getBytes(charset);\n int headersOffset = newFileNameBytes.length - fileHeader.getFileNameLength();\n\n currentFileCopyPointer = copyEntryAndChangeFileName(newFileNameBytes, fileHeader, currentFileCopyPointer, lengthToCopy,\n inputStream, outputStream, progressMonitor);\n\n updateHeadersInZipModel(fileHeader, newFileName, newFileNameBytes, headersOffset);\n }\n\n verifyIfTaskIsCancelled();\n }\n\n headerWriter.finalizeZipFile(zipModel, outputStream, charset);\n successFlag = true;\n } finally {\n cleanupFile(successFlag, zipModel.getZipFile(), temporaryFile);\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static boolean isWindows() {\n String os = System.getProperty(\"os.name\").toLowerCase();\n return isWindows(os);\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static boolean isWindows() {\n return (OPERATING_SYSTEM_NAME.contains(\"win\"));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private DecompressedInputStream initializeEntryInputStream(LocalFileHeader localFileHeader) throws IOException {\n ZipEntryInputStream zipEntryInputStream = new ZipEntryInputStream(inputStream);\n CipherInputStream cipherInputStream = initializeCipherInputStream(zipEntryInputStream, localFileHeader);\n return initializeDecompressorForThisEntry(cipherInputStream, localFileHeader);\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private DecompressedInputStream initializeEntryInputStream(LocalFileHeader localFileHeader) throws IOException {\n ZipEntryInputStream zipEntryInputStream = new ZipEntryInputStream(inputStream, getCompressedSize(localFileHeader));\n CipherInputStream cipherInputStream = initializeCipherInputStream(zipEntryInputStream, localFileHeader);\n return initializeDecompressorForThisEntry(cipherInputStream, localFileHeader);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void setFileAttributes(Path file, byte[] fileAttributes) {\n if (fileAttributes == null || fileAttributes.length == 0) {\n return;\n }\n\n String os = System.getProperty(\"os.name\").toLowerCase();\n if (isWindows(os)) {\n applyWindowsFileAttributes(file, fileAttributes);\n } else if (isMac(os) || isUnix(os)) {\n applyPosixFileAttributes(file, fileAttributes);\n }\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static void setFileAttributes(Path file, byte[] fileAttributes) {\n if (fileAttributes == null || fileAttributes.length == 0) {\n return;\n }\n\n if (isWindows()) {\n applyWindowsFileAttributes(file, fileAttributes);\n } else if (isMac() || isUnix()) {\n applyPosixFileAttributes(file, fileAttributes);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected ZipInputStream createZipInputStream(FileHeader fileHeader) throws IOException {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n return new ZipInputStream(splitInputStream, password);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n SplitInputStream splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n } \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private ZipInputStream prepareZipInputStream() throws ZipException {\n try {\n splitInputStream = new SplitInputStream(getZipModel().getZipFile(),\n getZipModel().isSplitArchive(), getZipModel().getEndOfCentralDirectoryRecord().getNumberOfThisDisk());\n\n FileHeader fileHeader = getFirstFileHeader(getZipModel());\n if (fileHeader != null) {\n splitInputStream.prepareExtractionForFileHeader(fileHeader);\n }\n\n return new ZipInputStream(splitInputStream, password);\n } catch (IOException e) {\n throw new ZipException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void bidiBackpressure() throws InterruptedException {\n Object lock = new Object();\n BackpressureDetector clientReqBPDetector = new BackpressureDetector(madMultipleCutoff);\n BackpressureDetector clientRespBPDetector = new BackpressureDetector(madMultipleCutoff);\n\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n\n Flowable rxRequest = Flowable\n .fromIterable(new Sequence(180, clientReqBPDetector))\n .doOnNext(i -> System.out.println(i + \" -->\"))\n .map(BackpressureIntegrationTest::protoNum);\n\n Flowable rxResponse = stub.twoWayPressure(rxRequest);\n\n rxResponse.subscribe(\n n -> {\n clientRespBPDetector.tick();\n System.out.println(\" \" + n.getNumber(0) + \" <--\");\n try { Thread.sleep(50); } catch (InterruptedException e) {}\n },\n t -> {\n t.printStackTrace();\n synchronized (lock) {\n lock.notify();\n }\n },\n () -> {\n System.out.println(\"Client done.\");\n synchronized (lock) {\n lock.notify();\n }\n });\n\n synchronized (lock) {\n lock.wait(TimeUnit.SECONDS.toMillis(20));\n }\n\n assertThat(clientReqBPDetector.backpressureDelayOcurred()).isTrue();\n assertThat(serverRespBPDetector.backpressureDelayOcurred()).isTrue();\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void bidiBackpressure() throws InterruptedException {\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n\n Flowable rxRequest = Flowable\n .fromIterable(IntStream.range(0, NUMBER_OF_STREAM_ELEMENTS)::iterator)\n .doOnNext(i -> System.out.println(i + \" --> \"))\n .doOnNext(i -> updateNumberOfWaits(clientLastValueTime, clientNbOfWaits))\n .map(BackpressureIntegrationTest::protoNum);\n\n TestSubscriber rxResponse = stub.twoWayPressure(rxRequest)\n .doOnNext(n -> System.out.println(n.getNumber(0) + \" <--\"))\n .doOnNext(n -> waitIfValuesAreEqual(n.getNumber(0), 3))\n .test();\n\n rxResponse.awaitTerminalEvent(5, TimeUnit.SECONDS);\n rxResponse.assertComplete().assertValueCount(NUMBER_OF_STREAM_ELEMENTS);\n\n assertThat(clientNbOfWaits.get()).isEqualTo(1);\n assertThat(serverNumberOfWaits.get()).isEqualTo(1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void serverToClientBackpressure() throws InterruptedException {\n Object lock = new Object();\n BackpressureDetector clientBackpressureDetector = new BackpressureDetector(madMultipleCutoff);\n\n ReactorNumbersGrpc.ReactorNumbersStub stub = ReactorNumbersGrpc.newReactorStub(channel);\n\n Mono reactorRequest = Mono.just(Empty.getDefaultInstance());\n\n Flux reactorResponse = stub.responsePressure(reactorRequest);\n reactorResponse.subscribe(\n n -> {\n clientBackpressureDetector.tick();\n System.out.println(n.getNumber(0) + \" <--\");\n try { Thread.sleep(50); } catch (InterruptedException e) {}\n },\n t -> {\n t.printStackTrace();\n synchronized (lock) {\n lock.notify();\n }\n },\n () -> {\n System.out.println(\"Client done.\");\n synchronized (lock) {\n lock.notify();\n }\n });\n\n synchronized (lock) {\n lock.wait(TimeUnit.SECONDS.toMillis(20));\n }\n\n assertThat(serverRespBPDetector.backpressureDelayOcurred()).isTrue();\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void serverToClientBackpressure() throws InterruptedException {\n ReactorNumbersGrpc.ReactorNumbersStub stub = ReactorNumbersGrpc.newReactorStub(channel);\n\n Mono reactorRequest = Mono.just(Empty.getDefaultInstance());\n\n Flux reactorResponse = stub.responsePressure(reactorRequest)\n .doOnNext(n -> System.out.println(n.getNumber(0) + \" <--\"))\n .doOnNext(n -> waitIfValuesAreEqual(n.getNumber(0), 3));\n\n StepVerifier.create(reactorResponse)\n .expectNextCount(NUMBER_OF_STREAM_ELEMENTS)\n .expectComplete()\n .verify(Duration.ofSeconds(5));\n\n assertThat(numberOfWaits.get()).isEqualTo(1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void clientToServerBackpressure() throws InterruptedException {\n Object lock = new Object();\n\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n BackpressureDetector clientBackpressureDetector = new BackpressureDetector(madMultipleCutoff);\n Sequence seq = new Sequence(200, clientBackpressureDetector);\n\n Flowable rxRequest = Flowable\n .fromIterable(seq)\n .doOnNext(i -> System.out.println(i + \" -->\"))\n .map(BackpressureIntegrationTest::protoNum);\n\n\n Single rxResponse = stub.requestPressure(rxRequest);\n\n rxResponse.subscribe(\n n -> {\n System.out.println(\"Client done. \" + n.getNumber(0));\n synchronized (lock) {\n lock.notify();\n }\n },\n t -> {\n t.printStackTrace();\n synchronized (lock) {\n lock.notify();\n }\n });\n\n synchronized (lock) {\n lock.wait(TimeUnit.SECONDS.toMillis(20));\n }\n\n assertThat(clientBackpressureDetector.backpressureDelayOcurred()).isTrue();\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void clientToServerBackpressure() throws InterruptedException {\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n\n Flowable rxRequest = Flowable\n .fromIterable(IntStream.range(0, NUMBER_OF_STREAM_ELEMENTS)::iterator)\n .doOnNext(i -> System.out.println(i + \" --> \"))\n .doOnNext(i -> updateNumberOfWaits(clientLastValueTime, clientNbOfWaits))\n .map(BackpressureIntegrationTest::protoNum);\n\n TestObserver rxResponse = stub.requestPressure(rxRequest).test();\n\n rxResponse.awaitTerminalEvent(5, TimeUnit.SECONDS);\n rxResponse.assertComplete()\n .assertValue(v -> v.getNumber(0) == NUMBER_OF_STREAM_ELEMENTS - 1);\n\n assertThat(clientNbOfWaits.get()).isEqualTo(1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void clientToServerBackpressure() throws InterruptedException {\n Object lock = new Object();\n\n ReactorNumbersGrpc.ReactorNumbersStub stub = ReactorNumbersGrpc.newReactorStub(channel);\n BackpressureDetector clientBackpressureDetector = new BackpressureDetector(madMultipleCutoff);\n Sequence seq = new Sequence(200, clientBackpressureDetector);\n\n Flux reactorRequest = Flux\n .fromIterable(seq)\n .doOnNext(i -> System.out.println(i + \" -->\"))\n .map(BackpressureIntegrationTest::protoNum);\n\n\n Mono reactorResponse = stub.requestPressure(reactorRequest);\n\n reactorResponse.subscribe(\n n -> {\n System.out.println(\"Client done. \" + n.getNumber(0));\n synchronized (lock) {\n lock.notify();\n }\n },\n t -> {\n t.printStackTrace();\n synchronized (lock) {\n lock.notify();\n }\n });\n\n synchronized (lock) {\n lock.wait(TimeUnit.SECONDS.toMillis(20));\n }\n\n assertThat(clientBackpressureDetector.backpressureDelayOcurred()).isTrue();\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void clientToServerBackpressure() throws InterruptedException {\n ReactorNumbersGrpc.ReactorNumbersStub stub = ReactorNumbersGrpc.newReactorStub(channel);\n\n Flux reactorRequest = Flux\n .fromIterable(IntStream.range(0, NUMBER_OF_STREAM_ELEMENTS)::iterator)\n .doOnNext(i -> System.out.println(i + \" --> \"))\n .doOnNext(i -> updateNumberOfWaits(lastValueTime, numberOfWaits))\n .map(BackpressureIntegrationTest::protoNum);\n\n Mono reactorResponse = stub.requestPressure(reactorRequest);\n\n StepVerifier.create(reactorResponse)\n .expectNextMatches(v -> v.getNumber(0) == NUMBER_OF_STREAM_ELEMENTS - 1)\n .expectComplete()\n .verify(Duration.ofSeconds(5));\n\n assertThat(numberOfWaits.get()).isEqualTo(1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void serverToClientBackpressure() throws InterruptedException {\n Object lock = new Object();\n BackpressureDetector clientBackpressureDetector = new BackpressureDetector(madMultipleCutoff);\n\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n\n Single rxRequest = Single.just(Empty.getDefaultInstance());\n\n Flowable rxResponse = stub.responsePressure(rxRequest);\n rxResponse.subscribe(\n n -> {\n clientBackpressureDetector.tick();\n System.out.println(n.getNumber(0) + \" <--\");\n try { Thread.sleep(50); } catch (InterruptedException e) {}\n },\n t -> {\n t.printStackTrace();\n synchronized (lock) {\n lock.notify();\n }\n },\n () -> {\n System.out.println(\"Client done.\");\n synchronized (lock) {\n lock.notify();\n }\n });\n\n synchronized (lock) {\n lock.wait(TimeUnit.SECONDS.toMillis(20));\n }\n\n assertThat(serverRespBPDetector.backpressureDelayOcurred()).isTrue();\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void serverToClientBackpressure() throws InterruptedException {\n RxNumbersGrpc.RxNumbersStub stub = RxNumbersGrpc.newRxStub(channel);\n\n Single rxRequest = Single.just(Empty.getDefaultInstance());\n\n TestSubscriber rxResponse = stub.responsePressure(rxRequest)\n .doOnNext(n -> System.out.println(n.getNumber(0) + \" <--\"))\n .doOnNext(n -> waitIfValuesAreEqual(n.getNumber(0), 3))\n .test();\n\n rxResponse.awaitTerminalEvent(5, TimeUnit.SECONDS);\n rxResponse.assertComplete()\n .assertValueCount(NUMBER_OF_STREAM_ELEMENTS);\n\n assertThat(serverNumberOfWaits.get()).isEqualTo(1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public String render(ClassModel model, int index, int size, Map session) {\n\n if (isExcludedClass(model.getType().getName())) {\n return null;\n }\n\n StringWriter sw = new StringWriter();\n PrintWriter writer = new PrintWriter(sw);\n\n ClassTypeInfo type = model.getType();\n\n if (index == 0) {\n Util.generateLicense(writer);\n registerJvmClasses();\n for (Object fqcn : jvmClasses()) {\n JVMClass.generateDTS(writer, fqcn.toString());\n }\n\n // include a file if present\n writer.print(includeFileIfPresent(\"index.header.d.ts\"));\n\n if (!type.getModuleName().equals(\"vertx\")) {\n if (isOptionalModule(\"@vertx/core\")) {\n writer.println(\"// @ts-ignore\");\n }\n // hard coded imports for non codegen types\n writer.print(\"import { Handler, AsyncResult } from '@vertx/core';\\n\\n\");\n }\n } else {\n writer.print(\"\\n\");\n }\n\n boolean imports = false;\n\n @SuppressWarnings(\"unchecked\")\n Map aliasMap = (Map) session.computeIfAbsent(\"aliasMap\", (a) -> new HashMap());\n for (ApiTypeInfo referencedType : model.getReferencedTypes()) {\n if (!isImported(referencedType, session)) {\n if (!referencedType.getRaw().getModuleName().equals(type.getModuleName())) {\n String simpleName = referencedType.getSimpleName();\n if (simpleName.equals(model.getIfaceSimpleName())) {\n String aliasName = simpleName + \"Super\";\n simpleName = simpleName + \" as \" + aliasName;\n aliasMap.put(referencedType.getName(), aliasName);\n }\n // ignore missing imports\n if (isOptionalModule(getNPMScope(referencedType.getRaw().getModule()))) {\n writer.println(\"// @ts-ignore\");\n }\n writer.printf(\"import { %s } from '%s';\\n\", simpleName, getNPMScope(referencedType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n for (ClassTypeInfo dataObjectType : model.getReferencedDataObjectTypes()) {\n if (!isImported(dataObjectType, session)) {\n if (dataObjectType.getRaw().getModuleName().equals(type.getModuleName())) {\n writer.printf(\"import { %s } from './options';\\n\", dataObjectType.getSimpleName());\n imports = true;\n } else {\n writer.printf(\"import { %s } from '%s/options';\\n\", dataObjectType.getSimpleName(), getNPMScope(dataObjectType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n for (EnumTypeInfo enumType : model.getReferencedEnumTypes()) {\n if (!isImported(enumType, session)) {\n if (enumType.getRaw().getModuleName().equals(type.getModuleName())) {\n writer.printf(\"import { %s } from './enums';\\n\", enumType.getSimpleName());\n imports = true;\n } else {\n writer.printf(\"import { %s } from '%s/enums';\\n\", enumType.getSimpleName(), getNPMScope(enumType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n\n if (imports) {\n writer.print(\"\\n\");\n }\n\n final Set superTypes = new HashSet<>();\n model.getAbstractSuperTypes().forEach(ti -> superTypes.add(genType(ti)));\n\n if (model.isHandler()) {\n if (model.isConcrete()) {\n superTypes.add(\"Handler<\" + genType(model.getHandlerArg()) + \">\");\n }\n }\n\n generateDoc(writer, model.getDoc(), \"\");\n\n writer.printf(\"export %s %s%s\", model.isConcrete() ? \"abstract class\" : \"interface\", type.getSimpleName(), genGeneric(type.getParams()));\n\n if (model.isConcrete()) {\n if (model.getConcreteSuperType() != null) {\n String simpleName = aliasMap.get(model.getConcreteSuperType().getName());\n writer.printf(\" extends %s\", simpleName != null ? simpleName : genType(model.getConcreteSuperType()));\n }\n if (!superTypes.isEmpty()) {\n writer.printf(\" implements %s\", String.join(\", \", superTypes));\n }\n } else {\n if (model.isHandler()) {\n writer.printf(\" extends Handler<%s>\", genType(model.getHandlerArg()));\n if (!superTypes.isEmpty()) {\n writer.printf(\", %s\", String.join(\", \", superTypes));\n }\n } else {\n if (!superTypes.isEmpty()) {\n writer.printf(\" extends %s\", String.join(\", \", superTypes));\n }\n }\n }\n\n writer.print(\" {\\n\");\n\n boolean moreConstants = false;\n boolean hasConstantInInterface = !model.isConcrete() && model.getConstants().size() > 0;\n\n // this looks awkward (and it is) but TS does not allow static constants in interfaces\n // so they get listed on the abstract classes.\n if (model.isConcrete()) {\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n }\n\n boolean moreMethods = false;\n boolean hasStaticMethodsInInterface = false;\n\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!model.isConcrete() && method.isStaticMethod()) {\n hasStaticMethodsInInterface = true;\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n // BEGIN of non polyglot methods...\n\n for (MethodInfo method : model.getAnyJavaTypeMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n\n\n // if the model is not concrete (interface) we need to merge types to allow declaring the constants\n // from the java interface\n\n if (hasConstantInInterface || hasStaticMethodsInInterface) {\n writer.print(\"\\n\");\n writer.printf(\"export abstract class %s%s implements %s%s {\\n\", type.getSimpleName(), genGeneric(type.getParams()), type.getSimpleName(), genGeneric(type.getParams()));\n\n moreConstants = false;\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n\n moreMethods = false;\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!method.isStaticMethod()) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n }\n\n if (index == size - 1) {\n // include a file if present\n writer.print(includeFileIfPresent(\"index.footer.d.ts\"));\n }\n\n return sw.toString();\n } \n #location 216 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n public String render(ClassModel model, int index, int size, Map session) {\n\n if (isExcludedClass(model.getType().getName())) {\n return null;\n }\n\n StringWriter sw = new StringWriter();\n PrintWriter writer = new PrintWriter(sw);\n\n ClassTypeInfo type = model.getType();\n\n if (index == 0) {\n Util.generateLicense(writer);\n registerJvmClasses();\n for (Object fqcn : jvmClasses(\"api\")) {\n JVMClass.generateDTS(writer, fqcn.toString());\n }\n\n // include a file if present\n writer.print(includeFileIfPresent(\"index.header.d.ts\"));\n\n if (!type.getModuleName().equals(\"vertx\")) {\n if (isOptionalModule(\"@vertx/core\")) {\n writer.println(\"// @ts-ignore\");\n }\n // hard coded imports for non codegen types\n writer.print(\"import { Handler, AsyncResult } from '@vertx/core';\\n\\n\");\n }\n } else {\n writer.print(\"\\n\");\n }\n\n boolean imports = false;\n\n @SuppressWarnings(\"unchecked\")\n Map aliasMap = (Map) session.computeIfAbsent(\"aliasMap\", (a) -> new HashMap());\n for (ApiTypeInfo referencedType : model.getReferencedTypes()) {\n if (!sameModule(type, referencedType.getRaw())) {\n String simpleName = referencedType.getSimpleName();\n if (simpleName.equals(model.getIfaceSimpleName())) {\n String aliasName = simpleName + \"Super\";\n simpleName = simpleName + \" as \" + aliasName;\n aliasMap.put(referencedType.getName(), aliasName);\n }\n importType(writer, session, referencedType, simpleName, getNPMScope(referencedType.getRaw().getModule()));\n imports = true;\n }\n }\n for (ClassTypeInfo dataObjectType : model.getReferencedDataObjectTypes()) {\n if (sameModule(type, dataObjectType.getRaw())) {\n importType(writer, session, dataObjectType, dataObjectType.getSimpleName(), \"./options\");\n imports = true;\n } else {\n importType(writer, session, dataObjectType, dataObjectType.getSimpleName(), getNPMScope(dataObjectType.getRaw().getModule()) + \"/options\");\n imports = true;\n }\n }\n for (EnumTypeInfo enumType : model.getReferencedEnumTypes()) {\n if (enumType.getRaw().getModuleName() == null) {\n System.err.println(\"@@@ Missing module for ENUM: \" + enumType);\n continue;\n }\n if (sameModule(type, enumType.getRaw())) {\n importType(writer, session, enumType, enumType.getSimpleName(), \"./enums\");\n imports = true;\n } else {\n importType(writer, session, enumType, enumType.getSimpleName(), getNPMScope(enumType.getRaw().getModule()) + \"/enums\");\n imports = true;\n }\n }\n\n final Set superTypes = new HashSet<>();\n // ensure that all super types are also imported\n model.getAbstractSuperTypes().forEach(ti -> {\n if (!sameModule(type, ti.getRaw())) {\n importType(writer, session, ti, ti.getSimpleName(), getNPMScope(ti.getRaw().getModule()));\n }\n superTypes.add(genType(ti));\n });\n\n imports |= superTypes.size() > 0;\n\n if (model.isHandler()) {\n if (model.isConcrete()) {\n TypeInfo ti = model.getHandlerArg();\n if (!sameModule(type, ti.getRaw())) {\n importType(writer, session, ti, ti.getSimpleName(), getNPMScope(ti.getRaw().getModule()) + (ti.isDataObjectHolder() ? \"/options\" : \"\"));\n imports = true;\n }\n superTypes.add(\"Handler<\" + genType(ti) + \">\");\n }\n }\n\n if (imports) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, model.getDoc(), \"\");\n\n writer.printf(\"export %s %s%s\", model.isConcrete() ? \"abstract class\" : \"interface\", type.getSimpleName(), genGeneric(type.getParams()));\n\n if (model.isConcrete()) {\n if (model.getConcreteSuperType() != null) {\n String simpleName = aliasMap.get(model.getConcreteSuperType().getName());\n writer.printf(\" extends %s\", simpleName != null ? simpleName : genType(model.getConcreteSuperType()));\n }\n if (!superTypes.isEmpty()) {\n writer.printf(\" implements %s\", String.join(\", \", superTypes));\n }\n } else {\n if (model.isHandler()) {\n writer.printf(\" extends Handler<%s>\", genType(model.getHandlerArg()));\n if (!superTypes.isEmpty()) {\n writer.printf(\", %s\", String.join(\", \", superTypes));\n }\n } else {\n if (!superTypes.isEmpty()) {\n writer.printf(\" extends %s\", String.join(\", \", superTypes));\n }\n }\n }\n\n writer.print(\" {\\n\");\n\n boolean moreConstants = false;\n boolean hasConstantInInterface = !model.isConcrete() && model.getConstants().size() > 0;\n\n // this looks awkward (and it is) but TS does not allow static constants in interfaces\n // so they get listed on the abstract classes.\n if (model.isConcrete()) {\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n }\n\n boolean moreMethods = false;\n boolean hasStaticMethodsInInterface = false;\n\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!model.isConcrete() && method.isStaticMethod()) {\n hasStaticMethodsInInterface = true;\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n // BEGIN of non polyglot methods...\n\n for (MethodInfo method : model.getAnyJavaTypeMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n\n\n // if the model is not concrete (interface) we need to merge types to allow declaring the constants\n // from the java interface\n\n if (hasConstantInInterface || hasStaticMethodsInInterface) {\n writer.print(\"\\n\");\n writer.printf(\"export abstract class %s%s implements %s%s {\\n\", type.getSimpleName(), genGeneric(type.getParams()), type.getSimpleName(), genGeneric(type.getParams()));\n\n moreConstants = false;\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n\n moreMethods = false;\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!method.isStaticMethod()) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n }\n\n if (index == size - 1) {\n // include a file if present\n writer.print(includeFileIfPresent(\"index.footer.d.ts\"));\n }\n\n return sw.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n final Set artifacts = new HashSet<>();\n installNodeModules(artifacts);\n\n final File base = new File(cwd, \"node_modules\");\n final File libs = new File(base, \".lib\");\n\n if (force || libs.exists()) {\n final double version = Double.parseDouble(System.getProperty(\"java.specification.version\"));\n final String vm = System.getProperty(\"java.vm.name\");\n // from graal 20.0.0 the vm name doesn't contain graalvm in the name\n // but it is now part of the vendor version\n final String vendor = System.getProperty(\"java.vendor.version\");\n if (!vm.toLowerCase().contains(\"graalvm\") || !vendor.toLowerCase().contains(\"graalvm\")) {\n\n // not on graal, install graaljs and dependencies\n warn(\"Installing GraalJS...\");\n // graaljs + dependencies\n installGraalJS(artifacts);\n\n if (version >= 11) {\n // verify if the current JDK contains the jdk.internal.vm.ci module\n try {\n String modules = exec(javaHomePrefix() + \"java\", \"--list-modules\");\n if (modules.contains(\"jdk.internal.vm.ci\")) {\n warn(\"Installing JVMCI Compiler...\");\n // jvmci compiler + dependencies\n installGraalJMVCICompiler();\n }\n } catch (IOException | InterruptedException e) {\n err(e.getMessage());\n }\n } else {\n warn(\"Current JDK only supports GraalJS in Interpreted mode!\");\n }\n }\n }\n\n // always create a launcher even if no dependencies are needed\n createLauncher(artifacts);\n // always install the es4x type definitions\n installTypeDefinitions();\n } \n #location 15 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void run() {\n final Set artifacts = new HashSet<>();\n installNodeModules(artifacts);\n\n final File base = new File(cwd, \"node_modules\");\n final File libs = new File(base, \".lib\");\n\n if (force || libs.exists()) {\n final double version = Double.parseDouble(System.getProperty(\"java.specification.version\"));\n final String vm = System.getProperty(\"java.vm.name\");\n // from graal 20.0.0 the vm name doesn't contain graalvm in the name\n // but it is now part of the vendor version\n final String vendor = System.getProperty(\"java.vendor.version\");\n if (!vm.toLowerCase().contains(\"graalvm\") && vendor != null && !vendor.toLowerCase().contains(\"graalvm\")) {\n\n // not on graal, install graaljs and dependencies\n warn(\"Installing GraalJS...\");\n // graaljs + dependencies\n installGraalJS(artifacts);\n\n if (version >= 11) {\n // verify if the current JDK contains the jdk.internal.vm.ci module\n try {\n String modules = exec(javaHomePrefix() + \"java\", \"--list-modules\");\n if (modules.contains(\"jdk.internal.vm.ci\")) {\n warn(\"Installing JVMCI Compiler...\");\n // jvmci compiler + dependencies\n installGraalJMVCICompiler();\n }\n } catch (IOException | InterruptedException e) {\n err(e.getMessage());\n }\n } else {\n warn(\"Current JDK only supports GraalJS in Interpreted mode!\");\n }\n }\n }\n\n // always create a launcher even if no dependencies are needed\n createLauncher(artifacts);\n // always install the es4x type definitions\n installTypeDefinitions();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public String render(ClassModel model, int index, int size, Map session) {\n\n if (isExcludedClass(model.getType().getName())) {\n return null;\n }\n\n StringWriter sw = new StringWriter();\n PrintWriter writer = new PrintWriter(sw);\n\n ClassTypeInfo type = model.getType();\n\n if (index == 0) {\n Util.generateLicense(writer);\n registerJvmClasses();\n for (Object fqcn : jvmClasses()) {\n JVMClass.generateDTS(writer, fqcn.toString());\n }\n\n // include a file if present\n writer.print(includeFileIfPresent(\"index.header.d.ts\"));\n\n if (!type.getModuleName().equals(\"vertx\")) {\n if (isOptionalModule(\"@vertx/core\")) {\n writer.println(\"// @ts-ignore\");\n }\n // hard coded imports for non codegen types\n writer.print(\"import { Handler, AsyncResult } from '@vertx/core';\\n\\n\");\n }\n } else {\n writer.print(\"\\n\");\n }\n\n boolean imports = false;\n\n @SuppressWarnings(\"unchecked\")\n Map aliasMap = (Map) session.computeIfAbsent(\"aliasMap\", (a) -> new HashMap());\n for (ApiTypeInfo referencedType : model.getReferencedTypes()) {\n if (!isImported(referencedType, session)) {\n if (!referencedType.getRaw().getModuleName().equals(type.getModuleName())) {\n String simpleName = referencedType.getSimpleName();\n if (simpleName.equals(model.getIfaceSimpleName())) {\n String aliasName = simpleName + \"Super\";\n simpleName = simpleName + \" as \" + aliasName;\n aliasMap.put(referencedType.getName(), aliasName);\n }\n // ignore missing imports\n if (isOptionalModule(getNPMScope(referencedType.getRaw().getModule()))) {\n writer.println(\"// @ts-ignore\");\n }\n writer.printf(\"import { %s } from '%s';\\n\", simpleName, getNPMScope(referencedType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n for (ClassTypeInfo dataObjectType : model.getReferencedDataObjectTypes()) {\n if (!isImported(dataObjectType, session)) {\n if (dataObjectType.getRaw().getModuleName().equals(type.getModuleName())) {\n writer.printf(\"import { %s } from './options';\\n\", dataObjectType.getSimpleName());\n imports = true;\n } else {\n writer.printf(\"import { %s } from '%s/options';\\n\", dataObjectType.getSimpleName(), getNPMScope(dataObjectType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n for (EnumTypeInfo enumType : model.getReferencedEnumTypes()) {\n if (!isImported(enumType, session)) {\n if (enumType.getRaw().getModuleName().equals(type.getModuleName())) {\n writer.printf(\"import { %s } from './enums';\\n\", enumType.getSimpleName());\n imports = true;\n } else {\n writer.printf(\"import { %s } from '%s/enums';\\n\", enumType.getSimpleName(), getNPMScope(enumType.getRaw().getModule()));\n imports = true;\n }\n }\n }\n\n if (imports) {\n writer.print(\"\\n\");\n }\n\n final Set superTypes = new HashSet<>();\n model.getAbstractSuperTypes().forEach(ti -> superTypes.add(genType(ti)));\n\n if (model.isHandler()) {\n if (model.isConcrete()) {\n superTypes.add(\"Handler<\" + genType(model.getHandlerArg()) + \">\");\n }\n }\n\n generateDoc(writer, model.getDoc(), \"\");\n\n writer.printf(\"export %s %s%s\", model.isConcrete() ? \"abstract class\" : \"interface\", type.getSimpleName(), genGeneric(type.getParams()));\n\n if (model.isConcrete()) {\n if (model.getConcreteSuperType() != null) {\n String simpleName = aliasMap.get(model.getConcreteSuperType().getName());\n writer.printf(\" extends %s\", simpleName != null ? simpleName : genType(model.getConcreteSuperType()));\n }\n if (!superTypes.isEmpty()) {\n writer.printf(\" implements %s\", String.join(\", \", superTypes));\n }\n } else {\n if (model.isHandler()) {\n writer.printf(\" extends Handler<%s>\", genType(model.getHandlerArg()));\n if (!superTypes.isEmpty()) {\n writer.printf(\", %s\", String.join(\", \", superTypes));\n }\n } else {\n if (!superTypes.isEmpty()) {\n writer.printf(\" extends %s\", String.join(\", \", superTypes));\n }\n }\n }\n\n writer.print(\" {\\n\");\n\n boolean moreConstants = false;\n boolean hasConstantInInterface = !model.isConcrete() && model.getConstants().size() > 0;\n\n // this looks awkward (and it is) but TS does not allow static constants in interfaces\n // so they get listed on the abstract classes.\n if (model.isConcrete()) {\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n }\n\n boolean moreMethods = false;\n boolean hasStaticMethodsInInterface = false;\n\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!model.isConcrete() && method.isStaticMethod()) {\n hasStaticMethodsInInterface = true;\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n // BEGIN of non polyglot methods...\n\n for (MethodInfo method : model.getAnyJavaTypeMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n\n\n // if the model is not concrete (interface) we need to merge types to allow declaring the constants\n // from the java interface\n\n if (hasConstantInInterface || hasStaticMethodsInInterface) {\n writer.print(\"\\n\");\n writer.printf(\"export abstract class %s%s implements %s%s {\\n\", type.getSimpleName(), genGeneric(type.getParams()), type.getSimpleName(), genGeneric(type.getParams()));\n\n moreConstants = false;\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n\n moreMethods = false;\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!method.isStaticMethod()) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n }\n\n if (index == size - 1) {\n // include a file if present\n writer.print(includeFileIfPresent(\"index.footer.d.ts\"));\n }\n\n return sw.toString();\n } \n #location 218 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n public String render(ClassModel model, int index, int size, Map session) {\n\n if (isExcludedClass(model.getType().getName())) {\n return null;\n }\n\n StringWriter sw = new StringWriter();\n PrintWriter writer = new PrintWriter(sw);\n\n ClassTypeInfo type = model.getType();\n\n if (index == 0) {\n Util.generateLicense(writer);\n registerJvmClasses();\n for (Object fqcn : jvmClasses(\"api\")) {\n JVMClass.generateDTS(writer, fqcn.toString());\n }\n\n // include a file if present\n writer.print(includeFileIfPresent(\"index.header.d.ts\"));\n\n if (!type.getModuleName().equals(\"vertx\")) {\n if (isOptionalModule(\"@vertx/core\")) {\n writer.println(\"// @ts-ignore\");\n }\n // hard coded imports for non codegen types\n writer.print(\"import { Handler, AsyncResult } from '@vertx/core';\\n\\n\");\n }\n } else {\n writer.print(\"\\n\");\n }\n\n boolean imports = false;\n\n @SuppressWarnings(\"unchecked\")\n Map aliasMap = (Map) session.computeIfAbsent(\"aliasMap\", (a) -> new HashMap());\n for (ApiTypeInfo referencedType : model.getReferencedTypes()) {\n if (!sameModule(type, referencedType.getRaw())) {\n String simpleName = referencedType.getSimpleName();\n if (simpleName.equals(model.getIfaceSimpleName())) {\n String aliasName = simpleName + \"Super\";\n simpleName = simpleName + \" as \" + aliasName;\n aliasMap.put(referencedType.getName(), aliasName);\n }\n importType(writer, session, referencedType, simpleName, getNPMScope(referencedType.getRaw().getModule()));\n imports = true;\n }\n }\n for (ClassTypeInfo dataObjectType : model.getReferencedDataObjectTypes()) {\n if (sameModule(type, dataObjectType.getRaw())) {\n importType(writer, session, dataObjectType, dataObjectType.getSimpleName(), \"./options\");\n imports = true;\n } else {\n importType(writer, session, dataObjectType, dataObjectType.getSimpleName(), getNPMScope(dataObjectType.getRaw().getModule()) + \"/options\");\n imports = true;\n }\n }\n for (EnumTypeInfo enumType : model.getReferencedEnumTypes()) {\n if (enumType.getRaw().getModuleName() == null) {\n System.err.println(\"@@@ Missing module for ENUM: \" + enumType);\n continue;\n }\n if (sameModule(type, enumType.getRaw())) {\n importType(writer, session, enumType, enumType.getSimpleName(), \"./enums\");\n imports = true;\n } else {\n importType(writer, session, enumType, enumType.getSimpleName(), getNPMScope(enumType.getRaw().getModule()) + \"/enums\");\n imports = true;\n }\n }\n\n final Set superTypes = new HashSet<>();\n // ensure that all super types are also imported\n model.getAbstractSuperTypes().forEach(ti -> {\n if (!sameModule(type, ti.getRaw())) {\n importType(writer, session, ti, ti.getSimpleName(), getNPMScope(ti.getRaw().getModule()));\n }\n superTypes.add(genType(ti));\n });\n\n imports |= superTypes.size() > 0;\n\n if (model.isHandler()) {\n if (model.isConcrete()) {\n TypeInfo ti = model.getHandlerArg();\n if (!sameModule(type, ti.getRaw())) {\n importType(writer, session, ti, ti.getSimpleName(), getNPMScope(ti.getRaw().getModule()) + (ti.isDataObjectHolder() ? \"/options\" : \"\"));\n imports = true;\n }\n superTypes.add(\"Handler<\" + genType(ti) + \">\");\n }\n }\n\n if (imports) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, model.getDoc(), \"\");\n\n writer.printf(\"export %s %s%s\", model.isConcrete() ? \"abstract class\" : \"interface\", type.getSimpleName(), genGeneric(type.getParams()));\n\n if (model.isConcrete()) {\n if (model.getConcreteSuperType() != null) {\n String simpleName = aliasMap.get(model.getConcreteSuperType().getName());\n writer.printf(\" extends %s\", simpleName != null ? simpleName : genType(model.getConcreteSuperType()));\n }\n if (!superTypes.isEmpty()) {\n writer.printf(\" implements %s\", String.join(\", \", superTypes));\n }\n } else {\n if (model.isHandler()) {\n writer.printf(\" extends Handler<%s>\", genType(model.getHandlerArg()));\n if (!superTypes.isEmpty()) {\n writer.printf(\", %s\", String.join(\", \", superTypes));\n }\n } else {\n if (!superTypes.isEmpty()) {\n writer.printf(\" extends %s\", String.join(\", \", superTypes));\n }\n }\n }\n\n writer.print(\" {\\n\");\n\n boolean moreConstants = false;\n boolean hasConstantInInterface = !model.isConcrete() && model.getConstants().size() > 0;\n\n // this looks awkward (and it is) but TS does not allow static constants in interfaces\n // so they get listed on the abstract classes.\n if (model.isConcrete()) {\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n }\n\n boolean moreMethods = false;\n boolean hasStaticMethodsInInterface = false;\n\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!model.isConcrete() && method.isStaticMethod()) {\n hasStaticMethodsInInterface = true;\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n // BEGIN of non polyglot methods...\n\n for (MethodInfo method : model.getAnyJavaTypeMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n\n\n // if the model is not concrete (interface) we need to merge types to allow declaring the constants\n // from the java interface\n\n if (hasConstantInInterface || hasStaticMethodsInInterface) {\n writer.print(\"\\n\");\n writer.printf(\"export abstract class %s%s implements %s%s {\\n\", type.getSimpleName(), genGeneric(type.getParams()), type.getSimpleName(), genGeneric(type.getParams()));\n\n moreConstants = false;\n for (ConstantInfo constant : model.getConstants()) {\n if (moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateDoc(writer, constant.getDoc(), \" \");\n\n writer.printf(\" static readonly %s : %s;\\n\", constant.getName(), genType(constant.getType()));\n moreConstants = true;\n }\n\n moreMethods = false;\n for (MethodInfo method : model.getMethods()) {\n if (isExcluded(type.getSimpleName(), method.getName(), method.getParams())) {\n continue;\n }\n\n if (!method.isStaticMethod()) {\n continue;\n }\n\n if (moreMethods || moreConstants) {\n writer.print(\"\\n\");\n }\n\n generateMethod(writer, type, method);\n moreMethods = true;\n }\n\n writer.print(\"}\\n\");\n }\n\n if (index == size - 1) {\n // include a file if present\n writer.print(includeFileIfPresent(\"index.footer.d.ts\"));\n }\n\n return sw.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n final Set artifacts = new HashSet<>();\n installNodeModules(artifacts);\n\n final File base = new File(cwd, \"node_modules\");\n final File libs = new File(base, \".lib\");\n\n if (force || libs.exists()) {\n final double version = Double.parseDouble(System.getProperty(\"java.specification.version\"));\n final String vm = System.getProperty(\"java.vm.name\");\n // from graal 20.0.0 the vm name doesn't contain graalvm in the name\n // but it is now part of the vendor version\n final String vendor = System.getProperty(\"java.vendor.version\");\n if (!vm.toLowerCase().contains(\"graalvm\") && vendor != null && !vendor.toLowerCase().contains(\"graalvm\")) {\n\n // not on graal, install graaljs and dependencies\n warn(\"Installing GraalJS...\");\n // graaljs + dependencies\n installGraalJS(artifacts);\n\n if (version >= 11) {\n // verify if the current JDK contains the jdk.internal.vm.ci module\n try {\n String modules = exec(javaHomePrefix() + \"java\", \"--list-modules\");\n if (modules.contains(\"jdk.internal.vm.ci\")) {\n warn(\"Installing JVMCI Compiler...\");\n // jvmci compiler + dependencies\n installGraalJMVCICompiler();\n }\n } catch (IOException | InterruptedException e) {\n err(e.getMessage());\n }\n } else {\n warn(\"Current JDK only supports GraalJS in Interpreted mode!\");\n }\n }\n }\n\n // always create a launcher even if no dependencies are needed\n createLauncher(artifacts);\n // always install the es4x type definitions\n installTypeDefinitions();\n } \n #location 15 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void run() {\n final Set artifacts = new HashSet<>();\n installNodeModules(artifacts);\n\n final File base = new File(cwd, \"node_modules\");\n final File libs = new File(base, \".lib\");\n\n if (force || libs.exists()) {\n final double version = Double.parseDouble(System.getProperty(\"java.specification.version\"));\n final boolean isGraalVM =\n System.getProperty(\"java.vm.name\", \"\").toLowerCase().contains(\"graalvm\") ||\n // from graal 20.0.0 the vm name doesn't contain graalvm in the name\n // but it is now part of the vendor version\n System.getProperty(\"java.vendor.version\", \"\").toLowerCase().contains(\"graalvm\");\n\n if (!isGraalVM) {\n\n // not on graal, install graaljs and dependencies\n warn(\"Installing GraalJS...\");\n // graaljs + dependencies\n installGraalJS(artifacts);\n\n if (version >= 11) {\n // verify if the current JDK contains the jdk.internal.vm.ci module\n try {\n String modules = exec(javaHomePrefix() + \"java\", \"--list-modules\");\n if (modules.contains(\"jdk.internal.vm.ci\")) {\n warn(\"Installing JVMCI Compiler...\");\n // jvmci compiler + dependencies\n installGraalJMVCICompiler();\n }\n } catch (IOException | InterruptedException e) {\n err(e.getMessage());\n }\n } else {\n warn(\"Current JDK only supports GraalJS in Interpreted mode!\");\n }\n }\n }\n\n // always create a launcher even if no dependencies are needed\n createLauncher(artifacts);\n // always install the es4x type definitions\n installTypeDefinitions();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String injectVersion(String resourcePath) {\n URL resourceUrl = getResourceUrl(resourcePath);\n try {\n long lastModified = resourceUrl.openConnection().getLastModified();\n\n // check for extension\n int extensionAt = resourcePath.lastIndexOf('.');\n\n StringBuilder versionedResourcePath = new StringBuilder();\n\n if (extensionAt == -1) {\n versionedResourcePath.append(resourcePath);\n versionedResourcePath.append(\"-ver-\").append(lastModified);\n } else {\n versionedResourcePath.append(resourcePath.substring(0, extensionAt));\n versionedResourcePath.append(\"-ver-\").append(lastModified);\n versionedResourcePath.append(resourcePath.substring(extensionAt, resourcePath.length()));\n }\n\n log.trace(\"Inject version in resource path: '{}' => '{}'\", resourcePath, versionedResourcePath);\n\n return versionedResourcePath.toString();\n } catch (IOException e) {\n throw new PippoRuntimeException(\"Failed to read lastModified property for {}\", e, resourceUrl);\n }\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public String injectVersion(String resourcePath) {\n String version = getResourceVersion(resourcePath);\n if (StringUtils.isNullOrEmpty(version)) {\n // unversioned, pass-through resource path\n return resourcePath;\n }\n\n // check for extension\n int extensionAt = resourcePath.lastIndexOf('.');\n\n StringBuilder versionedResourcePath = new StringBuilder();\n\n if (extensionAt == -1) {\n versionedResourcePath.append(resourcePath);\n versionedResourcePath.append(\"-ver-\").append(version);\n } else {\n versionedResourcePath.append(resourcePath.substring(0, extensionAt));\n versionedResourcePath.append(\"-ver-\").append(version);\n versionedResourcePath.append(resourcePath.substring(extensionAt, resourcePath.length()));\n }\n\n log.trace(\"Inject version in resource path: '{}' => '{}'\", resourcePath, versionedResourcePath);\n\n return versionedResourcePath.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @BeforeClass\n public static void setUpClass() {\n application = new Application();\n client = XmemcachedFactory.create(application.getPippoSettings());\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @BeforeClass\n public static void setUpClass() throws IOException {\n MemcachedStarter runtime = MemcachedStarter.getDefaultInstance();\n memcachedExe = runtime.prepare(\n new MemcachedConfig(Version.Main.PRODUCTION, PORT));\n memcached = memcachedExe.start();\n client = new XMemcachedClient(new InetSocketAddress(HOST, PORT));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public TemplateEngine getTemplateEngine() {\n if (templateEngine == null) {\n TemplateEngine engine = ServiceLocator.locate(TemplateEngine.class);\n setTemplateEngine(engine);\n }\n\n return templateEngine;\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public TemplateEngine getTemplateEngine() {\n return templateEngine;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @BeforeClass\n public static void setUpClass() {\n application = new Application();\n client = SpymemcachedFactory.create(application.getPippoSettings());\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @BeforeClass\n public static void setUpClass() throws IOException {\n MemcachedStarter runtime = MemcachedStarter.getDefaultInstance();\n memcachedExe = runtime.prepare(\n new MemcachedConfig(Version.Main.PRODUCTION, PORT));\n memcached = memcachedExe.start();\n client = new MemcachedClient(new InetSocketAddress(HOST, PORT));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void classpathResourceHandlerTest() throws URISyntaxException {\n ClasspathResourceHandler handler = new ClasspathResourceHandler(\"/\", \"/public\");\n\n URL resourceUrl = handler.getResourceUrl(\"VISIBLE\");\n assertNotNull(resourceUrl);\n Path visibleFile = Paths.get(resourceUrl.toURI());\n assertNotNull(visibleFile);\n Path basePath = visibleFile.getParent();\n URL url = handler.getResourceUrl(\"../HIDDEN\");\n assertNotNull(url);\n assertTrue(\"Path traversal security issue\", Paths.get(url.toURI()).startsWith(basePath));\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void classpathResourceHandlerTest() throws URISyntaxException {\n ClasspathResourceHandler handler = new ClasspathResourceHandler(\"/\", \"/public\");\n\n URL resourceUrl = handler.getResourceUrl(\"VISIBLE\");\n assertNotNull(resourceUrl);\n Path visibleFile = Paths.get(resourceUrl.toURI());\n assertNotNull(visibleFile);\n\n URL url = handler.getResourceUrl(\"../HIDDEN\");\n assertNull(url);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List toList(List defaultValue) {\n if (isNull() || (values.length == 1 && StringUtils.isNullOrEmpty(values[0]))) {\n return defaultValue;\n }\n\n if (values.length == 1) {\n String tmp = values[0];\n tmp = StringUtils.removeStart(tmp, \"[\");\n tmp = StringUtils.removeEnd(tmp, \"]\");\n\n return Arrays.asList(tmp.split(\"(,|\\\\|)\"));\n }\n\n return Arrays.asList(values);\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public List toList(List defaultValue) {\n if (isNull() || (values.length == 1 && StringUtils.isNullOrEmpty(values[0]))) {\n return defaultValue;\n }\n\n if (values.length == 1) {\n String tmp = values[0];\n tmp = StringUtils.removeStart(tmp, \"[\");\n tmp = StringUtils.removeEnd(tmp, \"]\");\n\n return StringUtils.getList(tmp, \"(,|\\\\|)\");\n }\n\n return Arrays.asList(values);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void publicResourceHandlerTest() throws URISyntaxException {\n PublicResourceHandler handler = new PublicResourceHandler();\n\n URL resourceUrl = handler.getResourceUrl(\"VISIBLE\");\n assertNotNull(resourceUrl);\n Path visibleFile = Paths.get(resourceUrl.toURI());\n assertNotNull(visibleFile);\n Path basePath = visibleFile.getParent();\n URL url = handler.getResourceUrl(\"../HIDDEN\");\n assertNotNull(url);\n assertTrue(\"Path traversal security issue\", Paths.get(url.toURI()).startsWith(basePath));\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void publicResourceHandlerTest() throws URISyntaxException {\n PublicResourceHandler handler = new PublicResourceHandler();\n\n URL resourceUrl = handler.getResourceUrl(\"VISIBLE\");\n assertNotNull(resourceUrl);\n Path visibleFile = Paths.get(resourceUrl.toURI());\n assertNotNull(visibleFile);\n\n URL url = handler.getResourceUrl(\"../HIDDEN\");\n assertNull(url);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String injectVersion(String resourcePath) {\n URL resourceUrl = getResourceUrl(resourcePath);\n try {\n long lastModified = resourceUrl.openConnection().getLastModified();\n\n // check for extension\n int extensionAt = resourcePath.lastIndexOf('.');\n\n StringBuilder versionedResourcePath = new StringBuilder();\n\n if (extensionAt == -1) {\n versionedResourcePath.append(resourcePath);\n versionedResourcePath.append(\"-ver-\").append(lastModified);\n } else {\n versionedResourcePath.append(resourcePath.substring(0, extensionAt));\n versionedResourcePath.append(\"-ver-\").append(lastModified);\n versionedResourcePath.append(resourcePath.substring(extensionAt, resourcePath.length()));\n }\n\n log.trace(\"Inject version in resource path: '{}' => '{}'\", resourcePath, versionedResourcePath);\n\n return versionedResourcePath.toString();\n } catch (IOException e) {\n throw new PippoRuntimeException(\"Failed to read lastModified property for {}\", e, resourceUrl);\n }\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public String injectVersion(String resourcePath) {\n String version = getResourceVersion(resourcePath);\n if (StringUtils.isNullOrEmpty(version)) {\n // unversioned, pass-through resource path\n return resourcePath;\n }\n\n // check for extension\n int extensionAt = resourcePath.lastIndexOf('.');\n\n StringBuilder versionedResourcePath = new StringBuilder();\n\n if (extensionAt == -1) {\n versionedResourcePath.append(resourcePath);\n versionedResourcePath.append(\"-ver-\").append(version);\n } else {\n versionedResourcePath.append(resourcePath.substring(0, extensionAt));\n versionedResourcePath.append(\"-ver-\").append(version);\n versionedResourcePath.append(resourcePath.substring(extensionAt, resourcePath.length()));\n }\n\n log.trace(\"Inject version in resource path: '{}' => '{}'\", resourcePath, versionedResourcePath);\n\n return versionedResourcePath.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n String buildRealData(final ConditionZkDTO condition, final ServerWebExchange exchange) {\n String realData = \"\";\n if (condition.getParamType().equals(ParamTypeEnum.QUERY.getName())) {\n final MultiValueMap queryParams = exchange.getRequest().getQueryParams();\n realData = queryParams.getFirst(condition.getParamName());\n } else if (Objects.equals(ParamTypeEnum.HOST.getName(), condition.getParamType())) {\n realData = exchange.getRequest().getRemoteAddress().getHostString();\n } else if (Objects.equals(ParamTypeEnum.IP.getName(), condition.getParamType())) {\n realData = exchange.getRequest().getRemoteAddress().getAddress().getHostAddress();\n } else if (Objects.equals(ParamTypeEnum.HEADER.getName(), condition.getParamType())) {\n final HttpHeaders headers = exchange.getRequest().getHeaders();\n final List list = headers.get(condition.getParamName());\n if (CollectionUtils.isEmpty(list)) {\n return realData;\n }\n realData = headers.get(condition.getParamName()).stream().findFirst().orElse(\"\");\n }\n return realData;\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n String buildRealData(final ConditionZkDTO condition, final ServerWebExchange exchange) {\n String realData = \"\";\n if (condition.getParamType().equals(ParamTypeEnum.QUERY.getName())) {\n final MultiValueMap queryParams = exchange.getRequest().getQueryParams();\n realData = queryParams.getFirst(condition.getParamName());\n } else if (Objects.equals(ParamTypeEnum.HOST.getName(), condition.getParamType())) {\n realData = Objects.requireNonNull(exchange.getRequest().getRemoteAddress()).getHostString();\n } else if (Objects.equals(ParamTypeEnum.IP.getName(), condition.getParamType())) {\n realData = Objects.requireNonNull(exchange.getRequest().getRemoteAddress()).getAddress().getHostAddress();\n } else if (Objects.equals(ParamTypeEnum.HEADER.getName(), condition.getParamType())) {\n final HttpHeaders headers = exchange.getRequest().getHeaders();\n final List list = headers.get(condition.getParamName());\n if (CollectionUtils.isEmpty(list)) {\n return realData;\n }\n realData = Objects.requireNonNull(headers.get(condition.getParamName())).stream().findFirst().orElse(\"\");\n }\n return realData;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void roundRobinLoadBalanceTest() {\n\n List divideUpstreamList =\n Arrays.asList(50, 20, 30).stream()\n .map(weight -> {\n DivideUpstream divideUpstream = new DivideUpstream();\n divideUpstream.setUpstreamUrl(\"divide-upstream-\" + weight);\n divideUpstream.setWeight(weight);\n return divideUpstream;\n })\n .collect(Collectors.toList());\n\n RoundRobinLoadBalance roundRobinLoadBalance = new RoundRobinLoadBalance();\n Map countMap = new HashMap<>();\n for(int i=0; i<100; i++) {\n DivideUpstream result = roundRobinLoadBalance.select(divideUpstreamList, \"\");\n int count = countMap.getOrDefault(result.getUpstreamUrl(), 0);\n countMap.put(result.getUpstreamUrl(), ++count);\n }\n\n Assert.assertEquals(50, countMap.get(\"divide-upstream-50\").intValue());\n } \n #location 22 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void roundRobinLoadBalanceTest() {\n\n List divideUpstreamList =\n Stream.of(50, 20, 30)\n .map(weight -> {\n DivideUpstream divideUpstream = new DivideUpstream();\n divideUpstream.setUpstreamUrl(\"divide-upstream-\" + weight);\n divideUpstream.setWeight(weight);\n return divideUpstream;\n })\n .collect(Collectors.toList());\n\n RoundRobinLoadBalance roundRobinLoadBalance = new RoundRobinLoadBalance();\n Map countMap = new HashMap<>();\n for (int i = 0; i < 120; i++) {\n DivideUpstream result = roundRobinLoadBalance.select(divideUpstreamList, \"\");\n int count = countMap.getOrDefault(result.getUpstreamUrl(), 0);\n countMap.put(result.getUpstreamUrl(), ++count);\n }\n\n Assert.assertEquals(50, countMap.get(\"divide-upstream-50\").intValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n int port;\n InetSocketAddress socket;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n socket = new InetSocketAddress(args[0], port);\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n socket = new InetSocketAddress(port);\n file = args[1];\n }\n\n new JmxCollector(new File(file)).register();\n DefaultExports.initialize();\n\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n pool.setMaxThreads(10);\n pool.setName(\"jmx_exporter\");\n server = new Server(pool);\n\n ServerConnector cnx = new ServerConnector(server);\n cnx.setReuseAddress(true);\n cnx.setHost(socket.getHostName());\n cnx.setPort(port);\n\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n context.addFilter(GzipFilter.class, \"/*\", null);\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n } \n #location 34 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n String host;\n int port;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n host = args[0];\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n host = \"0.0.0.0\";\n file = args[1];\n }\n\n new JmxCollector(new File(file)).register();\n DefaultExports.initialize();\n\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n pool.setMaxThreads(10);\n pool.setName(\"jmx_exporter\");\n server = new Server(pool);\n\n ServerConnector connector = new ServerConnector(server);\n connector.setReuseAddress(true);\n connector.setHost(host);\n connector.setPort(port);\n server.setConnectors(new Connector[]{connector});\n\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n context.addFilter(GzipFilter.class, \"/*\", null);\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n\n server.start();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = getClass().getClassLoader().getResource(\"test.yml\").getFile();\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n\n final String javaHome = System.getenv(\"JAVA_HOME\");\n final String java;\n if (javaHome != null && javaHome.equals(\"\")) {\n java = javaHome + \"/bin/java\";\n } else {\n java = \"java\";\n }\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n InputStream stream = new URL(\"http://localhost:\" + port + \"/metrics\").openStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n } \n #location 47 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = getClass().getClassLoader().getResource(\"test.yml\").getFile();\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n\n final String javaHome = System.getenv(\"JAVA_HOME\");\n final String java;\n if (javaHome != null && javaHome.equals(\"\")) {\n java = javaHome + \"/bin/java\";\n } else {\n java = \"java\";\n }\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n URL uri = new URL(\"http://localhost:\" + port + \"/metrics\");\n HttpURLConnection cnx = (HttpURLConnection) uri.openConnection();\n InputStream stream = cnx.getInputStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n cnx.disconnect();\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } catch (Throwable ex) {\n assertThat(\"Expection caught during scraping\", false);\n ex.printStackTrace();\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] args) throws Exception {\n if (args.length < 2) {\n System.err.println(\"Usage: WebServer \");\n System.exit(1);\n }\n JmxCollector jc = new JmxCollector(new FileReader(args[1])).register();\n\n int port = Integer.parseInt(args[0]);\n Server server = new Server(port);\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n server.join();\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void main(String[] args) throws Exception {\n if (args.length < 2) {\n System.err.println(\"Usage: WebServer \");\n System.exit(1);\n }\n JmxCollector jc = new JmxCollector(new File(args[1])).register();\n\n int port = Integer.parseInt(args[0]);\n Server server = new Server(port);\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n server.join();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = getClass().getClassLoader().getResource(\"test.yml\").getFile();\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n\n final String javaHome = System.getenv(\"JAVA_HOME\");\n final String java;\n if (javaHome != null && javaHome.equals(\"\")) {\n java = javaHome + \"/bin/java\";\n } else {\n java = \"java\";\n }\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n InputStream stream = new URL(\"http://localhost:\" + port + \"/metrics\").openStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = getClass().getClassLoader().getResource(\"test.yml\").getFile();\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n\n final String javaHome = System.getenv(\"JAVA_HOME\");\n final String java;\n if (javaHome != null && javaHome.equals(\"\")) {\n java = javaHome + \"/bin/java\";\n } else {\n java = \"java\";\n }\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n URL uri = new URL(\"http://localhost:\" + port + \"/metrics\");\n HttpURLConnection cnx = (HttpURLConnection) uri.openConnection();\n InputStream stream = cnx.getInputStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n cnx.disconnect();\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } catch (Throwable ex) {\n assertThat(\"Expection caught during scraping\", false);\n ex.printStackTrace();\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = resolveRelativePathToResource(\"test.yml\");\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n\n final String javaHome = System.getenv(\"JAVA_HOME\");\n final String java;\n if (javaHome != null && javaHome.equals(\"\")) {\n java = javaHome + \"/bin/java\";\n } else {\n java = \"java\";\n }\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n InputStream stream = new URL(\"http://localhost:\" + port + \"/metrics\").openStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void agentLoads() throws IOException, InterruptedException {\n // If not starting the testcase via Maven, set the buildDirectory and finalName system properties manually.\n final String buildDirectory = (String) System.getProperties().get(\"buildDirectory\");\n final String finalName = (String) System.getProperties().get(\"finalName\");\n final int port = Integer.parseInt((String) System.getProperties().get(\"it.port\"));\n final String config = resolveRelativePathToResource(\"test.yml\");\n final String javaagent = \"-javaagent:\" + buildDirectory + \"/\" + finalName + \".jar=\" + port + \":\" + config;\n final String java = buildJavaPath(System.getenv(\"JAVA_HOME\"));\n\n final Process app = new ProcessBuilder()\n .command(java, javaagent, \"-cp\", buildClasspath(), \"io.prometheus.jmx.TestApplication\")\n .start();\n try {\n // Wait for application to start\n app.getInputStream().read();\n\n InputStream stream = new URL(\"http://localhost:\" + port + \"/metrics\").openStream();\n BufferedReader contents = new BufferedReader(new InputStreamReader(stream));\n boolean found = false;\n while (!found) {\n String line = contents.readLine();\n if (line == null) {\n break;\n }\n if (line.contains(\"jmx_scrape_duration_seconds\")) {\n found = true;\n }\n }\n\n assertThat(\"Expected metric not found\", found);\n\n // Tell application to stop\n app.getOutputStream().write('\\n');\n try {\n app.getOutputStream().flush();\n } catch (IOException ignored) {\n }\n } finally {\n final int exitcode = app.waitFor();\n // Log any errors printed\n int len;\n byte[] buffer = new byte[100];\n while ((len = app.getErrorStream().read(buffer)) != -1) {\n System.out.write(buffer, 0, len);\n }\n\n assertThat(\"Application did not exit cleanly\", exitcode == 0);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n String host;\n int port;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n host = args[0];\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n host = \"0.0.0.0\";\n file = args[1];\n }\n\n new JmxCollector(new File(file)).register();\n DefaultExports.initialize();\n\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n pool.setMaxThreads(10);\n pool.setName(\"jmx_exporter\");\n server = new Server(pool);\n\n ServerConnector connector = new ServerConnector(server);\n connector.setReuseAddress(true);\n connector.setHost(host);\n connector.setPort(port);\n server.setConnectors(new Connector[]{connector});\n\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n context.addFilter(GzipFilter.class, \"/*\", null);\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n\n server.start();\n } \n #location 35 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n int port;\n InetSocketAddress socket;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n socket = new InetSocketAddress(args[0], port);\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n socket = new InetSocketAddress(port);\n file = args[1];\n }\n\n new JmxCollector(new File(file)).register();\n DefaultExports.initialize();\n\n server = new Server();\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n pool.setMaxThreads(10);\n pool.setMaxQueued(10);\n pool.setName(\"jmx_exporter\");\n server.setThreadPool(pool);\n SelectChannelConnector connector = new SelectChannelConnector();\n connector.setHost(socket.getHostName());\n connector.setPort(socket.getPort());\n connector.setAcceptors(1);\n server.addConnector(connector);\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n int port;\n InetSocketAddress socket;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n socket = new InetSocketAddress(args[0], port);\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n socket = new InetSocketAddress(port);\n file = args[1];\n }\n\n new JmxCollector(new FileReader(file)).register();\n DefaultExports.initialize();\n\n server = new Server(socket);\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n server.setThreadPool(pool);\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n } \n #location 22 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void premain(String agentArgument, Instrumentation instrumentation) throws Exception {\n String[] args = agentArgument.split(\":\");\n if (args.length < 2 || args.length > 3) {\n System.err.println(\"Usage: -javaagent:/path/to/JavaAgent.jar=[host:]:\");\n System.exit(1);\n }\n\n int port;\n InetSocketAddress socket;\n String file;\n\n if (args.length == 3) {\n port = Integer.parseInt(args[1]);\n socket = new InetSocketAddress(args[0], port);\n file = args[2];\n } else {\n port = Integer.parseInt(args[0]);\n socket = new InetSocketAddress(port);\n file = args[1];\n }\n\n new JmxCollector(new File(file)).register();\n DefaultExports.initialize();\n\n server = new Server(socket);\n QueuedThreadPool pool = new QueuedThreadPool();\n pool.setDaemon(true);\n server.setThreadPool(pool);\n ServletContextHandler context = new ServletContextHandler();\n context.setContextPath(\"/\");\n server.setHandler(context);\n context.addServlet(new ServletHolder(new MetricsServlet()), \"/metrics\");\n server.start();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @BeforeClass\n public static void beforeClass() {\n for (File file : customFileLog(\"\").listFiles()) {\n if (file.getPath().contains(\"tracer-self.log\") || file.getPath().contains(\"sync.log\")\n || file.getPath().contains(\"rpc-profile.log\")\n || file.getPath().contains(\"middleware_error.log\")) {\n continue;\n }\n FileUtils.deleteQuietly(file);\n }\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @BeforeClass\n public static void beforeClass() {\n File[] traceFiles = customFileLog(\"\").listFiles();\n if (traceFiles == null) {\n return;\n }\n for (File file : traceFiles) {\n if (file.getPath().contains(\"tracer-self.log\") || file.getPath().contains(\"sync.log\")\n || file.getPath().contains(\"rpc-profile.log\")\n || file.getPath().contains(\"middleware_error.log\")) {\n continue;\n }\n FileUtils.deleteQuietly(file);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected Map customSettingsFlat() {\n return ImmutableMap.builder()\n .put(HTTP_INCOMING_AUTH_TYPE, IlpOverHttpLinkSettings.AuthType.JWT_HS_256.name())\n .put(HTTP_INCOMING_TOKEN_ISSUER, \"https://incoming-issuer.example.com/\")\n .put(HTTP_INCOMING_SHARED_SECRET, \"incoming-credential\")\n .put(HTTP_INCOMING_TOKEN_AUDIENCE, \"https://incoming-audience.example.com/\")\n\n .put(HTTP_OUTGOING_AUTH_TYPE, IlpOverHttpLinkSettings.AuthType.SIMPLE.name())\n .put(HTTP_OUTGOING_TOKEN_SUBJECT, \"outgoing-subject\")\n .put(HTTP_OUTGOING_SHARED_SECRET, \"outgoing-credential\")\n .put(HTTP_OUTGOING_TOKEN_ISSUER, \"https://outgoing-issuer.example.com/\")\n .put(HTTP_OUTGOING_TOKEN_AUDIENCE, \"https://outgoing-audience.example.com/\")\n .put(HTTP_OUTGOING_TOKEN_EXPIRY, Duration.ofDays(1).toString())\n .put(HTTP_OUTGOING_URL, \"https://outgoing.example.com\")\n\n .build();\n } \n #location 1 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n protected Map customSettingsFlat() {\n return customSettingsFlat(IlpOverHttpLinkSettings.AuthType.JWT_HS_256, IlpOverHttpLinkSettings.AuthType.JWT_HS_256);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Node next() {\n // Take the next node from the stack.\n Node current = popUnvisited();\n // Take the associated state\n S currentState = current.transition().to();\n // Explore the adjacent neighbors\n for(Transition successor : this.successors.from(currentState)){\n // If the neighbor is still unexplored\n if (!this.visited.containsKey(successor.to())){\n // Create the associated neighbor\n Node successorNode = factory.node(current, successor);\n this.stack.push(successorNode);\n }\n }\n this.visited.put(currentState, current);\n return current;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Node next(){\n if (next != null){\n Node e = next;\n next = nextUnvisited();\n return e;\n } else {\n return nextUnvisited();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public GraphEdge connect(V v1, V v2, E value){\n //check input\n if(v1 == null || v2 == null) throw new IllegalArgumentException(\"Vertices cannot be null\");\n GraphEdge edge = new GraphEdge(v1, v2, value);\n GraphEdge edgeReverse = new GraphEdge(v2, v1, value);\n //add edges to the graph (if not present before)\n connected.get(v1).add(edge);\n connected.get(v2).add(edgeReverse);\n return edge;\n } \n #location 8 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public GraphEdge connect(V v1, V v2, E value){\n // Check non-null arguments\n if(v1 == null || v2 == null) throw new IllegalArgumentException(\"Vertices cannot be null\");\n // Ensure that the vertices are in the graph\n add(v1);\n add(v2);\n GraphEdge edge = new GraphEdge(v1, v2, value);\n GraphEdge reversedEdge = new GraphEdge(v2, v1, value);\n // Add edges to the graph\n connected.get(v1).add(edge);\n connected.get(v2).add(reversedEdge);\n return edge;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void test() {\n String[] testMaze = {\n \"XX@XXXXXXXXXXXXXXXXXXXXXXXXXXXXX\",\n \"XX XXXXXXXXXXXXX XXXXXXXXXXX\",\n \"XX XXXXXXXXXX XXX XX XXXX\",\n \"XXXXX XXXXXX XXX XX XXX XXXX\",\n \"XXX XX XXXXXX XX XXX XX XX XXXX\",\n \"XXX XXXXX XXXXXX XXXXXX XXXX\",\n \"XXXXXXX XXXXXX XXXX\",\n \"XXXXXXXXXX XXXXX XXXXXXXXXXXXXXX\",\n \"XXXXXXXXXX XX XXXXX XXXX\",\n \"XXXXXXXXXX XXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXX XXXXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXXXXXXXXXXXXXXX XX XXXX\",\n \"XXXXXX XXXX XX XXXX\",\n \"XXXXXX XXXXXXXXXXXX XX XXXX\",\n \"XXXXXX XXO XXXXXX XXXX XXXXXXX\",\n \"XXXXXX XXXXX XXX XX\",\n \"XXXXXX XXXXXXX XXXXXXXXXXX XXXXX\",\n \"XXXXXX XXXXXXX XXXXXXXXXXXXXXXXX\",\n \"XXXXXX XXXXXXXXXXXXXX\"};\n StringMaze maze = new StringMaze(testMaze);\n // Valid cells\n assertTrue(maze.getMaze()[1][2]);\n assertTrue(maze.getMaze()[0][2]);\n assertTrue(maze.getMaze()[5][4]);\n // Invalid cells\n assertFalse(maze.getMaze()[0][0]);\n assertFalse(maze.getMaze()[1][1]);\n assertFalse(maze.getMaze()[5][12]);\n // Initial loc\n assertEquals(maze.getInitialLoc(), new Point(2, 0));\n assertEquals(maze.getGoalLoc(), new Point(9, 15));\n // Print valid moves from initial and goal\n System.out.println(maze.validLocationsFrom(maze.getInitialLoc()));\n System.out.println(maze.validLocationsFrom(maze.getGoalLoc()));\n System.out.println(maze.validLocationsFrom(new Point(14, 3)));\n } \n #location 26 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void test() {\n String[] testMaze = {\n \"XX@XXXXXXXXXXXXXXXXXXXXXXXXXXXXX\",\n \"XX XXXXXXXXXXXXX XXXXXXXXXXX\",\n \"XX XXXXXXXXXX XXX XX XXXX\",\n \"XXXXX XXXXXX XXX XX XXX XXXX\",\n \"XXX XX XXXXXX XX XXX XX XX XXXX\",\n \"XXX XXXXX XXXXXX XXXXXX XXXX\",\n \"XXXXXXX XXXXXX XXXX\",\n \"XXXXXXXXXX XXXXX XXXXXXXXXXXXXXX\",\n \"XXXXXXXXXX XX XXXXX XXXX\",\n \"XXXXXXXXXX XXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXX XXXXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXX XXXX XXXX\",\n \"XXXXXXXXXXXXXXXXXXXXXXXX XX XXXX\",\n \"XXXXXX XXXX XX XXXX\",\n \"XXXXXX XXXXXXXXXXXX XX XXXX\",\n \"XXXXXX XXO XXXXXX XXXX XXXXXXX\",\n \"XXXXXX XXXXX XXX XX\",\n \"XXXXXX XXXXXXX XXXXXXXXXXX XXXXX\",\n \"XXXXXX XXXXXXX XXXXXXXXXXXXXXXXX\",\n \"XXXXXX XXXXXXXXXXXXXX\"};\n StringMaze maze = new StringMaze(testMaze);\n // Valid cells\n assertTrue(maze.validLocation(new Point(2,1)));\n assertTrue(maze.validLocation(new Point(2,0)));\n assertTrue(maze.validLocation(new Point(4,5)));\n // Invalid cells\n assertTrue(!maze.validLocation(new Point(0,0)));\n assertTrue(!maze.validLocation(new Point(1,1)));\n assertTrue(!maze.validLocation(new Point(12,5)));\n // Initial loc\n assertEquals(maze.getInitialLoc(), new Point(2, 0));\n assertEquals(maze.getGoalLoc(), new Point(9, 15));\n // Print valid moves from initial and goal\n System.out.println(maze.validLocationsFrom(maze.getInitialLoc()));\n System.out.println(maze.validLocationsFrom(maze.getGoalLoc()));\n System.out.println(maze.validLocationsFrom(new Point(14, 3)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public GraphEdge connect(V v1, V v2, E value){\n //check input\n if(v1 == null || v2 == null) throw new IllegalArgumentException(\"Vertices cannot be null\");\n GraphEdge edge = new GraphEdge(v1, v2, value);\n GraphEdge edgeReverse = new GraphEdge(v2, v1, value);\n //add edges to the graph (if not present before)\n connected.get(v1).add(edge);\n connected.get(v2).add(edgeReverse);\n return edge;\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public GraphEdge connect(V v1, V v2, E value){\n // Check non-null arguments\n if(v1 == null || v2 == null) throw new IllegalArgumentException(\"Vertices cannot be null\");\n // Ensure that the vertices are in the graph\n add(v1);\n add(v2);\n GraphEdge edge = new GraphEdge(v1, v2, value);\n GraphEdge reversedEdge = new GraphEdge(v2, v1, value);\n // Add edges to the graph\n connected.get(v1).add(edge);\n connected.get(v2).add(reversedEdge);\n return edge;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void benchmark() throws InterruptedException {\n System.out.println(\"Maze | Hipster-Dijkstra (ms) | JUNG-Dijkstra (ms)\");\n System.out.println(\"-------------------------------------------------\");\n final int times = 5;\n for (int i = 10; i < 300; i += 10) {\n Maze2D maze = Maze2D.random(i, 0.9);\n // Repeat 5 times\n //Double mean1 = 0d, mean2 = 0d;\n double min2 = Double.MAX_VALUE, min1 = Double.MAX_VALUE;\n DirectedGraph> graph = JungDirectedGraphFromMazeCreator.create(maze);\n for (int j = 0; j < times; j++) {\n //AStar it = AStarIteratorFromMazeCreator.create(maze, false);\n AStar it = AlgorithmIteratorFromMazeCreator.astar(maze, false);\n Stopwatch w1 = new Stopwatch().start();\n MazeSearch.Result resultJung = MazeSearch.executeJungSearch(graph, maze);\n //In case there is no possible result in the random maze\n if(resultJung.equals(MazeSearch.Result.NO_RESULT)){\n maze = Maze2D.random(i, 0.9);\n graph = JungDirectedGraphFromMazeCreator.create(maze);\n j--;\n continue;\n }\n long result1 = w1.stop().elapsed(TimeUnit.MILLISECONDS);\n if (result1 < min1) {\n min1 = result1;\n }\n Stopwatch w2 = new Stopwatch().start();\n MazeSearch.Result resultIterator = MazeSearch.executeIteratorSearch(it, maze);\n long result2 = w2.stop().elapsed(TimeUnit.MILLISECONDS);\n if (result2 < min2) {\n min2 = result2;\n }\n assertEquals(resultIterator.getCost(), resultJung.getCost(), 0.001);\n }\n System.out.println(String.format(\"%d \\t\\t %.5g \\t\\t %.5g\", i, min2, min1));\n }\n } \n #location 34 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void benchmark() throws InterruptedException {\n Benchmark bench = new Benchmark();\n \n // Hipster-Dijkstra\n bench.add(\"Hipster-Dijkstra\", new Algorithm() {\t\n\t\t\tAStar it; Maze2D maze;\n \tpublic void initialize(Maze2D maze) {\n\t\t\t\tit= AlgorithmIteratorFromMazeCreator.astar(maze, false);\n\t\t\t\tthis.maze = maze;\n\t\t\t}\n\t\t\tpublic Result evaluate() {\n\t\t\t\treturn MazeSearch.executeIteratorSearch(it, maze);\n\t\t\t}\n\t\t});\n \n // JUNG-Dijkstra\n bench.add(\"JUNG-Dijkstra\", new Algorithm() {\n\t\t\tMaze2D maze;DirectedGraph> graph;\n\t\t\tpublic void initialize(Maze2D maze) {\n\t\t\t\tthis.maze = maze;\n\t\t\t\tthis.graph = JungDirectedGraphFromMazeCreator.create(maze);\n\t\t\t}\n\t\t\tpublic Result evaluate() {\n\t\t\t\treturn MazeSearch.executeJungSearch(graph, maze);\n\t\t\t}\n\t\t});\n\n int index = 0;\n for(String algName : bench.algorithms.keySet()){\n \tSystem.out.println((++index) + \" = \" + algName);\n }\n \n for (int i = 10; i < 300; i += 10) {\n \tMaze2D maze = Maze2D.empty(i);\n // Test over an empty maze\n Map results = bench.run(maze);\n // Check results and print scores. We take JUNG as baseline\n Benchmark.Score jungScore = results.get(\"JUNG-Dijkstra\");\n String scores = \"\";\n for(String algName : bench.algorithms.keySet()){\n \tBenchmark.Score score = results.get(algName);\n \tassertEquals(jungScore.result.getCost(),score.result.getCost(), 0.0001);\n \tscores += score.time + \" ms\\t\";\n }\n System.out.println(scores);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testRestartAuditorBookieAfterCrashing() throws Exception {\n BookieServer auditor = verifyAuditor();\n\n shudownBookie(auditor);\n\n // restarting Bookie with same configurations.\n int indexOfDownBookie = bs.indexOf(auditor);\n ServerConfiguration serverConfiguration = bsConfs\n .get(indexOfDownBookie);\n bs.remove(indexOfDownBookie);\n bsConfs.remove(indexOfDownBookie);\n tmpDirs.remove(indexOfDownBookie);\n startBookie(serverConfiguration);\n // starting corresponding auditor elector\n StringBuilder sb = new StringBuilder();\n StringUtils.addrToString(sb, auditor.getLocalAddress());\n LOG.debug(\"Performing Auditor Election:\" + sb.toString());\n auditorElectors.get(sb.toString()).doElection();\n\n // waiting for new auditor to come\n BookieServer newAuditor = waitForNewAuditor(auditor);\n Assert.assertNotSame(\n \"Auditor re-election is not happened for auditor failure!\",\n auditor, newAuditor);\n Assert.assertFalse(\"No relection after old auditor rejoins\", auditor\n .getLocalAddress().getPort() == newAuditor.getLocalAddress()\n .getPort());\n } \n #location 19 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testRestartAuditorBookieAfterCrashing() throws Exception {\n BookieServer auditor = verifyAuditor();\n\n shudownBookie(auditor);\n\n // restarting Bookie with same configurations.\n int indexOfDownBookie = bs.indexOf(auditor);\n ServerConfiguration serverConfiguration = bsConfs\n .get(indexOfDownBookie);\n bs.remove(indexOfDownBookie);\n bsConfs.remove(indexOfDownBookie);\n tmpDirs.remove(indexOfDownBookie);\n startBookie(serverConfiguration);\n // starting corresponding auditor elector\n String addr = StringUtils.addrToString(auditor.getLocalAddress());\n LOG.debug(\"Performing Auditor Election:\" + addr);\n auditorElectors.get(addr).doElection();\n\n // waiting for new auditor to come\n BookieServer newAuditor = waitForNewAuditor(auditor);\n Assert.assertNotSame(\n \"Auditor re-election is not happened for auditor failure!\",\n auditor, newAuditor);\n Assert.assertFalse(\"No relection after old auditor rejoins\", auditor\n .getLocalAddress().getPort() == newAuditor.getLocalAddress()\n .getPort());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void handleSubscribeMessage(PubSubResponse response) {\n if (logger.isDebugEnabled())\n logger.debug(\"Handling a Subscribe message in response: \" + response + \", topic: \"\n + origSubData.topic.toStringUtf8() + \", subscriberId: \" + origSubData.subscriberId.toStringUtf8());\n Message message = response.getMessage();\n\n synchronized (this) {\n // Consume the message asynchronously that the client is subscribed\n // to. Do this only if delivery for the subscription has started and\n // a MessageHandler has been registered for the TopicSubscriber.\n if (messageHandler != null) {\n asyncMessageConsume(message);\n } else {\n // MessageHandler has not yet been registered so queue up these\n // messages for the Topic Subscription. Make the initial lazy\n // creation of the message queue thread safe just so we don't\n // run into a race condition where two simultaneous threads process\n // a received message and both try to create a new instance of\n // the message queue. Performance overhead should be okay\n // because the delivery of the topic has not even started yet\n // so these messages are not consumed and just buffered up here.\n if (subscribeMsgQueue == null)\n subscribeMsgQueue = new LinkedList();\n if (logger.isDebugEnabled())\n logger\n .debug(\"Message has arrived but Subscribe channel does not have a registered MessageHandler yet so queueing up the message: \"\n + message);\n subscribeMsgQueue.add(message);\n }\n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void handleSubscribeMessage(PubSubResponse response) {\n if (logger.isDebugEnabled()) {\n logger.debug(\"Handling a Subscribe message in response: {}, topic: {}, subscriberId: {}\",\n new Object[] { response, getOrigSubData().topic.toStringUtf8(),\n getOrigSubData().subscriberId.toStringUtf8() });\n }\n Message message = response.getMessage();\n\n synchronized (this) {\n // Consume the message asynchronously that the client is subscribed\n // to. Do this only if delivery for the subscription has started and\n // a MessageHandler has been registered for the TopicSubscriber.\n if (messageHandler != null) {\n asyncMessageConsume(message);\n } else {\n // MessageHandler has not yet been registered so queue up these\n // messages for the Topic Subscription. Make the initial lazy\n // creation of the message queue thread safe just so we don't\n // run into a race condition where two simultaneous threads process\n // a received message and both try to create a new instance of\n // the message queue. Performance overhead should be okay\n // because the delivery of the topic has not even started yet\n // so these messages are not consumed and just buffered up here.\n if (subscribeMsgQueue == null)\n subscribeMsgQueue = new LinkedList();\n if (logger.isDebugEnabled())\n logger\n .debug(\"Message has arrived but Subscribe channel does not have a registered MessageHandler yet so queueing up the message: \"\n + message);\n subscribeMsgQueue.add(message);\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void close() {\n synchronized (this) {\n state = ConnectionState.DISCONNECTED;\n }\n if (channel != null) {\n channel.close().awaitUninterruptibly();\n }\n if (readTimeoutTimer != null) {\n readTimeoutTimer.stop();\n readTimeoutTimer = null;\n }\n } \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void close() {\n closeInternal(true);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n while (running) {\n synchronized (this) {\n try {\n wait(gcWaitTime);\n } catch (InterruptedException e) {\n Thread.currentThread().interrupt();\n continue;\n }\n }\n\n // Dependency check.\n if (null == zk) {\n continue;\n }\n\n // Extract all of the ledger ID's that comprise all of the entry logs\n // (except for the current new one which is still being written to).\n try {\n entryLogMetaMap = entryLogger.extractMetaFromEntryLogs(entryLogMetaMap);\n } catch (IOException ie) {\n LOG.warn(\"Exception when extracting entry log meta from entry logs : \", ie);\n }\n\n // gc inactive/deleted ledgers\n doGcLedgers();\n\n // gc entry logs\n doGcEntryLogs();\n\n long curTime = System.currentTimeMillis();\n if (enableMajorCompaction &&\n curTime - lastMajorCompactionTime > majorCompactionInterval) {\n // enter major compaction\n LOG.info(\"Enter major compaction\");\n doCompactEntryLogs(majorCompactionThreshold);\n lastMajorCompactionTime = System.currentTimeMillis();\n // also move minor compaction time\n lastMinorCompactionTime = lastMajorCompactionTime;\n continue;\n }\n\n if (enableMinorCompaction &&\n curTime - lastMinorCompactionTime > minorCompactionInterval) {\n // enter minor compaction\n LOG.info(\"Enter minor compaction\");\n doCompactEntryLogs(minorCompactionThreshold);\n lastMinorCompactionTime = System.currentTimeMillis();\n }\n }\n } \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run() {\n while (running) {\n synchronized (this) {\n try {\n wait(gcWaitTime);\n } catch (InterruptedException e) {\n Thread.currentThread().interrupt();\n continue;\n }\n }\n\n // Dependency check.\n if (null == zk) {\n continue;\n }\n\n // Extract all of the ledger ID's that comprise all of the entry logs\n // (except for the current new one which is still being written to).\n try {\n entryLogMetaMap = extractMetaFromEntryLogs(entryLogMetaMap);\n } catch (IOException ie) {\n LOG.warn(\"Exception when extracting entry log meta from entry logs : \", ie);\n }\n\n // gc inactive/deleted ledgers\n doGcLedgers();\n\n // gc entry logs\n doGcEntryLogs();\n\n long curTime = System.currentTimeMillis();\n if (enableMajorCompaction &&\n curTime - lastMajorCompactionTime > majorCompactionInterval) {\n // enter major compaction\n LOG.info(\"Enter major compaction\");\n doCompactEntryLogs(majorCompactionThreshold);\n lastMajorCompactionTime = System.currentTimeMillis();\n // also move minor compaction time\n lastMinorCompactionTime = lastMajorCompactionTime;\n continue;\n }\n\n if (enableMinorCompaction &&\n curTime - lastMinorCompactionTime > minorCompactionInterval) {\n // enter minor compaction\n LOG.info(\"Enter minor compaction\");\n doCompactEntryLogs(minorCompactionThreshold);\n lastMinorCompactionTime = System.currentTimeMillis();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public byte[] readMasterKey(long ledgerId) throws IOException, BookieException {\n synchronized(fileInfoCache) {\n FileInfo fi = fileInfoCache.get(ledgerId);\n if (fi == null) {\n File lf = findIndexFile(ledgerId);\n if (lf == null) {\n throw new Bookie.NoLedgerException(ledgerId);\n }\n if (openLedgers.size() > openFileLimit) {\n fileInfoCache.remove(openLedgers.removeFirst()).close();\n }\n fi = new FileInfo(lf, null);\n byte[] key = fi.getMasterKey();\n fileInfoCache.put(ledgerId, fi);\n openLedgers.add(ledgerId);\n return key;\n }\n return fi.getMasterKey();\n }\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public byte[] readMasterKey(long ledgerId) throws IOException, BookieException {\n synchronized(fileInfoCache) {\n FileInfo fi = fileInfoCache.get(ledgerId);\n if (fi == null) {\n File lf = findIndexFile(ledgerId);\n if (lf == null) {\n throw new Bookie.NoLedgerException(ledgerId);\n }\n evictFileInfoIfNecessary(); \n fi = new FileInfo(lf, null);\n byte[] key = fi.getMasterKey();\n fileInfoCache.put(ledgerId, fi);\n openLedgers.add(ledgerId);\n return key;\n }\n return fi.getMasterKey();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void writeIndexFileForLedger(File indexDir, long ledgerId,\n byte[] masterKey)\n throws Exception {\n File fn = new File(indexDir, LedgerCache.getLedgerName(ledgerId));\n fn.getParentFile().mkdirs();\n FileInfo fi = new FileInfo(fn);\n fi.writeMasterKey(masterKey);\n fi.close();\n } \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void writeIndexFileForLedger(File indexDir, long ledgerId,\n byte[] masterKey)\n throws Exception {\n File fn = new File(indexDir, LedgerCache.getLedgerName(ledgerId));\n fn.getParentFile().mkdirs();\n FileInfo fi = new FileInfo(fn, masterKey);\n // force creation of index file\n fi.write(new ByteBuffer[]{ ByteBuffer.allocate(0) }, 0);\n fi.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void channelDisconnected(ChannelHandlerContext ctx, ChannelStateEvent e) throws Exception {\n LOG.info(\"Disconnected from bookie: \" + addr);\n errorOutOutstandingEntries();\n channel.close();\n state = ConnectionState.DISCONNECTED;\n\n // we don't want to reconnect right away. If someone sends a request to\n // this address, we will reconnect.\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void channelDisconnected(ChannelHandlerContext ctx, ChannelStateEvent e) throws Exception {\n LOG.info(\"Disconnected from bookie: \" + addr);\n errorOutOutstandingEntries();\n channel.close();\n synchronized (this) {\n state = ConnectionState.DISCONNECTED;\n }\n\n // we don't want to reconnect right away. If someone sends a request to\n // this address, we will reconnect.\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteSyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n entries.add(entry.array());\n lh.addEntry(entry.array());\n }\n lh.close();\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i++));\n Integer origEntry = origbb.getInt();\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 26 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteSyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n entries.add(entry.array());\n lh.addEntry(entry.array());\n }\n lh.close();\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i++));\n Integer origEntry = origbb.getInt();\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 15 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws Exception {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n } \n #location 48 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void close() {\n synchronized (this) {\n state = ConnectionState.DISCONNECTED;\n }\n if (channel != null) {\n channel.close().awaitUninterruptibly();\n }\n if (readTimeoutTimer != null) {\n readTimeoutTimer.stop();\n readTimeoutTimer = null;\n }\n } \n #location 9 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void close() {\n closeInternal(true);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if(rc != BKException.Code.OK) fail(\"Return code is not OK: \" + rc);\n\n ls = seq;\n\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n SyncObj sync = (SyncObj) ctx;\n sync.setLedgerEntries(seq);\n sync.setReturnCode(rc);\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public StatsLogger getStatsLogger(String name) {\n initIfNecessary();\n return new CodahaleStatsLogger(metrics, name);\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public StatsLogger getStatsLogger(String name) {\n initIfNecessary();\n return new CodahaleStatsLogger(getMetrics(), name);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n FileInfo getFileInfo(Long ledger, byte masterKey[]) throws IOException {\n synchronized(fileInfoCache) {\n FileInfo fi = fileInfoCache.get(ledger);\n if (fi == null) {\n File lf = findIndexFile(ledger);\n if (lf == null) {\n if (masterKey == null) {\n throw new Bookie.NoLedgerException(ledger);\n }\n File dir = pickDirs(ledgerDirectories);\n String ledgerName = getLedgerName(ledger);\n lf = new File(dir, ledgerName);\n // A new ledger index file has been created for this Bookie.\n // Add this new ledger to the set of active ledgers.\n if (LOG.isDebugEnabled()) {\n LOG.debug(\"New ledger index file created for ledgerId: \" + ledger);\n }\n activeLedgerManager.addActiveLedger(ledger, true);\n }\n if (openLedgers.size() > openFileLimit) {\n fileInfoCache.remove(openLedgers.removeFirst()).close();\n }\n fi = new FileInfo(lf, masterKey);\n fileInfoCache.put(ledger, fi);\n openLedgers.add(ledger);\n }\n if (fi != null) {\n fi.use();\n }\n return fi;\n }\n } \n #location 21 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n FileInfo getFileInfo(Long ledger, byte masterKey[]) throws IOException {\n synchronized(fileInfoCache) {\n FileInfo fi = fileInfoCache.get(ledger);\n if (fi == null) {\n File lf = findIndexFile(ledger);\n if (lf == null) {\n if (masterKey == null) {\n throw new Bookie.NoLedgerException(ledger);\n }\n File dir = pickDirs(ledgerDirectories);\n String ledgerName = getLedgerName(ledger);\n lf = new File(dir, ledgerName);\n // A new ledger index file has been created for this Bookie.\n // Add this new ledger to the set of active ledgers.\n if (LOG.isDebugEnabled()) {\n LOG.debug(\"New ledger index file created for ledgerId: \" + ledger);\n }\n activeLedgerManager.addActiveLedger(ledger, true);\n }\n evictFileInfoIfNecessary();\n fi = new FileInfo(lf, masterKey);\n fileInfoCache.put(ledger, fi);\n openLedgers.add(ledger);\n }\n if (fi != null) {\n fi.use();\n }\n return fi;\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public String toString() {\n StringBuilder sb = new StringBuilder();\n sb.append(\"Latency min/avg/max: \" + getMinLatency() + \"/\" + getAvgLatency() + \"/\" + getMaxLatency() + \"\\n\");\n sb.append(\"Received: \" + getPacketsReceived() + \"\\n\");\n sb.append(\"Sent: \" + getPacketsSent() + \"\\n\");\n if (provider != null) {\n sb.append(\"Outstanding: \" + getOutstandingRequests() + \"\\n\");\n sb.append(\"Zxid: 0x\" + Long.toHexString(getLastProcessedZxid()) + \"\\n\");\n }\n sb.append(\"Mode: \" + getServerState() + \"\\n\");\n return sb.toString();\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public String toString() {\n StringBuilder sb = new StringBuilder();\n sb.append(\"Latency min/avg/max: \" + getMinLatency() + \"/\" + getAvgLatency() + \"/\" + getMaxLatency() + \"\\n\");\n sb.append(\"Received: \" + getPacketsReceived() + \"\\n\");\n sb.append(\"Sent: \" + getPacketsSent() + \"\\n\");\n return sb.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void connectIfNeededAndDoOp(GenericCallback op) {\n boolean doOpNow;\n\n // common case without lock first\n if (channel != null && state == ConnectionState.CONNECTED) {\n doOpNow = true;\n } else {\n\n synchronized (this) {\n // check again under lock\n if (channel != null && state == ConnectionState.CONNECTED) {\n doOpNow = true;\n } else {\n\n // if reached here, channel is either null (first connection\n // attempt),\n // or the channel is disconnected\n doOpNow = false;\n\n // connection attempt is still in progress, queue up this\n // op. Op will be executed when connection attempt either\n // fails\n // or\n // succeeds\n pendingOps.add(op);\n\n connect();\n }\n }\n }\n\n if (doOpNow) {\n op.operationComplete(BKException.Code.OK, null);\n }\n\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n void connectIfNeededAndDoOp(GenericCallback op) {\n boolean doOpNow;\n\n synchronized (this) {\n if (channel != null && state == ConnectionState.CONNECTED) {\n doOpNow = true;\n } else {\n // if reached here, channel is either null (first connection\n // attempt),\n // or the channel is disconnected\n doOpNow = false;\n\n // connection attempt is still in progress, queue up this\n // op. Op will be executed when connection attempt either\n // fails\n // or\n // succeeds\n pendingOps.add(op);\n\n connect();\n }\n }\n\n if (doOpNow) {\n op.operationComplete(BKException.Code.OK, null);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testSimpleBookieLedgerMapping() throws Exception {\n LedgerManagerFactory newLedgerManagerFactory = LedgerManagerFactory\n .newLedgerManagerFactory(baseConf, zkc);\n LedgerManager ledgerManager = newLedgerManagerFactory\n .newLedgerManager();\n\n List ledgerList = new ArrayList(3);\n LedgerHandle lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n\n Map> bookieToLedgerIndex = bookieLedgerIndex\n .getBookieToLedgerIndex();\n\n assertEquals(\"Missed few bookies in the bookie-ledger mapping!\", 3,\n bookieToLedgerIndex.size());\n Collection> bk2ledgerEntry = bookieToLedgerIndex.values();\n for (Set ledgers : bk2ledgerEntry) {\n assertEquals(\"Missed few ledgers in the bookie-ledger mapping!\", 3,\n ledgers.size());\n for (Long ledgerId : ledgers) {\n assertTrue(\"Unknown ledger-bookie mapping\", ledgerList\n .contains(ledgerId));\n }\n }\n } \n #location 25 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testSimpleBookieLedgerMapping() throws Exception {\n\n for (int i = 0; i < numberOfLedgers; i++) {\n createAndAddEntriesToLedger().close();\n }\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n\n Map> bookieToLedgerIndex = bookieLedgerIndex\n .getBookieToLedgerIndex();\n\n assertEquals(\"Missed few bookies in the bookie-ledger mapping!\", 3,\n bookieToLedgerIndex.size());\n Collection> bk2ledgerEntry = bookieToLedgerIndex.values();\n for (Set ledgers : bk2ledgerEntry) {\n assertEquals(\"Missed few ledgers in the bookie-ledger mapping!\", 3,\n ledgers.size());\n for (Long ledgerId : ledgers) {\n assertTrue(\"Unknown ledger-bookie mapping\", ledgerList\n .contains(ledgerId));\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteZero() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n }\n\n /*\n * Write a non-zero entry\n */\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n entries.add(entry.array());\n lh.addEntry(entry.array());\n\n lh.close();\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == numEntriesToWrite);\n\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteZero() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n }\n\n /*\n * Write a non-zero entry\n */\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n entries.add(entry.array());\n lh.addEntry(entry.array());\n\n lh.close();\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == numEntriesToWrite);\n\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void setMessageHandler(MessageHandler messageHandler) {\n if (logger.isDebugEnabled())\n logger.debug(\"Setting the messageHandler for topic: \" + origSubData.topic.toStringUtf8()\n + \", subscriberId: \" + origSubData.subscriberId.toStringUtf8());\n synchronized (this) {\n this.messageHandler = messageHandler;\n // Once the MessageHandler is registered, see if we have any queued up\n // subscription messages sent to us already from the server. If so,\n // consume those first. Do this only if the MessageHandler registered is\n // not null (since that would be the HedwigSubscriber.stopDelivery\n // call).\n if (messageHandler != null && subscribeMsgQueue != null && subscribeMsgQueue.size() > 0) {\n if (logger.isDebugEnabled())\n logger.debug(\"Consuming \" + subscribeMsgQueue.size() + \" queued up messages for topic: \"\n + origSubData.topic.toStringUtf8() + \", subscriberId: \"\n + origSubData.subscriberId.toStringUtf8());\n for (Message message : subscribeMsgQueue) {\n asyncMessageConsume(message);\n }\n // Now we can remove the queued up messages since they are all\n // consumed.\n subscribeMsgQueue.clear();\n }\n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void setMessageHandler(MessageHandler messageHandler) {\n if (logger.isDebugEnabled()) {\n logger.debug(\"Setting the messageHandler for topic: {}, subscriberId: {}\",\n getOrigSubData().topic.toStringUtf8(),\n getOrigSubData().subscriberId.toStringUtf8());\n }\n synchronized (this) {\n this.messageHandler = messageHandler;\n // Once the MessageHandler is registered, see if we have any queued up\n // subscription messages sent to us already from the server. If so,\n // consume those first. Do this only if the MessageHandler registered is\n // not null (since that would be the HedwigSubscriber.stopDelivery\n // call).\n if (messageHandler != null && subscribeMsgQueue != null && subscribeMsgQueue.size() > 0) {\n if (logger.isDebugEnabled())\n logger.debug(\"Consuming \" + subscribeMsgQueue.size() + \" queued up messages for topic: \"\n + origSubData.topic.toStringUtf8() + \", subscriberId: \"\n + origSubData.subscriberId.toStringUtf8());\n for (Message message : subscribeMsgQueue) {\n asyncMessageConsume(message);\n }\n // Now we can remove the queued up messages since they are all\n // consumed.\n subscribeMsgQueue.clear();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if(rc != BKException.Code.OK) fail(\"Return code is not OK: \" + rc);\n\n ls = seq;\n\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n SyncObj sync = (SyncObj) ctx;\n sync.setLedgerEntries(seq);\n sync.setReturnCode(rc);\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteAsyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 55 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteAsyncSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n Enumeration ls = sync.getLedgerEntries();\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testGarbageCollectLedgers() throws Exception {\n int numLedgers = 100;\n int numRemovedLedgers = 10;\n\n final Set createdLedgers = new HashSet();\n final Set removedLedgers = new HashSet();\n\n // create 100 ledgers\n createLedgers(numLedgers, createdLedgers);\n\n Random r = new Random(System.currentTimeMillis());\n final List tmpList = new ArrayList();\n tmpList.addAll(createdLedgers);\n Collections.shuffle(tmpList, r);\n // random remove several ledgers\n for (int i=0; i() {\n @Override\n public void operationComplete(int rc, Void result) {\n synchronized (removedLedgers) {\n removedLedgers.notify();\n }\n }\n });\n synchronized (removedLedgers) {\n removedLedgers.wait();\n }\n removedLedgers.add(ledgerId);\n createdLedgers.remove(ledgerId);\n }\n final CountDownLatch inGcProgress = new CountDownLatch(1);\n final CountDownLatch createLatch = new CountDownLatch(1);\n final CountDownLatch endLatch = new CountDownLatch(2);\n\n Thread gcThread = new Thread() {\n @Override\n public void run() {\n getActiveLedgerManager().garbageCollectLedgers(new GarbageCollector() {\n boolean paused = false;\n @Override\n public void gc(long ledgerId) {\n if (!paused) {\n inGcProgress.countDown();\n try {\n createLatch.await();\n } catch (InterruptedException ie) {\n }\n paused = true;\n }\n LOG.info(\"Garbage Collected ledger {}\", ledgerId);\n }\n });\n LOG.info(\"Gc Thread quits.\");\n endLatch.countDown();\n }\n };\n\n Thread createThread = new Thread() {\n @Override\n public void run() {\n try {\n inGcProgress.await();\n // create 10 more ledgers\n createLedgers(10, createdLedgers);\n LOG.info(\"Finished creating 10 more ledgers.\");\n createLatch.countDown();\n } catch (Exception e) {\n }\n LOG.info(\"Create Thread quits.\");\n endLatch.countDown();\n }\n };\n\n createThread.start();\n gcThread.start();\n\n endLatch.await();\n\n // test ledgers\n for (Long ledger : removedLedgers) {\n assertFalse(getActiveLedgerManager().containsActiveLedger(ledger));\n }\n for (Long ledger : createdLedgers) {\n assertTrue(getActiveLedgerManager().containsActiveLedger(ledger));\n }\n } \n #location 19 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testGarbageCollectLedgers() throws Exception {\n int numLedgers = 100;\n int numRemovedLedgers = 10;\n\n final Set createdLedgers = new HashSet();\n final Set removedLedgers = new HashSet();\n\n // create 100 ledgers\n createLedgers(numLedgers, createdLedgers);\n\n Random r = new Random(System.currentTimeMillis());\n final List tmpList = new ArrayList();\n tmpList.addAll(createdLedgers);\n Collections.shuffle(tmpList, r);\n // random remove several ledgers\n for (int i=0; i() {\n @Override\n public void operationComplete(int rc, Void result) {\n synchronized (removedLedgers) {\n removedLedgers.notify();\n }\n }\n });\n removedLedgers.wait();\n }\n removedLedgers.add(ledgerId);\n createdLedgers.remove(ledgerId);\n }\n final CountDownLatch inGcProgress = new CountDownLatch(1);\n final CountDownLatch createLatch = new CountDownLatch(1);\n final CountDownLatch endLatch = new CountDownLatch(2);\n\n Thread gcThread = new Thread() {\n @Override\n public void run() {\n getActiveLedgerManager().garbageCollectLedgers(new GarbageCollector() {\n boolean paused = false;\n @Override\n public void gc(long ledgerId) {\n if (!paused) {\n inGcProgress.countDown();\n try {\n createLatch.await();\n } catch (InterruptedException ie) {\n }\n paused = true;\n }\n LOG.info(\"Garbage Collected ledger {}\", ledgerId);\n }\n });\n LOG.info(\"Gc Thread quits.\");\n endLatch.countDown();\n }\n };\n\n Thread createThread = new Thread() {\n @Override\n public void run() {\n try {\n inGcProgress.await();\n // create 10 more ledgers\n createLedgers(10, createdLedgers);\n LOG.info(\"Finished creating 10 more ledgers.\");\n createLatch.countDown();\n } catch (Exception e) {\n }\n LOG.info(\"Create Thread quits.\");\n endLatch.countDown();\n }\n };\n\n createThread.start();\n gcThread.start();\n\n endLatch.await();\n\n // test ledgers\n for (Long ledger : removedLedgers) {\n assertFalse(getActiveLedgerManager().containsActiveLedger(ledger));\n }\n for (Long ledger : createdLedgers) {\n assertTrue(getActiveLedgerManager().containsActiveLedger(ledger));\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void start(Configuration conf) {\n initIfNecessary();\n\n int metricsOutputFrequency = conf.getInt(\"codahaleStatsOutputFrequencySeconds\", 60);\n String prefix = conf.getString(\"codahaleStatsPrefix\", \"\");\n String graphiteHost = conf.getString(\"codahaleStatsGraphiteEndpoint\");\n String csvDir = conf.getString(\"codahaleStatsCSVEndpoint\");\n String slf4jCat = conf.getString(\"codahaleStatsSlf4jEndpoint\");\n\n if (!Strings.isNullOrEmpty(graphiteHost)) {\n LOG.info(\"Configuring stats with graphite\");\n HostAndPort addr = HostAndPort.fromString(graphiteHost);\n final Graphite graphite = new Graphite(\n new InetSocketAddress(addr.getHostText(), addr.getPort()));\n reporters.add(GraphiteReporter.forRegistry(metrics)\n .prefixedWith(prefix)\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .filter(MetricFilter.ALL)\n .build(graphite));\n }\n if (!Strings.isNullOrEmpty(csvDir)) {\n // NOTE: 1/ metrics output files are exclusive to a given process\n // 2/ the output directory must exist\n // 3/ if output files already exist they are not overwritten and there is no metrics output\n File outdir;\n if (Strings.isNullOrEmpty(prefix)) {\n outdir = new File(csvDir, prefix);\n } else {\n outdir = new File(csvDir);\n }\n LOG.info(\"Configuring stats with csv output to directory [{}]\", outdir.getAbsolutePath());\n reporters.add(CsvReporter.forRegistry(metrics)\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build(outdir));\n }\n if (!Strings.isNullOrEmpty(slf4jCat)) {\n LOG.info(\"Configuring stats with slf4j\");\n reporters.add(Slf4jReporter.forRegistry(metrics)\n .outputTo(LoggerFactory.getLogger(slf4jCat))\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build());\n }\n for (ScheduledReporter r : reporters) {\n r.start(metricsOutputFrequency, TimeUnit.SECONDS);\n }\n } \n #location 41 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void start(Configuration conf) {\n initIfNecessary();\n\n int metricsOutputFrequency = conf.getInt(\"codahaleStatsOutputFrequencySeconds\", 60);\n String prefix = conf.getString(\"codahaleStatsPrefix\", \"\");\n String graphiteHost = conf.getString(\"codahaleStatsGraphiteEndpoint\");\n String csvDir = conf.getString(\"codahaleStatsCSVEndpoint\");\n String slf4jCat = conf.getString(\"codahaleStatsSlf4jEndpoint\");\n\n if (!Strings.isNullOrEmpty(graphiteHost)) {\n LOG.info(\"Configuring stats with graphite\");\n HostAndPort addr = HostAndPort.fromString(graphiteHost);\n final Graphite graphite = new Graphite(\n new InetSocketAddress(addr.getHostText(), addr.getPort()));\n reporters.add(GraphiteReporter.forRegistry(getMetrics())\n .prefixedWith(prefix)\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .filter(MetricFilter.ALL)\n .build(graphite));\n }\n if (!Strings.isNullOrEmpty(csvDir)) {\n // NOTE: 1/ metrics output files are exclusive to a given process\n // 2/ the output directory must exist\n // 3/ if output files already exist they are not overwritten and there is no metrics output\n File outdir;\n if (Strings.isNullOrEmpty(prefix)) {\n outdir = new File(csvDir, prefix);\n } else {\n outdir = new File(csvDir);\n }\n LOG.info(\"Configuring stats with csv output to directory [{}]\", outdir.getAbsolutePath());\n reporters.add(CsvReporter.forRegistry(getMetrics())\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build(outdir));\n }\n if (!Strings.isNullOrEmpty(slf4jCat)) {\n LOG.info(\"Configuring stats with slf4j\");\n reporters.add(Slf4jReporter.forRegistry(getMetrics())\n .outputTo(LoggerFactory.getLogger(slf4jCat))\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build());\n }\n for (ScheduledReporter r : reporters) {\n r.start(metricsOutputFrequency, TimeUnit.SECONDS);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n // get back to prev value\n lh.lastAddConfirmed--;\n if (rc == BKException.Code.OK) {\n LedgerEntry entry = seq.nextElement();\n byte[] data = entry.getEntry();\n\n /*\n * We will add this entry again to make sure it is written to enough\n * replicas. We subtract the length of the data itself, since it will\n * be added again when processing the call to add it.\n */\n synchronized (lh) {\n lh.length = entry.getLength() - (long) data.length;\n }\n lh.asyncRecoveryAddEntry(data, 0, data.length, this, null);\n return;\n }\n\n if (rc == BKException.Code.NoSuchEntryException || rc == BKException.Code.NoSuchLedgerExistsException) {\n lh.asyncCloseInternal(new CloseCallback() {\n @Override\n public void closeComplete(int rc, LedgerHandle lh, Object ctx) {\n if (rc != KeeperException.Code.OK.intValue()) {\n LOG.warn(\"Close failed: \" + BKException.getMessage(rc));\n cb.operationComplete(BKException.Code.ZKException, null);\n } else {\n cb.operationComplete(BKException.Code.OK, null);\n LOG.debug(\"After closing length is: {}\", lh.getLength());\n }\n }\n }, null, BKException.Code.LedgerClosedException);\n return;\n }\n\n // otherwise, some other error, we can't handle\n LOG.error(\"Failure \" + BKException.getMessage(rc) + \" while reading entry: \" + (lh.lastAddConfirmed + 1)\n + \" ledger: \" + lh.ledgerId + \" while recovering ledger\");\n cb.operationComplete(rc, null);\n return;\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if (rc == BKException.Code.OK) {\n LedgerEntry entry = seq.nextElement();\n byte[] data = entry.getEntry();\n\n /*\n * We will add this entry again to make sure it is written to enough\n * replicas. We subtract the length of the data itself, since it will\n * be added again when processing the call to add it.\n */\n synchronized (lh) {\n lh.length = entry.getLength() - (long) data.length;\n }\n lh.asyncRecoveryAddEntry(data, 0, data.length, this, null);\n return;\n }\n\n if (rc == BKException.Code.NoSuchEntryException || rc == BKException.Code.NoSuchLedgerExistsException) {\n lh.asyncCloseInternal(new CloseCallback() {\n @Override\n public void closeComplete(int rc, LedgerHandle lh, Object ctx) {\n if (rc != KeeperException.Code.OK.intValue()) {\n LOG.warn(\"Close failed: \" + BKException.getMessage(rc));\n cb.operationComplete(BKException.Code.ZKException, null);\n } else {\n cb.operationComplete(BKException.Code.OK, null);\n LOG.debug(\"After closing length is: {}\", lh.getLength());\n }\n }\n }, null, BKException.Code.LedgerClosedException);\n return;\n }\n\n // otherwise, some other error, we can't handle\n LOG.error(\"Failure \" + BKException.getMessage(rc) + \" while reading entry: \" + (lh.lastAddConfirmed + 1)\n + \" ledger: \" + lh.ledgerId + \" while recovering ledger\");\n cb.operationComplete(rc, null);\n return;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void doPublish(PubSubData pubSubData, Channel channel) {\n // Create a PubSubRequest\n PubSubRequest.Builder pubsubRequestBuilder = PubSubRequest.newBuilder();\n pubsubRequestBuilder.setProtocolVersion(ProtocolVersion.VERSION_ONE);\n pubsubRequestBuilder.setType(OperationType.PUBLISH);\n if (pubSubData.triedServers != null && pubSubData.triedServers.size() > 0) {\n pubsubRequestBuilder.addAllTriedServers(pubSubData.triedServers);\n }\n long txnId = client.globalCounter.incrementAndGet();\n pubsubRequestBuilder.setTxnId(txnId);\n pubsubRequestBuilder.setShouldClaim(pubSubData.shouldClaim);\n pubsubRequestBuilder.setTopic(pubSubData.topic);\n\n // Now create the PublishRequest\n PublishRequest.Builder publishRequestBuilder = PublishRequest.newBuilder();\n\n publishRequestBuilder.setMsg(pubSubData.msg);\n\n // Set the PublishRequest into the outer PubSubRequest\n pubsubRequestBuilder.setPublishRequest(publishRequestBuilder);\n\n // Update the PubSubData with the txnId and the requestWriteTime\n pubSubData.txnId = txnId;\n pubSubData.requestWriteTime = MathUtils.now();\n\n // Before we do the write, store this information into the\n // ResponseHandler so when the server responds, we know what\n // appropriate Callback Data to invoke for the given txn ID.\n HedwigClientImpl.getResponseHandlerFromChannel(channel).txn2PubSubData.put(txnId, pubSubData);\n\n // Finally, write the Publish request through the Channel.\n if (logger.isDebugEnabled())\n logger.debug(\"Writing a Publish request to host: \" + HedwigClientImpl.getHostFromChannel(channel)\n + \" for pubSubData: \" + pubSubData);\n ChannelFuture future = channel.write(pubsubRequestBuilder.build());\n future.addListener(new WriteCallback(pubSubData, client));\n } \n #location 20 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void doPublish(PubSubData pubSubData, Channel channel) {\n // Create a PubSubRequest\n PubSubRequest.Builder pubsubRequestBuilder = PubSubRequest.newBuilder();\n pubsubRequestBuilder.setProtocolVersion(ProtocolVersion.VERSION_ONE);\n pubsubRequestBuilder.setType(OperationType.PUBLISH);\n if (pubSubData.triedServers != null && pubSubData.triedServers.size() > 0) {\n pubsubRequestBuilder.addAllTriedServers(pubSubData.triedServers);\n }\n long txnId = client.globalCounter.incrementAndGet();\n pubsubRequestBuilder.setTxnId(txnId);\n pubsubRequestBuilder.setShouldClaim(pubSubData.shouldClaim);\n pubsubRequestBuilder.setTopic(pubSubData.topic);\n\n // Now create the PublishRequest\n PublishRequest.Builder publishRequestBuilder = PublishRequest.newBuilder();\n\n publishRequestBuilder.setMsg(pubSubData.msg);\n\n // Set the PublishRequest into the outer PubSubRequest\n pubsubRequestBuilder.setPublishRequest(publishRequestBuilder);\n\n // Update the PubSubData with the txnId and the requestWriteTime\n pubSubData.txnId = txnId;\n pubSubData.requestWriteTime = MathUtils.now();\n\n // Before we do the write, store this information into the\n // ResponseHandler so when the server responds, we know what\n // appropriate Callback Data to invoke for the given txn ID.\n try {\n HedwigClientImpl.getResponseHandlerFromChannel(channel).txn2PubSubData.put(txnId, pubSubData);\n } catch (NoResponseHandlerException e) {\n logger.error(\"No response handler found while storing the publish callback.\");\n // Callback on pubsubdata indicating failure.\n pubSubData.getCallback().operationFailed(pubSubData.context, new CouldNotConnectException(\"No response \" +\n \"handler found while attempting to publish. So could not connect.\"));\n return;\n }\n\n // Finally, write the Publish request through the Channel.\n if (logger.isDebugEnabled())\n logger.debug(\"Writing a Publish request to host: \" + HedwigClientImpl.getHostFromChannel(channel)\n + \" for pubSubData: \" + pubSubData);\n ChannelFuture future = channel.write(pubsubRequestBuilder.build());\n future.addListener(new WriteCallback(pubSubData, client));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void setLastLogId(File dir, long logId) throws IOException {\n FileOutputStream fos;\n fos = new FileOutputStream(new File(dir, \"lastId\"));\n BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos));\n try {\n bw.write(Long.toHexString(logId) + \"\\n\");\n bw.flush();\n } finally {\n try {\n fos.close();\n } catch (IOException e) {\n }\n }\n } \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void setLastLogId(File dir, long logId) throws IOException {\n FileOutputStream fos;\n fos = new FileOutputStream(new File(dir, \"lastId\"));\n BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos));\n try {\n bw.write(Long.toHexString(logId) + \"\\n\");\n bw.flush();\n } finally {\n try {\n bw.close();\n } catch (IOException e) {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteRangeAsyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n byte bytes[] = {'a','b','c','d','e','f','g','h','i'};\n\n lh.asyncAddEntry(bytes, 0, bytes.length, this, sync);\n lh.asyncAddEntry(bytes, 0, 4, this, sync); // abcd\n lh.asyncAddEntry(bytes, 3, 4, this, sync); // defg\n lh.asyncAddEntry(bytes, 3, (bytes.length-3), this, sync); // defghi\n int numEntries = 4;\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntries) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length, this, sync);\n fail(\"Shouldn't be able to use negative offset\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 0, bytes.length+1, this, sync);\n fail(\"Shouldn't be able to use that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length+2, this, sync);\n fail(\"Shouldn't be able to use negative offset \"\n + \"with that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 4, -3, this, sync);\n fail(\"Shouldn't be able to use negative length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -4, -3, this, sync);\n fail(\"Shouldn't be able to use negative offset & length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\",\n lh.getLastAddConfirmed() == (numEntries - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntries - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] expected = null;\n byte[] entry = ls.nextElement().getEntry();\n\n switch (i) {\n case 0:\n expected = Arrays.copyOfRange(bytes, 0, bytes.length);\n break;\n case 1:\n expected = Arrays.copyOfRange(bytes, 0, 4);\n break;\n case 2:\n expected = Arrays.copyOfRange(bytes, 3, 3+4);\n break;\n case 3:\n expected = Arrays.copyOfRange(bytes, 3, 3+(bytes.length-3));\n break;\n }\n assertNotNull(\"There are more checks than writes\", expected);\n\n String message = \"Checking entry \" + i + \" for equality [\"\n + new String(entry, \"UTF-8\") + \",\"\n + new String(expected, \"UTF-8\") + \"]\";\n assertTrue(message, Arrays.equals(entry, expected));\n\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntries);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 86 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteRangeAsyncSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n byte bytes[] = {'a','b','c','d','e','f','g','h','i'};\n\n lh.asyncAddEntry(bytes, 0, bytes.length, this, sync);\n lh.asyncAddEntry(bytes, 0, 4, this, sync); // abcd\n lh.asyncAddEntry(bytes, 3, 4, this, sync); // defg\n lh.asyncAddEntry(bytes, 3, (bytes.length-3), this, sync); // defghi\n int numEntries = 4;\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntries) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length, this, sync);\n fail(\"Shouldn't be able to use negative offset\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 0, bytes.length+1, this, sync);\n fail(\"Shouldn't be able to use that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length+2, this, sync);\n fail(\"Shouldn't be able to use negative offset \"\n + \"with that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 4, -3, this, sync);\n fail(\"Shouldn't be able to use negative length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -4, -3, this, sync);\n fail(\"Shouldn't be able to use negative offset & length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\",\n lh.getLastAddConfirmed() == (numEntries - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntries - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n Enumeration ls = sync.getLedgerEntries();\n while (ls.hasMoreElements()) {\n byte[] expected = null;\n byte[] entry = ls.nextElement().getEntry();\n\n switch (i) {\n case 0:\n expected = Arrays.copyOfRange(bytes, 0, bytes.length);\n break;\n case 1:\n expected = Arrays.copyOfRange(bytes, 0, 4);\n break;\n case 2:\n expected = Arrays.copyOfRange(bytes, 3, 3+4);\n break;\n case 3:\n expected = Arrays.copyOfRange(bytes, 3, 3+(bytes.length-3));\n break;\n }\n assertNotNull(\"There are more checks than writes\", expected);\n\n String message = \"Checking entry \" + i + \" for equality [\"\n + new String(entry, \"UTF-8\") + \",\"\n + new String(expected, \"UTF-8\") + \"]\";\n assertTrue(message, Arrays.equals(entry, expected));\n\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntries);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if (rc != 0)\n fail(\"Failed to write entry\");\n ls = seq;\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n SyncObj x = (SyncObj) ctx;\n if (rc != 0) {\n LOG.error(\"Failure during add {}\", rc);\n x.failureOccurred = true;\n }\n synchronized (x) {\n x.value = true;\n x.ls = seq;\n x.notify();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected synchronized void messageConsumed(Message message) {\n if (logger.isDebugEnabled())\n logger.debug(\"Message has been successfully consumed by the client app for message: \" + message\n + \", topic: \" + origSubData.topic.toStringUtf8() + \", subscriberId: \"\n + origSubData.subscriberId.toStringUtf8());\n // Update the consumed messages buffer variables\n if (responseHandler.getConfiguration().isAutoSendConsumeMessageEnabled()) {\n // Update these variables only if we are auto-sending consume\n // messages to the server. Otherwise the onus is on the client app\n // to call the Subscriber consume API to let the server know which\n // messages it has successfully consumed.\n numConsumedMessagesInBuffer++;\n lastMessageSeqId = message.getMsgId();\n }\n // Remove this consumed message from the outstanding Message Set.\n outstandingMsgSet.remove(message);\n\n // For consume response to server, there is a config param on how many\n // messages to consume and buffer up before sending the consume request.\n // We just need to keep a count of the number of messages consumed\n // and the largest/latest msg ID seen so far in this batch. Messages\n // should be delivered in order and without gaps. Do this only if\n // auto-sending of consume messages is enabled.\n if (responseHandler.getConfiguration().isAutoSendConsumeMessageEnabled()\n && numConsumedMessagesInBuffer >= responseHandler.getConfiguration().getConsumedMessagesBufferSize()) {\n // Send the consume request and reset the consumed messages buffer\n // variables. We will use the same Channel created from the\n // subscribe request for the TopicSubscriber.\n if (logger.isDebugEnabled())\n logger\n .debug(\"Consumed message buffer limit reached so send the Consume Request to the server with lastMessageSeqId: \"\n + lastMessageSeqId);\n responseHandler.getSubscriber().doConsume(origSubData, subscribeChannel, lastMessageSeqId);\n numConsumedMessagesInBuffer = 0;\n lastMessageSeqId = null;\n }\n\n // Check if we throttled message consumption previously when the\n // outstanding message limit was reached. For now, only turn the\n // delivery back on if there are no more outstanding messages to\n // consume. We could make this a configurable parameter if needed.\n if (!subscribeChannel.isReadable() && outstandingMsgSet.isEmpty()) {\n if (logger.isDebugEnabled())\n logger\n .debug(\"Message consumption has caught up so okay to turn off throttling of messages on the subscribe channel for topic: \"\n + origSubData.topic.toStringUtf8()\n + \", subscriberId: \"\n + origSubData.subscriberId.toStringUtf8());\n subscribeChannel.setReadable(true);\n }\n } \n #location 33 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected synchronized void messageConsumed(Message message) {\n if (logger.isDebugEnabled())\n logger.debug(\"Message has been successfully consumed by the client app for message: \" + message\n + \", topic: \" + origSubData.topic.toStringUtf8() + \", subscriberId: \"\n + origSubData.subscriberId.toStringUtf8());\n // Update the consumed messages buffer variables\n if (responseHandler.getConfiguration().isAutoSendConsumeMessageEnabled()) {\n // Update these variables only if we are auto-sending consume\n // messages to the server. Otherwise the onus is on the client app\n // to call the Subscriber consume API to let the server know which\n // messages it has successfully consumed.\n numConsumedMessagesInBuffer++;\n lastMessageSeqId = message.getMsgId();\n }\n // Remove this consumed message from the outstanding Message Set.\n outstandingMsgSet.remove(message);\n\n // For consume response to server, there is a config param on how many\n // messages to consume and buffer up before sending the consume request.\n // We just need to keep a count of the number of messages consumed\n // and the largest/latest msg ID seen so far in this batch. Messages\n // should be delivered in order and without gaps. Do this only if\n // auto-sending of consume messages is enabled.\n if (responseHandler.getConfiguration().isAutoSendConsumeMessageEnabled()\n && numConsumedMessagesInBuffer >= responseHandler.getConfiguration().getConsumedMessagesBufferSize()) {\n // Send the consume request and reset the consumed messages buffer\n // variables. We will use the same Channel created from the\n // subscribe request for the TopicSubscriber.\n logger.debug(\"Consumed message buffer limit reached so send the Consume Request to the \"\n + \"server with lastMessageSeqId: {}\", lastMessageSeqId);\n responseHandler.getSubscriber().doConsume(origSubData, subscribeChannel, lastMessageSeqId);\n numConsumedMessagesInBuffer = 0;\n lastMessageSeqId = null;\n }\n\n // Check if we throttled message consumption previously when the\n // outstanding message limit was reached. For now, only turn the\n // delivery back on if there are no more outstanding messages to\n // consume. We could make this a configurable parameter if needed.\n if (!subscribeChannel.isReadable() && outstandingMsgSet.isEmpty()) {\n if (logger.isDebugEnabled())\n logger.debug(\"Message consumption has caught up so okay to turn off throttling of \" +\n \"messages on the subscribe channel for topic: \" + origSubData.topic.toStringUtf8()\n + \", subscriberId: \" + origSubData.subscriberId.toStringUtf8());\n subscribeChannel.setReadable(true);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout=60000)\n public void testReadFromOpenLedger() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n if(i == numEntriesToWrite/2) {\n LedgerHandle lhOpen = bkc.openLedgerNoRecovery(ledgerId, digestType, ledgerPassword);\n // no recovery opened ledger 's last confirmed entry id is less than written\n // and it just can read until (i-1)\n int toRead = i - 1;\n Enumeration readEntry = lhOpen.readEntries(toRead, toRead);\n assertTrue(\"Enumeration of ledger entries has no element\", readEntry.hasMoreElements() == true);\n LedgerEntry e = readEntry.nextElement();\n assertEquals(toRead, e.getEntryId());\n Assert.assertArrayEquals(entries.get(toRead), e.getEntry());\n // should not written to a read only ledger\n try {\n lhOpen.addEntry(entry.array());\n fail(\"Should have thrown an exception here\");\n } catch (BKException.BKIllegalOpException bkioe) {\n // this is the correct response\n } catch (Exception ex) {\n LOG.error(\"Unexpected exception\", ex);\n fail(\"Unexpected exception\");\n }\n // close read only ledger should not change metadata\n lhOpen.close();\n }\n }\n\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == -1) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 15 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test(timeout=60000)\n public void testReadFromOpenLedger() throws Exception {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n long lac = writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n LedgerHandle lhOpen = bkc.openLedgerNoRecovery(ledgerId, digestType, ledgerPassword);\n // no recovery opened ledger 's last confirmed entry id is less than written\n // and it just can read until (i-1)\n long toRead = lac - 1;\n\n Enumeration readEntry = lhOpen.readEntries(toRead, toRead);\n assertTrue(\"Enumeration of ledger entries has no element\", readEntry.hasMoreElements() == true);\n LedgerEntry e = readEntry.nextElement();\n assertEquals(toRead, e.getEntryId());\n Assert.assertArrayEquals(entries.get((int)toRead), e.getEntry());\n // should not written to a read only ledger\n try {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n lhOpen.addEntry(entry.array());\n fail(\"Should have thrown an exception here\");\n } catch (BKException.BKIllegalOpException bkioe) {\n // this is the correct response\n } catch (Exception ex) {\n LOG.error(\"Unexpected exception\", ex);\n fail(\"Unexpected exception\");\n }\n // close read only ledger should not change metadata\n lhOpen.close();\n\n lac = writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n assertEquals(\"Last confirmed add: \", lac, (numEntriesToWrite * 2) - 1);\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == -1) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertEquals(\"Last confirmed add\", sync.lastConfirmed, (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void processResult(int rc, String path, Object ctx, List children) {\n\n if (rc != KeeperException.Code.OK.intValue()) {\n //logger.error(\"Error while reading bookies\", KeeperException.create(Code.get(rc), path));\n // try the read after a second again\n scheduler.schedule(reReadTask, ZK_CONNECT_BACKOFF_SEC, TimeUnit.SECONDS);\n return;\n }\n\n // Read the bookie addresses into a set for efficient lookup\n HashSet newBookieAddrs = new HashSet();\n for (String bookieAddrString : children) {\n InetSocketAddress bookieAddr;\n try {\n bookieAddr = StringUtils.parseAddr(bookieAddrString);\n } catch (IOException e) {\n logger.error(\"Could not parse bookie address: \" + bookieAddrString + \", ignoring this bookie\");\n continue;\n }\n newBookieAddrs.add(bookieAddr);\n }\n\n HashSet deadBookies = (HashSet)knownBookies.clone();\n deadBookies.removeAll(newBookieAddrs);\n\n synchronized (this) {\n knownBookies = newBookieAddrs;\n }\n\n if (bk.getBookieClient() != null) {\n bk.getBookieClient().closeClients(deadBookies);\n }\n } \n #location 24 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void processResult(int rc, String path, Object ctx, List children) {\n\n if (rc != KeeperException.Code.OK.intValue()) {\n //logger.error(\"Error while reading bookies\", KeeperException.create(Code.get(rc), path));\n // try the read after a second again\n scheduler.schedule(reReadTask, ZK_CONNECT_BACKOFF_SEC, TimeUnit.SECONDS);\n return;\n }\n\n // Read the bookie addresses into a set for efficient lookup\n HashSet newBookieAddrs = new HashSet();\n for (String bookieAddrString : children) {\n InetSocketAddress bookieAddr;\n try {\n bookieAddr = StringUtils.parseAddr(bookieAddrString);\n } catch (IOException e) {\n logger.error(\"Could not parse bookie address: \" + bookieAddrString + \", ignoring this bookie\");\n continue;\n }\n newBookieAddrs.add(bookieAddr);\n }\n\n final HashSet deadBookies;\n synchronized (this) {\n deadBookies = (HashSet)knownBookies.clone();\n deadBookies.removeAll(newBookieAddrs);\n knownBookies = newBookieAddrs;\n }\n\n if (bk.getBookieClient() != null) {\n bk.getBookieClient().closeClients(deadBookies);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n } \n #location 20 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void auxTestReadWriteAsyncSingleClient(BookieServer bs) throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(3, 2, digestType, ledgerPassword);\n\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n }\n\n LOG.info(\"Wrote \" + numEntriesToWrite + \" and now going to fail bookie.\");\n // Bookie fail\n bs.shutdown();\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n bkc.close();\n bkc = new BookKeeperTestClient(baseClientConf);\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait(10000);\n assertTrue(\"Haven't received entries\", sync.value);\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + i);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n LOG.info(\"Verified that entries are ok, and now closing ledger\");\n lh.close();\n } catch (KeeperException e) {\n LOG.error(\"Caught KeeperException\", e);\n fail(e.toString());\n } catch (BKException e) {\n LOG.error(\"Caught BKException\", e);\n fail(e.toString());\n } catch (InterruptedException e) {\n LOG.error(\"Caught InterruptedException\", e);\n fail(e.toString());\n }\n\n } \n #location 24 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n void auxTestReadWriteAsyncSingleClient(BookieServer bs) throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(3, 2, digestType, ledgerPassword);\n\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n }\n\n LOG.info(\"Wrote \" + numEntriesToWrite + \" and now going to fail bookie.\");\n // Bookie fail\n bs.shutdown();\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait(10000);\n assertFalse(\"Failure occurred during write\", sync.failureOccurred);\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n bkc.close();\n bkc = new BookKeeperTestClient(baseClientConf);\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait(10000);\n assertTrue(\"Haven't received entries\", sync.value);\n assertFalse(\"Failure occurred during read\", sync.failureOccurred);\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (sync.ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = sync.ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + i);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n LOG.info(\"Verified that entries are ok, and now closing ledger\");\n lh.close();\n } catch (KeeperException e) {\n LOG.error(\"Caught KeeperException\", e);\n fail(e.toString());\n } catch (BKException e) {\n LOG.error(\"Caught BKException\", e);\n fail(e.toString());\n } catch (InterruptedException e) {\n LOG.error(\"Caught InterruptedException\", e);\n fail(e.toString());\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 11 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws Exception {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void doPublish(PubSubData pubSubData, Channel channel) {\n // Create a PubSubRequest\n PubSubRequest.Builder pubsubRequestBuilder = PubSubRequest.newBuilder();\n pubsubRequestBuilder.setProtocolVersion(ProtocolVersion.VERSION_ONE);\n pubsubRequestBuilder.setType(OperationType.PUBLISH);\n if (pubSubData.triedServers != null && pubSubData.triedServers.size() > 0) {\n pubsubRequestBuilder.addAllTriedServers(pubSubData.triedServers);\n }\n long txnId = client.globalCounter.incrementAndGet();\n pubsubRequestBuilder.setTxnId(txnId);\n pubsubRequestBuilder.setShouldClaim(pubSubData.shouldClaim);\n pubsubRequestBuilder.setTopic(pubSubData.topic);\n\n // Now create the PublishRequest\n PublishRequest.Builder publishRequestBuilder = PublishRequest.newBuilder();\n\n publishRequestBuilder.setMsg(pubSubData.msg);\n\n // Set the PublishRequest into the outer PubSubRequest\n pubsubRequestBuilder.setPublishRequest(publishRequestBuilder);\n\n // Update the PubSubData with the txnId and the requestWriteTime\n pubSubData.txnId = txnId;\n pubSubData.requestWriteTime = MathUtils.now();\n\n // Before we do the write, store this information into the\n // ResponseHandler so when the server responds, we know what\n // appropriate Callback Data to invoke for the given txn ID.\n HedwigClientImpl.getResponseHandlerFromChannel(channel).txn2PubSubData.put(txnId, pubSubData);\n\n // Finally, write the Publish request through the Channel.\n if (logger.isDebugEnabled())\n logger.debug(\"Writing a Publish request to host: \" + HedwigClientImpl.getHostFromChannel(channel)\n + \" for pubSubData: \" + pubSubData);\n ChannelFuture future = channel.write(pubsubRequestBuilder.build());\n future.addListener(new WriteCallback(pubSubData, client));\n } \n #location 35 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void doPublish(PubSubData pubSubData, Channel channel) {\n // Create a PubSubRequest\n PubSubRequest.Builder pubsubRequestBuilder = PubSubRequest.newBuilder();\n pubsubRequestBuilder.setProtocolVersion(ProtocolVersion.VERSION_ONE);\n pubsubRequestBuilder.setType(OperationType.PUBLISH);\n if (pubSubData.triedServers != null && pubSubData.triedServers.size() > 0) {\n pubsubRequestBuilder.addAllTriedServers(pubSubData.triedServers);\n }\n long txnId = client.globalCounter.incrementAndGet();\n pubsubRequestBuilder.setTxnId(txnId);\n pubsubRequestBuilder.setShouldClaim(pubSubData.shouldClaim);\n pubsubRequestBuilder.setTopic(pubSubData.topic);\n\n // Now create the PublishRequest\n PublishRequest.Builder publishRequestBuilder = PublishRequest.newBuilder();\n\n publishRequestBuilder.setMsg(pubSubData.msg);\n\n // Set the PublishRequest into the outer PubSubRequest\n pubsubRequestBuilder.setPublishRequest(publishRequestBuilder);\n\n // Update the PubSubData with the txnId and the requestWriteTime\n pubSubData.txnId = txnId;\n pubSubData.requestWriteTime = MathUtils.now();\n\n // Before we do the write, store this information into the\n // ResponseHandler so when the server responds, we know what\n // appropriate Callback Data to invoke for the given txn ID.\n try {\n HedwigClientImpl.getResponseHandlerFromChannel(channel).txn2PubSubData.put(txnId, pubSubData);\n } catch (NoResponseHandlerException e) {\n logger.error(\"No response handler found while storing the publish callback.\");\n // Callback on pubsubdata indicating failure.\n pubSubData.getCallback().operationFailed(pubSubData.context, new CouldNotConnectException(\"No response \" +\n \"handler found while attempting to publish. So could not connect.\"));\n return;\n }\n\n // Finally, write the Publish request through the Channel.\n if (logger.isDebugEnabled())\n logger.debug(\"Writing a Publish request to host: \" + HedwigClientImpl.getHostFromChannel(channel)\n + \" for pubSubData: \" + pubSubData);\n ChannelFuture future = channel.write(pubsubRequestBuilder.build());\n future.addListener(new WriteCallback(pubSubData, client));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private long readLastLogId(File f) {\n FileInputStream fis;\n try {\n fis = new FileInputStream(new File(f, \"lastId\"));\n } catch (FileNotFoundException e) {\n return -1;\n }\n BufferedReader br = new BufferedReader(new InputStreamReader(fis));\n try {\n String lastIdString = br.readLine();\n return Long.parseLong(lastIdString, 16);\n } catch (IOException e) {\n return -1;\n } catch(NumberFormatException e) {\n return -1;\n } finally {\n try {\n fis.close();\n } catch (IOException e) {\n }\n }\n } \n #location 10 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private long readLastLogId(File f) {\n FileInputStream fis;\n try {\n fis = new FileInputStream(new File(f, \"lastId\"));\n } catch (FileNotFoundException e) {\n return -1;\n }\n BufferedReader br = new BufferedReader(new InputStreamReader(fis));\n try {\n String lastIdString = br.readLine();\n return Long.parseLong(lastIdString, 16);\n } catch (IOException e) {\n return -1;\n } catch(NumberFormatException e) {\n return -1;\n } finally {\n try {\n br.close();\n } catch (IOException e) {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n } \n #location 39 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testSyncReadAsyncWriteStringsSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n LOG.info(\"TEST READ WRITE STRINGS MIXED SINGLE CLIENT\");\n String charset = \"utf-8\";\n LOG.debug(\"Default charset: \" + Charset.defaultCharset());\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n int randomInt = rng.nextInt(maxInt);\n byte[] entry = new String(Integer.toString(randomInt)).getBytes(charset);\n entries.add(entry);\n lh.asyncAddEntry(entry, this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** ASYNC WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETED // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n\n LOG.debug(\"*** SYNC READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] origEntryBytes = entries.get(i++);\n byte[] retrEntryBytes = ls.nextElement().getEntry();\n\n LOG.debug(\"Original byte entry size: \" + origEntryBytes.length);\n LOG.debug(\"Saved byte entry size: \" + retrEntryBytes.length);\n\n String origEntry = new String(origEntryBytes, charset);\n String retrEntry = new String(retrEntryBytes, charset);\n\n LOG.debug(\"Original entry: \" + origEntry);\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n // get back to prev value\n lh.lastAddConfirmed--;\n if (rc == BKException.Code.OK) {\n LedgerEntry entry = seq.nextElement();\n byte[] data = entry.getEntry();\n\n /*\n * We will add this entry again to make sure it is written to enough\n * replicas. We subtract the length of the data itself, since it will\n * be added again when processing the call to add it.\n */\n synchronized (lh) {\n lh.length = entry.getLength() - (long) data.length;\n }\n lh.asyncRecoveryAddEntry(data, 0, data.length, this, null);\n return;\n }\n\n if (rc == BKException.Code.NoSuchEntryException || rc == BKException.Code.NoSuchLedgerExistsException) {\n lh.asyncCloseInternal(new CloseCallback() {\n @Override\n public void closeComplete(int rc, LedgerHandle lh, Object ctx) {\n if (rc != KeeperException.Code.OK.intValue()) {\n LOG.warn(\"Close failed: \" + BKException.getMessage(rc));\n cb.operationComplete(BKException.Code.ZKException, null);\n } else {\n cb.operationComplete(BKException.Code.OK, null);\n LOG.debug(\"After closing length is: {}\", lh.getLength());\n }\n }\n }, null, BKException.Code.LedgerClosedException);\n return;\n }\n\n // otherwise, some other error, we can't handle\n LOG.error(\"Failure \" + BKException.getMessage(rc) + \" while reading entry: \" + (lh.lastAddConfirmed + 1)\n + \" ledger: \" + lh.ledgerId + \" while recovering ledger\");\n cb.operationComplete(rc, null);\n return;\n } \n #location 38 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if (rc == BKException.Code.OK) {\n LedgerEntry entry = seq.nextElement();\n byte[] data = entry.getEntry();\n\n /*\n * We will add this entry again to make sure it is written to enough\n * replicas. We subtract the length of the data itself, since it will\n * be added again when processing the call to add it.\n */\n synchronized (lh) {\n lh.length = entry.getLength() - (long) data.length;\n }\n lh.asyncRecoveryAddEntry(data, 0, data.length, this, null);\n return;\n }\n\n if (rc == BKException.Code.NoSuchEntryException || rc == BKException.Code.NoSuchLedgerExistsException) {\n lh.asyncCloseInternal(new CloseCallback() {\n @Override\n public void closeComplete(int rc, LedgerHandle lh, Object ctx) {\n if (rc != KeeperException.Code.OK.intValue()) {\n LOG.warn(\"Close failed: \" + BKException.getMessage(rc));\n cb.operationComplete(BKException.Code.ZKException, null);\n } else {\n cb.operationComplete(BKException.Code.OK, null);\n LOG.debug(\"After closing length is: {}\", lh.getLength());\n }\n }\n }, null, BKException.Code.LedgerClosedException);\n return;\n }\n\n // otherwise, some other error, we can't handle\n LOG.error(\"Failure \" + BKException.getMessage(rc) + \" while reading entry: \" + (lh.lastAddConfirmed + 1)\n + \" ledger: \" + lh.ledgerId + \" while recovering ledger\");\n cb.operationComplete(rc, null);\n return;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteRangeAsyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n byte bytes[] = {'a','b','c','d','e','f','g','h','i'};\n\n lh.asyncAddEntry(bytes, 0, bytes.length, this, sync);\n lh.asyncAddEntry(bytes, 0, 4, this, sync); // abcd\n lh.asyncAddEntry(bytes, 3, 4, this, sync); // defg\n lh.asyncAddEntry(bytes, 3, (bytes.length-3), this, sync); // defghi\n int numEntries = 4;\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntries) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length, this, sync);\n fail(\"Shouldn't be able to use negative offset\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 0, bytes.length+1, this, sync);\n fail(\"Shouldn't be able to use that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length+2, this, sync);\n fail(\"Shouldn't be able to use negative offset \"\n + \"with that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 4, -3, this, sync);\n fail(\"Shouldn't be able to use negative length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -4, -3, this, sync);\n fail(\"Shouldn't be able to use negative offset & length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\",\n lh.getLastAddConfirmed() == (numEntries - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntries - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n byte[] expected = null;\n byte[] entry = ls.nextElement().getEntry();\n\n switch (i) {\n case 0:\n expected = Arrays.copyOfRange(bytes, 0, bytes.length);\n break;\n case 1:\n expected = Arrays.copyOfRange(bytes, 0, 4);\n break;\n case 2:\n expected = Arrays.copyOfRange(bytes, 3, 3+4);\n break;\n case 3:\n expected = Arrays.copyOfRange(bytes, 3, 3+(bytes.length-3));\n break;\n }\n assertNotNull(\"There are more checks than writes\", expected);\n\n String message = \"Checking entry \" + i + \" for equality [\"\n + new String(entry, \"UTF-8\") + \",\"\n + new String(expected, \"UTF-8\") + \"]\";\n assertTrue(message, Arrays.equals(entry, expected));\n\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntries);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 18 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteRangeAsyncSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n byte bytes[] = {'a','b','c','d','e','f','g','h','i'};\n\n lh.asyncAddEntry(bytes, 0, bytes.length, this, sync);\n lh.asyncAddEntry(bytes, 0, 4, this, sync); // abcd\n lh.asyncAddEntry(bytes, 3, 4, this, sync); // defg\n lh.asyncAddEntry(bytes, 3, (bytes.length-3), this, sync); // defghi\n int numEntries = 4;\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntries) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length, this, sync);\n fail(\"Shouldn't be able to use negative offset\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 0, bytes.length+1, this, sync);\n fail(\"Shouldn't be able to use that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -1, bytes.length+2, this, sync);\n fail(\"Shouldn't be able to use negative offset \"\n + \"with that much length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, 4, -3, this, sync);\n fail(\"Shouldn't be able to use negative length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n try {\n lh.asyncAddEntry(bytes, -4, -3, this, sync);\n fail(\"Shouldn't be able to use negative offset & length\");\n } catch (ArrayIndexOutOfBoundsException aiob) {\n // expected\n }\n\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\",\n lh.getLastAddConfirmed() == (numEntries - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntries - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n Enumeration ls = sync.getLedgerEntries();\n while (ls.hasMoreElements()) {\n byte[] expected = null;\n byte[] entry = ls.nextElement().getEntry();\n\n switch (i) {\n case 0:\n expected = Arrays.copyOfRange(bytes, 0, bytes.length);\n break;\n case 1:\n expected = Arrays.copyOfRange(bytes, 0, 4);\n break;\n case 2:\n expected = Arrays.copyOfRange(bytes, 3, 3+4);\n break;\n case 3:\n expected = Arrays.copyOfRange(bytes, 3, 3+(bytes.length-3));\n break;\n }\n assertNotNull(\"There are more checks than writes\", expected);\n\n String message = \"Checking entry \" + i + \" for equality [\"\n + new String(entry, \"UTF-8\") + \",\"\n + new String(expected, \"UTF-8\") + \"]\";\n assertTrue(message, Arrays.equals(entry, expected));\n\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntries);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteAsyncLength() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n long length = numEntriesToWrite * 4;\n assertTrue(\"Ledger length before closing: \" + lh.getLength(), lh.getLength() == length);\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n assertTrue(\"Ledger length after opening: \" + lh.getLength(), lh.getLength() == length);\n\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 20 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteAsyncLength() throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n long length = numEntriesToWrite * 4;\n assertTrue(\"Ledger length before closing: \" + lh.getLength(), lh.getLength() == length);\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n assertTrue(\"Ledger length after opening: \" + lh.getLength(), lh.getLength() == length);\n\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void run() {\n LOG.info(\"Running...\");\n long start = previous = System.currentTimeMillis();\n\n byte messageCount = 0;\n int sent = 0;\n\n Thread reporter = new Thread() {\n public void run() {\n try {\n while(true) {\n Thread.sleep(200);\n LOG.info(\"ms: {} req: {}\", System.currentTimeMillis(), completedRequests.getAndSet(0));\n }\n } catch (InterruptedException ie) {\n LOG.info(\"Caught interrupted exception, going away\");\n }\n }\n };\n reporter.start();\n long beforeSend = System.nanoTime();\n\n while(!Thread.currentThread().isInterrupted() && sent < sendLimit) {\n try {\n sem.acquire();\n if (sent == 10000) {\n long afterSend = System.nanoTime();\n long time = afterSend - beforeSend;\n LOG.info(\"Time to send first batch: {}s {}ns \",\n time/1000/1000/1000, time);\n }\n } catch (InterruptedException e) {\n break;\n }\n\n final int index = getRandomLedger();\n LedgerHandle h = lh[index];\n if (h == null) {\n LOG.error(\"Handle \" + index + \" is null!\");\n } else {\n long nanoTime = System.nanoTime();\n lh[index].asyncAddEntry(bytes, this, new Context(sent, nanoTime));\n counter.incrementAndGet();\n }\n sent++;\n }\n LOG.info(\"Sent: \" + sent);\n try {\n synchronized (this) {\n while(this.counter.get() > 0)\n Thread.sleep(1000);\n }\n } catch(InterruptedException e) {\n LOG.error(\"Interrupted while waiting\", e);\n }\n synchronized(this) {\n duration = System.currentTimeMillis() - start;\n }\n throughput = sent*1000/duration;\n\n reporter.interrupt();\n try {\n reporter.join();\n } catch (InterruptedException ie) {\n // ignore\n }\n LOG.info(\"Finished processing in ms: \" + duration + \" tp = \" + throughput);\n } \n #location 67 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void run() {\n LOG.info(\"Running...\");\n long start = previous = System.currentTimeMillis();\n\n int sent = 0;\n\n Thread reporter = new Thread() {\n public void run() {\n try {\n while(true) {\n Thread.sleep(200);\n LOG.info(\"ms: {} req: {}\", System.currentTimeMillis(), completedRequests.getAndSet(0));\n }\n } catch (InterruptedException ie) {\n LOG.info(\"Caught interrupted exception, going away\");\n }\n }\n };\n reporter.start();\n long beforeSend = System.nanoTime();\n\n while(!Thread.currentThread().isInterrupted() && sent < sendLimit) {\n try {\n sem.acquire();\n if (sent == 10000) {\n long afterSend = System.nanoTime();\n long time = afterSend - beforeSend;\n LOG.info(\"Time to send first batch: {}s {}ns \",\n time/1000/1000/1000, time);\n }\n } catch (InterruptedException e) {\n break;\n }\n\n final int index = getRandomLedger();\n LedgerHandle h = lh[index];\n if (h == null) {\n LOG.error(\"Handle \" + index + \" is null!\");\n } else {\n long nanoTime = System.nanoTime();\n lh[index].asyncAddEntry(bytes, this, new Context(sent, nanoTime));\n counter.incrementAndGet();\n }\n sent++;\n }\n LOG.info(\"Sent: \" + sent);\n try {\n synchronized (this) {\n while (this.counter.get() > 0) {\n waitFor(1000);\n }\n }\n } catch(InterruptedException e) {\n LOG.error(\"Interrupted while waiting\", e);\n }\n synchronized(this) {\n duration = System.currentTimeMillis() - start;\n }\n throughput = sent*1000/getDuration();\n\n reporter.interrupt();\n try {\n reporter.join();\n } catch (InterruptedException ie) {\n // ignore\n }\n LOG.info(\"Finished processing in ms: \" + getDuration() + \" tp = \" + throughput);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testEnsembleReformation() throws Exception {\n try {\n LedgerManagerFactory newLedgerManagerFactory = LedgerManagerFactory\n .newLedgerManagerFactory(baseConf, zkc);\n LedgerManager ledgerManager = newLedgerManagerFactory\n .newLedgerManager();\n\n List ledgerList = new ArrayList(3);\n LedgerHandle lh1 = createAndAddEntriesToLedger();\n ledgerList.add(lh1.getId());\n LedgerHandle lh2 = createAndAddEntriesToLedger();\n ledgerList.add(lh2.getId());\n\n startNewBookie();\n shutdownBookie(bs.size() - 2);\n\n // add few more entries after ensemble reformation\n for (int i = 0; i < 10; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(Integer.MAX_VALUE));\n entry.position(0);\n\n entries.add(entry.array());\n lh1.addEntry(entry.array());\n lh2.addEntry(entry.array());\n }\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n\n Map> bookieToLedgerIndex = bookieLedgerIndex\n .getBookieToLedgerIndex();\n assertEquals(\"Missed few bookies in the bookie-ledger mapping!\", 4,\n bookieToLedgerIndex.size());\n Collection> bk2ledgerEntry = bookieToLedgerIndex.values();\n for (Set ledgers : bk2ledgerEntry) {\n assertEquals(\n \"Missed few ledgers in the bookie-ledger mapping!\", 2,\n ledgers.size());\n for (Long ledgerNode : ledgers) {\n assertTrue(\"Unknown ledger-bookie mapping\", ledgerList\n .contains(ledgerNode));\n }\n }\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 46 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testEnsembleReformation() throws Exception {\n try {\n LedgerHandle lh1 = createAndAddEntriesToLedger();\n LedgerHandle lh2 = createAndAddEntriesToLedger();\n\n startNewBookie();\n shutdownBookie(bs.size() - 2);\n\n // add few more entries after ensemble reformation\n for (int i = 0; i < 10; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(Integer.MAX_VALUE));\n entry.position(0);\n\n entries.add(entry.array());\n lh1.addEntry(entry.array());\n lh2.addEntry(entry.array());\n }\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n\n Map> bookieToLedgerIndex = bookieLedgerIndex\n .getBookieToLedgerIndex();\n assertEquals(\"Missed few bookies in the bookie-ledger mapping!\", 4,\n bookieToLedgerIndex.size());\n Collection> bk2ledgerEntry = bookieToLedgerIndex.values();\n for (Set ledgers : bk2ledgerEntry) {\n assertEquals(\n \"Missed few ledgers in the bookie-ledger mapping!\", 2,\n ledgers.size());\n for (Long ledgerNode : ledgers) {\n assertTrue(\"Unknown ledger-bookie mapping\", ledgerList\n .contains(ledgerNode));\n }\n }\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void handleBookieFailure(InetSocketAddress addr, final int bookieIndex) {\n InetSocketAddress newBookie;\n\n if (LOG.isDebugEnabled()) {\n LOG.debug(\"Handling failure of bookie: \" + addr + \" index: \"\n + bookieIndex);\n }\n\n try {\n newBookie = bk.bookieWatcher\n .getAdditionalBookie(metadata.currentEnsemble);\n } catch (BKNotEnoughBookiesException e) {\n LOG\n .error(\"Could not get additional bookie to remake ensemble, closing ledger: \"\n + ledgerId);\n handleUnrecoverableErrorDuringAdd(e.getCode());\n return;\n }\n\n final ArrayList newEnsemble = new ArrayList(\n metadata.currentEnsemble);\n newEnsemble.set(bookieIndex, newBookie);\n\n if (LOG.isDebugEnabled()) {\n LOG.debug(\"Changing ensemble from: \" + metadata.currentEnsemble + \" to: \"\n + newEnsemble + \" for ledger: \" + ledgerId + \" starting at entry: \"\n + (lastAddConfirmed + 1));\n }\n\n final long newEnsembleStartEntry = lastAddConfirmed + 1;\n metadata.addEnsemble(newEnsembleStartEntry, newEnsemble);\n\n final class ChangeEnsembleCb implements GenericCallback {\n @Override\n public void operationComplete(final int rc, Void result) {\n\n bk.mainWorkerPool.submitOrdered(ledgerId, new SafeRunnable() {\n @Override\n public void safeRun() {\n if (rc == BKException.Code.MetadataVersionException) {\n rereadMetadata(new GenericCallback() {\n @Override\n public void operationComplete(int newrc, LedgerMetadata newMeta) {\n if (newrc != BKException.Code.OK) {\n LOG.error(\"Error reading new metadata from ledger after changing ensemble, code=\" + newrc);\n handleUnrecoverableErrorDuringAdd(rc);\n } else {\n // a new ensemble is added only when the start entry is larger than zero\n if (newEnsembleStartEntry > 0) {\n metadata.getEnsembles().remove(newEnsembleStartEntry);\n }\n if (metadata.resolveConflict(newMeta)) {\n metadata.addEnsemble(newEnsembleStartEntry, newEnsemble);\n writeLedgerConfig(new ChangeEnsembleCb());\n return;\n } else {\n LOG.error(\"Could not resolve ledger metadata conflict while changing ensemble to: \"\n + newEnsemble + \", old meta data is \\n\" + new String(metadata.serialize())\n + \"\\n, new meta data is \\n\" + new String(newMeta.serialize()) + \"\\n ,closing ledger\");\n handleUnrecoverableErrorDuringAdd(rc);\n }\n }\n }\n });\n return;\n } else if (rc != BKException.Code.OK) {\n LOG.error(\"Could not persist ledger metadata while changing ensemble to: \"\n + newEnsemble + \" , closing ledger\");\n handleUnrecoverableErrorDuringAdd(rc);\n return;\n }\n\n for (PendingAddOp pendingAddOp : pendingAddOps) {\n pendingAddOp.unsetSuccessAndSendWriteRequest(bookieIndex);\n }\n }\n });\n\n }\n };\n\n writeLedgerConfig(new ChangeEnsembleCb());\n } \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n LedgerHandle(BookKeeper bk, long ledgerId, LedgerMetadata metadata,\n DigestType digestType, byte[] password)\n throws GeneralSecurityException, NumberFormatException {\n this.bk = bk;\n this.metadata = metadata;\n\n if (metadata.isClosed()) {\n lastAddConfirmed = lastAddPushed = metadata.getLastEntryId();\n length = metadata.getLength();\n } else {\n lastAddConfirmed = lastAddPushed = INVALID_ENTRY_ID;\n length = 0;\n }\n\n this.ledgerId = ledgerId;\n\n this.throttling = bk.getConf().getThrottleValue();\n this.opCounterSem = new Semaphore(throttling);\n\n macManager = DigestManager.instantiate(ledgerId, password, digestType);\n this.ledgerKey = MacDigestManager.genDigest(\"ledger\", password);\n distributionSchedule = new RoundRobinDistributionSchedule(\n metadata.getQuorumSize(), metadata.getEnsembleSize());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void setLastLogId(File dir, long logId) throws IOException {\n FileOutputStream fos;\n fos = new FileOutputStream(new File(dir, \"lastId\"));\n BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos));\n try {\n bw.write(Long.toHexString(logId) + \"\\n\");\n bw.flush();\n } finally {\n try {\n fos.close();\n } catch (IOException e) {\n }\n }\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void setLastLogId(File dir, long logId) throws IOException {\n FileOutputStream fos;\n fos = new FileOutputStream(new File(dir, \"lastId\"));\n BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos));\n try {\n bw.write(Long.toHexString(logId) + \"\\n\");\n bw.flush();\n } finally {\n try {\n bw.close();\n } catch (IOException e) {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n if (rc != 0)\n fail(\"Failed to write entry\");\n ls = seq;\n synchronized (sync) {\n sync.value = true;\n sync.notify();\n }\n\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void readComplete(int rc, LedgerHandle lh, Enumeration seq, Object ctx) {\n SyncObj x = (SyncObj) ctx;\n if (rc != 0) {\n LOG.error(\"Failure during add {}\", rc);\n x.failureOccurred = true;\n }\n synchronized (x) {\n x.value = true;\n x.ls = seq;\n x.notify();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout = 60000)\n public void testWhenNoLogsToCompact() throws Exception {\n tearDown(); // I dont want the test infrastructure\n ServerConfiguration conf = new ServerConfiguration();\n File tmpDir = File.createTempFile(\"bkTest\", \".dir\");\n tmpDir.delete();\n tmpDir.mkdir();\n File curDir = Bookie.getCurrentDirectory(tmpDir);\n Bookie.checkDirectoryStructure(curDir);\n conf.setLedgerDirNames(new String[] { tmpDir.toString() });\n\n LedgerDirsManager dirs = new LedgerDirsManager(conf);\n final Set ledgers = Collections\n .newSetFromMap(new ConcurrentHashMap());\n LedgerManager manager = getLedgerManager(ledgers);\n CheckpointSource checkpointSource = new CheckpointSource() {\n\n @Override\n public Checkpoint newCheckpoint() {\n return null;\n }\n\n @Override\n public void checkpointComplete(Checkpoint checkpoint,\n boolean compact) throws IOException {\n }\n };\n InterleavedLedgerStorage storage = new InterleavedLedgerStorage(conf,\n manager, dirs, checkpointSource);\n\n double threshold = 0.1;\n // shouldn't throw exception\n storage.gcThread.doCompactEntryLogs(threshold);\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeout = 60000)\n public void testWhenNoLogsToCompact() throws Exception {\n tearDown(); // I dont want the test infrastructure\n ServerConfiguration conf = new ServerConfiguration();\n File tmpDir = File.createTempFile(\"bkTest\", \".dir\");\n tmpDir.delete();\n tmpDir.mkdir();\n File curDir = Bookie.getCurrentDirectory(tmpDir);\n Bookie.checkDirectoryStructure(curDir);\n conf.setLedgerDirNames(new String[] { tmpDir.toString() });\n\n LedgerDirsManager dirs = new LedgerDirsManager(conf, conf.getLedgerDirs());\n final Set ledgers = Collections\n .newSetFromMap(new ConcurrentHashMap());\n LedgerManager manager = getLedgerManager(ledgers);\n CheckpointSource checkpointSource = new CheckpointSource() {\n\n @Override\n public Checkpoint newCheckpoint() {\n return null;\n }\n\n @Override\n public void checkpointComplete(Checkpoint checkpoint,\n boolean compact) throws IOException {\n }\n };\n InterleavedLedgerStorage storage = new InterleavedLedgerStorage(conf,\n manager, dirs, checkpointSource);\n\n double threshold = 0.1;\n // shouldn't throw exception\n storage.gcThread.doCompactEntryLogs(threshold);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void handleBookieFailure(final InetSocketAddress addr, final int bookieIndex) {\n InetSocketAddress newBookie;\n\n LOG.debug(\"Handling failure of bookie: {} index: {}\", addr, bookieIndex);\n final ArrayList newEnsemble = new ArrayList();\n blockAddCompletions.incrementAndGet();\n final long newEnsembleStartEntry = lastAddConfirmed + 1;\n\n // avoid parallel ensemble changes to same ensemble.\n synchronized (metadata) {\n if (!metadata.currentEnsemble.get(bookieIndex).equals(addr)) {\n // ensemble has already changed, failure of this addr is immaterial\n LOG.warn(\"Write did not succeed to {}, bookieIndex {}, but we have already fixed it.\",\n addr, bookieIndex);\n blockAddCompletions.decrementAndGet();\n return;\n }\n\n try {\n newBookie = bk.bookieWatcher\n .getAdditionalBookie(metadata.currentEnsemble);\n } catch (BKNotEnoughBookiesException e) {\n LOG.error(\"Could not get additional bookie to \"\n + \"remake ensemble, closing ledger: \" + ledgerId);\n handleUnrecoverableErrorDuringAdd(e.getCode());\n return;\n }\n\n newEnsemble.addAll(metadata.currentEnsemble);\n newEnsemble.set(bookieIndex, newBookie);\n\n if (LOG.isDebugEnabled()) {\n LOG.debug(\"Changing ensemble from: \" + metadata.currentEnsemble\n + \" to: \" + newEnsemble + \" for ledger: \" + ledgerId\n + \" starting at entry: \" + (lastAddConfirmed + 1));\n }\n\n metadata.addEnsemble(newEnsembleStartEntry, newEnsemble);\n }\n\n EnsembleInfo ensembleInfo = new EnsembleInfo(newEnsemble, bookieIndex,\n addr);\n writeLedgerConfig(new ChangeEnsembleCb(ensembleInfo));\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n LedgerHandle(BookKeeper bk, long ledgerId, LedgerMetadata metadata,\n DigestType digestType, byte[] password)\n throws GeneralSecurityException, NumberFormatException {\n this.bk = bk;\n this.metadata = metadata;\n\n if (metadata.isClosed()) {\n lastAddConfirmed = lastAddPushed = metadata.getLastEntryId();\n length = metadata.getLength();\n } else {\n lastAddConfirmed = lastAddPushed = INVALID_ENTRY_ID;\n length = 0;\n }\n\n this.ledgerId = ledgerId;\n\n this.throttler = RateLimiter.create(bk.getConf().getThrottleValue());\n\n macManager = DigestManager.instantiate(ledgerId, password, digestType);\n this.ledgerKey = MacDigestManager.genDigest(\"ledger\", password);\n distributionSchedule = new RoundRobinDistributionSchedule(\n metadata.getWriteQuorumSize(), metadata.getAckQuorumSize(), metadata.getEnsembleSize());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.addEntry(entry.array());\n }\n\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 14 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test(timeout=60000)\n public void testLastConfirmedAdd() throws Exception {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n long last = lh.readLastConfirmed();\n assertTrue(\"Last confirmed add: \" + last, last == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n /*\n * Asynchronous call to read last confirmed entry\n */\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n writeNEntriesLastWriteSync(lh, numEntriesToWrite);\n\n SyncObj sync = new SyncObj();\n lh.asyncReadLastConfirmed(this, sync);\n\n // Wait for for last confirmed\n synchronized (sync) {\n while (sync.lastConfirmed == LedgerHandle.INVALID_ENTRY_ID) {\n LOG.debug(\"Counter = \" + sync.lastConfirmed);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n assertTrue(\"Last confirmed add: \" + sync.lastConfirmed, sync.lastConfirmed == (numEntriesToWrite - 2));\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void compactEntryLog(long entryLogId) {\n EntryLogMetadata entryLogMeta = entryLogMetaMap.get(entryLogId);\n if (null == entryLogMeta) {\n LOG.warn(\"Can't get entry log meta when compacting entry log \" + entryLogId + \".\");\n return;\n }\n\n // Similar with Sync Thread\n // try to mark compacting flag to make sure it would not be interrupted\n // by shutdown during compaction. otherwise it will receive\n // ClosedByInterruptException which may cause index file & entry logger\n // closed and corrupted.\n if (!compacting.compareAndSet(false, true)) {\n // set compacting flag failed, means compacting is true now\n // indicates another thread wants to interrupt gc thread to exit\n return;\n }\n\n LOG.info(\"Compacting entry log : \" + entryLogId);\n\n try {\n entryLogger.scanEntryLog(entryLogId, new CompactionScanner(entryLogMeta));\n // after moving entries to new entry log, remove this old one\n removeEntryLog(entryLogId);\n } catch (IOException e) {\n LOG.info(\"Premature exception when compacting \" + entryLogId, e);\n } finally {\n // clear compacting flag\n compacting.set(false);\n }\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void compactEntryLog(long entryLogId) {\n EntryLogMetadata entryLogMeta = entryLogMetaMap.get(entryLogId);\n if (null == entryLogMeta) {\n LOG.warn(\"Can't get entry log meta when compacting entry log \" + entryLogId + \".\");\n return;\n }\n\n // Similar with Sync Thread\n // try to mark compacting flag to make sure it would not be interrupted\n // by shutdown during compaction. otherwise it will receive\n // ClosedByInterruptException which may cause index file & entry logger\n // closed and corrupted.\n if (!compacting.compareAndSet(false, true)) {\n // set compacting flag failed, means compacting is true now\n // indicates another thread wants to interrupt gc thread to exit\n return;\n }\n\n LOG.info(\"Compacting entry log : \" + entryLogId);\n\n try {\n CompactionScanner scanner = new CompactionScanner(entryLogMeta);\n entryLogger.scanEntryLog(entryLogId, scanner);\n scanner.awaitComplete();\n // after moving entries to new entry log, remove this old one\n removeEntryLog(entryLogId);\n } catch (IOException e) {\n LOG.info(\"Premature exception when compacting \" + entryLogId, e);\n } catch (InterruptedException ie) {\n Thread.currentThread().interrupt();\n LOG.warn(\"Interrupted while compacting\", ie);\n } finally {\n // clear compacting flag\n compacting.set(false);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testMultiLedger() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n lh2 = bkc.createLedger(digestType, ledgerPassword);\n\n long ledgerId = lh.getId();\n long ledgerId2 = lh2.getId();\n\n // bkc.initMessageDigest(\"SHA1\");\n LOG.info(\"Ledger ID 1: \" + lh.getId() + \", Ledger ID 2: \" + lh2.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n lh2.addEntry(new byte[0]);\n }\n\n lh.close();\n lh2.close();\n\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n lh2 = bkc.openLedger(ledgerId2, digestType, ledgerPassword);\n\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed() + \", \" + lh2.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written lh (\" + lh.getLastAddConfirmed() + \")\", lh\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n assertTrue(\"Verifying number of entries written lh2 (\" + lh2.getLastAddConfirmed() + \")\", lh2\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n ls = lh2.readEntries(0, numEntriesToWrite - 1);\n i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh2.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testMultiLedger() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n lh2 = bkc.createLedger(digestType, ledgerPassword);\n\n long ledgerId = lh.getId();\n long ledgerId2 = lh2.getId();\n\n // bkc.initMessageDigest(\"SHA1\");\n LOG.info(\"Ledger ID 1: \" + lh.getId() + \", Ledger ID 2: \" + lh2.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n lh2.addEntry(new byte[0]);\n }\n\n lh.close();\n lh2.close();\n\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n lh2 = bkc.openLedger(ledgerId2, digestType, ledgerPassword);\n\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed() + \", \" + lh2.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written lh (\" + lh.getLastAddConfirmed() + \")\", lh\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n assertTrue(\"Verifying number of entries written lh2 (\" + lh2.getLastAddConfirmed() + \")\", lh2\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n ls = lh2.readEntries(0, numEntriesToWrite - 1);\n i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh2.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void auxTestReadWriteAsyncSingleClient(BookieServer bs) throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(3, 2, digestType, ledgerPassword);\n\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n }\n\n LOG.info(\"Wrote \" + numEntriesToWrite + \" and now going to fail bookie.\");\n // Bookie fail\n bs.shutdown();\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n bkc.close();\n bkc = new BookKeeperTestClient(baseClientConf);\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait(10000);\n assertTrue(\"Haven't received entries\", sync.value);\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + i);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n LOG.info(\"Verified that entries are ok, and now closing ledger\");\n lh.close();\n } catch (KeeperException e) {\n LOG.error(\"Caught KeeperException\", e);\n fail(e.toString());\n } catch (BKException e) {\n LOG.error(\"Caught BKException\", e);\n fail(e.toString());\n } catch (InterruptedException e) {\n LOG.error(\"Caught InterruptedException\", e);\n fail(e.toString());\n }\n\n } \n #location 63 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n void auxTestReadWriteAsyncSingleClient(BookieServer bs) throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(3, 2, digestType, ledgerPassword);\n\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n }\n\n LOG.info(\"Wrote \" + numEntriesToWrite + \" and now going to fail bookie.\");\n // Bookie fail\n bs.shutdown();\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait(10000);\n assertFalse(\"Failure occurred during write\", sync.failureOccurred);\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n bkc.close();\n bkc = new BookKeeperTestClient(baseClientConf);\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait(10000);\n assertTrue(\"Haven't received entries\", sync.value);\n assertFalse(\"Failure occurred during read\", sync.failureOccurred);\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (sync.ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = sync.ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + i);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n LOG.info(\"Verified that entries are ok, and now closing ledger\");\n lh.close();\n } catch (KeeperException e) {\n LOG.error(\"Caught KeeperException\", e);\n fail(e.toString());\n } catch (BKException e) {\n LOG.error(\"Caught BKException\", e);\n fail(e.toString());\n } catch (InterruptedException e) {\n LOG.error(\"Caught InterruptedException\", e);\n fail(e.toString());\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testWithoutZookeeper() throws Exception {\n LedgerManagerFactory newLedgerManagerFactory = LedgerManagerFactory\n .newLedgerManagerFactory(baseConf, zkc);\n LedgerManager ledgerManager = newLedgerManagerFactory\n .newLedgerManager();\n\n List ledgerList = new ArrayList(3);\n LedgerHandle lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n lh = createAndAddEntriesToLedger();\n lh.close();\n ledgerList.add(lh.getId());\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n stopZKCluster();\n try {\n bookieLedgerIndex.getBookieToLedgerIndex();\n fail(\"Must throw exception as bookies are not running!\");\n } catch (BKAuditException bkAuditException) {\n // expected behaviour\n }\n } \n #location 25 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testWithoutZookeeper() throws Exception {\n for (int i = 0; i < numberOfLedgers; i++) {\n createAndAddEntriesToLedger().close();\n }\n\n BookieLedgerIndexer bookieLedgerIndex = new BookieLedgerIndexer(\n ledgerManager);\n stopZKCluster();\n try {\n bookieLedgerIndex.getBookieToLedgerIndex();\n fail(\"Must throw exception as bookies are not running!\");\n } catch (BKAuditException bkAuditException) {\n // expected behaviour\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteAsyncSingleClient() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 20 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteAsyncSingleClient() throws IOException {\n SyncObj sync = new SyncObj();\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n lh.asyncReadEntries(0, numEntriesToWrite - 1, this, sync);\n\n synchronized (sync) {\n while (sync.value == false) {\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n // at this point, Enumeration ls is filled with the returned\n // values\n int i = 0;\n Enumeration ls = sync.getLedgerEntries();\n while (ls.hasMoreElements()) {\n ByteBuffer origbb = ByteBuffer.wrap(entries.get(i));\n Integer origEntry = origbb.getInt();\n byte[] entry = ls.nextElement().getEntry();\n ByteBuffer result = ByteBuffer.wrap(entry);\n LOG.debug(\"Length of result: \" + result.capacity());\n LOG.debug(\"Original entry: \" + origEntry);\n\n Integer retrEntry = result.getInt();\n LOG.debug(\"Retrieved entry: \" + retrEntry);\n assertTrue(\"Checking entry \" + i + \" for equality\", origEntry.equals(retrEntry));\n assertTrue(\"Checking entry \" + i + \" for size\", entry.length == entriesSize.get(i).intValue());\n i++;\n }\n assertTrue(\"Checking number of read entries\", i == numEntriesToWrite);\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void initiate() {\n /** \n * Enable fencing on this op. When the read request reaches the bookies\n * server it will fence off the ledger, stopping any subsequent operation\n * from writing to it.\n */\n int flags = BookieProtocol.FLAG_DO_FENCING;\n for (int i = 0; i < lh.metadata.currentEnsemble.size(); i++) {\n lh.bk.bookieClient.readEntry(lh.metadata.currentEnsemble.get(i), lh.ledgerId, \n BookieProtocol.LAST_ADD_CONFIRMED, this, i, flags);\n }\n } \n #location 9 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void initiate() {\n ReadLastConfirmedOp rlcop = new ReadLastConfirmedOp(lh,\n new ReadLastConfirmedOp.LastConfirmedDataCallback() {\n public void readLastConfirmedDataComplete(int rc, RecoveryData data) {\n if (rc == BKException.Code.OK) {\n lh.lastAddPushed = lh.lastAddConfirmed = data.lastAddConfirmed;\n lh.length = data.length;\n doRecoveryRead();\n } else {\n cb.operationComplete(BKException.Code.ReadException, null);\n }\n }\n });\n\n /**\n * Enable fencing on this op. When the read request reaches the bookies\n * server it will fence off the ledger, stopping any subsequent operation\n * from writing to it.\n */\n rlcop.initiateWithFencing();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReadWriteAsyncSingleClientThrottle() throws\n IOException, NoSuchFieldException, IllegalAccessException {\n try {\n\n Integer throttle = 100;\n ThrottleTestCallback tcb = new ThrottleTestCallback(throttle);\n // Create a ledger\n bkc.getConf().setThrottleValue(throttle);\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n numEntriesToWrite = 8000;\n for (int i = 0; i < (numEntriesToWrite - 2000); i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n /*\n * Check that the difference is no larger than the throttling threshold\n */\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n\n for (int i = 0; i < 2000; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n /*\n * Check that the difference is no larger than the throttling threshold\n */\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n sync.counter = 0;\n for (int i = 0; i < numEntriesToWrite; i+=throttle) {\n lh.asyncReadEntries(i, i + throttle - 1, tcb, sync);\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.info(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 49 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testReadWriteAsyncSingleClientThrottle() throws\n IOException, NoSuchFieldException, IllegalAccessException {\n SyncObj sync = new SyncObj();\n try {\n\n Integer throttle = 100;\n ThrottleTestCallback tcb = new ThrottleTestCallback(throttle);\n // Create a ledger\n bkc.getConf().setThrottleValue(throttle);\n lh = bkc.createLedger(digestType, ledgerPassword);\n // bkc.initMessageDigest(\"SHA1\");\n ledgerId = lh.getId();\n LOG.info(\"Ledger ID: \" + lh.getId());\n\n numEntriesToWrite = 8000;\n for (int i = 0; i < (numEntriesToWrite - 2000); i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n /*\n * Check that the difference is no larger than the throttling threshold\n */\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n\n for (int i = 0; i < 2000; i++) {\n ByteBuffer entry = ByteBuffer.allocate(4);\n entry.putInt(rng.nextInt(maxInt));\n entry.position(0);\n\n entries.add(entry.array());\n entriesSize.add(entry.array().length);\n lh.asyncAddEntry(entry.array(), this, sync);\n\n /*\n * Check that the difference is no larger than the throttling threshold\n */\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n // wait for all entries to be acknowledged\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.debug(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error adding\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** WRITE COMPLETE ***\");\n // close ledger\n lh.close();\n\n // *** WRITING PART COMPLETE // READ PART BEGINS ***\n\n // open ledger\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n LOG.debug(\"Number of entries written: \" + (lh.getLastAddConfirmed() + 1));\n assertTrue(\"Verifying number of entries written\", lh.getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n // read entries\n sync.counter = 0;\n for (int i = 0; i < numEntriesToWrite; i+=throttle) {\n lh.asyncReadEntries(i, i + throttle - 1, tcb, sync);\n int testValue = getAvailablePermits(lh);\n assertTrue(\"Difference is incorrect : \" + i + \", \" + sync.counter + \", \" + testValue, testValue <= throttle);\n }\n\n synchronized (sync) {\n while (sync.counter < numEntriesToWrite) {\n LOG.info(\"Entries counter = \" + sync.counter);\n sync.wait();\n }\n assertEquals(\"Error reading\", BKException.Code.OK, sync.getReturnCode());\n }\n\n LOG.debug(\"*** READ COMPLETE ***\");\n\n lh.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testMultiLedger() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n lh2 = bkc.createLedger(digestType, ledgerPassword);\n\n long ledgerId = lh.getId();\n long ledgerId2 = lh2.getId();\n\n // bkc.initMessageDigest(\"SHA1\");\n LOG.info(\"Ledger ID 1: \" + lh.getId() + \", Ledger ID 2: \" + lh2.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n lh2.addEntry(new byte[0]);\n }\n\n lh.close();\n lh2.close();\n\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n lh2 = bkc.openLedger(ledgerId2, digestType, ledgerPassword);\n\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed() + \", \" + lh2.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written lh (\" + lh.getLastAddConfirmed() + \")\", lh\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n assertTrue(\"Verifying number of entries written lh2 (\" + lh2.getLastAddConfirmed() + \")\", lh2\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n ls = lh2.readEntries(0, numEntriesToWrite - 1);\n i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh2.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n } \n #location 33 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Test\n public void testMultiLedger() throws IOException {\n try {\n // Create a ledger\n lh = bkc.createLedger(digestType, ledgerPassword);\n lh2 = bkc.createLedger(digestType, ledgerPassword);\n\n long ledgerId = lh.getId();\n long ledgerId2 = lh2.getId();\n\n // bkc.initMessageDigest(\"SHA1\");\n LOG.info(\"Ledger ID 1: \" + lh.getId() + \", Ledger ID 2: \" + lh2.getId());\n for (int i = 0; i < numEntriesToWrite; i++) {\n lh.addEntry(new byte[0]);\n lh2.addEntry(new byte[0]);\n }\n\n lh.close();\n lh2.close();\n\n lh = bkc.openLedger(ledgerId, digestType, ledgerPassword);\n lh2 = bkc.openLedger(ledgerId2, digestType, ledgerPassword);\n\n LOG.debug(\"Number of entries written: \" + lh.getLastAddConfirmed() + \", \" + lh2.getLastAddConfirmed());\n assertTrue(\"Verifying number of entries written lh (\" + lh.getLastAddConfirmed() + \")\", lh\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n assertTrue(\"Verifying number of entries written lh2 (\" + lh2.getLastAddConfirmed() + \")\", lh2\n .getLastAddConfirmed() == (numEntriesToWrite - 1));\n\n Enumeration ls = lh.readEntries(0, numEntriesToWrite - 1);\n int i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh.close();\n ls = lh2.readEntries(0, numEntriesToWrite - 1);\n i = 0;\n while (ls.hasMoreElements()) {\n ByteBuffer result = ByteBuffer.wrap(ls.nextElement().getEntry());\n LOG.debug(\"Length of result: \" + result.capacity());\n\n assertTrue(\"Checking if entry \" + i + \" has zero bytes\", result.capacity() == 0);\n }\n lh2.close();\n } catch (BKException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to BookKeeper exception\");\n } catch (InterruptedException e) {\n LOG.error(\"Test failed\", e);\n fail(\"Test failed due to interruption\");\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Around(\"within(@org.springframework.stereotype.Repository *)\")\n public Object invoke(ProceedingJoinPoint joinPoint) throws Throwable {\n if (this.isEnabled) {\n StopWatch sw = new StopWatch(joinPoint.toShortString());\n\n sw.start(\"invoke\");\n try {\n return joinPoint.proceed();\n } finally {\n sw.stop();\n synchronized (this) {\n this.callCount++;\n this.accumulatedCallTime += sw.getTotalTimeMillis();\n }\n }\n } else {\n return joinPoint.proceed();\n }\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Around(\"within(@org.springframework.stereotype.Repository *)\")\n public Object invoke(ProceedingJoinPoint joinPoint) throws Throwable {\n if (this.enabled) {\n StopWatch sw = new StopWatch(joinPoint.toShortString());\n\n sw.start(\"invoke\");\n try {\n return joinPoint.proceed();\n } finally {\n sw.stop();\n synchronized (this) {\n this.callCount++;\n this.accumulatedCallTime += sw.getTotalTimeMillis();\n }\n }\n } else {\n return joinPoint.proceed();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public Object eval(final String js) {\n try {\n Object _xblockexpression = null;\n {\n this.assertScriptEngine();\n if (((this.maxCPUTimeInMs).longValue() == 0)) {\n return this.scriptEngine.eval(js);\n }\n Object _xsynchronizedexpression = null;\n synchronized (this) {\n Object _xblockexpression_1 = null;\n {\n final Value resVal = new Value(null);\n final Value exceptionVal = new Value(null);\n final MonitorThread monitorThread = new MonitorThread(((this.maxCPUTimeInMs).longValue() * 1000000));\n if ((this.exectuor == null)) {\n throw new IllegalStateException(\n \"When a CPU time limit is set, an executor needs to be provided by calling .setExecutor(...)\");\n }\n final Object monitor = new Object();\n final Runnable _function = new Runnable() {\n @Override\n public void run() {\n try {\n boolean _contains = js.contains(\"intCheckForInterruption\");\n if (_contains) {\n throw new IllegalArgumentException(\n \"Script contains the illegal string [intCheckForInterruption]\");\n }\n Object _eval = NashornSandboxImpl.this.scriptEngine.eval(\"window.js_beautify;\");\n final ScriptObjectMirror jsBeautify = ((ScriptObjectMirror) _eval);\n Object _call = jsBeautify.call(\"beautify\", js);\n final String beautifiedJs = ((String) _call);\n Random _random = new Random();\n int _nextInt = _random.nextInt();\n final int randomToken = Math.abs(_nextInt);\n StringConcatenation _builder = new StringConcatenation();\n _builder.append(\"var InterruptTest = Java.type(\\'\");\n String _name = InterruptTest.class.getName();\n _builder.append(_name, \"\");\n _builder.append(\"\\');\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"var isInterrupted = InterruptTest.isInterrupted;\");\n _builder.newLine();\n _builder.append(\"var intCheckForInterruption\");\n _builder.append(randomToken, \"\");\n _builder.append(\" = function() {\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"\\t\");\n _builder.append(\"if (isInterrupted()) {\");\n _builder.newLine();\n _builder.append(\"\\t \");\n _builder.append(\"throw new Error(\\'Interrupted\");\n _builder.append(randomToken, \"\\t \");\n _builder.append(\"\\')\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"\\t\");\n _builder.append(\"}\");\n _builder.newLine();\n _builder.append(\"};\");\n _builder.newLine();\n String preamble = _builder.toString();\n String _replace = preamble.replace(\"\\n\", \"\");\n preamble = _replace;\n String _injectInterruptionCalls = NashornSandboxImpl.injectInterruptionCalls(beautifiedJs, randomToken);\n final String securedJs = (preamble + _injectInterruptionCalls);\n final Thread mainThread = Thread.currentThread();\n Thread _currentThread = Thread.currentThread();\n monitorThread.setThreadToMonitor(_currentThread);\n final Runnable _function = new Runnable() {\n @Override\n public void run() {\n mainThread.interrupt();\n }\n };\n monitorThread.setOnInvalidHandler(_function);\n monitorThread.start();\n try {\n if (NashornSandboxImpl.this.debug) {\n InputOutput.println(\"--- Running JS ---\");\n InputOutput.println(securedJs);\n InputOutput.println(\"--- JS END ---\");\n }\n final Object res = NashornSandboxImpl.this.scriptEngine.eval(securedJs);\n resVal.set(res);\n } catch (final Throwable _t) {\n if (_t instanceof ScriptException) {\n final ScriptException e = (ScriptException)_t;\n String _message = e.getMessage();\n boolean _contains_1 = _message.contains((\"Interrupted\" + Integer.valueOf(randomToken)));\n if (_contains_1) {\n monitorThread.notifyOperationInterrupted();\n } else {\n exceptionVal.set(e);\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n return;\n }\n } else {\n throw Exceptions.sneakyThrow(_t);\n }\n } finally {\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n }\n } catch (final Throwable _t_1) {\n if (_t_1 instanceof Throwable) {\n final Throwable t = (Throwable)_t_1;\n exceptionVal.set(t);\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n } else {\n throw Exceptions.sneakyThrow(_t_1);\n }\n }\n }\n };\n this.exectuor.execute(_function);\n synchronized (monitor) {\n monitor.wait();\n }\n boolean _isCPULimitExceeded = monitorThread.isCPULimitExceeded();\n if (_isCPULimitExceeded) {\n String notGraceful = \"\";\n boolean _gracefullyInterrputed = monitorThread.gracefullyInterrputed();\n boolean _not = (!_gracefullyInterrputed);\n if (_not) {\n notGraceful = \" The operation could not be gracefully interrupted.\";\n }\n Throwable _get = exceptionVal.get();\n throw new ScriptCPUAbuseException(\n (((\"Script used more than the allowed [\" + this.maxCPUTimeInMs) + \" ms] of CPU time. \") + notGraceful), _get);\n }\n Throwable _get_1 = exceptionVal.get();\n boolean _tripleNotEquals = (_get_1 != null);\n if (_tripleNotEquals) {\n throw exceptionVal.get();\n }\n _xblockexpression_1 = resVal.get();\n }\n _xsynchronizedexpression = _xblockexpression_1;\n }\n _xblockexpression = _xsynchronizedexpression;\n }\n return _xblockexpression;\n } catch (Throwable _e) {\n throw Exceptions.sneakyThrow(_e);\n }\n } \n #location 8 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public Object eval(final String js) {\n try {\n Object _xblockexpression = null;\n {\n this.assertScriptEngine();\n if (((this.maxCPUTimeInMs).longValue() == 0)) {\n if (this.debug) {\n InputOutput.println(\"--- Running JS ---\");\n InputOutput.println(js);\n InputOutput.println(\"--- JS END ---\");\n }\n return this.scriptEngine.eval(js);\n }\n Object _xsynchronizedexpression = null;\n synchronized (this) {\n Object _xblockexpression_1 = null;\n {\n final Value resVal = new Value(null);\n final Value exceptionVal = new Value(null);\n final MonitorThread monitorThread = new MonitorThread(((this.maxCPUTimeInMs).longValue() * 1000000));\n if ((this.exectuor == null)) {\n throw new IllegalStateException(\n \"When a CPU time limit is set, an executor needs to be provided by calling .setExecutor(...)\");\n }\n final Object monitor = new Object();\n final Runnable _function = new Runnable() {\n @Override\n public void run() {\n try {\n boolean _contains = js.contains(\"intCheckForInterruption\");\n if (_contains) {\n throw new IllegalArgumentException(\n \"Script contains the illegal string [intCheckForInterruption]\");\n }\n Object _eval = NashornSandboxImpl.this.scriptEngine.eval(\"window.js_beautify;\");\n final ScriptObjectMirror jsBeautify = ((ScriptObjectMirror) _eval);\n Object _call = jsBeautify.call(\"beautify\", js);\n final String beautifiedJs = ((String) _call);\n Random _random = new Random();\n int _nextInt = _random.nextInt();\n final int randomToken = Math.abs(_nextInt);\n StringConcatenation _builder = new StringConcatenation();\n _builder.append(\"var InterruptTest = Java.type(\\'\");\n String _name = InterruptTest.class.getName();\n _builder.append(_name, \"\");\n _builder.append(\"\\');\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"var isInterrupted = InterruptTest.isInterrupted;\");\n _builder.newLine();\n _builder.append(\"var intCheckForInterruption\");\n _builder.append(randomToken, \"\");\n _builder.append(\" = function() {\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"\\t\");\n _builder.append(\"if (isInterrupted()) {\");\n _builder.newLine();\n _builder.append(\"\\t \");\n _builder.append(\"throw new Error(\\'Interrupted\");\n _builder.append(randomToken, \"\\t \");\n _builder.append(\"\\')\");\n _builder.newLineIfNotEmpty();\n _builder.append(\"\\t\");\n _builder.append(\"}\");\n _builder.newLine();\n _builder.append(\"};\");\n _builder.newLine();\n String preamble = _builder.toString();\n String _replace = preamble.replace(\"\\n\", \"\");\n preamble = _replace;\n String _injectInterruptionCalls = NashornSandboxImpl.injectInterruptionCalls(beautifiedJs, randomToken);\n final String securedJs = (preamble + _injectInterruptionCalls);\n final Thread mainThread = Thread.currentThread();\n Thread _currentThread = Thread.currentThread();\n monitorThread.setThreadToMonitor(_currentThread);\n final Runnable _function = new Runnable() {\n @Override\n public void run() {\n mainThread.interrupt();\n }\n };\n monitorThread.setOnInvalidHandler(_function);\n monitorThread.start();\n try {\n if (NashornSandboxImpl.this.debug) {\n InputOutput.println(\"--- Running JS ---\");\n InputOutput.println(securedJs);\n InputOutput.println(\"--- JS END ---\");\n }\n final Object res = NashornSandboxImpl.this.scriptEngine.eval(securedJs);\n resVal.set(res);\n } catch (final Throwable _t) {\n if (_t instanceof ScriptException) {\n final ScriptException e = (ScriptException)_t;\n String _message = e.getMessage();\n boolean _contains_1 = _message.contains((\"Interrupted\" + Integer.valueOf(randomToken)));\n if (_contains_1) {\n monitorThread.notifyOperationInterrupted();\n } else {\n exceptionVal.set(e);\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n return;\n }\n } else {\n throw Exceptions.sneakyThrow(_t);\n }\n } finally {\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n }\n } catch (final Throwable _t_1) {\n if (_t_1 instanceof Throwable) {\n final Throwable t = (Throwable)_t_1;\n exceptionVal.set(t);\n monitorThread.stopMonitor();\n synchronized (monitor) {\n monitor.notify();\n }\n } else {\n throw Exceptions.sneakyThrow(_t_1);\n }\n }\n }\n };\n this.exectuor.execute(_function);\n synchronized (monitor) {\n monitor.wait();\n }\n boolean _isCPULimitExceeded = monitorThread.isCPULimitExceeded();\n if (_isCPULimitExceeded) {\n String notGraceful = \"\";\n boolean _gracefullyInterrputed = monitorThread.gracefullyInterrputed();\n boolean _not = (!_gracefullyInterrputed);\n if (_not) {\n notGraceful = \" The operation could not be gracefully interrupted.\";\n }\n Throwable _get = exceptionVal.get();\n throw new ScriptCPUAbuseException(\n (((\"Script used more than the allowed [\" + this.maxCPUTimeInMs) + \" ms] of CPU time. \") + notGraceful), _get);\n }\n Throwable _get_1 = exceptionVal.get();\n boolean _tripleNotEquals = (_get_1 != null);\n if (_tripleNotEquals) {\n throw exceptionVal.get();\n }\n _xblockexpression_1 = resVal.get();\n }\n _xsynchronizedexpression = _xblockexpression_1;\n }\n _xblockexpression = _xsynchronizedexpression;\n }\n return _xblockexpression;\n } catch (Throwable _e) {\n throw Exceptions.sneakyThrow(_e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void callOnError(final ExecutionError error) {\n if (onError != null) {\n onError.call(error);\n }\n\n synchronized (error.getContext()) {\n callOnTerminate((C) error.getContext());\n error.getContext().notifyAll();\n }\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void callOnError(final ExecutionError error) {\n if (onError != null) {\n onError.call(error);\n }\n callOnTerminate((C) error.getContext());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void callOnFinalState(final State state, final C context) {\n try {\n if (onFinalStateHandler != null) {\n if (isTrace())\n log.debug(\"when final state {} for {} <<<\", state, context);\n\n onFinalStateHandler.call(state, context);\n\n if (isTrace())\n log.debug(\"when final state {} for {} >>>\", state, context);\n }\n\n synchronized (context) {\n callOnTerminate(context);\n context.notifyAll();\n }\n\n } catch (Exception e) {\n callOnError(new ExecutionError(state, null, e,\n \"Execution Error in [EasyFlow.whenFinalState] handler\", context));\n }\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void callOnFinalState(final State state, final C context) {\n try {\n if (onFinalStateHandler != null) {\n if (isTrace())\n log.debug(\"when final state {} for {} <<<\", state, context);\n\n onFinalStateHandler.call(state, context);\n\n if (isTrace())\n log.debug(\"when final state {} for {} >>>\", state, context);\n }\n\n callOnTerminate(context);\n } catch (Exception e) {\n callOnError(new ExecutionError(state, null, e,\n \"Execution Error in [EasyFlow.whenFinalState] handler\", context));\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void callOnFinalState(final State state, final C context) {\n try {\n if (onFinalStateHandler != null) {\n if (isTrace())\n log.debug(\"when final state {} for {} <<<\", state, context);\n\n onFinalStateHandler.call(state, context);\n\n if (isTrace())\n log.debug(\"when final state {} for {} >>>\", state, context);\n }\n\n synchronized (context) {\n callOnTerminate(context);\n context.notifyAll();\n }\n\n } catch (Exception e) {\n callOnError(new ExecutionError(state, null, e,\n \"Execution Error in [EasyFlow.whenFinalState] handler\", context));\n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void callOnFinalState(final State state, final C context) {\n try {\n if (onFinalStateHandler != null) {\n if (isTrace())\n log.debug(\"when final state {} for {} <<<\", state, context);\n\n onFinalStateHandler.call(state, context);\n\n if (isTrace())\n log.debug(\"when final state {} for {} >>>\", state, context);\n }\n\n callOnTerminate(context);\n } catch (Exception e) {\n callOnError(new ExecutionError(state, null, e,\n \"Execution Error in [EasyFlow.whenFinalState] handler\", context));\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void tableWrite() {\n String fileName = TestFileUtil.getPath() + \"tableWrite\" + System.currentTimeMillis() + \".xlsx\";\n // \u8fd9\u91cc\u76f4\u63a5\u5199\u591a\u4e2atable\u7684\u6848\u4f8b\u4e86\uff0c\u5982\u679c\u53ea\u6709\u4e00\u4e2a \u4e5f\u53ef\u4ee5\u76f4\u4e00\u884c\u4ee3\u7801\u641e\u5b9a\uff0c\u53c2\u7167\u5176\u4ed6\u6848\u4f8b\n // \u8fd9\u91cc \u9700\u8981\u6307\u5b9a\u5199\u7528\u54ea\u4e2aclass\u53bb\u5199\n ExcelWriter excelWriter = null;\n try {\n EasyExcel.write(fileName, DemoData.class).build();\n // \u628asheet\u8bbe\u7f6e\u4e3a\u4e0d\u9700\u8981\u5934 \u4e0d\u7136\u4f1a\u8f93\u51fasheet\u7684\u5934 \u8fd9\u6837\u770b\u8d77\u6765\u7b2c\u4e00\u4e2atable \u5c31\u67092\u4e2a\u5934\u4e86\n WriteSheet writeSheet = EasyExcel.writerSheet(\"\u6a21\u677f\").needHead(Boolean.FALSE).build();\n // \u8fd9\u91cc\u5fc5\u987b\u6307\u5b9a\u9700\u8981\u5934\uff0ctable \u4f1a\u7ee7\u627fsheet\u7684\u914d\u7f6e\uff0csheet\u914d\u7f6e\u4e86\u4e0d\u9700\u8981\uff0ctable \u9ed8\u8ba4\u4e5f\u662f\u4e0d\u9700\u8981\n WriteTable writeTable0 = EasyExcel.writerTable(0).needHead(Boolean.TRUE).build();\n WriteTable writeTable1 = EasyExcel.writerTable(1).needHead(Boolean.TRUE).build();\n // \u7b2c\u4e00\u6b21\u5199\u5165\u4f1a\u521b\u5efa\u5934\n excelWriter.write(data(), writeSheet, writeTable0);\n // \u7b2c\u4e8c\u6b21\u5199\u5982\u4e5f\u4f1a\u521b\u5efa\u5934\uff0c\u7136\u540e\u5728\u7b2c\u4e00\u6b21\u7684\u540e\u9762\u5199\u5165\u6570\u636e\n excelWriter.write(data(), writeSheet, writeTable1);\n } finally {\n // \u5343\u4e07\u522b\u5fd8\u8bb0finish \u4f1a\u5e2e\u5fd9\u5173\u95ed\u6d41\n if (excelWriter != null) {\n excelWriter.finish();\n }\n }\n } \n #location 15 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void tableWrite() {\n String fileName = TestFileUtil.getPath() + \"tableWrite\" + System.currentTimeMillis() + \".xlsx\";\n // \u8fd9\u91cc\u76f4\u63a5\u5199\u591a\u4e2atable\u7684\u6848\u4f8b\u4e86\uff0c\u5982\u679c\u53ea\u6709\u4e00\u4e2a \u4e5f\u53ef\u4ee5\u76f4\u4e00\u884c\u4ee3\u7801\u641e\u5b9a\uff0c\u53c2\u7167\u5176\u4ed6\u6848\u4f8b\n // \u8fd9\u91cc \u9700\u8981\u6307\u5b9a\u5199\u7528\u54ea\u4e2aclass\u53bb\u5199\n ExcelWriter excelWriter = null;\n try {\n excelWriter=EasyExcel.write(fileName, DemoData.class).build();\n // \u628asheet\u8bbe\u7f6e\u4e3a\u4e0d\u9700\u8981\u5934 \u4e0d\u7136\u4f1a\u8f93\u51fasheet\u7684\u5934 \u8fd9\u6837\u770b\u8d77\u6765\u7b2c\u4e00\u4e2atable \u5c31\u67092\u4e2a\u5934\u4e86\n WriteSheet writeSheet = EasyExcel.writerSheet(\"\u6a21\u677f\").needHead(Boolean.FALSE).build();\n // \u8fd9\u91cc\u5fc5\u987b\u6307\u5b9a\u9700\u8981\u5934\uff0ctable \u4f1a\u7ee7\u627fsheet\u7684\u914d\u7f6e\uff0csheet\u914d\u7f6e\u4e86\u4e0d\u9700\u8981\uff0ctable \u9ed8\u8ba4\u4e5f\u662f\u4e0d\u9700\u8981\n WriteTable writeTable0 = EasyExcel.writerTable(0).needHead(Boolean.TRUE).build();\n WriteTable writeTable1 = EasyExcel.writerTable(1).needHead(Boolean.TRUE).build();\n // \u7b2c\u4e00\u6b21\u5199\u5165\u4f1a\u521b\u5efa\u5934\n excelWriter.write(data(), writeSheet, writeTable0);\n // \u7b2c\u4e8c\u6b21\u5199\u5982\u4e5f\u4f1a\u521b\u5efa\u5934\uff0c\u7136\u540e\u5728\u7b2c\u4e00\u6b21\u7684\u540e\u9762\u5199\u5165\u6570\u636e\n excelWriter.write(data(), writeSheet, writeTable1);\n } finally {\n // \u5343\u4e07\u522b\u5fd8\u8bb0finish \u4f1a\u5e2e\u5fd9\u5173\u95ed\u6d41\n if (excelWriter != null) {\n excelWriter.finish();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @GET\n @Path(\"/result_counter/{identifier}\")\n @Produces(\"application/json\")\n public EnumMap getCounterResults(@PathParam(\"identifier\") String executionIdentifier) {\n try {\n return AlgorithmExecutionCache.getResultCounter(executionIdentifier).getResults();\n } catch (Exception e) {\n throw new WebException(\"Could not find any progress to the given identifier\",\n Response.Status.BAD_REQUEST);\n }\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @GET\n @Path(\"/result_counter/{identifier}\")\n @Produces(\"application/json\")\n public EnumMap getCounterResults(@PathParam(\"identifier\") String executionIdentifier) {\n try {\n return this.resultCounts.get(executionIdentifier);\n } catch (Exception e) {\n throw new WebException(\"Could not find any progress to the given identifier\",\n Response.Status.BAD_REQUEST);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected AlgorithmExecutor buildExecutor(String algorithmName) throws FileNotFoundException, UnsupportedEncodingException {\n\t\tFunctionalDependencyResultReceiver fdResultReceiver = \n\t\t\t\tnew FunctionalDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tInclusionDependencyResultReceiver indResultReceiver = \n\t\t\t\tnew InclusionDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tUniqueColumnCombinationResultReceiver uccResultReceiver = \n\t\t\t\tnew UniqueColumnCombinationPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tFileGenerator fileGenerator = new TempFileGenerator();\n\t\t\n\t\treturn new AlgorithmExecutor(fdResultReceiver, indResultReceiver, uccResultReceiver, fileGenerator);\n\t} \n #location 10 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected AlgorithmExecutor buildExecutor(String algorithmName) throws FileNotFoundException, UnsupportedEncodingException {\n\t\tLinkedList resultPrinters = new LinkedList();\n\t\t\n\t\tFunctionalDependencyPrinter fdResultReceiver = \n\t\t\t\tnew FunctionalDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(fdResultReceiver);\n\t\t\n\t\tInclusionDependencyPrinter indResultReceiver = \n\t\t\t\tnew InclusionDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(indResultReceiver);\n\t\t\n\t\tUniqueColumnCombinationPrinter uccResultReceiver = \n\t\t\t\tnew UniqueColumnCombinationPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(uccResultReceiver);\n\t\t\n\t\tFileGenerator fileGenerator = new TempFileGenerator();\n\t\t\n\t\tAlgorithmExecutor executor = new AlgorithmExecutor(fdResultReceiver, indResultReceiver, uccResultReceiver, fileGenerator);\n\t\tcurrentResultPrinters.put(algorithmName, resultPrinters);\n\t\treturn executor;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void executeUniqueColumnCombinationsAlgorithmTest() {\n\t\t// Setup\n\t\tAlgorithmExecuter executer = new AlgorithmExecuter();\n\t\tByteArrayOutputStream outStream = new ByteArrayOutputStream();\n\t\tList configs = new ArrayList();\n\t\tconfigs.add(new ConfigurationValueString(\"pathToInputFile\", \"blub\"));\n\n\t\t// Expected values\n\t\tColumnCombination columnCombination = new ColumnCombination(\n\t\t\t\tnew ColumnIdentifier(\"table1\", \"column1\"), \n\t\t\t\tnew ColumnIdentifier(\"table2\", \"column2\"));\n\t\t\t\t\n\t\t// Execute\n\t\texecuter.executeUniqueColumnCombinationsAlgorithm(\"example_algorithm-0.0.1-SNAPSHOT-jar-with-dependencies.jar\", configs, \n\t\t\t\tnew UniqueColumnCombinationPrinter(new PrintStream(outStream)));\n\t\t\n\t\t// Check result\n\t\tassertTrue(outStream.toString().contains(columnCombination.toString()));\n\t} \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void executeUniqueColumnCombinationsAlgorithmTest() {\n\t\t// Setup\n\t\tList configs = new ArrayList();\n\t\tconfigs.add(new ConfigurationValueString(\"pathToInputFile\", \"blub\"));\n\t\tUniqueColumnCombinationResultReceiver resultReceiver = mock(UniqueColumnCombinationFileWriter.class);\n\t\t\t\t\n\t\t// Execute\n\t\texecuter.executeUniqueColumnCombinationsAlgorithm(\"example_algorithm-0.0.1-SNAPSHOT-jar-with-dependencies.jar\", configs, \n\t\t\t\tresultReceiver);\n\t\t\n\t\t// Check result\n\t\tverify(resultReceiver).receiveResult(isA(ColumnCombination.class));\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testGenerateNewCsvFile() throws IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCsvFile();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCsvFile();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t} \n #location 13 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void receiveResult(ColumnCombination columnCombination) {\n\t\ttry {\n\t\t\tFileWriter writer = new FileWriter(this.file, true);\n\t\t\twriter.write(columnCombination.toString() + \"\\n\");\n\t\t\twriter.close();\n\t\t} catch (IOException e) {\n\t\t\t// TODO Auto-generated catch block\n\t\t\te.printStackTrace();\n\t\t}\n\t} \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tpublic void receiveResult(ColumnCombination columnCombination) {\n\t\tappendToResultFile(columnCombination.toString());\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected AlgorithmExecutor buildExecutor(String algorithmName) throws FileNotFoundException, UnsupportedEncodingException {\n\t\tFunctionalDependencyResultReceiver fdResultReceiver = \n\t\t\t\tnew FunctionalDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tInclusionDependencyResultReceiver indResultReceiver = \n\t\t\t\tnew InclusionDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tUniqueColumnCombinationResultReceiver uccResultReceiver = \n\t\t\t\tnew UniqueColumnCombinationPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tFileGenerator fileGenerator = new TempFileGenerator();\n\t\t\n\t\treturn new AlgorithmExecutor(fdResultReceiver, indResultReceiver, uccResultReceiver, fileGenerator);\n\t} \n #location 10 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected AlgorithmExecutor buildExecutor(String algorithmName) throws FileNotFoundException, UnsupportedEncodingException {\n\t\tLinkedList resultPrinters = new LinkedList();\n\t\t\n\t\tFunctionalDependencyPrinter fdResultReceiver = \n\t\t\t\tnew FunctionalDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(fdResultReceiver);\n\t\t\n\t\tInclusionDependencyPrinter indResultReceiver = \n\t\t\t\tnew InclusionDependencyPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(indResultReceiver);\n\t\t\n\t\tUniqueColumnCombinationPrinter uccResultReceiver = \n\t\t\t\tnew UniqueColumnCombinationPrinter(getResultFileName(algorithmName), getResultDirectoryName());\n\t\tresultPrinters.add(uccResultReceiver);\n\t\t\n\t\tFileGenerator fileGenerator = new TempFileGenerator();\n\t\t\n\t\tAlgorithmExecutor executor = new AlgorithmExecutor(fdResultReceiver, indResultReceiver, uccResultReceiver, fileGenerator);\n\t\tcurrentResultPrinters.put(algorithmName, resultPrinters);\n\t\treturn executor;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testGenerateNewCsvFile() throws IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCsvFile();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCsvFile();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t} \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public T loadAlgorithm(String path) throws IOException, ClassNotFoundException, InstantiationException, IllegalAccessException, IllegalArgumentException, SecurityException, InvocationTargetException, NoSuchMethodException {\n\t\tString pathToFolder = ClassLoader.getSystemResource(\"algorithms\").getPath();\n\t\t\n\t\tFile file = new File(URLDecoder.decode(pathToFolder + \"/\" + path, \"utf-8\"));\n\t\tJarFile jar = new JarFile(file);\n\t\t\n\t\tManifest man = jar.getManifest();\n Attributes attr = man.getMainAttributes();\n String className = attr.getValue(bootstrapClassTagName);\n \n URL[] url = {file.toURI().toURL()};\n ClassLoader loader = new URLClassLoader(url, algorithmSubclass.getClassLoader());\n \n Class algorithmClass = \n \t\tClass.forName(className, true, loader).asSubclass(algorithmSubclass);\n \n\t\treturn algorithmClass.getConstructor().newInstance();\n\t} \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public T loadAlgorithm(String path) throws IOException, ClassNotFoundException, InstantiationException, IllegalAccessException, IllegalArgumentException, SecurityException, InvocationTargetException, NoSuchMethodException {\n\t\tString pathToFolder = ClassLoader.getSystemResource(\"algorithms\").getPath();\n\t\t\n\t\tFile file = new File(URLDecoder.decode(pathToFolder + \"/\" + path, \"utf-8\"));\n\t\tJarFile jar = new JarFile(file);\n\t\t\n\t\tManifest man = jar.getManifest();\n Attributes attr = man.getMainAttributes();\n String className = attr.getValue(bootstrapClassTagName);\n \n URL[] url = {file.toURI().toURL()};\n ClassLoader loader = new URLClassLoader(url, algorithmSubclass.getClassLoader());\n \n Class algorithmClass = \n \t\tClass.forName(className, true, loader).asSubclass(algorithmSubclass);\n \n jar.close();\n \n\t\treturn algorithmClass.getConstructor().newInstance();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testAddAlgorithm() throws EntityStorageException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"someFileName.jar\");\n algorithm.setInd(true);\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n } \n #location 16 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testAddAlgorithm() throws EntityStorageException, AlgorithmLoadingException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"example_ind_algorithm.jar\");\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void executeAlgorithm(String algorithmName, List parameters) throws AlgorithmConfigurationException, AlgorithmLoadingException, AlgorithmExecutionException {\n\t\t\n\t\tList configs = convertInputParameters(parameters);\n\n\t\ttry {\n\t\t\tbuildExecutor(algorithmName).executeAlgorithm(algorithmName, configs);\n\t\t} catch (FileNotFoundException e) {\n\t\t\tthrow new AlgorithmExecutionException(\"Could not generate result file.\");\n\t\t} catch (UnsupportedEncodingException e) {\n\t\t\tthrow new AlgorithmExecutionException(\"Could not build temporary file generator.\");\n\t\t}\n\t} \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tpublic void executeAlgorithm(String algorithmName, List parameters) throws AlgorithmConfigurationException, AlgorithmLoadingException, AlgorithmExecutionException {\n\t\t\n\t\tList configs = convertInputParameters(parameters);\n\t\tAlgorithmExecutor executor = null;\n\t\t\n\t\ttry {\n\t\t\texecutor = buildExecutor(algorithmName);\n\t\t} catch (FileNotFoundException e) {\n\t\t\tthrow new AlgorithmExecutionException(\"Could not generate result file.\");\n\t\t} catch (UnsupportedEncodingException e) {\n\t\t\tthrow new AlgorithmExecutionException(\"Could not build temporary file generator.\");\n\t\t}\n\t\tSystem.out.println(\"before execution\");\n\t\texecutor.executeAlgorithm(algorithmName, configs);\n\t\tSystem.out.println(\"after execution & wait\");\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ConfigurationSettingCsvFile getValues() {\n if (this.listbox.getSelectedValue().equals(\"--\")) {\n this.messageReceiver.addError(\"You must choose a CSV file!\");\n return null;\n }\n\n FileInput currentFileInput = this.fileInputs.get(\n this.listbox.getSelectedValue());\n\n return getCurrentSetting(currentFileInput);\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ConfigurationSettingCsvFile getValues() throws InputValidationException {\n String selectedValue = this.listbox.getSelectedValue();\n\n if (selectedValue.equals(\"--\")) {\n throw new InputValidationException(\"You must choose a CSV file!\");\n }\n\n FileInput currentFileInput = this.fileInputs.get(selectedValue);\n\n return getCurrentSetting(currentFileInput);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t} \n #location 13 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, InputIterationException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testUpdateOnSuccess() {\n // Set up\n TestHelper.resetDatabaseSync();\n\n Execution execution = new Execution(null, 12);\n execution.setEnd(2345);\n\n BasePage parent = new BasePage();\n ResultsPage page = new ResultsPage(parent);\n page.setMessageReceiver(new TabWrapper());\n page.setExecutionParameter(\"identifier\", \"name\");\n\n page.startPolling(true);\n\n // Expected Values\n // Execute\n page.updateOnSuccess(null);\n\n // Check\n assertEquals(2, page.getWidgetCount());\n assertTrue(page.getWidget(1) instanceof TabLayoutPanel);\n assertEquals(2, ((TabLayoutPanel) page.getWidget(1)).getWidgetCount());\n\n // Cleanup\n TestHelper.resetDatabaseSync();\n } \n #location 17 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testUpdateOnSuccess() {\n // Set up\n TestHelper.resetDatabaseSync();\n\n Algorithm algorithm = new Algorithm(\"example_ind_algorithm.jar\");\n Execution execution = new Execution(algorithm, 12);\n execution.setEnd(2345);\n\n BasePage parent = new BasePage();\n ResultsPage page = new ResultsPage(parent);\n page.setMessageReceiver(new TabWrapper());\n page.setExecutionParameter(\"identifier\", \"name\");\n\n page.startPolling(true);\n\n // Expected Values\n // Execute\n page.updateOnSuccess(execution);\n\n // Check\n assertEquals(2, page.getWidgetCount());\n assertTrue(page.getWidget(1) instanceof TabLayoutPanel);\n assertEquals(2, ((TabLayoutPanel) page.getWidget(1)).getWidgetCount());\n\n // Cleanup\n TestHelper.resetDatabaseSync();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List fetchNewResults(String algorithmName){\n\t\tList newResults = new LinkedList();\n\t\t\n\t\tfor (ResultPrinter printer : currentResultPrinters.get(algorithmName)) {\n//\t\t\tnewResults.addAll(printer.getNewResults());\n\t\t}\n\t\tnewResults.add(new UniqueColumnCombination(new ColumnIdentifier(\"table\", \"col1\")));\n\t\t\n\t\treturn newResults;\n\t} \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public List fetchNewResults(String algorithmName){\n\t\tList newResults = new LinkedList();\n\t\t\n\t\t//newResults.add(currentResultReceivers.get(algorithmName).getNewResults());\n\t\tnewResults.add(new UniqueColumnCombination(new ColumnIdentifier(\"table\", \"col1\")));\n\t\t\n\t\treturn newResults;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testAddAlgorithm() throws EntityStorageException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"someFileName.jar\");\n algorithm.setInd(true);\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n } \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testAddAlgorithm() throws EntityStorageException, AlgorithmLoadingException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"example_ind_algorithm.jar\");\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List> getAlgorithmInterfaces(File file) throws IOException, ClassNotFoundException {\n\t\tJarFile jar = new JarFile(file);\n\t\t\n\t\tManifest man = jar.getManifest();\n Attributes attr = man.getMainAttributes();\n String className = attr.getValue(bootstrapClassTagName);\n \n URL[] url = {file.toURI().toURL()};\n ClassLoader loader = new URLClassLoader(url, Algorithm.class.getClassLoader());\n \n Class algorithmClass = Class.forName(className, false, loader);\n \n\t\treturn Arrays.asList(algorithmClass.getInterfaces());\n\t} \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List> getAlgorithmInterfaces(File file) throws IOException, ClassNotFoundException {\n\t\tJarFile jar = new JarFile(file);\n\t\t\n\t\tManifest man = jar.getManifest();\n Attributes attr = man.getMainAttributes();\n String className = attr.getValue(bootstrapClassTagName);\n \n URL[] url = {file.toURI().toURL()};\n ClassLoader loader = new URLClassLoader(url, Algorithm.class.getClassLoader());\n \n Class algorithmClass = Class.forName(className, false, loader);\n \n jar.close();\n \n\t\treturn Arrays.asList(algorithmClass.getInterfaces());\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, IOException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t} \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void testGenerateNewCsvFile() throws SimpleRelationalInputGenerationException, InputIterationException {\n\t\t// Setup\n\t\tSimpleRelationalInput csv = generator.generateNewCopy();\n\t\t\n\t\t// Check result\n\t\t// The csv should contain both lines and iterate through them with next.\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv.next());\n\t\t// A new CsvFile should iterate from the start.\n\t\tSimpleRelationalInput csv2 = generator.generateNewCopy();\n\t\tassertEquals(csvFileFixture.expectedFirstLine(), csv2.next());\n\t\tassertEquals(csvFileFixture.expectedSecondLine(), csv2.next());\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected AlgorithmExecutor buildExecutor(String executionIdentifier)\n throws FileNotFoundException, UnsupportedEncodingException {\n ResultPrinter resultPrinter = new ResultPrinter(executionIdentifier, \"results\");\n ResultsCache resultsCache = new ResultsCache();\n ResultsHub resultsHub = new ResultsHub();\n resultsHub.addSubscriber(resultPrinter);\n resultsHub.addSubscriber(resultsCache);\n\n FileGenerator fileGenerator = new TempFileGenerator();\n ProgressCache progressCache = new ProgressCache();\n\n AlgorithmExecutor executor = new AlgorithmExecutor(resultsHub, progressCache, fileGenerator);\n AlgorithmExecutionCache.add(executionIdentifier, resultsCache, progressCache);\n\n return executor;\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected AlgorithmExecutor buildExecutor(String executionIdentifier)\n throws FileNotFoundException, UnsupportedEncodingException {\n ResultPrinter resultPrinter = new ResultPrinter(executionIdentifier);\n ResultsCache resultsCache = new ResultsCache();\n ResultsHub resultsHub = new ResultsHub();\n resultsHub.addSubscriber(resultPrinter);\n resultsHub.addSubscriber(resultsCache);\n\n FileGenerator fileGenerator = new TempFileGenerator();\n ProgressCache progressCache = new ProgressCache();\n\n AlgorithmExecutor executor = new AlgorithmExecutor(resultsHub, progressCache, fileGenerator);\n executor.setResultPathPrefix(resultPrinter.getOutputFilePathPrefix());\n AlgorithmExecutionCache.add(executionIdentifier, resultsCache, progressCache);\n\n return executor;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testStoreTableInput() throws EntityStorageException, InputValidationException {\n // Setup\n TestHelper.resetDatabaseSync();\n\n BasePage parent = new BasePage();\n InputConfigurationPage page = new InputConfigurationPage(parent);\n page.setErrorReceiver(new TabWrapper());\n\n DatabaseConnection dbConnection = new DatabaseConnection();\n dbConnection.setId(1);\n dbConnection.setUrl(\"url\");\n dbConnection.setPassword(\"password\");\n dbConnection.setUsername(\"db\");\n TestHelper.storeDatabaseConnectionSync(dbConnection);\n\n page.tableInputField.setValues(\"1: url\", \"table\");\n page.tableInputFieldSelected = true;\n page.dbFieldSelected = false;\n page.fileInputFieldSelected = false;\n page.content.clear();\n page.content.add(page.tableInputField);\n\n // Execute\n page.saveObject();\n\n // Expected values\n TableInput expectedInput = page.tableInputField.getValue();\n\n // Check result\n assertTrue(TestHelper.getAllTableInputs().contains(expectedInput));\n\n // Cleanup\n TestHelper.resetDatabaseSync();\n } \n #location 28 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testStoreTableInput() throws EntityStorageException, InputValidationException {\n // Setup\n TestHelper.resetDatabaseSync();\n final boolean[] blocked = {true};\n\n BasePage parent = new BasePage();\n InputConfigurationPage page = new InputConfigurationPage(parent);\n page.setErrorReceiver(new TabWrapper());\n\n DatabaseConnection dbConnection = new DatabaseConnection();\n dbConnection.setUrl(\"url\");\n dbConnection.setPassword(\"password\");\n dbConnection.setUsername(\"db\");\n TestHelper.storeDatabaseConnectionSync(dbConnection);\n\n page.tableInputField.setValues(\"1: url\", \"table\");\n page.tableInputFieldSelected = true;\n page.dbFieldSelected = false;\n page.fileInputFieldSelected = false;\n page.content.clear();\n page.content.add(page.tableInputField);\n\n // Execute\n page.saveObject();\n\n // Expected values\n final TableInput expectedInput = page.tableInputField.getValue();\n\n // Check result\n TestHelper.getAllTableInputs(\n new AsyncCallback>() {\n @Override\n public void onFailure(Throwable throwable) {\n fail();\n }\n\n @Override\n public void onSuccess(List con) {\n blocked[0] = false;\n assertTrue(con.contains(expectedInput));\n }\n });\n\n Timer rpcCheck = new Timer() {\n @Override\n public void run() {\n if (blocked[0]) {\n this.schedule(100);\n }\n }\n };\n rpcCheck.schedule(100);\n\n // Cleanup\n TestHelper.resetDatabaseSync();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testNextSeparator() throws IOException {\n\t\t// Setup\n\t\tCsvFileOneLineFixture fixtureSeparator = new CsvFileOneLineFixture(';');\n\t\tCsvFile csvFileSeparator = fixtureSeparator.getTestData();\n\t\t\n\t\t// Check result \n\t\tassertEquals(fixtureSeparator.getExpectedStrings(), csvFileSeparator.next());\n\t} \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n\tpublic void testNextSeparator() throws InputIterationException {\n\t\t// Setup\n\t\tCsvFileOneLineFixture fixtureSeparator = new CsvFileOneLineFixture(';');\n\t\tCsvFile csvFileSeparator = fixtureSeparator.getTestData();\n\t\t\n\t\t// Check result \n\t\tassertEquals(fixtureSeparator.getExpectedStrings(), csvFileSeparator.next());\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testAddAlgorithm() throws EntityStorageException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"someFileName.jar\");\n algorithm.setInd(true);\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n } \n #location 17 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testAddAlgorithm() throws EntityStorageException, AlgorithmLoadingException {\n // Setup\n HibernateUtil.clear();\n\n AlgorithmServiceImpl finderService = new AlgorithmServiceImpl();\n\n // Execute functionality: add an IND algorithm\n Algorithm algorithm = new Algorithm(\"example_ind_algorithm.jar\");\n finderService.addAlgorithm(algorithm);\n\n // Check result\n assertTrue(finderService.listAllAlgorithms().contains(algorithm));\n assertTrue(\n finderService.listAlgorithms(InclusionDependencyAlgorithm.class).contains(algorithm));\n assertFalse(finderService.listAlgorithms(FunctionalDependencyAlgorithm.class).contains(\n algorithm));\n\n // Cleanup\n HibernateUtil.clear();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void executeUniqueColumnCombinationsAlgorithm(String algorithmName,\n\t\t\tList parameters) {\n\t\tList configs = convertInputParameters(parameters);\n\t\tUniqueColumnCombinationResultReceiver resultReceiver = new UniqueColumnCombinationPrinter(\n\t\t\t\tnew PrintStream(new ByteArrayOutputStream())); //TODO instantiate useful one\n\t\t\n\t\texecuter.executeUniqueColumnCombinationsAlgorithm(algorithmName, configs, resultReceiver);\n\t\tSystem.out.println(\"Successfully executed \" + algorithmName);\n\t} \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tpublic void executeUniqueColumnCombinationsAlgorithm(String algorithmName,\n\t\t\tList parameters) {\n\t\tList configs = convertInputParameters(parameters);\n\t\tUniqueColumnCombinationResultReceiver resultReceiver = new UniqueColumnCombinationFileWriter(\n\t\t\t\tgetResultFileName(algorithmName));\n\t\t\n\t\texecuter.executeUniqueColumnCombinationsAlgorithm(algorithmName, configs, resultReceiver);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List buildResolverArguments(ArgumentBuilderParams params) {\n Method resolverMethod = params.getResolverMethod();\n List operationArguments = new ArrayList<>(resolverMethod.getParameterCount());\n AnnotatedType[] parameterTypes = ClassUtils.getParameterTypes(resolverMethod, params.getDeclaringType());\n for (int i = 0; i < resolverMethod.getParameterCount(); i++) {\n Parameter parameter = resolverMethod.getParameters()[i];\n if (parameter.isSynthetic() || parameter.isImplicit()) continue;\n AnnotatedType parameterType;\n try {\n parameterType = params.getTypeTransformer().transform(parameterTypes[i]);\n } catch (TypeMappingException e) {\n throw new TypeMappingException(resolverMethod, parameter, e);\n }\n parameterType = ClassUtils.addAnnotations(parameterType, parameter.getAnnotations());\n operationArguments.add(buildResolverArgument(parameter, parameterType, params.getInclusionStrategy(), params.getEnvironment()));\n }\n return operationArguments;\n } \n #location 16 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List buildResolverArguments(ArgumentBuilderParams params) {\n Method resolverMethod = params.getResolverMethod();\n List operationArguments = new ArrayList<>(resolverMethod.getParameterCount());\n AnnotatedType[] parameterTypes = ClassUtils.getParameterTypes(resolverMethod, params.getDeclaringType());\n for (int i = 0; i < resolverMethod.getParameterCount(); i++) {\n Parameter parameter = resolverMethod.getParameters()[i];\n if (parameter.isSynthetic() || parameter.isImplicit()) continue;\n AnnotatedType parameterType;\n try {\n parameterType = params.getTypeTransformer().transform(parameterTypes[i]);\n } catch (TypeMappingException e) {\n throw new TypeMappingException(resolverMethod, parameter, e);\n }\n operationArguments.add(buildResolverArgument(parameter, parameterType, params.getInclusionStrategy(), params.getEnvironment()));\n }\n return operationArguments;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List buildResolverArguments(ArgumentBuilderParams params) {\n Method resolverMethod = params.getResolverMethod();\n List operationArguments = new ArrayList<>(resolverMethod.getParameterCount());\n AnnotatedType[] parameterTypes = ClassUtils.getParameterTypes(resolverMethod, params.getDeclaringType());\n for (int i = 0; i < resolverMethod.getParameterCount(); i++) {\n Parameter parameter = resolverMethod.getParameters()[i];\n if (parameter.isSynthetic() || parameter.isImplicit()) continue;\n AnnotatedType parameterType;\n try {\n parameterType = params.getTypeTransformer().transform(parameterTypes[i]);\n } catch (TypeMappingException e) {\n throw new TypeMappingException(resolverMethod, parameter, e);\n }\n parameterType = ClassUtils.addAnnotations(parameterType, parameter.getAnnotations());\n operationArguments.add(new OperationArgument(\n parameterType,\n getArgumentName(parameter, parameterType, params.getInclusionStrategy()),\n getArgumentDescription(parameter, parameterType),\n defaultValue(parameter, parameterType),\n parameter,\n parameter.isAnnotationPresent(GraphQLContext.class),\n params.getInclusionStrategy().includeArgument(parameter, parameterType)\n ));\n }\n return operationArguments;\n } \n #location 18 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List buildResolverArguments(ArgumentBuilderParams params) {\n Method resolverMethod = params.getResolverMethod();\n List operationArguments = new ArrayList<>(resolverMethod.getParameterCount());\n AnnotatedType[] parameterTypes = ClassUtils.getParameterTypes(resolverMethod, params.getDeclaringType());\n for (int i = 0; i < resolverMethod.getParameterCount(); i++) {\n Parameter parameter = resolverMethod.getParameters()[i];\n if (parameter.isSynthetic() || parameter.isImplicit()) continue;\n AnnotatedType parameterType;\n try {\n parameterType = params.getTypeTransformer().transform(parameterTypes[i]);\n } catch (TypeMappingException e) {\n throw new TypeMappingException(resolverMethod, parameter, e);\n }\n parameterType = ClassUtils.addAnnotations(parameterType, parameter.getAnnotations());\n operationArguments.add(buildResolverArgument(parameter, parameterType, params.getInclusionStrategy()));\n }\n return operationArguments;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testConflictingConnections() {\n try (TestLog log = new TestLog(OperationMapper.class)) {\n new TestSchemaGenerator()\n .withOperationsFromSingleton(new ConflictingBookService())\n .generate();\n assertEquals(1, log.getEvents().size());\n ILoggingEvent event = log.getEvents().get(0);\n assertThat(event.getLevel(), is(Level.WARN));\n assertThat(event.getMessage(), containsString(Urls.Errors.NON_UNIQUE_TYPE_NAME));\n }\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testConflictingConnections() {\n try (TestLog log = new TestLog(OperationMapper.class)) {\n new TestSchemaGenerator()\n .withOperationsFromSingleton(new ConflictingBookService())\n .generate();\n assertWarningsLogged(log.getEvents(), Urls.Errors.NON_UNIQUE_TYPE_NAME);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void startDb() {\n postgres = (PostgreSQLContainer) new PostgreSQLContainer()\n .withDatabaseName(TEST_SCHEMA_NAME)\n .withUsername(\"SA\")\n .withPassword(\"pass\")\n .withLogConsumer(new Consumer() {\n @Override\n public void accept(OutputFrame outputFrame) {\n logger.debug(outputFrame.getUtf8String());\n }\n });\n postgres.start();\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void startDb() {\n postgres = new MyPostgreSQLContainer()\n .withDatabaseName(TEST_SCHEMA_NAME)\n .withUsername(\"SA\")\n .withPassword(\"pass\")\n .withLogConsumer(new Consumer() {\n @Override\n public void accept(OutputFrame outputFrame) {\n logger.debug(outputFrame.getUtf8String());\n }\n });\n postgres.start();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static void copyResources(URL resourceUrl, File targetPath) throws IOException, URISyntaxException {\n if (resourceUrl == null) {\n return;\n }\n\n URLConnection urlConnection = resourceUrl.openConnection();\n\n /**\n * Copy resources either from inside jar or from project folder.\n */\n if (urlConnection instanceof JarURLConnection) {\n copyJarResourceToPath((JarURLConnection) urlConnection, targetPath);\n } else if (VFS_PROTOCOL.equals(resourceUrl.getProtocol())) {\n VirtualFile virtualFileOrFolder = VFS.getChild(resourceUrl.toURI());\n copyFromWarToFolder(virtualFileOrFolder, targetPath);\n } else {\n File file = new File(resourceUrl.getPath());\n if (file.isDirectory()) {\n for (File resourceFile : file.listFiles()) {\n File targetFile = new File(targetPath, resourceFile.getName());\n if (!targetFile.exists() || targetFile.length() != resourceFile.length()) {\n FileUtils.copyFile(resourceFile, targetFile);\n }\n }\n } else {\n FileUtils.copyFile(file, targetPath);\n }\n }\n } \n #location 19 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n static void copyResources(URL resourceUrl, File targetPath) throws IOException, URISyntaxException {\n if (resourceUrl == null) {\n return;\n }\n\n URLConnection urlConnection = resourceUrl.openConnection();\n\n /**\n * Copy resources either from inside jar or from project folder.\n */\n if (urlConnection instanceof JarURLConnection) {\n copyJarResourceToPath((JarURLConnection) urlConnection, targetPath);\n } else if (VFS_PROTOCOL.equals(resourceUrl.getProtocol())) {\n VirtualFile virtualFileOrFolder = VFS.getChild(resourceUrl.toURI());\n copyFromWarToFolder(virtualFileOrFolder, targetPath);\n } else {\n File file = new File(resourceUrl.getPath());\n if (file.isDirectory()) {\n for (File resourceFile : FileUtils.listFiles(file, null, true)) {\n File targetFile = new File(targetPath, resourceFile.getName());\n if (!targetFile.exists() || targetFile.length() != resourceFile.length()) {\n if (resourceFile.isFile()) {\n FileUtils.copyFile(resourceFile, targetFile);\n }\n }\n }\n } else {\n if (!targetPath.exists() || targetPath.length() != file.length()) {\n FileUtils.copyFile(file, targetPath);\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 15 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 17 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n long st = System.currentTimeMillis();\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setConv(conv);\n ku.setMinRto(minRto);\n ku.setStream(stream);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n if (ku.isClosed())\n {\n temp = ku;\n } else\n {\n ku.update();\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n if (inputs.isEmpty())//\u5982\u679c\u8f93\u5165\u4e3a\u7a7a\u5219\u8003\u8651wait\n {\n long end = System.currentTimeMillis();\n if (end - st < this.interval)\n {\n synchronized (this.lock)\n {\n try\n {\n lock.wait(interval - end + st);\n } catch (InterruptedException e)\n {\n }\n }\n }\n }\n }\n release();\n } \n #location 18 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n long st = System.currentTimeMillis();\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n ByteBuf content = dp.content();\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n // conv\u5e94\u8be5\u5728\u5ba2\u6237\u7aef\u7b2c\u4e00\u6b21\u5efa\u7acb\u65f6\u83b7\u53d6\n int conv = content.getIntLE(0);\n ku.setConv(conv);\n ku.setMinRto(minRto);\n ku.setStream(stream);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(content);\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n if (ku.isClosed())\n {\n temp = ku;\n } else\n {\n ku.update();\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n if (inputs.isEmpty())//\u5982\u679c\u8f93\u5165\u4e3a\u7a7a\u5219\u8003\u8651wait\n {\n long end = System.currentTimeMillis();\n if (end - st < this.interval)\n {\n synchronized (this.lock)\n {\n try\n {\n lock.wait(interval - end + st);\n } catch (InterruptedException e)\n {\n }\n }\n }\n }\n }\n release();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 16 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n long st = System.currentTimeMillis();\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setConv(conv);\n ku.setOrder(order);\n ku.setMinRto(minRto);\n ku.setStream(stream);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n if (ku.isClosed())\n {\n temp = ku;\n } else\n {\n ku.update();\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n if (inputs.isEmpty())//\u5982\u679c\u8f93\u5165\u4e3a\u7a7a\u5219\u8003\u8651wait\n {\n long end = System.currentTimeMillis();\n if (end - st < this.interval)\n {\n synchronized (this.lock)\n {\n try\n {\n lock.wait(interval - end + st);\n } catch (InterruptedException e)\n {\n }\n }\n }\n }\n }\n release();\n } \n #location 19 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n long st = System.currentTimeMillis();\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setConv(conv);\n ku.setMinRto(minRto);\n ku.setStream(stream);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n if (ku.isClosed())\n {\n temp = ku;\n } else\n {\n ku.update();\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n if (inputs.isEmpty())//\u5982\u679c\u8f93\u5165\u4e3a\u7a7a\u5219\u8003\u8651wait\n {\n long end = System.currentTimeMillis();\n if (end - st < this.interval)\n {\n synchronized (this.lock)\n {\n try\n {\n lock.wait(interval - end + st);\n } catch (InterruptedException e)\n {\n }\n }\n }\n }\n }\n release();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 41 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (running)\n {\n if (this.kcp.isClosed())\n {\n this.running = false;\n continue;\n }\n long st = System.currentTimeMillis();\n this.kcp.update();\n if (this.kcp.needUpdate())\n {\n continue;\n }\n long end = System.currentTimeMillis();\n while ((end - st) < this.interval)\n {\n synchronized (waitLock)\n {\n try\n {\n waitLock.wait(this.interval - end + st);\n } catch (Exception ex)\n {\n }\n }\n break;\n }\n }\n nioEventLoopGroup.shutdownGracefully();\n this.channel.close();\n } \n #location 18 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (running)\n {\n if (this.kcp.isClosed())\n {\n this.running = false;\n continue;\n }\n this.kcp.update();\n if (this.kcp.needUpdate())\n {\n continue;\n }\n synchronized (waitLock)\n {\n try\n {\n waitLock.wait(this.interval);\n } catch (Exception ex)\n {\n System.out.println(\"error..........\");\n }\n }\n }\n nioEventLoopGroup.shutdownGracefully();\n this.channel.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 27 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 43 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n pqueue.add(ku);\n }\n ku.input(dp.content());\n }\n \n //\u9009\u51fa\u7b2c\u4e00\u4e2akcp\u66f4\u65b0\u72b6\u6001\n KcpOnUdp first = pqueue.poll();\n if(first != null && first.getTimeout() < System.currentTimeMillis()) {\n first.update();\n if(!first.isClosed()) {\n pqueue.add(first);\n } else {\n this.kcps.remove((InetSocketAddress) first.getKcp().getUser());\n }\n }\n \n //\u6bcf30s\uff0c\u66f4\u65b0\u4e00\u904d\u6240\u6709\u7684kcp\u72b6\u6001\n if(System.currentTimeMillis()%(1000*30) == 0) {\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed()) {//\u5220\u6389\u8fc7\u65f6\u7684kcp\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n pqueue.remove(ku);\n }\n }\n }\n \n //\u7b49\u5f85 \n try { \n synchronized(wakeup){ \n wakeup.wait(5*60*1000);\n }\n } catch (InterruptedException ex) {\n Logger.getLogger(KcpThread.class.getName()).log(Level.SEVERE, null, ex);\n }\n \n }\n } \n #location 14 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run()\n {\n while (this.running)\n {\n //input\n while (!this.inputs.isEmpty())\n {\n DatagramPacket dp = this.inputs.remove();\n KcpOnUdp ku = this.kcps.get(dp.sender());\n if (ku == null)\n {\n ku = new KcpOnUdp(this.out, dp.sender(), this.listerner);//\u521d\u59cb\u5316\n ku.noDelay(nodelay, interval, resend, nc);\n ku.wndSize(sndwnd, rcvwnd);\n ku.setMtu(mtu);\n ku.setTimeout(timeout);\n this.kcps.put(dp.sender(), ku);\n }\n ku.input(dp.content());\n }\n //update\n KcpOnUdp temp = null;\n for (KcpOnUdp ku : this.kcps.values())\n {\n ku.update();\n if (ku.isClosed())\n {\n temp = ku;\n }\n }\n if (temp != null)//\u5220\u6389\u8fc7\u65f6\u7684kcp\n {\n this.kcps.remove((InetSocketAddress) temp.getKcp().getUser());\n }\n try\n {\n Thread.sleep(this.interval);\n } catch (InterruptedException ex)\n {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static Instances createBootstrapSample(Instances instances) {\n\t\tRandom rand = Random.getInstance();\n\t\tMap map = new HashMap<>();\n\t\tfor (int i = 0; i < instances.size(); i++) {\n\t\t\tint idx = rand.nextInt(instances.size());\n\t\t\tif (!map.containsKey(idx)) {\n\t\t\t\tmap.put(idx, 0);\n\t\t\t}\n\t\t\tmap.put(idx, map.get(idx) + 1);\n\t\t}\n\t\tInstances bag = new Instances(instances.getAttributes(), instances.getTargetAttribute(), map.size());\n\t\tfor (Integer idx : map.keySet()) {\n\t\t\tint weight = map.get(idx);\n\t\t\tInstance instance = instances.get(idx).clone();\n\t\t\tinstance.setWeight(weight);\n\t\t\tbag.add(instance);\n\t\t}\n\t\treturn bag;\n\t} \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static Instances createBootstrapSample(Instances instances) {\n\t\tRandom rand = Random.getInstance();\n\t\tMap map = new HashMap<>();\n\t\tfor (int i = 0; i < instances.size(); i++) {\n\t\t\tint idx = rand.nextInt(instances.size());\n\t\t\tmap.put(idx, map.getOrDefault(idx, 0) + 1);\n\t\t}\n\t\tInstances bag = new Instances(instances.getAttributes(), instances.getTargetAttribute(), map.size());\n\t\tfor (Integer idx : map.keySet()) {\n\t\t\tint weight = map.get(idx);\n\t\t\tInstance instance = instances.get(idx).clone();\n\t\t\tinstance.setWeight(weight);\n\t\t\tbag.add(instance);\n\t\t}\n\t\treturn bag;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout = 60000)\n public void testCommitFailWhenTSOIsDown() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf)\n .withCommitTableClient(getCommitTable().getClient().get()).build();\n \n long ts1 = client.createTransaction().get();\n pauseTSO();\n TSOFuture future = client.commit(ts1, Sets.newSet(c1, c2));\n while(!isTsoBlockingRequest()) {}\n try {\n future.get();\n } catch(ExecutionException e) {\n assertEquals(\"Should be a ServiceUnavailableExeption\",\n ServiceUnavailableException.class, e.getCause().getClass());\n }\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeout = 60000)\n public void testCommitFailWhenTSOIsDown() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf).build();\n \n long ts1 = client.createTransaction().get();\n pauseTSO();\n TSOFuture future = client.commit(ts1, Sets.newSet(c1, c2));\n while(!isTsoBlockingRequest()) {}\n try {\n future.get();\n } catch(ExecutionException e) {\n assertEquals(\"Should be a ServiceUnavailableExeption\",\n ServiceUnavailableException.class, e.getCause().getClass());\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommittedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test public void testMultiPutSameRow() throws Exception {\n try{\n TransactionManager tm = new TransactionManager(hbaseConf);\n TransactionalTable table1 = new TransactionalTable(hbaseConf, TEST_TABLE);\n\n int num=10;\n TransactionState t=tm.beginTransaction();\n for(int j=0;j raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % BKT_NUMBER)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n } \n #location 14 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testShadowCellIsHealedAfterCommitCrash() throws Exception {\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .withCommitTableClient(commitTableClient).build();\n TransactionManager tm = spy(TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client).build());\n doNothing().when(tm).postCommit(any(Transaction.class));\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n tm.commit(t1);\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell should not be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n Transaction t2 = tm.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n // This get should heal the shadow cell\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n\n // Allow the healer thread to put the shadow cell back\n table.shadowCellHealerExecutor.submit(new Runnable() {\n @Override\n public void run() {\n\n }\n }).get();\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there after being healed\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // As the shadow cell is healed, this get shouldn't have to hit the storage,\n // so the number of invocations to commitTableClient.getCommitTimestamp()\n // should remain the same\n getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testShadowCellIsHealedAfterCommitCrash() throws Exception {\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .build();\n TransactionManager tm = spy(TransactionManager.newBuilder()\n .withConfiguration(hbaseConf)\n .withCommitTableClient(commitTableClient)\n .withTSOClient(client).build());\n doNothing().when(tm).postCommit(any(Transaction.class));\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n tm.commit(t1);\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell should not be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n Transaction t2 = tm.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n // This get should heal the shadow cell\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n\n // Allow the healer thread to put the shadow cell back\n table.shadowCellHealerExecutor.submit(new Runnable() {\n @Override\n public void run() {\n\n }\n }).get();\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there after being healed\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // As the shadow cell is healed, this get shouldn't have to hit the storage,\n // so the number of invocations to commitTableClient.getCommitTimestamp()\n // should remain the same\n getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n // *** Start the Netty configuration ***\n // Start server with Nb of active threads = 2*NB CPU + 1 as maximum.\n ChannelFactory factory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"worker-%d\").build()), (Runtime\n .getRuntime().availableProcessors() * 2 + 1) * 2);\n\n ServerBootstrap bootstrap = new ServerBootstrap(factory);\n // Create the global ChannelGroup\n ChannelGroup channelGroup = new DefaultChannelGroup(TSOServer.class.getName());\n // threads max\n // int maxThreads = Runtime.getRuntime().availableProcessors() *2 + 1;\n int maxThreads = 5;\n // Memory limitation: 1MB by channel, 1GB global, 100 ms of timeout\n ThreadPoolExecutor pipelineExecutor = new OrderedMemoryAwareThreadPoolExecutor(maxThreads, 1048576, 1073741824,\n 100, TimeUnit.MILLISECONDS, new ObjectSizeEstimator() {\n @Override\n public int estimateSize(Object o) {\n return 1000;\n }\n }, new ThreadFactoryBuilder().setNameFormat(\"executor-%d\").build());\n\n // TODO use dependency injection\n if (config.getFsLog() != null) {\n state = FileSystemTimestampOnlyStateBuilder.getState(config);\n } else {\n state = BookKeeperStateBuilder.getState(this.config);\n }\n\n if (state == null) {\n LOG.error(\"Couldn't build state\");\n return;\n }\n\n state.addRecord(new byte[] { LoggerProtocol.LOGSTART }, new AddRecordCallback() {\n @Override\n public void addRecordComplete(int rc, Object ctx) {\n }\n }, null);\n\n String metricsConfig = config.getMetrics();\n if (metricsConfig != null) {\n MetricsUtils.initMetrics(metricsConfig);\n }\n\n TSOState.BATCH_SIZE = config.getBatchSize();\n LOG.info(\"PARAM MAX_ITEMS: \" + TSOState.MAX_ITEMS);\n LOG.info(\"PARAM BATCH_SIZE: \" + TSOState.BATCH_SIZE);\n LOG.info(\"PARAM LOAD_FACTOR: \" + TSOState.LOAD_FACTOR);\n LOG.info(\"PARAM MAX_THREADS: \" + maxThreads);\n\n final TSOHandler handler = new TSOHandler(channelGroup, state);\n handler.start();\n\n bootstrap.setPipelineFactory(new TSOPipelineFactory(pipelineExecutor, handler));\n bootstrap.setOption(\"tcpNoDelay\", true);\n // setting buffer size can improve I/O\n bootstrap.setOption(\"child.sendBufferSize\", 1048576);\n bootstrap.setOption(\"child.receiveBufferSize\", 1048576);\n // better to have an receive buffer predictor\n bootstrap.setOption(\"receiveBufferSizePredictorFactory\", new AdaptiveReceiveBufferSizePredictorFactory());\n // if the server is sending 1000 messages per sec, optimum write buffer water marks will\n // prevent unnecessary throttling, Check NioSocketChannelConfig doc\n bootstrap.setOption(\"writeBufferLowWaterMark\", 32 * 1024);\n bootstrap.setOption(\"writeBufferHighWaterMark\", 64 * 1024);\n\n bootstrap.setOption(\"child.tcpNoDelay\", true);\n bootstrap.setOption(\"child.keepAlive\", true);\n bootstrap.setOption(\"child.reuseAddress\", true);\n bootstrap.setOption(\"child.connectTimeoutMillis\", 60000);\n\n // *** Start the Netty running ***\n\n // Add the parent channel to the group\n Channel channel = bootstrap.bind(new InetSocketAddress(config.getPort()));\n channelGroup.add(channel);\n\n // Compacter handler\n ChannelFactory comFactory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-worker-%d\").build()),\n (Runtime.getRuntime().availableProcessors() * 2 + 1) * 2);\n ServerBootstrap comBootstrap = new ServerBootstrap(comFactory);\n ChannelGroup comGroup = new DefaultChannelGroup(\"compacter\");\n final CompacterHandler comHandler = new CompacterHandler(comGroup, state);\n comBootstrap.setPipelineFactory(new ChannelPipelineFactory() {\n\n @Override\n public ChannelPipeline getPipeline() throws Exception {\n ChannelPipeline pipeline = Channels.pipeline();\n pipeline.addLast(\"decoder\", new ObjectDecoder());\n pipeline.addLast(\"encoder\", new ObjectEncoder());\n pipeline.addLast(\"handler\", comHandler);\n return pipeline;\n }\n });\n comBootstrap.setOption(\"tcpNoDelay\", true);\n comBootstrap.setOption(\"child.tcpNoDelay\", true);\n comBootstrap.setOption(\"child.keepAlive\", true);\n comBootstrap.setOption(\"child.reuseAddress\", true);\n comBootstrap.setOption(\"child.connectTimeoutMillis\", 100);\n comBootstrap.setOption(\"readWriteFair\", true);\n channel = comBootstrap.bind(new InetSocketAddress(config.getPort() + 1));\n\n synchronized (lock) {\n while (!finish) {\n try {\n lock.wait();\n } catch (InterruptedException e) {\n break;\n }\n }\n }\n\n // timestampOracle.stop();\n handler.stop();\n comHandler.stop();\n state.stop();\n state = null;\n\n // *** Start the Netty shutdown ***\n\n // Now close all channels\n LOG.info(\"End of channel group\");\n channelGroup.close().awaitUninterruptibly();\n comGroup.close().awaitUninterruptibly();\n // Close the executor for Pipeline\n LOG.info(\"End of pipeline executor\");\n pipelineExecutor.shutdownNow();\n // Now release resources\n LOG.info(\"End of resources\");\n factory.releaseExternalResources();\n comFactory.releaseExternalResources();\n comBootstrap.releaseExternalResources();\n } \n #location 48 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run() {\n // *** Start the Netty configuration ***\n // Start server with Nb of active threads = 2*NB CPU + 1 as maximum.\n ChannelFactory factory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"worker-%d\").build()), (Runtime\n .getRuntime().availableProcessors() * 2 + 1) * 2);\n\n ServerBootstrap bootstrap = new ServerBootstrap(factory);\n // Create the global ChannelGroup\n ChannelGroup channelGroup = new DefaultChannelGroup(TSOServer.class.getName());\n // threads max\n // int maxThreads = Runtime.getRuntime().availableProcessors() *2 + 1;\n int maxThreads = 5;\n // Memory limitation: 1MB by channel, 1GB global, 100 ms of timeout\n ThreadPoolExecutor pipelineExecutor = new OrderedMemoryAwareThreadPoolExecutor(maxThreads, 1048576, 1073741824,\n 100, TimeUnit.MILLISECONDS, new ObjectSizeEstimator() {\n @Override\n public int estimateSize(Object o) {\n return 1000;\n }\n }, new ThreadFactoryBuilder().setNameFormat(\"executor-%d\").build());\n\n // TODO use dependency injection\n if (config.getFsLog() != null) {\n state = FileSystemTimestampOnlyStateBuilder.getState(config);\n } else {\n state = BookKeeperStateBuilder.getState(this.config);\n }\n\n if (state == null) {\n LOG.error(\"Couldn't build state\");\n return;\n }\n\n state.addRecord(new byte[] { LoggerProtocol.LOGSTART }, new AddRecordCallback() {\n @Override\n public void addRecordComplete(int rc, Object ctx) {\n }\n }, null);\n\n String metricsConfig = config.getMetrics();\n if (metricsConfig != null) {\n MetricsUtils.initMetrics(metricsConfig);\n }\n\n LOG.info(\"PARAM MAX_ITEMS: \" + state.maxItems);\n LOG.info(\"PARAM BATCH_SIZE: \" + state.batchSize);\n LOG.info(\"PARAM LOAD_FACTOR: \" + TSOState.LOAD_FACTOR);\n LOG.info(\"PARAM MAX_THREADS: \" + maxThreads);\n\n final TSOHandler handler = new TSOHandler(channelGroup, state);\n handler.start();\n\n bootstrap.setPipelineFactory(new TSOPipelineFactory(pipelineExecutor, handler));\n bootstrap.setOption(\"tcpNoDelay\", true);\n // setting buffer size can improve I/O\n bootstrap.setOption(\"child.sendBufferSize\", 1048576);\n bootstrap.setOption(\"child.receiveBufferSize\", 1048576);\n // better to have an receive buffer predictor\n bootstrap.setOption(\"receiveBufferSizePredictorFactory\", new AdaptiveReceiveBufferSizePredictorFactory());\n // if the server is sending 1000 messages per sec, optimum write buffer water marks will\n // prevent unnecessary throttling, Check NioSocketChannelConfig doc\n bootstrap.setOption(\"writeBufferLowWaterMark\", 32 * 1024);\n bootstrap.setOption(\"writeBufferHighWaterMark\", 64 * 1024);\n\n bootstrap.setOption(\"child.tcpNoDelay\", true);\n bootstrap.setOption(\"child.keepAlive\", true);\n bootstrap.setOption(\"child.reuseAddress\", true);\n bootstrap.setOption(\"child.connectTimeoutMillis\", 60000);\n\n // *** Start the Netty running ***\n\n // Add the parent channel to the group\n Channel channel = bootstrap.bind(new InetSocketAddress(config.getPort()));\n channelGroup.add(channel);\n\n // Compacter handler\n ChannelFactory comFactory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-worker-%d\").build()),\n (Runtime.getRuntime().availableProcessors() * 2 + 1) * 2);\n ServerBootstrap comBootstrap = new ServerBootstrap(comFactory);\n ChannelGroup comGroup = new DefaultChannelGroup(\"compacter\");\n final CompacterHandler comHandler = new CompacterHandler(comGroup, state);\n comBootstrap.setPipelineFactory(new ChannelPipelineFactory() {\n\n @Override\n public ChannelPipeline getPipeline() throws Exception {\n ChannelPipeline pipeline = Channels.pipeline();\n pipeline.addLast(\"decoder\", new ObjectDecoder());\n pipeline.addLast(\"encoder\", new ObjectEncoder());\n pipeline.addLast(\"handler\", comHandler);\n return pipeline;\n }\n });\n comBootstrap.setOption(\"tcpNoDelay\", true);\n comBootstrap.setOption(\"child.tcpNoDelay\", true);\n comBootstrap.setOption(\"child.keepAlive\", true);\n comBootstrap.setOption(\"child.reuseAddress\", true);\n comBootstrap.setOption(\"child.connectTimeoutMillis\", 100);\n comBootstrap.setOption(\"readWriteFair\", true);\n channel = comBootstrap.bind(new InetSocketAddress(config.getPort() + 1));\n\n synchronized (lock) {\n while (!finish) {\n try {\n lock.wait();\n } catch (InterruptedException e) {\n break;\n }\n }\n }\n\n // timestampOracle.stop();\n handler.stop();\n comHandler.stop();\n state.stop();\n state = null;\n\n // *** Start the Netty shutdown ***\n\n // Now close all channels\n LOG.info(\"End of channel group\");\n channelGroup.close().awaitUninterruptibly();\n comGroup.close().awaitUninterruptibly();\n // Close the executor for Pipeline\n LOG.info(\"End of pipeline executor\");\n pipelineExecutor.shutdownNow();\n // Now release resources\n LOG.info(\"End of resources\");\n factory.releaseExternalResources();\n comFactory.releaseExternalResources();\n comBootstrap.releaseExternalResources();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeOut = 30_000)\n public void runTestInterleaveScanWhenATransactionAborts() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n TTable tt = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n LOG.info(\"Transaction created \" + t1);\n\n byte[] fam = Bytes.toBytes(TEST_FAMILY);\n byte[] col = Bytes.toBytes(\"testdata\");\n byte[] data1 = Bytes.toBytes(\"testWrite-1\");\n byte[] data2 = Bytes.toBytes(\"testWrite-2\");\n\n byte[] startrow = Bytes.toBytes(\"test-scan\" + 0);\n byte[] stoprow = Bytes.toBytes(\"test-scan\" + 9);\n byte[] modrow = Bytes.toBytes(\"test-scan\" + 3);\n for (int i = 0; i < 10; i++) {\n byte[] row = Bytes.toBytes(\"test-scan\" + i);\n\n Put p = new Put(row);\n p.add(fam, col, data1);\n tt.put(t1, p);\n }\n tm.commit(t1);\n\n Transaction t2 = tm.begin();\n Put p = new Put(modrow);\n p.add(fam, col, data2);\n tt.put(t2, p);\n\n int modifiedrows = 0;\n ResultScanner rs = tt.getScanner(t2, new Scan().setStartRow(startrow).setStopRow(stoprow).addColumn(fam, col));\n Result r = rs.next();\n while (r != null) {\n if (Bytes.equals(data2, r.getValue(fam, col))) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Modified :\" + Bytes.toString(r.getRow()));\n }\n modifiedrows++;\n }\n\n r = rs.next();\n }\n\n assertTrue(modifiedrows == 1, \"Expected 1 row modified, but \" + modifiedrows + \" are.\");\n tm.rollback(t2);\n\n Transaction tscan = tm.begin();\n rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow).addColumn(fam, col));\n r = rs.next();\n while (r != null) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Scan1 :\" + Bytes.toString(r.getRow()) + \" => \" + Bytes.toString(r.getValue(fam, col)));\n }\n\n assertTrue(Bytes.equals(data1, r.getValue(fam, col)),\n \"Unexpected value for SI scan \" + tscan + \": \" + Bytes.toString(r.getValue(fam, col)));\n r = rs.next();\n }\n\n } \n #location 46 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeOut = 30_000)\n public void runTestInterleaveScanWhenATransactionAborts() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n TTable tt = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n LOG.info(\"Transaction created \" + t1);\n\n byte[] fam = Bytes.toBytes(TEST_FAMILY);\n byte[] col = Bytes.toBytes(\"testdata\");\n byte[] data1 = Bytes.toBytes(\"testWrite-1\");\n byte[] data2 = Bytes.toBytes(\"testWrite-2\");\n\n byte[] startrow = Bytes.toBytes(\"test-scan\" + 0);\n byte[] stoprow = Bytes.toBytes(\"test-scan\" + 9);\n byte[] modrow = Bytes.toBytes(\"test-scan\" + 3);\n for (int i = 0; i < 10; i++) {\n byte[] row = Bytes.toBytes(\"test-scan\" + i);\n\n Put p = new Put(row);\n p.add(fam, col, data1);\n tt.put(t1, p);\n }\n tm.commit(t1);\n\n Transaction t2 = tm.begin();\n Put p = new Put(modrow);\n p.add(fam, col, data2);\n tt.put(t2, p);\n\n int modifiedrows = 0;\n ResultScanner rs = tt.getScanner(t2, new Scan().setStartRow(startrow).setStopRow(stoprow).addColumn(fam, col));\n Result r = rs.next();\n while (r != null) {\n if (Bytes.equals(data2, r.getValue(fam, col))) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Modified :\" + Bytes.toString(r.getRow()));\n }\n modifiedrows++;\n }\n\n r = rs.next();\n }\n\n assertTrue(modifiedrows == 1, \"Expected 1 row modified, but \" + modifiedrows + \" are.\");\n tm.rollback(t2);\n\n Transaction tscan = tm.begin();\n rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow).addColumn(fam, col));\n r = rs.next();\n while (r != null) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Scan1 :\" + Bytes.toString(r.getRow()) + \" => \" + Bytes.toString(r.getValue(fam, col)));\n }\n\n assertTrue(Bytes.equals(data1, r.getValue(fam, col)),\n \"Unexpected value for SI scan \" + tscan + \": \" + Bytes.toString(r.getValue(fam, col)));\n r = rs.next();\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout = 60000)\n public void testTimestampRequestSucceedWithMultipleTimeouts() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10000);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf)\n .withCommitTableClient(getCommitTable().getClient().get()).build();\n \n pauseTSO();\n Future future = client.createTransaction();\n while(!isTsoBlockingRequest()) {}\n Thread.sleep(1000);\n resumeTSO();\n future.get();\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeout = 60000)\n public void testTimestampRequestSucceedWithMultipleTimeouts() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10000);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf).build();\n \n pauseTSO();\n Future future = client.createTransaction();\n while(!isTsoBlockingRequest()) {}\n Thread.sleep(1000);\n resumeTSO();\n future.get();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testShadowCellsBasics() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell shouldn't be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n tm.commit(t1);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // Test that we can make a valid read after adding a shadow cell without hitting the commit table\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .withCommitTableClient(commitTableClient).build();\n TransactionManager tm2 = TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client).build();\n\n Transaction t2 = tm2.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, never()).getCommitTimestamp(anyLong());\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testShadowCellsBasics() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell shouldn't be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n tm.commit(t1);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // Test that we can make a valid read after adding a shadow cell without hitting the commit table\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .build();\n TransactionManager tm2 = TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client)\n .withCommitTableClient(commitTableClient).build();\n\n Transaction t2 = tm2.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, never()).getCommitTimestamp(anyLong());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % BKT_NUMBER)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeout = 60000)\n public void testCommitCanSucceedWithMultipleTimeouts() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10000);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf)\n .withCommitTableClient(getCommitTable().getClient().get()).build();\n \n long ts1 = client.createTransaction().get();\n pauseTSO();\n TSOFuture future = client.commit(ts1, Sets.newSet(c1, c2));\n while(!isTsoBlockingRequest()) {}\n Thread.sleep(1000);\n resumeTSO();\n future.get();\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeout = 60000)\n public void testCommitCanSucceedWithMultipleTimeouts() throws Exception {\n Configuration clientConfiguration = getClientConfiguration();\n clientConfiguration.setProperty(TSOClient.REQUEST_TIMEOUT_IN_MS_CONFKEY, 100);\n clientConfiguration.setProperty(TSOClient.REQUEST_MAX_RETRIES_CONFKEY, 10000);\n \n TSOClient client = TSOClient.newBuilder().withConfiguration(clientConf).build();\n \n long ts1 = client.createTransaction().get();\n pauseTSO();\n TSOFuture future = client.commit(ts1, Sets.newSet(c1, c2));\n while(!isTsoBlockingRequest()) {}\n Thread.sleep(1000);\n resumeTSO();\n future.get();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n // *** Start the Netty configuration ***\n // Start server with Nb of active threads = 2*NB CPU + 1 as maximum.\n ChannelFactory factory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"worker-%d\").build()), (Runtime\n .getRuntime().availableProcessors() * 2 + 1) * 2);\n\n ServerBootstrap bootstrap = new ServerBootstrap(factory);\n // Create the global ChannelGroup\n ChannelGroup channelGroup = new DefaultChannelGroup(TSOServer.class.getName());\n // threads max\n // int maxThreads = Runtime.getRuntime().availableProcessors() *2 + 1;\n int maxThreads = 5;\n // Memory limitation: 1MB by channel, 1GB global, 100 ms of timeout\n ThreadPoolExecutor pipelineExecutor = new OrderedMemoryAwareThreadPoolExecutor(maxThreads, 1048576, 1073741824,\n 100, TimeUnit.MILLISECONDS, new ObjectSizeEstimator() {\n @Override\n public int estimateSize(Object o) {\n return 1000;\n }\n }, new ThreadFactoryBuilder().setNameFormat(\"executor-%d\").build());\n\n // TODO use dependency injection\n if (config.getFsLog() != null) {\n state = FileSystemTimestampOnlyStateBuilder.getState(config);\n } else {\n state = BookKeeperStateBuilder.getState(this.config);\n }\n\n if (state == null) {\n LOG.error(\"Couldn't build state\");\n return;\n }\n\n state.addRecord(new byte[] { LoggerProtocol.LOGSTART }, new AddRecordCallback() {\n @Override\n public void addRecordComplete(int rc, Object ctx) {\n }\n }, null);\n\n String metricsConfig = config.getMetrics();\n if (metricsConfig != null) {\n MetricsUtils.initMetrics(metricsConfig);\n }\n\n TSOState.BATCH_SIZE = config.getBatchSize();\n LOG.info(\"PARAM MAX_ITEMS: \" + TSOState.MAX_ITEMS);\n LOG.info(\"PARAM BATCH_SIZE: \" + TSOState.BATCH_SIZE);\n LOG.info(\"PARAM LOAD_FACTOR: \" + TSOState.LOAD_FACTOR);\n LOG.info(\"PARAM MAX_THREADS: \" + maxThreads);\n\n final TSOHandler handler = new TSOHandler(channelGroup, state);\n handler.start();\n\n bootstrap.setPipelineFactory(new TSOPipelineFactory(pipelineExecutor, handler));\n bootstrap.setOption(\"tcpNoDelay\", true);\n // setting buffer size can improve I/O\n bootstrap.setOption(\"child.sendBufferSize\", 1048576);\n bootstrap.setOption(\"child.receiveBufferSize\", 1048576);\n // better to have an receive buffer predictor\n bootstrap.setOption(\"receiveBufferSizePredictorFactory\", new AdaptiveReceiveBufferSizePredictorFactory());\n // if the server is sending 1000 messages per sec, optimum write buffer water marks will\n // prevent unnecessary throttling, Check NioSocketChannelConfig doc\n bootstrap.setOption(\"writeBufferLowWaterMark\", 32 * 1024);\n bootstrap.setOption(\"writeBufferHighWaterMark\", 64 * 1024);\n\n bootstrap.setOption(\"child.tcpNoDelay\", true);\n bootstrap.setOption(\"child.keepAlive\", true);\n bootstrap.setOption(\"child.reuseAddress\", true);\n bootstrap.setOption(\"child.connectTimeoutMillis\", 60000);\n\n // *** Start the Netty running ***\n\n // Add the parent channel to the group\n Channel channel = bootstrap.bind(new InetSocketAddress(config.getPort()));\n channelGroup.add(channel);\n\n // Compacter handler\n ChannelFactory comFactory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-worker-%d\").build()),\n (Runtime.getRuntime().availableProcessors() * 2 + 1) * 2);\n ServerBootstrap comBootstrap = new ServerBootstrap(comFactory);\n ChannelGroup comGroup = new DefaultChannelGroup(\"compacter\");\n final CompacterHandler comHandler = new CompacterHandler(comGroup, state);\n comBootstrap.setPipelineFactory(new ChannelPipelineFactory() {\n\n @Override\n public ChannelPipeline getPipeline() throws Exception {\n ChannelPipeline pipeline = Channels.pipeline();\n pipeline.addLast(\"decoder\", new ObjectDecoder());\n pipeline.addLast(\"encoder\", new ObjectEncoder());\n pipeline.addLast(\"handler\", comHandler);\n return pipeline;\n }\n });\n comBootstrap.setOption(\"tcpNoDelay\", true);\n comBootstrap.setOption(\"child.tcpNoDelay\", true);\n comBootstrap.setOption(\"child.keepAlive\", true);\n comBootstrap.setOption(\"child.reuseAddress\", true);\n comBootstrap.setOption(\"child.connectTimeoutMillis\", 100);\n comBootstrap.setOption(\"readWriteFair\", true);\n channel = comBootstrap.bind(new InetSocketAddress(config.getPort() + 1));\n\n synchronized (lock) {\n while (!finish) {\n try {\n lock.wait();\n } catch (InterruptedException e) {\n break;\n }\n }\n }\n\n // timestampOracle.stop();\n handler.stop();\n comHandler.stop();\n state.stop();\n state = null;\n\n // *** Start the Netty shutdown ***\n\n // Now close all channels\n LOG.info(\"End of channel group\");\n channelGroup.close().awaitUninterruptibly();\n comGroup.close().awaitUninterruptibly();\n // Close the executor for Pipeline\n LOG.info(\"End of pipeline executor\");\n pipelineExecutor.shutdownNow();\n // Now release resources\n LOG.info(\"End of resources\");\n factory.releaseExternalResources();\n comFactory.releaseExternalResources();\n comBootstrap.releaseExternalResources();\n } \n #location 50 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public void run() {\n // *** Start the Netty configuration ***\n // Start server with Nb of active threads = 2*NB CPU + 1 as maximum.\n ChannelFactory factory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"worker-%d\").build()), (Runtime\n .getRuntime().availableProcessors() * 2 + 1) * 2);\n\n ServerBootstrap bootstrap = new ServerBootstrap(factory);\n // Create the global ChannelGroup\n ChannelGroup channelGroup = new DefaultChannelGroup(TSOServer.class.getName());\n // threads max\n // int maxThreads = Runtime.getRuntime().availableProcessors() *2 + 1;\n int maxThreads = 5;\n // Memory limitation: 1MB by channel, 1GB global, 100 ms of timeout\n ThreadPoolExecutor pipelineExecutor = new OrderedMemoryAwareThreadPoolExecutor(maxThreads, 1048576, 1073741824,\n 100, TimeUnit.MILLISECONDS, new ObjectSizeEstimator() {\n @Override\n public int estimateSize(Object o) {\n return 1000;\n }\n }, new ThreadFactoryBuilder().setNameFormat(\"executor-%d\").build());\n\n // TODO use dependency injection\n if (config.getFsLog() != null) {\n state = FileSystemTimestampOnlyStateBuilder.getState(config);\n } else {\n state = BookKeeperStateBuilder.getState(this.config);\n }\n\n if (state == null) {\n LOG.error(\"Couldn't build state\");\n return;\n }\n\n state.addRecord(new byte[] { LoggerProtocol.LOGSTART }, new AddRecordCallback() {\n @Override\n public void addRecordComplete(int rc, Object ctx) {\n }\n }, null);\n\n String metricsConfig = config.getMetrics();\n if (metricsConfig != null) {\n MetricsUtils.initMetrics(metricsConfig);\n }\n\n LOG.info(\"PARAM MAX_ITEMS: \" + state.maxItems);\n LOG.info(\"PARAM BATCH_SIZE: \" + state.batchSize);\n LOG.info(\"PARAM LOAD_FACTOR: \" + TSOState.LOAD_FACTOR);\n LOG.info(\"PARAM MAX_THREADS: \" + maxThreads);\n\n final TSOHandler handler = new TSOHandler(channelGroup, state);\n handler.start();\n\n bootstrap.setPipelineFactory(new TSOPipelineFactory(pipelineExecutor, handler));\n bootstrap.setOption(\"tcpNoDelay\", true);\n // setting buffer size can improve I/O\n bootstrap.setOption(\"child.sendBufferSize\", 1048576);\n bootstrap.setOption(\"child.receiveBufferSize\", 1048576);\n // better to have an receive buffer predictor\n bootstrap.setOption(\"receiveBufferSizePredictorFactory\", new AdaptiveReceiveBufferSizePredictorFactory());\n // if the server is sending 1000 messages per sec, optimum write buffer water marks will\n // prevent unnecessary throttling, Check NioSocketChannelConfig doc\n bootstrap.setOption(\"writeBufferLowWaterMark\", 32 * 1024);\n bootstrap.setOption(\"writeBufferHighWaterMark\", 64 * 1024);\n\n bootstrap.setOption(\"child.tcpNoDelay\", true);\n bootstrap.setOption(\"child.keepAlive\", true);\n bootstrap.setOption(\"child.reuseAddress\", true);\n bootstrap.setOption(\"child.connectTimeoutMillis\", 60000);\n\n // *** Start the Netty running ***\n\n // Add the parent channel to the group\n Channel channel = bootstrap.bind(new InetSocketAddress(config.getPort()));\n channelGroup.add(channel);\n\n // Compacter handler\n ChannelFactory comFactory = new NioServerSocketChannelFactory(\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-boss-%d\").build()),\n Executors.newCachedThreadPool(new ThreadFactoryBuilder().setNameFormat(\"compacter-worker-%d\").build()),\n (Runtime.getRuntime().availableProcessors() * 2 + 1) * 2);\n ServerBootstrap comBootstrap = new ServerBootstrap(comFactory);\n ChannelGroup comGroup = new DefaultChannelGroup(\"compacter\");\n final CompacterHandler comHandler = new CompacterHandler(comGroup, state);\n comBootstrap.setPipelineFactory(new ChannelPipelineFactory() {\n\n @Override\n public ChannelPipeline getPipeline() throws Exception {\n ChannelPipeline pipeline = Channels.pipeline();\n pipeline.addLast(\"decoder\", new ObjectDecoder());\n pipeline.addLast(\"encoder\", new ObjectEncoder());\n pipeline.addLast(\"handler\", comHandler);\n return pipeline;\n }\n });\n comBootstrap.setOption(\"tcpNoDelay\", true);\n comBootstrap.setOption(\"child.tcpNoDelay\", true);\n comBootstrap.setOption(\"child.keepAlive\", true);\n comBootstrap.setOption(\"child.reuseAddress\", true);\n comBootstrap.setOption(\"child.connectTimeoutMillis\", 100);\n comBootstrap.setOption(\"readWriteFair\", true);\n channel = comBootstrap.bind(new InetSocketAddress(config.getPort() + 1));\n\n synchronized (lock) {\n while (!finish) {\n try {\n lock.wait();\n } catch (InterruptedException e) {\n break;\n }\n }\n }\n\n // timestampOracle.stop();\n handler.stop();\n comHandler.stop();\n state.stop();\n state = null;\n\n // *** Start the Netty shutdown ***\n\n // Now close all channels\n LOG.info(\"End of channel group\");\n channelGroup.close().awaitUninterruptibly();\n comGroup.close().awaitUninterruptibly();\n // Close the executor for Pipeline\n LOG.info(\"End of pipeline executor\");\n pipelineExecutor.shutdownNow();\n // Now release resources\n LOG.info(\"End of resources\");\n factory.releaseExternalResources();\n comFactory.releaseExternalResources();\n comBootstrap.releaseExternalResources();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testCrashAfterCommit() throws Exception {\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .withCommitTableClient(commitTableClient).build();\n TransactionManager tm = spy(TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client).build());\n doNothing().when(tm).postCommit(any(Transaction.class));\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n tm.commit(t1);\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell should not be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n Transaction t2 = tm.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testCrashAfterCommit() throws Exception {\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .build();\n TransactionManager tm = spy(TransactionManager.newBuilder()\n .withConfiguration(hbaseConf)\n .withCommitTableClient(commitTableClient)\n .withTSOClient(client).build());\n doNothing().when(tm).postCommit(any(Transaction.class));\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n tm.commit(t1);\n\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell should not be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n Transaction t2 = tm.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, times(1)).getCommitTimestamp(anyLong());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % BKT_NUMBER)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n } \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void stop() {\n if (clientThread != null) {\n clientThread.interrupt();\n }\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void stop() {\n for (NotificationClient client : clients.values()) {\n client.stop();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testBasicBehaviour() throws Throwable {\n HTable table = new HTable(hbaseConf, TEST_TABLE);\n HBaseCommitTable commitTable = new HBaseCommitTable(table);\n\n ListenableFuture futureWriter = commitTable.getWriter();\n Writer writer = futureWriter.get();\n ListenableFuture futureClient = commitTable.getClient();\n Client client = futureClient.get();\n\n // Test that the first time the table is empty\n assertEquals(\"Rows should be 0!\", 0, rowCount());\n\n // Test the successful creation of 1000 txs in the table\n for (int i = 0; i < 1000; i++) {\n writer.addCommittedTransaction(i, i + 1);\n }\n writer.flush().get();\n assertEquals(\"Rows should be 1000!\", 1000, rowCount());\n\n // Test the we get the right commit timestamps for each previously inserted tx\n for (long i = 0; i < 1000; i++) {\n ListenableFuture> ctf = client.getCommitTimestamp(i);\n Optional optional = ctf.get();\n Long ct = optional.get();\n assertEquals(\"Commit timestamp should be \" + (i + 1), (i + 1), (long) ct);\n }\n assertEquals(\"Rows should be 1000!\", 1000, rowCount());\n\n // Test the successful deletion of the 1000 txs\n Future f = null;\n for (long i = 0; i < 1000; i++) {\n f = client.completeTransaction(i);\n }\n f.get();\n assertEquals(\"Rows should be 0!\", 0, rowCount());\n\n // Test we don't get a commit timestamp for a non-existent transaction id in the table\n ListenableFuture> ctf = client.getCommitTimestamp(0);\n Optional optional = ctf.get();\n assertFalse(\"Commit timestamp should not be present\", optional.isPresent());\n\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testBasicBehaviour() throws Throwable {\n HBaseCommitTable commitTable = new HBaseCommitTable(hbaseConf, TEST_TABLE);\n\n ListenableFuture futureWriter = commitTable.getWriter();\n Writer writer = futureWriter.get();\n ListenableFuture futureClient = commitTable.getClient();\n Client client = futureClient.get();\n\n // Test that the first time the table is empty\n assertEquals(\"Rows should be 0!\", 0, rowCount());\n\n // Test the successful creation of 1000 txs in the table\n for (int i = 0; i < 1000; i++) {\n writer.addCommittedTransaction(i, i + 1);\n }\n writer.flush().get();\n assertEquals(\"Rows should be 1000!\", 1000, rowCount());\n\n // Test the we get the right commit timestamps for each previously inserted tx\n for (long i = 0; i < 1000; i++) {\n ListenableFuture> ctf = client.getCommitTimestamp(i);\n Optional optional = ctf.get();\n Long ct = optional.get();\n assertEquals(\"Commit timestamp should be \" + (i + 1), (i + 1), (long) ct);\n }\n assertEquals(\"Rows should be 1000!\", 1000, rowCount());\n\n // Test the successful deletion of the 1000 txs\n Future f = null;\n for (long i = 0; i < 1000; i++) {\n f = client.completeTransaction(i);\n }\n f.get();\n assertEquals(\"Rows should be 0!\", 0, rowCount());\n\n // Test we don't get a commit timestamp for a non-existent transaction id in the table\n ListenableFuture> ctf = client.getCommitTimestamp(0);\n Optional optional = ctf.get();\n assertFalse(\"Commit timestamp should not be present\", optional.isPresent());\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testShadowCellsBasics() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell shouldn't be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n tm.commit(t1);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // Test that we can make a valid read after adding a shadow cell without hitting the commit table\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .withCommitTableClient(commitTableClient).build();\n TransactionManager tm2 = TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client).build();\n\n Transaction t2 = tm2.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, never()).getCommitTimestamp(anyLong());\n } \n #location 17 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testShadowCellsBasics() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n\n TTable table = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n\n // Test shadow cell are created properly\n Put put = new Put(row);\n put.add(family, qualifier, data1);\n table.put(t1, put);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertFalse(\"Shadow cell shouldn't be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n tm.commit(t1);\n assertTrue(\"Cell should be there\",\n hasCell(table, row, family, qualifier, t1.getStartTimestamp()));\n assertTrue(\"Shadow cell should be there\",\n hasShadowCell(table, row, family, qualifier, t1.getStartTimestamp()));\n\n // Test that we can make a valid read after adding a shadow cell without hitting the commit table\n CommitTable.Client commitTableClient = spy(getTSO().getCommitTable().getClient().get());\n\n TSOClient client = TSOClient.newBuilder().withConfiguration(getTSO().getClientConfiguration())\n .build();\n TransactionManager tm2 = TransactionManager.newBuilder()\n .withConfiguration(hbaseConf).withTSOClient(client)\n .withCommitTableClient(commitTableClient).build();\n\n Transaction t2 = tm2.begin();\n Get get = new Get(row);\n get.addColumn(family, qualifier);\n\n Result getResult = table.get(t2, get);\n assertTrue(\"Values should be the same\", Arrays.equals(data1, getResult.getValue(family, qualifier)));\n verify(commitTableClient, never()).getCommitTimestamp(anyLong());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % BKT_NUMBER)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Set raiseLargestDeletedTransaction(long id) {\n if (firstUncommitedAbsolute > getAbsolutePosition(id))\n return Collections.emptySet();\n int maxBucket = getRelativePosition(id);\n Set aborted = new TreeSet();\n for (int i = firstUncommitedBucket; i != maxBucket ; i = (int)((i+1) % bucketNumber)) {\n Bucket bucket = buckets[i];\n if (bucket != null) {\n aborted.addAll(bucket.abortAllUncommited());\n buckets[i] = null;\n }\n }\n \n Bucket bucket = buckets[maxBucket];\n if (bucket != null) {\n aborted.addAll(bucket.abortUncommited(id));\n }\n \n increaseFirstUncommitedBucket();\n \n return aborted;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] args) throws Exception {\n Config config = new Config();\n new JCommander(config, args);\n\n Configuration hbaseConfig = HBaseConfiguration.create();\n HTable commitHTable = new HTable(hbaseConfig, COMMIT_TABLE_DEFAULT_NAME);\n if (config.writeBufferSize != -1) {\n commitHTable.setWriteBufferSize(config.writeBufferSize);\n }\n\n final KeyGenerator keygen;\n if (config.fullRandomAlgo) {\n keygen = new FullRandomKeyGenerator();\n } else if (config.badRandomAlgo) {\n keygen = new BadRandomKeyGenerator();\n } else if (config.bucketingAlgo) {\n keygen = new BucketKeyGenerator();\n } else if (config.seqAlgo) {\n keygen = new SeqKeyGenerator();\n } else {\n keygen = null;\n assert (false);\n }\n CommitTable commitTable = new HBaseCommitTable(commitHTable, keygen);\n CommitTable.Writer writer = commitTable.getWriter().get();\n\n MetricRegistry metrics = new MetricRegistry();\n if (config.graphite != null) {\n String parts[] = config.graphite.split(\":\");\n String host = parts[0];\n Integer port = Integer.valueOf(parts[1]);\n\n final Graphite graphite = new Graphite(new InetSocketAddress(host, port));\n final GraphiteReporter reporter = GraphiteReporter.forRegistry(metrics)\n .prefixedWith(\"omid-hbase.\" + keygen.getClass().getSimpleName())\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .filter(MetricFilter.ALL)\n .build(graphite);\n reporter.start(10, TimeUnit.SECONDS);\n }\n final ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics)\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build();\n reporter.start(10, TimeUnit.SECONDS);\n\n Timer flushTimer = metrics.timer(\"flush\");\n Meter commitsMeter = metrics.meter(\"commits\");\n int i = 0;\n long ts = 0;\n while (true) {\n writer.addCommittedTransaction(ts++, ts++);\n if (i++ == config.batchSize) {\n commitsMeter.mark(i);\n long start = System.nanoTime();\n writer.flush().get();\n flushTimer.update((System.nanoTime() - start), TimeUnit.NANOSECONDS);\n i = 0;\n }\n }\n } \n #location 22 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void main(String[] args) throws Exception {\n Config config = new Config();\n new JCommander(config, args);\n\n Configuration hbaseConfig = HBaseConfiguration.create();\n\n final KeyGenerator keygen;\n if (config.fullRandomAlgo) {\n keygen = new FullRandomKeyGenerator();\n } else if (config.badRandomAlgo) {\n keygen = new BadRandomKeyGenerator();\n } else if (config.bucketingAlgo) {\n keygen = new BucketKeyGenerator();\n } else if (config.seqAlgo) {\n keygen = new SeqKeyGenerator();\n } else {\n keygen = null;\n assert (false);\n }\n CommitTable commitTable = new HBaseCommitTable(hbaseConfig,\n COMMIT_TABLE_DEFAULT_NAME, keygen);\n CommitTable.Writer writer = commitTable.getWriter().get();\n\n MetricRegistry metrics = new MetricRegistry();\n if (config.graphite != null) {\n String parts[] = config.graphite.split(\":\");\n String host = parts[0];\n Integer port = Integer.valueOf(parts[1]);\n\n final Graphite graphite = new Graphite(new InetSocketAddress(host, port));\n final GraphiteReporter reporter = GraphiteReporter.forRegistry(metrics)\n .prefixedWith(\"omid-hbase.\" + keygen.getClass().getSimpleName())\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .filter(MetricFilter.ALL)\n .build(graphite);\n reporter.start(10, TimeUnit.SECONDS);\n }\n final ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics)\n .convertRatesTo(TimeUnit.SECONDS)\n .convertDurationsTo(TimeUnit.MILLISECONDS)\n .build();\n reporter.start(10, TimeUnit.SECONDS);\n\n Timer flushTimer = metrics.timer(\"flush\");\n Meter commitsMeter = metrics.meter(\"commits\");\n int i = 0;\n long ts = 0;\n while (true) {\n writer.addCommittedTransaction(ts++, ts++);\n if (i++ == config.batchSize) {\n commitsMeter.mark(i);\n long start = System.nanoTime();\n writer.flush().get();\n flushTimer.update((System.nanoTime() - start), TimeUnit.NANOSECONDS);\n i = 0;\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test(timeOut = 30_000)\n public void runTestInterleaveScan() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n TTable tt = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n LOG.info(\"Transaction created \" + t1);\n\n byte[] fam = Bytes.toBytes(TEST_FAMILY);\n byte[] col = Bytes.toBytes(\"testdata\");\n byte[] data1 = Bytes.toBytes(\"testWrite-1\");\n byte[] data2 = Bytes.toBytes(\"testWrite-2\");\n\n byte[] startrow = Bytes.toBytes(\"test-scan\" + 0);\n byte[] stoprow = Bytes.toBytes(\"test-scan\" + 9);\n byte[] modrow = Bytes.toBytes(\"test-scan\" + 3);\n for (int i = 0; i < 10; i++) {\n byte[] row = Bytes.toBytes(\"test-scan\" + i);\n\n Put p = new Put(row);\n p.add(fam, col, data1);\n tt.put(t1, p);\n }\n tm.commit(t1);\n\n Transaction t2 = tm.begin();\n Put p = new Put(modrow);\n p.add(fam, col, data2);\n tt.put(t2, p);\n\n Transaction tscan = tm.begin();\n ResultScanner rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow));\n Result r = rs.next();\n int i = 0;\n while (r != null) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Scan1 :\" + Bytes.toString(r.getRow()) + \" => \" + Bytes.toString(r.getValue(fam, col)));\n }\n LOG.debug(\"\" + ++i);\n\n assertTrue(Bytes.equals(data1, r.getValue(fam, col)),\n \"Unexpected value for SI scan \" + tscan + \": \" + Bytes.toString(r.getValue(fam, col)));\n r = rs.next();\n }\n tm.commit(t2);\n\n int modifiedrows = 0;\n tscan = tm.begin();\n rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow));\n r = rs.next();\n while (r != null) {\n if (Bytes.equals(data2, r.getValue(fam, col))) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Modified :\" + Bytes.toString(r.getRow()));\n }\n modifiedrows++;\n }\n\n r = rs.next();\n }\n\n assertTrue(modifiedrows == 1, \"Expected 1 row modified, but \" + modifiedrows + \" are.\");\n\n } \n #location 63 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test(timeOut = 30_000)\n public void runTestInterleaveScan() throws Exception {\n\n TransactionManager tm = newTransactionManager();\n TTable tt = new TTable(hbaseConf, TEST_TABLE);\n\n Transaction t1 = tm.begin();\n LOG.info(\"Transaction created \" + t1);\n\n byte[] fam = Bytes.toBytes(TEST_FAMILY);\n byte[] col = Bytes.toBytes(\"testdata\");\n byte[] data1 = Bytes.toBytes(\"testWrite-1\");\n byte[] data2 = Bytes.toBytes(\"testWrite-2\");\n\n byte[] startrow = Bytes.toBytes(\"test-scan\" + 0);\n byte[] stoprow = Bytes.toBytes(\"test-scan\" + 9);\n byte[] modrow = Bytes.toBytes(\"test-scan\" + 3);\n for (int i = 0; i < 10; i++) {\n byte[] row = Bytes.toBytes(\"test-scan\" + i);\n\n Put p = new Put(row);\n p.add(fam, col, data1);\n tt.put(t1, p);\n }\n tm.commit(t1);\n\n Transaction t2 = tm.begin();\n Put p = new Put(modrow);\n p.add(fam, col, data2);\n tt.put(t2, p);\n\n Transaction tscan = tm.begin();\n ResultScanner rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow));\n Result r = rs.next();\n int i = 0;\n while (r != null) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Scan1 :\" + Bytes.toString(r.getRow()) + \" => \" + Bytes.toString(r.getValue(fam, col)));\n }\n LOG.debug(\"\" + ++i);\n\n assertTrue(Bytes.equals(data1, r.getValue(fam, col)),\n \"Unexpected value for SI scan \" + tscan + \": \" + Bytes.toString(r.getValue(fam, col)));\n r = rs.next();\n }\n tm.commit(t2);\n\n int modifiedrows = 0;\n tscan = tm.begin();\n rs = tt.getScanner(tscan, new Scan().setStartRow(startrow).setStopRow(stoprow));\n r = rs.next();\n while (r != null) {\n if (Bytes.equals(data2, r.getValue(fam, col))) {\n if (LOG.isTraceEnabled()) {\n LOG.trace(\"Modified :\" + Bytes.toString(r.getRow()));\n }\n modifiedrows++;\n }\n\n r = rs.next();\n }\n\n assertTrue(modifiedrows == 1, \"Expected 1 row modified, but \" + modifiedrows + \" are.\");\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public TSOState buildState() \n throws LoggerException { \n try{\n CountDownLatch latch = new CountDownLatch(1);\n \n this.zk = new ZooKeeper(config.getZkServers(), \n Integer.parseInt(System.getProperty(\"SESSIONTIMEOUT\", Integer.toString(10000))), \n new LoggerWatcher(latch));\n \n latch.await();\n } catch (Exception e) {\n LOG.error(\"Exception while starting zookeeper client\", e);\n this.zk = null;\n throw LoggerException.create(Code.ZKOPFAILED);\n }\n \n LOG.info(\"Creating bookkeeper client\");\n \n try{\n bk = new BookKeeper(new ClientConfiguration(), this.zk); \n } catch (Exception e) {\n LOG.error(\"Error while creating bookkeeper object\", e);\n return null;\n }\n \n \n /*\n * Create ZooKeeper lock\n */\n \n Context ctx = new Context();\n \n zk.create(LoggerConstants.OMID_LOCK_PATH, \n new byte[0], \n Ids.OPEN_ACL_UNSAFE, \n CreateMode.EPHEMERAL, \n new LockCreateCallback(),\n ctx);\n \n new BookKeeperStateLogger(zk).initialize(new LoggerInitCallback(){\n public void loggerInitComplete(int rc, StateLogger sl, Object ctx){ \n if(rc == Code.OK){\n if(LOG.isDebugEnabled()){\n LOG.debug(\"Logger is ok.\");\n }\n ((Context) ctx).setLogger(sl); \n } else {\n LOG.error(\"Error when initializing logger: \" + LoggerException.getMessage(rc));\n }\n }\n \n }, ctx);\n \n try{\n synchronized(ctx){\n while(!ctx.isReady()){\n ctx.wait();\n } \n }\n } catch (InterruptedException e) {\n LOG.error(\"Interrupted while waiting for state to build up.\", e);\n ctx.setState(null);\n }\n \n return ctx.state;\n } \n #location 41 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public TSOState buildState() \n throws LoggerException { \n try{\n CountDownLatch latch = new CountDownLatch(1);\n \n this.zk = new ZooKeeper(config.getZkServers(), \n Integer.parseInt(System.getProperty(\"SESSIONTIMEOUT\", Integer.toString(10000))), \n new LoggerWatcher(latch));\n \n latch.await();\n } catch (Exception e) {\n LOG.error(\"Exception while starting zookeeper client\", e);\n this.zk = null;\n throw LoggerException.create(Code.ZKOPFAILED);\n }\n \n LOG.info(\"Creating bookkeeper client\");\n \n try{\n bk = new BookKeeper(new ClientConfiguration(), this.zk); \n } catch (Exception e) {\n LOG.error(\"Error while creating bookkeeper object\", e);\n return null;\n }\n \n \n /*\n * Create ZooKeeper lock\n */\n \n Context ctx = new Context();\n ctx.config = this.config;\n \n zk.create(LoggerConstants.OMID_LOCK_PATH, \n new byte[0], \n Ids.OPEN_ACL_UNSAFE, \n CreateMode.EPHEMERAL, \n new LockCreateCallback(),\n ctx);\n \n new BookKeeperStateLogger(zk).initialize(new LoggerInitCallback(){\n public void loggerInitComplete(int rc, StateLogger sl, Object ctx){ \n if(rc == Code.OK){\n if(LOG.isDebugEnabled()){\n LOG.debug(\"Logger is ok.\");\n }\n ((Context) ctx).setLogger(sl); \n } else {\n LOG.error(\"Error when initializing logger: \" + LoggerException.getMessage(rc));\n }\n }\n \n }, ctx);\n \n try{\n synchronized(ctx){\n if(!ctx.isReady()){\n // TODO make configurable maximum waiting\n ctx.wait();\n } \n }\n } catch (InterruptedException e) {\n LOG.error(\"Interrupted while waiting for state to build up.\", e);\n ctx.setState(null);\n }\n \n return ctx.state;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public byte[] getChannelConfigurationBytes() throws TransactionException {\n try {\n final Block configBlock = getConfigBlock(getShuffledPeers());\n\n Envelope envelopeRet = Envelope.parseFrom(configBlock.getData().getData(0));\n\n Payload payload = Payload.parseFrom(envelopeRet.getPayload());\n\n ConfigEnvelope configEnvelope = ConfigEnvelope.parseFrom(payload.getData());\n return configEnvelope.getConfig().toByteArray();\n\n } catch (Exception e) {\n throw new TransactionException(e);\n }\n\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public byte[] getChannelConfigurationBytes() throws InvalidArgumentException, TransactionException {\n return getChannelConfigurationBytes(client.getUserContext());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private Channel reconstructChannel(String name, HFClient client, SampleOrg sampleOrg) throws Exception {\n out(\"Reconstructing %s channel\", name);\n\n client.setUserContext(sampleOrg.getPeerAdmin());\n\n Channel newChannel;\n\n if (BAR_CHANNEL_NAME.equals(name)) { // bar channel was stored in samplestore in End2endIT testcase.\n\n /**\n * sampleStore.getChannel uses {@link HFClient#deSerializeChannel(byte[])}\n */\n newChannel = sampleStore.getChannel(client, name);\n\n if (!IS_FABRIC_V10) {\n // Make sure there is one of each type peer at the very least. see End2end for how peers were constructed.\n assertFalse(newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).isEmpty());\n assertFalse(newChannel.getPeers(PeerRole.NO_EVENT_SOURCE).isEmpty());\n\n }\n assertEquals(2, newChannel.getEventHubs().size());\n out(\"Retrieved channel %s from sample store.\", name);\n\n } else {\n // foo channel do manual reconstruction.\n\n newChannel = client.newChannel(name);\n\n for (String ordererName : sampleOrg.getOrdererNames()) {\n newChannel.addOrderer(client.newOrderer(ordererName, sampleOrg.getOrdererLocation(ordererName),\n testConfig.getOrdererProperties(ordererName)));\n }\n\n boolean everyOther = false;\n\n for (String peerName : sampleOrg.getPeerNames()) {\n String peerLocation = sampleOrg.getPeerLocation(peerName);\n Properties peerProperties = testConfig.getPeerProperties(peerName);\n Peer peer = client.newPeer(peerName, peerLocation, peerProperties);\n final PeerOptions peerEventingOptions = // we have two peers on one use block on other use filtered\n everyOther ?\n createPeerOptions().registerEventsForBlocks() :\n createPeerOptions().registerEventsForFilteredBlocks();\n\n newChannel.addPeer(peer, IS_FABRIC_V10 ?\n createPeerOptions().setPeerRoles(PeerRole.NO_EVENT_SOURCE) : peerEventingOptions);\n\n everyOther = !everyOther;\n }\n\n //For testing mix it up. For v1.1 use just peer eventing service for foo channel.\n if (IS_FABRIC_V10) {\n //Should have no peers with event sources.\n assertTrue(newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).isEmpty());\n //Should have two peers with all roles but event source.\n assertEquals(2, newChannel.getPeers(PeerRole.NO_EVENT_SOURCE).size());\n for (String eventHubName : sampleOrg.getEventHubNames()) {\n EventHub eventHub = client.newEventHub(eventHubName, sampleOrg.getEventHubLocation(eventHubName),\n testConfig.getEventHubProperties(eventHubName));\n newChannel.addEventHub(eventHub);\n }\n } else {\n //Peers should have all roles. Do some sanity checks that they do.\n\n //Should have two peers with event sources.\n assertEquals(2, newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).size());\n //Check some other roles too..\n assertEquals(2, newChannel.getPeers(EnumSet.of(PeerRole.CHAINCODE_QUERY, PeerRole.LEDGER_QUERY)).size());\n assertEquals(2, newChannel.getPeers(PeerRole.ALL).size()); //really same as newChannel.getPeers()\n }\n\n assertEquals(IS_FABRIC_V10 ? sampleOrg.getEventHubNames().size() : 0, newChannel.getEventHubs().size());\n }\n\n //Just some sanity check tests\n assertTrue(newChannel == client.getChannel(name));\n assertTrue(client == TestUtils.getField(newChannel, \"client\"));\n assertEquals(name, newChannel.getName());\n assertEquals(2, newChannel.getPeers().size());\n assertEquals(1, newChannel.getOrderers().size());\n assertFalse(newChannel.isShutdown());\n assertFalse(newChannel.isInitialized());\n byte[] serializedChannelBytes = newChannel.serializeChannel();\n\n //Just checks if channel can be serialized and deserialized .. otherwise this is just a waste :)\n // Get channel back.\n\n newChannel.shutdown(true);\n newChannel = client.deSerializeChannel(serializedChannelBytes);\n\n assertEquals(2, newChannel.getPeers().size());\n\n assertEquals(1, newChannel.getOrderers().size());\n\n assertNotNull(client.getChannel(name));\n assertEquals(newChannel, client.getChannel(name));\n assertFalse(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n newChannel.initialize();\n assertTrue(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n\n //Begin tests with de-serialized channel.\n\n //Query the actual peer for which channels it belongs to and check it belongs to this channel\n for (Peer peer : newChannel.getPeers()) {\n Set channels = client.queryChannels(peer);\n if (!channels.contains(name)) {\n throw new AssertionError(format(\"Peer %s does not appear to belong to channel %s\", peer.getName(), name));\n }\n }\n\n //Just see if we can get channelConfiguration. Not required for the rest of scenario but should work.\n final byte[] channelConfigurationBytes = newChannel.getChannelConfigurationBytes();\n Configtx.Config channelConfig = Configtx.Config.parseFrom(channelConfigurationBytes);\n\n assertNotNull(channelConfig);\n\n Configtx.ConfigGroup channelGroup = channelConfig.getChannelGroup();\n\n assertNotNull(channelGroup);\n\n Map groupsMap = channelGroup.getGroupsMap();\n\n assertNotNull(groupsMap.get(\"Orderer\"));\n\n assertNotNull(groupsMap.get(\"Application\"));\n\n //Before return lets see if we have the chaincode on the peers that we expect from End2endIT\n //And if they were instantiated too.\n\n for (Peer peer : newChannel.getPeers()) {\n\n if (!checkInstalledChaincode(client, peer, CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_VERSION)) {\n throw new AssertionError(format(\"Peer %s is missing chaincode name: %s, path:%s, version: %s\",\n peer.getName(), CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_PATH));\n }\n\n if (!checkInstantiatedChaincode(newChannel, peer, CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_VERSION)) {\n\n throw new AssertionError(format(\"Peer %s is missing instantiated chaincode name: %s, path:%s, version: %s\",\n peer.getName(), CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_PATH));\n }\n\n }\n\n assertTrue(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n\n out(\"Finished reconstructing channel %s.\", name);\n\n return newChannel;\n } \n #location 21 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private Channel reconstructChannel(String name, HFClient client, SampleOrg sampleOrg) throws Exception {\n out(\"Reconstructing %s channel\", name);\n\n client.setUserContext(sampleOrg.getPeerAdmin());\n\n Channel newChannel;\n\n if (BAR_CHANNEL_NAME.equals(name)) { // bar channel was stored in samplestore in End2endIT testcase.\n\n /**\n * sampleStore.getChannel uses {@link HFClient#deSerializeChannel(byte[])}\n */\n newChannel = sampleStore.getChannel(client, name);\n\n if (!IS_FABRIC_V10) {\n // Make sure there is one of each type peer at the very least. see End2end for how peers were constructed.\n assertFalse(newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).isEmpty());\n assertFalse(newChannel.getPeers(PeerRole.NO_EVENT_SOURCE).isEmpty());\n\n }\n assertEquals(2, newChannel.getEventHubs().size());\n out(\"Retrieved channel %s from sample store.\", name);\n\n } else {\n // foo channel do manual reconstruction.\n\n Properties clientTLSProperties = new Properties();\n\n final String clientPEMTLSCertificate = sampleStore.getClientPEMTLSCertificate(sampleOrg);\n if (clientPEMTLSCertificate != null) {\n clientTLSProperties.put(\"clientCertBytes\", clientPEMTLSCertificate.getBytes(UTF_8));\n }\n final String clientPEMTLSKey = sampleStore.getClientPEMTLSKey(sampleOrg);\n\n if (clientPEMTLSKey != null) {\n clientTLSProperties.put(\"clientKeyBytes\", clientPEMTLSKey.getBytes(UTF_8));\n }\n\n newChannel = client.newChannel(name);\n\n for (String ordererName : sampleOrg.getOrdererNames()) {\n Properties ordererProperties = (Properties) clientTLSProperties.clone();\n ordererProperties.putAll(testConfig.getOrdererProperties(ordererName));\n newChannel.addOrderer(client.newOrderer(ordererName, sampleOrg.getOrdererLocation(ordererName),\n ordererProperties));\n }\n\n boolean everyOther = false;\n\n for (String peerName : sampleOrg.getPeerNames()) {\n String peerLocation = sampleOrg.getPeerLocation(peerName);\n Properties peerProperties = testConfig.getPeerProperties(peerName);\n peerProperties.putAll(clientTLSProperties);\n Peer peer = client.newPeer(peerName, peerLocation, peerProperties);\n final PeerOptions peerEventingOptions = // we have two peers on one use block on other use filtered\n everyOther ?\n createPeerOptions().registerEventsForBlocks() :\n createPeerOptions().registerEventsForFilteredBlocks();\n\n newChannel.addPeer(peer, IS_FABRIC_V10 ?\n createPeerOptions().setPeerRoles(PeerRole.NO_EVENT_SOURCE) : peerEventingOptions);\n\n everyOther = !everyOther;\n }\n\n //For testing mix it up. For v1.1 use just peer eventing service for foo channel.\n if (IS_FABRIC_V10) {\n //Should have no peers with event sources.\n assertTrue(newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).isEmpty());\n //Should have two peers with all roles but event source.\n assertEquals(2, newChannel.getPeers(PeerRole.NO_EVENT_SOURCE).size());\n for (String eventHubName : sampleOrg.getEventHubNames()) {\n Properties eventhubProperties = (Properties) clientTLSProperties.clone();\n eventhubProperties.putAll(testConfig.getEventHubProperties(eventHubName));\n EventHub eventHub = client.newEventHub(eventHubName, sampleOrg.getEventHubLocation(eventHubName),\n eventhubProperties);\n newChannel.addEventHub(eventHub);\n }\n } else {\n //Peers should have all roles. Do some sanity checks that they do.\n\n //Should have two peers with event sources.\n assertEquals(2, newChannel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).size());\n //Check some other roles too..\n assertEquals(2, newChannel.getPeers(EnumSet.of(PeerRole.CHAINCODE_QUERY, PeerRole.LEDGER_QUERY)).size());\n assertEquals(2, newChannel.getPeers(PeerRole.ALL).size()); //really same as newChannel.getPeers()\n }\n\n assertEquals(IS_FABRIC_V10 ? sampleOrg.getEventHubNames().size() : 0, newChannel.getEventHubs().size());\n }\n\n //Just some sanity check tests\n assertTrue(newChannel == client.getChannel(name));\n assertTrue(client == TestUtils.getField(newChannel, \"client\"));\n assertEquals(name, newChannel.getName());\n assertEquals(2, newChannel.getPeers().size());\n assertEquals(1, newChannel.getOrderers().size());\n assertFalse(newChannel.isShutdown());\n assertFalse(newChannel.isInitialized());\n byte[] serializedChannelBytes = newChannel.serializeChannel();\n\n //Just checks if channel can be serialized and deserialized .. otherwise this is just a waste :)\n // Get channel back.\n\n newChannel.shutdown(true);\n newChannel = client.deSerializeChannel(serializedChannelBytes);\n\n assertEquals(2, newChannel.getPeers().size());\n\n assertEquals(1, newChannel.getOrderers().size());\n\n assertNotNull(client.getChannel(name));\n assertEquals(newChannel, client.getChannel(name));\n assertFalse(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n newChannel.initialize();\n assertTrue(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n\n //Begin tests with de-serialized channel.\n\n //Query the actual peer for which channels it belongs to and check it belongs to this channel\n for (Peer peer : newChannel.getPeers()) {\n Set channels = client.queryChannels(peer);\n if (!channels.contains(name)) {\n throw new AssertionError(format(\"Peer %s does not appear to belong to channel %s\", peer.getName(), name));\n }\n }\n\n //Just see if we can get channelConfiguration. Not required for the rest of scenario but should work.\n final byte[] channelConfigurationBytes = newChannel.getChannelConfigurationBytes();\n Configtx.Config channelConfig = Configtx.Config.parseFrom(channelConfigurationBytes);\n\n assertNotNull(channelConfig);\n\n Configtx.ConfigGroup channelGroup = channelConfig.getChannelGroup();\n\n assertNotNull(channelGroup);\n\n Map groupsMap = channelGroup.getGroupsMap();\n\n assertNotNull(groupsMap.get(\"Orderer\"));\n\n assertNotNull(groupsMap.get(\"Application\"));\n\n //Before return lets see if we have the chaincode on the peers that we expect from End2endIT\n //And if they were instantiated too.\n\n for (Peer peer : newChannel.getPeers()) {\n\n if (!checkInstalledChaincode(client, peer, CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_VERSION)) {\n throw new AssertionError(format(\"Peer %s is missing chaincode name: %s, path:%s, version: %s\",\n peer.getName(), CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_PATH));\n }\n\n if (!checkInstantiatedChaincode(newChannel, peer, CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_VERSION)) {\n\n throw new AssertionError(format(\"Peer %s is missing instantiated chaincode name: %s, path:%s, version: %s\",\n peer.getName(), CHAIN_CODE_NAME, CHAIN_CODE_PATH, CHAIN_CODE_PATH));\n }\n\n }\n\n assertTrue(newChannel.isInitialized());\n assertFalse(newChannel.isShutdown());\n\n out(\"Finished reconstructing channel %s.\", name);\n\n return newChannel;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n ExecutorService getChannelExecutorService() {\n return executorService;\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n Enrollment getEnrollment() {\n return client.getUserContext().getEnrollment();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Ab.BroadcastResponse sendTransaction(Common.Envelope transaction) throws Exception {\n if (shutdown) {\n throw new TransactionException(format(\"Orderer %s was shutdown.\", name));\n }\n\n logger.debug(format(\"Order.sendTransaction name: %s, url: %s\", name, url));\n\n OrdererClient localOrdererClient = ordererClient;\n\n if (localOrdererClient == null || !localOrdererClient.isChannelActive()) {\n ordererClient = new OrdererClient(this, new Endpoint(url, properties).getChannelBuilder());\n localOrdererClient = ordererClient;\n }\n\n try {\n Ab.BroadcastResponse resp = localOrdererClient.sendTransaction(transaction);\n\n return resp;\n } catch (TransactionException e) { //For any error lets start with a fresh connection.\n ordererClient = null;\n throw e;\n } catch (Throwable t) {\n ordererClient = null;\n throw t;\n\n }\n\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n Orderer(String name, String url, Properties properties) throws InvalidArgumentException {\n\n if (StringUtil.isNullOrEmpty(name)) {\n throw new InvalidArgumentException(\"Invalid name for orderer\");\n }\n Exception e = checkGrpcUrl(url);\n if (e != null) {\n throw new InvalidArgumentException(e);\n }\n\n this.name = name;\n this.url = url;\n this.properties = properties == null ? null : (Properties) properties.clone(); //keep our own copy.\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n ListenableFuture sendProposalAsync(FabricProposal.SignedProposal proposal)\n throws PeerException, InvalidArgumentException {\n checkSendProposal(proposal);\n\n logger.debug(format(\"peer.sendProposalAsync name:%s, url: %s\", name, url));\n\n return endorserClent.sendProposalAsync(proposal);\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n Peer(String name, String grpcURL, Properties properties) throws InvalidArgumentException {\n\n Exception e = checkGrpcUrl(grpcURL);\n if (e != null) {\n throw new InvalidArgumentException(\"Bad peer url.\", e);\n\n }\n\n if (StringUtil.isNullOrEmpty(name)) {\n throw new InvalidArgumentException(\"Invalid name for peer\");\n }\n\n this.url = grpcURL;\n this.name = name;\n this.properties = properties == null ? null : (Properties) properties.clone(); //keep our own copy.\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public byte[] getChannelConfigurationBytes() throws TransactionException {\n try {\n final Block configBlock = getConfigurationBlock();\n\n Envelope envelopeRet = Envelope.parseFrom(configBlock.getData().getData(0));\n\n Payload payload = Payload.parseFrom(envelopeRet.getPayload());\n\n ConfigEnvelope configEnvelope = ConfigEnvelope.parseFrom(payload.getData());\n return configEnvelope.getConfig().toByteArray();\n\n } catch (Exception e) {\n throw new TransactionException(e);\n }\n\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public byte[] getChannelConfigurationBytes() throws TransactionException {\n try {\n final Block configBlock = getConfigBlock(getRandomPeer());\n\n Envelope envelopeRet = Envelope.parseFrom(configBlock.getData().getData(0));\n\n Payload payload = Payload.parseFrom(envelopeRet.getPayload());\n\n ConfigEnvelope configEnvelope = ConfigEnvelope.parseFrom(payload.getData());\n return configEnvelope.getConfig().toByteArray();\n\n } catch (Exception e) {\n throw new TransactionException(e);\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testValidateInvalidCertificate() throws IOException, CertificateException {\n BufferedInputStream pem = new BufferedInputStream(new ByteArrayInputStream(invalidPemCert));\n\n assertFalse(crypto.validateCertificate(invalidPemCert));\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testValidateInvalidCertificate() throws IOException, CertificateException {\n assertFalse(crypto.validateCertificate(invalidPemCert));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void parseConfigBlock() throws TransactionException {\n\n try {\n\n final Block configBlock = getConfigurationBlock();\n\n logger.debug(format(\"Channel %s Got config block getting MSP data and anchorPeers data\", name));\n\n Envelope envelope = Envelope.parseFrom(configBlock.getData().getData(0));\n Payload payload = Payload.parseFrom(envelope.getPayload());\n ConfigEnvelope configEnvelope = ConfigEnvelope.parseFrom(payload.getData());\n ConfigGroup channelGroup = configEnvelope.getConfig().getChannelGroup();\n Map newMSPS = traverseConfigGroupsMSP(\"\", channelGroup, new HashMap<>(20));\n\n msps = Collections.unmodifiableMap(newMSPS);\n\n// anchorPeers = Collections.unmodifiableSet(traverseConfigGroupsAnchors(\"\", channelGroup, new HashSet<>()));\n\n } catch (TransactionException e) {\n logger.error(e.getMessage(), e);\n throw e;\n } catch (Exception e) {\n logger.error(e.getMessage(), e);\n throw new TransactionException(e);\n }\n\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void parseConfigBlock() throws TransactionException {\n\n try {\n\n Block parseFrom = getConfigBlock(getRandomPeer());\n\n // final Block configBlock = getConfigurationBlock();\n\n logger.debug(format(\"Channel %s Got config block getting MSP data and anchorPeers data\", name));\n\n Envelope envelope = Envelope.parseFrom(parseFrom.getData().getData(0));\n Payload payload = Payload.parseFrom(envelope.getPayload());\n ConfigEnvelope configEnvelope = ConfigEnvelope.parseFrom(payload.getData());\n ConfigGroup channelGroup = configEnvelope.getConfig().getChannelGroup();\n Map newMSPS = traverseConfigGroupsMSP(\"\", channelGroup, new HashMap<>(20));\n\n msps = Collections.unmodifiableMap(newMSPS);\n\n// anchorPeers = Collections.unmodifiableSet(traverseConfigGroupsAnchors(\"\", channelGroup, new HashSet<>()));\n\n } catch (Exception e) {\n logger.error(e.getMessage(), e);\n throw new TransactionException(e);\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void initiateEventing(TransactionContext transactionContext, PeerOptions peersOptions) throws TransactionException {\n\n this.transactionContext = transactionContext.retryTransactionSameContext();\n\n if (peerEventingClient == null) {\n\n //PeerEventServiceClient(Peer peer, ManagedChannelBuilder channelBuilder, Properties properties)\n // peerEventingClient = new PeerEventServiceClient(this, new HashSet(Arrays.asList(new Channel[] {channel})));\n\n peerEventingClient = new PeerEventServiceClient(this, Endpoint.createEndpoint(url, properties), properties, peersOptions);\n\n peerEventingClient.connect(transactionContext);\n\n }\n\n } \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n boolean hasConnected() {\n return connected;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n synchronized boolean connect(final TransactionContext transactionContext) throws EventHubException {\n if (connected) {\n logger.warn(format(\"%s already connected.\", toString()));\n return true;\n }\n eventStream = null;\n\n final CountDownLatch finishLatch = new CountDownLatch(1);\n\n logger.debug(format(\"EventHub %s is connecting.\", name));\n\n lastConnectedAttempt = System.currentTimeMillis();\n\n managedChannel = new Endpoint(url, properties).getChannelBuilder().build();\n\n events = EventsGrpc.newStub(managedChannel);\n\n final ArrayList threw = new ArrayList<>();\n\n final StreamObserver eventStreamLocal = new StreamObserver() {\n @Override\n public void onNext(PeerEvents.Event event) {\n\n logger.debug(format(\"EventHub %s got event type: %s\", EventHub.this.name, event.getEventCase().name()));\n\n if (event.getEventCase() == PeerEvents.Event.EventCase.BLOCK) {\n try {\n eventQue.addBEvent(new BlockEvent(EventHub.this, event)); //add to channel queue\n } catch (InvalidProtocolBufferException e) {\n EventHubException eventHubException = new EventHubException(format(\"%s onNext error %s\", this, e.getMessage()), e);\n logger.error(eventHubException.getMessage());\n threw.add(eventHubException);\n }\n } else if (event.getEventCase() == PeerEvents.Event.EventCase.REGISTER) {\n\n connected = true;\n connectedTime = System.currentTimeMillis();\n finishLatch.countDown();\n }\n }\n\n @Override\n public void onError(Throwable t) {\n if (shutdown) { //IF we're shutdown don't try anything more.\n logger.trace(format(\"%s was shutdown.\", EventHub.this.toString()));\n connected = false;\n eventStream = null;\n finishLatch.countDown();\n return;\n }\n\n final boolean isTerminated = managedChannel.isTerminated();\n final boolean isChannelShutdown = managedChannel.isShutdown();\n\n logger.error(format(\"%s terminated is %b shutdown is %b has error %s \", EventHub.this.toString(), isTerminated, isChannelShutdown,\n t.getMessage()), new EventHubException(t));\n threw.add(t);\n finishLatch.countDown();\n\n // logger.error(\"Error in stream: \" + t.getMessage(), new EventHubException(t));\n if (t instanceof StatusRuntimeException) {\n StatusRuntimeException sre = (StatusRuntimeException) t;\n Status sreStatus = sre.getStatus();\n logger.error(format(\"%s :StatusRuntimeException Status %s. Description %s \", EventHub.this, sreStatus + \"\", sreStatus.getDescription()));\n if (sre.getStatus().getCode() == Status.Code.INTERNAL || sre.getStatus().getCode() == Status.Code.UNAVAILABLE) {\n\n connected = false;\n eventStream = null;\n disconnectedTime = System.currentTimeMillis();\n try {\n if (!isChannelShutdown) {\n managedChannel.shutdownNow();\n }\n if (null != disconnectedHandler) {\n try {\n disconnectedHandler.disconnected(EventHub.this);\n } catch (Exception e) {\n logger.warn(format(\"Eventhub %s %s\", EventHub.this.name, e.getMessage()), e);\n eventQue.eventError(e);\n }\n }\n } catch (Exception e) {\n logger.warn(format(\"Eventhub %s Failed shutdown msg: %s\", EventHub.this.name, e.getMessage()), e);\n }\n }\n }\n\n }\n\n @Override\n public void onCompleted() {\n\n logger.warn(format(\"Stream completed %s\", EventHub.this.toString()));\n finishLatch.countDown();\n\n }\n };\n\n sender = events.chat(eventStreamLocal);\n try {\n blockListen(transactionContext);\n } catch (CryptoException e) {\n throw new EventHubException(e);\n }\n\n try {\n if (!finishLatch.await(EVENTHUB_CONNECTION_WAIT_TIME, TimeUnit.MILLISECONDS)) {\n EventHubException evh = new EventHubException(format(\"EventHub %s failed to connect in %s ms.\", name, EVENTHUB_CONNECTION_WAIT_TIME));\n logger.debug(evh.getMessage(), evh);\n\n throw evh;\n }\n logger.trace(format(\"Eventhub %s Done waiting for reply!\", name));\n\n } catch (InterruptedException e) {\n logger.error(e);\n }\n\n if (!threw.isEmpty()) {\n eventStream = null;\n connected = false;\n Throwable t = threw.iterator().next();\n\n EventHubException evh = new EventHubException(t.getMessage(), t);\n logger.error(format(\"EventHub %s Error in stream. error: \" + t.getMessage(), toString()), evh);\n throw evh;\n\n }\n\n logger.debug(format(\"Eventhub %s connect is done with connect status: %b \", name, connected));\n\n if (connected) {\n eventStream = eventStreamLocal;\n }\n\n return connected;\n\n } \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n synchronized boolean connect(final TransactionContext transactionContext) throws EventHubException {\n if (connected) {\n logger.warn(format(\"%s already connected.\", toString()));\n return true;\n }\n eventStream = null;\n\n final CountDownLatch finishLatch = new CountDownLatch(1);\n\n logger.debug(format(\"EventHub %s is connecting.\", name));\n\n lastConnectedAttempt = System.currentTimeMillis();\n\n Endpoint endpoint = new Endpoint(url, properties);\n managedChannel = endpoint.getChannelBuilder().build();\n\n clientTLSCertificateDigest = endpoint.getClientTLSCertificateDigest();\n\n events = EventsGrpc.newStub(managedChannel);\n\n final ArrayList threw = new ArrayList<>();\n\n final StreamObserver eventStreamLocal = new StreamObserver() {\n @Override\n public void onNext(PeerEvents.Event event) {\n\n logger.debug(format(\"EventHub %s got event type: %s\", EventHub.this.name, event.getEventCase().name()));\n\n if (event.getEventCase() == PeerEvents.Event.EventCase.BLOCK) {\n try {\n eventQue.addBEvent(new BlockEvent(EventHub.this, event)); //add to channel queue\n } catch (InvalidProtocolBufferException e) {\n EventHubException eventHubException = new EventHubException(format(\"%s onNext error %s\", this, e.getMessage()), e);\n logger.error(eventHubException.getMessage());\n threw.add(eventHubException);\n }\n } else if (event.getEventCase() == PeerEvents.Event.EventCase.REGISTER) {\n\n connected = true;\n connectedTime = System.currentTimeMillis();\n finishLatch.countDown();\n }\n }\n\n @Override\n public void onError(Throwable t) {\n if (shutdown) { //IF we're shutdown don't try anything more.\n logger.trace(format(\"%s was shutdown.\", EventHub.this.toString()));\n connected = false;\n eventStream = null;\n finishLatch.countDown();\n return;\n }\n\n final boolean isTerminated = managedChannel.isTerminated();\n final boolean isChannelShutdown = managedChannel.isShutdown();\n\n logger.error(format(\"%s terminated is %b shutdown is %b has error %s \", EventHub.this.toString(), isTerminated, isChannelShutdown,\n t.getMessage()), new EventHubException(t));\n threw.add(t);\n finishLatch.countDown();\n\n // logger.error(\"Error in stream: \" + t.getMessage(), new EventHubException(t));\n if (t instanceof StatusRuntimeException) {\n StatusRuntimeException sre = (StatusRuntimeException) t;\n Status sreStatus = sre.getStatus();\n logger.error(format(\"%s :StatusRuntimeException Status %s. Description %s \", EventHub.this, sreStatus + \"\", sreStatus.getDescription()));\n if (sre.getStatus().getCode() == Status.Code.INTERNAL || sre.getStatus().getCode() == Status.Code.UNAVAILABLE) {\n\n connected = false;\n eventStream = null;\n disconnectedTime = System.currentTimeMillis();\n try {\n if (!isChannelShutdown) {\n managedChannel.shutdownNow();\n }\n if (null != disconnectedHandler) {\n try {\n disconnectedHandler.disconnected(EventHub.this);\n } catch (Exception e) {\n logger.warn(format(\"Eventhub %s %s\", EventHub.this.name, e.getMessage()), e);\n eventQue.eventError(e);\n }\n }\n } catch (Exception e) {\n logger.warn(format(\"Eventhub %s Failed shutdown msg: %s\", EventHub.this.name, e.getMessage()), e);\n }\n }\n }\n\n }\n\n @Override\n public void onCompleted() {\n\n logger.warn(format(\"Stream completed %s\", EventHub.this.toString()));\n finishLatch.countDown();\n\n }\n };\n\n sender = events.chat(eventStreamLocal);\n try {\n blockListen(transactionContext);\n } catch (CryptoException e) {\n throw new EventHubException(e);\n }\n\n try {\n if (!finishLatch.await(EVENTHUB_CONNECTION_WAIT_TIME, TimeUnit.MILLISECONDS)) {\n EventHubException evh = new EventHubException(format(\"EventHub %s failed to connect in %s ms.\", name, EVENTHUB_CONNECTION_WAIT_TIME));\n logger.debug(evh.getMessage(), evh);\n\n throw evh;\n }\n logger.trace(format(\"Eventhub %s Done waiting for reply!\", name));\n\n } catch (InterruptedException e) {\n logger.error(e);\n }\n\n if (!threw.isEmpty()) {\n eventStream = null;\n connected = false;\n Throwable t = threw.iterator().next();\n\n EventHubException evh = new EventHubException(t.getMessage(), t);\n logger.error(format(\"EventHub %s Error in stream. error: \" + t.getMessage(), toString()), evh);\n throw evh;\n\n }\n\n logger.debug(format(\"Eventhub %s connect is done with connect status: %b \", name, connected));\n\n if (connected) {\n eventStream = eventStreamLocal;\n }\n\n return connected;\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void peerVent(TransactionContext transactionContext) throws TransactionException {\n logger.trace(toString() + \"peerVent transaction: \" + transactionContext);\n\n final Envelope envelope;\n try {\n\n Ab.SeekPosition.Builder start = Ab.SeekPosition.newBuilder();\n if (null != peerOptions.getNewest()) {\n start.setNewest(Ab.SeekNewest.getDefaultInstance());\n } else if (peerOptions.getStartEvents() != null) {\n start.setSpecified(Ab.SeekSpecified.newBuilder().setNumber(peerOptions.getStartEvents()));\n } else {\n start.setNewest(Ab.SeekNewest.getDefaultInstance());\n }\n\n envelope = createSeekInfoEnvelope(transactionContext,\n start.build(),\n Ab.SeekPosition.newBuilder()\n .setSpecified(Ab.SeekSpecified.newBuilder().setNumber(peerOptions.getStopEvents()).build())\n .build(),\n SeekInfo.SeekBehavior.BLOCK_UNTIL_READY,\n\n clientTLSCertificateDigest);\n connectEnvelope(envelope);\n } catch (Exception e) {\n throw new TransactionException(toString() + \" error message: \" + e.getMessage(), e);\n }\n\n } \n #location 24 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n PeerEventServiceClient(Peer peer, Endpoint endpoint, Properties properties, PeerOptions peerOptions) {\n\n this.channelBuilder = endpoint.getChannelBuilder();\n this.filterBlock = peerOptions.isRegisterEventsForFilteredBlocks();\n this.peer = peer;\n this.peerOptions = peerOptions;\n name = peer.getName();\n url = peer.getUrl();\n\n if (peer.isShutdown()) {\n logger.debug(\"PeerEventServiceClient not starting peer has shutdown.\");\n shutdown = true;\n toString = \"PeerEventServiceClient{\" + \"id: \" + config.getNextID() + \", channel: null\" + \", peerName: \" + name + \", url: \" + url + \"}\";\n return;\n }\n final Channel channel = peer.getChannel();\n if (channel == null) {\n logger.debug(\"Peer no longer associated with a channel not connecting.\");\n shutdown = true;\n toString = \"PeerEventServiceClient{\" + \"id: \" + config.getNextID() + \", channel: null\" + \", peerName: \" + name + \", url: \" + url + \"}\";\n return;\n }\n\n channelName = channel.getName();\n toString = \"PeerEventServiceClient{\" + \"id: \" + config.getNextID() + \", channel: \" + channelName + \", peerName: \" + name + \", url: \" + url + \"}\";\n\n clientTLSCertificateDigest = endpoint.getClientTLSCertificateDigest();\n\n this.channelEventQue = channel.getChannelEventQue();\n\n if (null == properties) {\n\n peerEventRegistrationWaitTimeMilliSecs = PEER_EVENT_REGISTRATION_WAIT_TIME;\n\n } else {\n\n String peerEventRegistrationWaitTime = properties.getProperty(\"peerEventRegistrationWaitTime\", Long.toString(PEER_EVENT_REGISTRATION_WAIT_TIME));\n\n long tempPeerWaitTimeMilliSecs = PEER_EVENT_REGISTRATION_WAIT_TIME;\n\n try {\n tempPeerWaitTimeMilliSecs = Long.parseLong(peerEventRegistrationWaitTime);\n } catch (NumberFormatException e) {\n logger.warn(format(\"Peer event service registration %s wait time %s not parsable.\", toString, peerEventRegistrationWaitTime), e);\n }\n\n peerEventRegistrationWaitTimeMilliSecs = tempPeerWaitTimeMilliSecs;\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void setTLSCertificateKeyPair(TLSCertificateKeyPair tlsCertificateKeyPair) {\n properties.put(\"clientKeyBytes\", tlsCertificateKeyPair.getKeyPemBytes());\n properties.put(\"clientCertBytes\", tlsCertificateKeyPair.getCertPEMBytes());\n\n Endpoint endpoint = Endpoint.createEndpoint(url, properties);\n foundClientTLSCertificateDigest = true;\n clientTLSCertificateDigest = endpoint.getClientTLSCertificateDigest();\n endorserClent = new EndorserClient(endpoint.getChannelBuilder());\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n boolean hasConnected() {\n return connected;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n DeliverResponse[] sendDeliver(Common.Envelope transaction) throws TransactionException {\n\n if (shutdown) {\n throw new TransactionException(format(\"Orderer %s was shutdown.\", name));\n }\n\n OrdererClient localOrdererClient = ordererClient;\n\n logger.debug(format(\"Order.sendDeliver name: %s, url: %s\", name, url));\n if (localOrdererClient == null || !localOrdererClient.isChannelActive()) {\n localOrdererClient = new OrdererClient(this, new Endpoint(url, properties).getChannelBuilder());\n ordererClient = localOrdererClient;\n }\n\n try {\n\n return localOrdererClient.sendDeliver(transaction);\n } catch (Throwable t) {\n ordererClient = null;\n throw t;\n\n }\n\n } \n #location 17 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n Orderer(String name, String url, Properties properties) throws InvalidArgumentException {\n\n if (StringUtil.isNullOrEmpty(name)) {\n throw new InvalidArgumentException(\"Invalid name for orderer\");\n }\n Exception e = checkGrpcUrl(url);\n if (e != null) {\n throw new InvalidArgumentException(e);\n }\n\n this.name = name;\n this.url = url;\n this.properties = properties == null ? null : (Properties) properties.clone(); //keep our own copy.\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void updateChannelConfiguration(UpdateChannelConfiguration updateChannelConfiguration, Orderer orderer, byte[]... signers) throws TransactionException, InvalidArgumentException {\n\n checkChannelState();\n\n checkOrderer(orderer);\n\n try {\n final long startLastConfigIndex = getLastConfigIndex(orderer);\n logger.trace(format(\"startLastConfigIndex: %d. Channel config wait time is: %d\",\n startLastConfigIndex, CHANNEL_CONFIG_WAIT_TIME));\n\n sendUpdateChannel(updateChannelConfiguration.getUpdateChannelConfigurationAsBytes(), signers, orderer);\n\n long currentLastConfigIndex = -1;\n final long nanoTimeStart = System.nanoTime();\n\n //Try to wait to see the channel got updated but don't fail if we don't see it.\n do {\n currentLastConfigIndex = getLastConfigIndex(orderer);\n if (currentLastConfigIndex == startLastConfigIndex) {\n\n final long duration = TimeUnit.MILLISECONDS.convert(System.nanoTime() - nanoTimeStart, TimeUnit.NANOSECONDS);\n\n if (duration > CHANNEL_CONFIG_WAIT_TIME) {\n logger.warn(format(\"Channel %s did not get updated last config after %d ms, Config wait time: %d ms. startLastConfigIndex: %d, currentLastConfigIndex: %d \",\n name, duration, CHANNEL_CONFIG_WAIT_TIME, startLastConfigIndex, currentLastConfigIndex));\n //waited long enough ..\n currentLastConfigIndex = startLastConfigIndex - 1L; // just bail don't throw exception.\n } else {\n\n try {\n Thread.sleep(ORDERER_RETRY_WAIT_TIME); //try again sleep\n } catch (InterruptedException e) {\n TransactionException te = new TransactionException(\"update channel thread Sleep\", e);\n logger.warn(te.getMessage(), te);\n }\n }\n\n }\n\n logger.trace(format(\"currentLastConfigIndex: %d\", currentLastConfigIndex));\n\n } while (currentLastConfigIndex == startLastConfigIndex);\n\n } catch (TransactionException e) {\n\n logger.error(format(\"Channel %s error: %s\", name, e.getMessage()), e);\n throw e;\n } catch (Exception e) {\n String msg = format(\"Channel %s error: %s\", name, e.getMessage());\n\n logger.error(msg, e);\n throw new TransactionException(msg, e);\n }\n\n } \n #location 12 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void updateChannelConfiguration(UpdateChannelConfiguration updateChannelConfiguration, Orderer orderer, byte[]... signers) throws TransactionException, InvalidArgumentException {\n updateChannelConfiguration(client.getUserContext(), updateChannelConfiguration, orderer, signers);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testGetInfo() throws Exception {\n\n if (testConfig.isRunningAgainstFabric10()) {\n HFCAInfo info = client.info();\n assertNull(info.getVersion());\n }\n\n if (!testConfig.isRunningAgainstFabric10()) {\n HFCAInfo info = client.info();\n assertTrue(info.getVersion().contains(\"1.1.0\"));\n }\n\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testGetInfo() throws Exception {\n\n if (testConfig.isRunningAgainstFabric10()) {\n HFCAInfo info = client.info();\n assertNull(info.getVersion());\n }\n\n if (!testConfig.isRunningAgainstFabric10()) {\n HFCAInfo info = client.info();\n assertNotNull(\"client.info returned null.\", info);\n String version = info.getVersion();\n assertNotNull(\"client.info.getVersion returned null.\", version);\n assertTrue(format(\"Version '%s' didn't match expected pattern\", version), version.matches(\"^\\\\d+\\\\.\\\\d+\\\\.\\\\d+($|-.*)\"));\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void connectEnvelope(Envelope envelope) throws TransactionException {\n\n if (shutdown) {\n logger.warn(format(\"Peer %s not connecting is shutdown \", peer));\n return;\n }\n\n ManagedChannel lmanagedChannel = managedChannel;\n\n if (lmanagedChannel == null || lmanagedChannel.isTerminated() || lmanagedChannel.isShutdown()) {\n\n lmanagedChannel = channelBuilder.build();\n managedChannel = lmanagedChannel;\n\n }\n\n try {\n\n DeliverGrpc.DeliverStub broadcast = DeliverGrpc.newStub(lmanagedChannel);\n\n // final DeliverResponse[] ret = new DeliverResponse[1];\n // final List retList = new ArrayList<>();\n final List throwableList = new ArrayList<>();\n final CountDownLatch finishLatch = new CountDownLatch(1);\n\n so = new StreamObserver() {\n\n @Override\n public void onNext(DeliverResponse resp) {\n\n // logger.info(\"Got Broadcast response: \" + resp);\n logger.trace(format(\"DeliverResponse channel %s peer %s resp status value:%d status %s, typecase %s \",\n channelName, peer.getName(), resp.getStatusValue(), resp.getStatus(), resp.getTypeCase()));\n\n final DeliverResponse.TypeCase typeCase = resp.getTypeCase();\n\n if (typeCase == STATUS) {\n\n logger.debug(format(\"DeliverResponse channel %s peer %s setting done.\",\n channelName, peer.getName()));\n\n if (resp.getStatus() == Common.Status.SUCCESS) { // unlike you may think this only happens when all blocks are fetched.\n peer.setLastConnectTime(System.currentTimeMillis());\n peer.resetReconnectCount();\n } else {\n\n throwableList.add(new TransactionException(format(\"Channel %s peer %s Status returned failure code %d (%s) during peer service event registration\",\n channelName, peer.getName(), resp.getStatusValue(), resp.getStatus().name())));\n }\n\n } else if (typeCase == FILTERED_BLOCK || typeCase == BLOCK) {\n if (typeCase == BLOCK) {\n logger.trace(format(\"Channel %s peer %s got event block hex hashcode: %016x, block number: %d\",\n channelName, peer.getName(), resp.getBlock().hashCode(), resp.getBlock().getHeader().getNumber()));\n } else {\n logger.trace(format(\"Channel %s peer %s got event block hex hashcode: %016x, block number: %d\",\n channelName, peer.getName(), resp.getFilteredBlock().hashCode(), resp.getFilteredBlock().getNumber()));\n }\n\n peer.setLastConnectTime(System.currentTimeMillis());\n long reconnectCount = peer.getReconnectCount();\n if (reconnectCount > 1) {\n\n logger.info(format(\"Peer eventing service reconnected after %d attempts on channel %s, peer %s, url %s\",\n reconnectCount, channelName, name, url));\n\n }\n peer.resetReconnectCount();\n\n BlockEvent blockEvent = new BlockEvent(peer, resp);\n peer.setLastBlockSeen(blockEvent);\n\n channelEventQue.addBEvent(blockEvent);\n } else {\n logger.error(format(\"Channel %s peer %s got event block with unknown type: %s, %d\",\n channelName, peer.getName(), typeCase.name(), typeCase.getNumber()));\n\n throwableList.add(new TransactionException(format(\"Channel %s peer %s Status got unknown type %s, %d\",\n channelName, peer.getName(), typeCase.name(), typeCase.getNumber())));\n\n }\n finishLatch.countDown();\n\n }\n\n @Override\n public void onError(Throwable t) {\n ManagedChannel llmanagedChannel = managedChannel;\n if (llmanagedChannel != null) {\n llmanagedChannel.shutdownNow();\n managedChannel = null;\n }\n if (!shutdown) {\n final long reconnectCount = peer.getReconnectCount();\n if (PEER_EVENT_RECONNECTION_WARNING_RATE > 1 && reconnectCount % PEER_EVENT_RECONNECTION_WARNING_RATE == 1) {\n logger.warn(format(\"Received error on peer eventing service on channel %s, peer %s, url %s, attempts %d. %s\",\n channelName, name, url, reconnectCount, t.getMessage()));\n\n } else {\n logger.trace(format(\"Received error on peer eventing service on channel %s, peer %s, url %s, attempts %d. %s\",\n channelName, name, url, reconnectCount, t.getMessage()));\n\n }\n\n peer.reconnectPeerEventServiceClient(PeerEventServiceClient.this, t);\n\n }\n finishLatch.countDown();\n }\n\n @Override\n public void onCompleted() {\n logger.debug(format(\"DeliverResponse onCompleted channel %s peer %s setting done.\",\n channelName, peer.getName()));\n // done = true;\n //There should have been a done before this...\n finishLatch.countDown();\n }\n };\n\n nso = filterBlock ? broadcast.deliverFiltered(so) : broadcast.deliver(so);\n\n nso.onNext(envelope);\n\n // try {\n if (!finishLatch.await(peerEventRegistrationWaitTimeMilliSecs, TimeUnit.MILLISECONDS)) {\n TransactionException ex = new TransactionException(format(\n \"Channel %s connect time exceeded for peer eventing service %s, timed out at %d ms.\", channelName, name, peerEventRegistrationWaitTimeMilliSecs));\n throwableList.add(0, ex);\n\n }\n logger.trace(\"Done waiting for reply!\");\n\n if (!throwableList.isEmpty()) {\n ManagedChannel llmanagedChannel = managedChannel;\n if (llmanagedChannel != null) {\n llmanagedChannel.shutdownNow();\n managedChannel = null;\n }\n Throwable throwable = throwableList.get(0);\n peer.reconnectPeerEventServiceClient(this, throwable);\n\n }\n\n } catch (InterruptedException e) {\n ManagedChannel llmanagedChannel = managedChannel;\n if (llmanagedChannel != null) {\n llmanagedChannel.shutdownNow();\n managedChannel = null;\n }\n logger.error(e); // not likely\n\n peer.reconnectPeerEventServiceClient(this, e);\n\n } finally {\n if (null != nso) {\n\n try {\n nso.onCompleted();\n } catch (Exception e) { //Best effort only report on debug\n logger.debug(format(\"Exception completing connect with channel %s, name %s, url %s %s\",\n channelName, name, url, e.getMessage()), e);\n }\n\n }\n }\n } \n #location 141 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n PeerEventServiceClient(Peer peer, Endpoint endpoint, Properties properties, PeerOptions peerOptions) {\n\n this.channelBuilder = endpoint.getChannelBuilder();\n this.filterBlock = peerOptions.isRegisterEventsForFilteredBlocks();\n this.peer = peer;\n name = peer.getName();\n url = peer.getUrl();\n channelName = peer.getChannel().getName();\n this.peerOptions = peerOptions;\n clientTLSCertificateDigest = endpoint.getClientTLSCertificateDigest();\n\n this.channelEventQue = peer.getChannel().getChannelEventQue();\n\n if (null == properties) {\n\n peerEventRegistrationWaitTimeMilliSecs = PEER_EVENT_REGISTRATION_WAIT_TIME;\n\n } else {\n\n String peerEventRegistrationWaitTime = properties.getProperty(\"peerEventRegistrationWaitTime\", Long.toString(PEER_EVENT_REGISTRATION_WAIT_TIME));\n\n long tempPeerWaitTimeMilliSecs = PEER_EVENT_REGISTRATION_WAIT_TIME;\n\n try {\n tempPeerWaitTimeMilliSecs = Long.parseLong(peerEventRegistrationWaitTime);\n } catch (NumberFormatException e) {\n logger.warn(format(\"Peer event service registration %s wait time %s not parsable.\", name, peerEventRegistrationWaitTime), e);\n }\n\n peerEventRegistrationWaitTimeMilliSecs = tempPeerWaitTimeMilliSecs;\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n TBSCertList.CRLEntry[] parseCRL(String crl) throws Exception {\n\n Base64.Decoder b64dec = Base64.getDecoder();\n final byte[] decode = b64dec.decode(crl.getBytes(UTF_8));\n\n ByteArrayInputStream inStream = new ByteArrayInputStream(decode);\n ASN1InputStream asnInputStream = new ASN1InputStream(inStream);\n\n return CertificateList.getInstance(asnInputStream.readObject()).getRevokedCertificates();\n } \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n TBSCertList.CRLEntry[] getRevokes(Date r) throws Exception {\n\n String crl = client.generateCRL(admin, r, null, null, null);\n\n return parseCRL(crl);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n DeliverResponse[] sendDeliver(Common.Envelope transaction) throws TransactionException {\n\n if (shutdown) {\n throw new TransactionException(format(\"Orderer %s was shutdown.\", name));\n }\n\n OrdererClient localOrdererClient = ordererClient;\n\n logger.debug(format(\"Order.sendDeliver name: %s, url: %s\", name, url));\n if (localOrdererClient == null || !localOrdererClient.isChannelActive()) {\n localOrdererClient = new OrdererClient(this, new Endpoint(url, properties).getChannelBuilder());\n ordererClient = localOrdererClient;\n }\n\n try {\n DeliverResponse[] response = localOrdererClient.sendDeliver(transaction);\n\n return response;\n } catch (TransactionException e) { //For any error lets start with a fresh connection.\n ordererClient = null;\n throw e;\n } catch (Throwable t) {\n ordererClient = null;\n throw t;\n\n }\n\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n Orderer(String name, String url, Properties properties) throws InvalidArgumentException {\n\n if (StringUtil.isNullOrEmpty(name)) {\n throw new InvalidArgumentException(\"Invalid name for orderer\");\n }\n Exception e = checkGrpcUrl(url);\n if (e != null) {\n throw new InvalidArgumentException(e);\n }\n\n this.name = name;\n this.url = url;\n this.properties = properties == null ? null : (Properties) properties.clone(); //keep our own copy.\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void updateChannelConfiguration(UpdateChannelConfiguration updateChannelConfiguration, byte[]... signers) throws TransactionException, InvalidArgumentException {\n\n updateChannelConfiguration(updateChannelConfiguration, getRandomOrderer(), signers);\n\n } \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void updateChannelConfiguration(UpdateChannelConfiguration updateChannelConfiguration, byte[]... signers) throws TransactionException, InvalidArgumentException {\n\n updateChannelConfiguration(client.getUserContext(), updateChannelConfiguration, getRandomOrderer(), signers);\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void setTLSCertificateKeyPair(TLSCertificateKeyPair tlsCertificateKeyPair) {\n properties.put(\"clientKeyBytes\", tlsCertificateKeyPair.getKeyPemBytes());\n properties.put(\"clientCertBytes\", tlsCertificateKeyPair.getCertPEMBytes());\n\n Endpoint endpoint = Endpoint.createEndpoint(url, properties);\n foundClientTLSCertificateDigest = true;\n clientTLSCertificateDigest = endpoint.getClientTLSCertificateDigest();\n endorserClent = new EndorserClient(endpoint.getChannelBuilder());\n } \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n boolean hasConnected() {\n return connected;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n TBSCertList.CRLEntry[] getRevokes(Date r) throws Exception {\n\n String crl = client.generateCRL(admin, r, null, null, null);\n\n Base64.Decoder b64dec = Base64.getDecoder();\n final byte[] decode = b64dec.decode(crl.getBytes(UTF_8));\n\n ByteArrayInputStream inStream = new ByteArrayInputStream(decode);\n ASN1InputStream asnInputStream = new ASN1InputStream(inStream);\n\n return CertificateList.getInstance(asnInputStream.readObject()).getRevokedCertificates();\n } \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n TBSCertList.CRLEntry[] getRevokes(Date r) throws Exception {\n\n String crl = client.generateCRL(admin, r, null, null, null);\n\n return parseCRL(crl);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void setProperties(Properties properties) {\n this.properties = properties;\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n boolean hasConnected() {\n return connected;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Map discoverEndorserEndpoints(TransactionContext transactionContext, List> chaincodeNames) throws ServiceDiscoveryException {\n if (null == chaincodeNames) {\n logger.warn(\"Discover of chaincode names was null.\");\n return Collections.emptyMap();\n }\n if (chaincodeNames.isEmpty()) {\n logger.warn(\"Discover of chaincode names was empty.\");\n return Collections.emptyMap();\n }\n if (DEBUG) {\n StringBuilder cns = new StringBuilder(1000);\n String sep = \"\";\n cns.append(\"[\");\n for (List s : chaincodeNames) {\n\n ServiceDiscoveryChaincodeCalls n = s.get(0);\n cns.append(sep).append(n.write(s.subList(1, s.size())));\n sep = \", \";\n }\n cns.append(\"]\");\n logger.debug(format(\"Channel %s doing discovery for chaincodes: %s\", channelName, cns.toString()));\n }\n\n ArrayList speers = new ArrayList<>(serviceDiscoveryPeers);\n Collections.shuffle(speers);\n final Map ret = new HashMap<>();\n SDNetwork sdNetwork = networkDiscovery(transactionContext, false);\n ServiceDiscoveryException serviceDiscoveryException = null;\n\n for (Peer serviceDiscoveryPeer : speers) {\n serviceDiscoveryException = null;\n try {\n logger.debug(format(\"Channel %s doing discovery for chaincodes on peer: %s\", channelName, serviceDiscoveryPeer.toString()));\n\n TransactionContext ltransactionContext = transactionContext.retryTransactionSameContext();\n final byte[] clientTLSCertificateDigest = serviceDiscoveryPeer.getClientTLSCertificateDigest();\n\n if (null == clientTLSCertificateDigest) {\n logger.warn(format(\"Channel %s peer %s requires mutual tls for service discovery.\", channelName, serviceDiscoveryPeer.toString()));\n continue;\n }\n\n ByteString clientIdent = ltransactionContext.getIdentity().toByteString();\n ByteString tlshash = ByteString.copyFrom(clientTLSCertificateDigest);\n Protocol.AuthInfo authentication = Protocol.AuthInfo.newBuilder().setClientIdentity(clientIdent).setClientTlsCertHash(tlshash).build();\n\n List fq = new ArrayList<>(chaincodeNames.size());\n\n for (List chaincodeName : chaincodeNames) {\n if (ret.containsKey(chaincodeName.get(0).getName())) {\n continue;\n }\n LinkedList chaincodeCalls = new LinkedList<>();\n chaincodeName.forEach(serviceDiscoveryChaincodeCalls -> chaincodeCalls.add(serviceDiscoveryChaincodeCalls.build()));\n List cinn = new ArrayList<>(1);\n chaincodeName.forEach(ServiceDiscoveryChaincodeCalls::build);\n Protocol.ChaincodeInterest cci = Protocol.ChaincodeInterest.newBuilder().addAllChaincodes(chaincodeCalls).build();\n cinn.add(cci);\n Protocol.ChaincodeQuery chaincodeQuery = Protocol.ChaincodeQuery.newBuilder().addAllInterests(cinn).build();\n\n fq.add(Protocol.Query.newBuilder().setChannel(channelName).setCcQuery(chaincodeQuery).build());\n }\n\n if (fq.size() == 0) {\n //this would be odd but lets take care of it.\n break;\n }\n\n Protocol.Request request = Protocol.Request.newBuilder().addAllQueries(fq).setAuthentication(authentication).build();\n ByteString payloadBytes = request.toByteString();\n ByteString signatureBytes = ltransactionContext.signByteStrings(payloadBytes);\n Protocol.SignedRequest sr = Protocol.SignedRequest.newBuilder()\n .setPayload(payloadBytes).setSignature(signatureBytes).build();\n if (IS_TRACE_LEVEL && null != diagnosticFileDumper) { // dump protobuf we sent\n logger.trace(format(\"Service discovery channel %s %s service chaincode query sent %s\", channelName, serviceDiscoveryPeer,\n diagnosticFileDumper.createDiagnosticProtobufFile(sr.toByteArray())));\n }\n\n logger.debug(format(\"Channel %s peer %s sending chaincode query request\", channelName, serviceDiscoveryPeer.toString()));\n final Protocol.Response response = serviceDiscoveryPeer.sendDiscoveryRequestAsync(sr).get(SERVICE_DISCOVERY_WAITTIME, TimeUnit.MILLISECONDS);\n if (IS_TRACE_LEVEL && null != diagnosticFileDumper) { // dump protobuf we get\n logger.trace(format(\"Service discovery channel %s %s service chaincode query returned %s\", channelName, serviceDiscoveryPeer,\n diagnosticFileDumper.createDiagnosticProtobufFile(response.toByteArray())));\n }\n logger.debug(format(\"Channel %s peer %s completed chaincode query request\", channelName, serviceDiscoveryPeer.toString()));\n serviceDiscoveryPeer.hasConnected();\n\n for (Protocol.QueryResult queryResult : response.getResultsList()) {\n if (queryResult.getResultCase().getNumber() == Protocol.QueryResult.ERROR_FIELD_NUMBER) {\n ServiceDiscoveryException discoveryException = new ServiceDiscoveryException(format(\"Error %s\", queryResult.getError().getContent()));\n logger.error(discoveryException.getMessage());\n continue;\n }\n\n if (queryResult.getResultCase().getNumber() != Protocol.QueryResult.CC_QUERY_RES_FIELD_NUMBER) {\n ServiceDiscoveryException discoveryException = new ServiceDiscoveryException(format(\"Error expected chaincode endorsement query but got %s : \", queryResult.getResultCase().toString()));\n logger.error(discoveryException.getMessage());\n continue;\n }\n\n Protocol.ChaincodeQueryResult ccQueryRes = queryResult.getCcQueryRes();\n if (ccQueryRes.getContentList().isEmpty()) {\n throw new ServiceDiscoveryException(format(\"Error %s\", queryResult.getError().getContent()));\n }\n\n for (Protocol.EndorsementDescriptor es : ccQueryRes.getContentList()) {\n final String chaincode = es.getChaincode();\n List layouts = new LinkedList<>();\n for (Protocol.Layout layout : es.getLayoutsList()) {\n SDLayout sdLayout = null;\n Map quantitiesByGroupMap = layout.getQuantitiesByGroupMap();\n for (Map.Entry qmap : quantitiesByGroupMap.entrySet()) {\n final String key = qmap.getKey();\n final int quantity = qmap.getValue();\n if (quantity < 1) {\n continue;\n }\n Protocol.Peers peers = es.getEndorsersByGroupsMap().get(key);\n if (peers == null || peers.getPeersCount() == 0) {\n continue;\n }\n\n List sdEndorsers = new LinkedList<>();\n\n for (Protocol.Peer pp : peers.getPeersList()) {\n SDEndorser ppp = new SDEndorser(pp, null, null, asLocalhost);\n final String endPoint = ppp.getEndpoint();\n SDEndorser nppp = sdNetwork.getEndorserByEndpoint(endPoint);\n if (null == nppp) {\n sdNetwork = networkDiscovery(transactionContext, true);\n if (null == sdNetwork) {\n throw new ServiceDiscoveryException(\"Failed to discover network resources.\");\n }\n nppp = sdNetwork.getEndorserByEndpoint(ppp.getEndpoint());\n if (null == nppp) {\n throw new ServiceDiscoveryException(format(\"Failed to discover peer endpoint information %s for chaincode %s \", endPoint, chaincode));\n }\n }\n sdEndorsers.add(nppp);\n }\n if (sdLayout == null) {\n sdLayout = new SDLayout();\n layouts.add(sdLayout);\n }\n sdLayout.addGroup(key, quantity, sdEndorsers);\n }\n }\n if (layouts.isEmpty()) {\n logger.warn(format(\"Channel %s chaincode %s discovered no layouts!\", channelName, chaincode));\n } else {\n if (DEBUG) {\n StringBuilder sb = new StringBuilder(1000);\n sb.append(\"Channel \").append(channelName)\n .append(\" found \").append(layouts.size()).append(\" layouts for chaincode: \").append(es.getChaincode());\n sb.append(\", layouts: [\");\n\n String sep = \"\";\n for (SDLayout layout : layouts) {\n sb.append(sep).append(layout);\n sep = \", \";\n }\n sb.append(\"]\");\n\n logger.debug(sb.toString());\n }\n ret.put(es.getChaincode(), new SDChaindcode(es.getChaincode(), layouts));\n }\n }\n }\n\n if (ret.size() == chaincodeNames.size()) {\n break; // found them all.\n }\n } catch (ServiceDiscoveryException e) {\n logger.warn(format(\"Service discovery error on peer %s. Error: %s\", serviceDiscoveryPeer.toString(), e.getMessage()));\n serviceDiscoveryException = e;\n } catch (Exception e) {\n logger.warn(format(\"Service discovery error on peer %s. Error: %s\", serviceDiscoveryPeer.toString(), e.getMessage()));\n serviceDiscoveryException = new ServiceDiscoveryException(e);\n }\n }\n\n if (null != serviceDiscoveryException) {\n throw serviceDiscoveryException;\n }\n if (ret.size() != chaincodeNames.size()) {\n logger.warn((format(\"Channel %s failed to find all layouts for chaincodes. Expected: %d and found: %d\", channelName, chaincodeNames.size(), ret.size())));\n }\n\n return ret;\n } \n #location 43 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n ServiceDiscovery(Channel channel, Collection serviceDiscoveryPeers, TransactionContext transactionContext) {\n this.serviceDiscoveryPeers = serviceDiscoveryPeers;\n this.channel = channel;\n this.channelName = channel.getName();\n this.transactionContext = transactionContext.retryTransactionSameContext();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n FabricProposalResponse.ProposalResponse sendProposal(FabricProposal.SignedProposal proposal)\n throws PeerException, InvalidArgumentException {\n checkSendProposal(proposal);\n\n logger.debug(format(\"peer.sendProposalAsync name: %s, url: %s\", name, url));\n\n return endorserClent.sendProposal(proposal);\n } \n #location 7 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n Peer(String name, String grpcURL, Properties properties) throws InvalidArgumentException {\n\n Exception e = checkGrpcUrl(grpcURL);\n if (e != null) {\n throw new InvalidArgumentException(\"Bad peer url.\", e);\n\n }\n\n if (StringUtil.isNullOrEmpty(name)) {\n throw new InvalidArgumentException(\"Invalid name for peer\");\n }\n\n this.url = grpcURL;\n this.name = name;\n this.properties = properties == null ? null : (Properties) properties.clone(); //keep our own copy.\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static final Collection createAreasForSimpleMultipolygon(OsmRelation relation,\n\t\t\tTLongObjectMap nodeIdMap, OsmEntityProvider db) throws EntityNotFoundException {\n\n\t\tassert isSimpleMultipolygon(relation, db);\n\n\t\tOsmEntity tagSource = null;\n\t\tList outerNodes = null;\n\t\tList> holes = new ArrayList>();\n\n\t\tfor (OsmRelationMember member : membersAsList(relation)) {\n\t\t\tif (member.getType() == EntityType.Way) {\n\n\t\t\t\tOsmWay way = db.getWay(member.getId());\n\n\t\t\t\tif (\"inner\".equals(member.getRole())) {\n\n\t\t\t\t\tList hole = new ArrayList(way.getNumberOfNodes());\n\n\t\t\t\t\tfor (long nodeId : nodesAsList(way).toArray()) {\n\t\t\t\t\t\thole.add(nodeIdMap.get(nodeId));\n\t\t\t\t\t}\n\n\t\t\t\t\tholes.add(hole);\n\n\t\t\t\t} else if (\"outer\".equals(member.getRole())) {\n\n\t\t\t\t\ttagSource = relation.getNumberOfTags() > 1 ? relation : way;\n\n\t\t\t\t\touterNodes = new ArrayList(way.getNumberOfNodes());\n\t\t\t\t\tfor (long nodeId : nodesAsList(way).toArray()) {\n\t\t\t\t\t\touterNodes.add(nodeIdMap.get(nodeId));\n\t\t\t\t\t}\n\n\t\t\t\t}\n\n\t\t\t}\n\t\t}\n\n\t\treturn singleton(new MapArea(tagSource, outerNodes, holes));\n\n\t} \n #location 39 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private static final Collection createAreasForSimpleMultipolygon(OsmRelation relation,\n\t\t\tTLongObjectMap nodeIdMap, OsmEntityProvider db) throws EntityNotFoundException {\n\n\t\tassert isSimpleMultipolygon(relation, db);\n\n\t\tOsmEntity tagSource = null;\n\t\tList outerNodes = null;\n\t\tList> holes = new ArrayList>();\n\n\t\tfor (OsmRelationMember member : membersAsList(relation)) {\n\t\t\tif (member.getType() == EntityType.Way) {\n\n\t\t\t\tOsmWay way = db.getWay(member.getId());\n\n\t\t\t\tif (\"inner\".equals(member.getRole())) {\n\n\t\t\t\t\tList hole = new ArrayList(way.getNumberOfNodes());\n\n\t\t\t\t\tfor (long nodeId : nodesAsList(way).toArray()) {\n\t\t\t\t\t\thole.add(nodeIdMap.get(nodeId));\n\t\t\t\t\t}\n\n\t\t\t\t\tholes.add(hole);\n\n\t\t\t\t} else if (\"outer\".equals(member.getRole())) {\n\n\t\t\t\t\ttagSource = relation.getNumberOfTags() > 1 ? relation : way;\n\n\t\t\t\t\touterNodes = new ArrayList(way.getNumberOfNodes());\n\t\t\t\t\tfor (long nodeId : nodesAsList(way).toArray()) {\n\t\t\t\t\t\touterNodes.add(nodeIdMap.get(nodeId));\n\t\t\t\t\t}\n\n\t\t\t\t}\n\n\t\t\t}\n\t\t}\n\n\t\treturn singleton(new MapArea(tagSource.getId(), tagSource instanceof OsmRelation,\n\t\t\t\tOSMToMapDataConverter.tagsOfEntity(tagSource), outerNodes, holes));\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] unparsedArgs) {\n\t\t\n\t\tProgramMode programMode;\n\t\tCLIArguments args = null;\n\t\t\n\t\t/* parse command line arguments */\n\t\t\n\t\tif (unparsedArgs.length > 0) {\n\t\t\t\n\t\t\ttry {\n\t\t\t\targs = CliFactory.parseArguments(CLIArguments.class, unparsedArgs);\n\t\t\t} catch (ArgumentValidationException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tif (!CLIArgumentsUtil.isValid(args)) {\n\t\t\t\tSystem.err.println(CLIArgumentsUtil.getErrorString(args));\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tprogramMode = CLIArgumentsUtil.getProgramMode(args);\n\t\t\t\n\t\t} else {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\tprogramMode = ProgramMode.GUI;\n\t\t\t\n\t\t}\n\t\t\n\t\t/* load configuration file */\n\n\t\tConfiguration config = new BaseConfiguration();\n\t\t\n\t\tif (args != null && args.isConfig()) {\n\t\t\ttry {\n\t\t\t\tconfig = new PropertiesConfiguration(args.getConfig());\n\t\t\t} catch (ConfigurationException e) {\n\t\t\t\tSystem.err.println(\"could not read config, ignoring it: \");\n\t\t\t\tSystem.err.println(e);\n\t\t\t}\n\t\t}\n\t\t\n\t\t/* run selected mode */\n\t\t\n\t\tswitch (programMode) {\n\t\t\n\t\tcase HELP:\n\t\t\t//parser.printHelp();\n\t\t\tSystem.out.println(\n\t\t\t\t\tCliFactory.createCli(CLIArguments.class).getHelpMessage()\n\t\t\t\t\t+ \"\\n\\nFor more information, see \" + GlobalValues.WIKI_URI);\n\t\t\tbreak;\n\t\t\t\n\t\tcase VERSION:\n\t\t\tSystem.out.println(\"OSM2World \" + VERSION_STRING);\n\t\t\tbreak;\n\t\t\n\t\tcase GUI:\n\t\t\ttry {\n\t\t\t\tUIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());\n\t\t\t} catch(Exception e) {\n\t\t\t\tSystem.out.println(\"Error setting native look and feel: \" + e);\n\t\t\t}\n\t\t\tnew ViewerFrame(new Data(), new MessageManager(),\n\t\t\t\t\tnew RenderOptions(), config).setVisible(true);\n\t\t\tbreak;\n\t\t\t\n\t\tcase CONVERT:\n\t\t\ttry {\n\t\t\t\tOutput.output(config, args);\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t\tbreak;\n\t\t\t\n\t\t}\n\t\t\n\t} \n #location 73 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static void main(String[] unparsedArgs) {\n\t\t\n\t\t/* assume --gui if no parameters are given */\n\t\t\n\t\tif (unparsedArgs.length == 0) {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\t\n\t\t\tunparsedArgs = new String[]{\"--gui\"};\n\t\t\t\n\t\t}\n\t\t\n\t\t/* parse command line arguments */\n\t\t\n\t\tCLIArguments args = null;\n\t\t\n\t\ttry {\n\t\t\targs = parseArguments(unparsedArgs);\n\t\t} catch (Exception e) {\n\t\t\tSystem.err.println(e.getMessage());\n\t\t\tSystem.exit(1);\n\t\t}\n\t\t\n\t\t/* parse lines from parameter file (if one exists) */\n\t\t\n\t\tList argumentsList = Collections.singletonList(args);\n\t\t\n\t\tif (args.isParameterFile()) {\n\t\t\t\n\t\t\targumentsList = new ArrayList();\n\t\t\t\n\t\t\ttry {\n\t\t\t\t\n\t\t\t\tList unparsedArgsLines = CLIArgumentsUtil\n\t\t\t\t\t.getUnparsedParameterGroups(args.getParameterFile());\n\t\t\t\t\n\t\t\t\tfor (String[] unparsedArgsLine : unparsedArgsLines) {\n\t\t\t\t\t\n\t\t\t\t\ttry {\n\t\t\t\t\t\targumentsList.add(parseArguments(unparsedArgsLine));\n\t\t\t\t\t} catch (Exception e) {\n\t\t\t\t\t\tSystem.err.println(\"Could not parse parameters from file:\");\n\t\t\t\t\t\tSystem.err.println(unparsedArgsLine);\n\t\t\t\t\t\tSystem.err.println(\"Ignoring it. Reason:\");\n\t\t\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\t\t}\n\t\t\t\t\t\n\t\t\t\t}\n\t\t\t\t\n\t\t\t} catch (IOException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t}\n\t\t\n\t\t/* collect parameter groups into compatible groups\n\t\t * (groups of parameter groups that use the same input and config files) */\n\t\t\n\t\tList argumentsGroups = new ArrayList();\n\t\t\n\t\tfor (CLIArguments arguments : argumentsList) {\n\t\t\t\n\t\t\tboolean added = false;\n\t\t\t\n\t\t\tfor (CLIArgumentsGroup compatibleGroup : argumentsGroups) {\n\t\t\t\tif (compatibleGroup.isCompatible(arguments)) {\n\t\t\t\t\t// add to existing compatible group\n\t\t\t\t\tcompatibleGroup.addCLIArguments(arguments);\n\t\t\t\t\tadded = true;\n\t\t\t\t\tbreak;\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\tif (!added) {\n\t\t\t\t// start a new compatible group\n\t\t\t\targumentsGroups.add(new CLIArgumentsGroup(arguments));\n\t\t\t}\n\t\t\t\n\t\t}\n\t\t\n\t\t/* execute conversions */\n\t\t\n\t\tfor (CLIArgumentsGroup argumentsGroup : argumentsGroups) {\n\t\t\t\t\t\t\n\t\t\tif (argumentsList.size() > 1) {\n\t\t\t\tSystem.out.print(\"executing conversion for these parameter lines: \");\n\t\t\t\tfor (CLIArguments p : argumentsGroup.getCLIArgumentsList()) {\n\t\t\t\t\tSystem.out.print(argumentsList.indexOf(p) + \" \");\n\t\t\t\t}\n\t\t\t\tSystem.out.print(\"\\n\");\n\t\t\t}\n\t\t\t\n\t\t\texecuteArgumentsGroup(argumentsGroup);\n\t\t\t\n\t\t}\n\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void addPrimitiveToValueBuffer(BufferT buffer,\n\t\t\tPrimitive primitive) {\n\t\t\t\t\t\n\t\t/*\n\t\t * rearrange the lists of vertices, normals and texture coordinates\n\t\t * to turn triangle strips and triangle fans into separate triangles\n\t\t */\n\n\t\tList primVertices = primitive.vertices;\n\t\tList primNormals = primitive.normals;\n\t\tList> primTexCoordLists = primitive.texCoordLists;\n\t\t\n\t\tif (primitive.type == Type.TRIANGLE_STRIP) {\n\t\t\t\n\t\t\tprimVertices = triangleVertexListFromTriangleStrip(primVertices);\n\t\t\tprimNormals = triangleNormalListFromTriangleStrip(primNormals);\n\t\t\t\n\t\t\tif (primTexCoordLists != null) {\n\t\t\t\tList> newPrimTexCoordLists = new ArrayList>();\n\t\t\t\tfor (List primTexCoordList : primTexCoordLists) {\n\t\t\t\t\tnewPrimTexCoordLists.add(triangleVertexListFromTriangleStrip(primTexCoordList));\n\t\t\t\t}\n\t\t\t\tprimTexCoordLists = newPrimTexCoordLists;\n\t\t\t}\n\t\t\t\n\t\t} else if (primitive.type == Type.TRIANGLE_FAN) {\n\t\t\t\n\t\t\tprimVertices = triangleVertexListFromTriangleFan(primVertices);\n\t\t\tprimNormals = triangleVertexListFromTriangleFan(primNormals);\n\t\t\t\n\t\t\tif (primTexCoordLists != null) {\n\t\t\t\tList> newPrimTexCoordLists = new ArrayList>();\n\t\t\t\tfor (List primTexCoordList : primTexCoordLists) {\n\t\t\t\t\tnewPrimTexCoordLists.add(triangleVertexListFromTriangleFan(primTexCoordList));\n\t\t\t\t}\n\t\t\t\tprimTexCoordLists = newPrimTexCoordLists;\n\t\t\t}\n\t\t\t\n\t\t}\n\t\t\n\t\tList primTangents = null;\n\t\tif (material.hasBumpMap()) {\n\t\t\tprimTangents = calculateTangentVectorsForTexLayer(primVertices, primNormals, primTexCoordLists.get(material.getBumpMapInd()));\n\t\t} else if (material.getNumTextureLayers() > 0) {\n\t\t\tprimTangents = calculateTangentVectorsForTexLayer(primVertices, primNormals, primTexCoordLists.get(0));\n\t\t}\n\t\t\t\n\t\t/* put the values into the buffer, in the right order */\n\t\t\n\t\tfor (int i = 0; i < primVertices.size(); i++) {\n\t\t\t\n\t\t\tint count = 0;\n\t\t\tassert (primTexCoordLists == null\n\t\t\t\t\t&& material.getNumTextureLayers() == 0)\n\t\t\t\t|| (primTexCoordLists != null\n\t\t\t\t\t&& primTexCoordLists.size() == material.getNumTextureLayers())\n\t\t\t\t: \"WorldModules need to provide the correct number of tex coords\";\n\t\t\t\n\t\t\tif (primTexCoordLists == null && material.getNumTextureLayers() > 0) {\n\t\t\t\tSystem.out.println(material);\n\t\t\t}\n\t\t\t\t\n\t\t\tfor (int t = 0; t < material.getNumTextureLayers(); t++) {\n\t\t\t\tif (!material.hasBumpMap() || t != material.getBumpMapInd()) {\n\t\t\t\t\tVectorXZ textureCoord =\tprimTexCoordLists.get(t).get(i);\n\t\t\t\t\tput(buffer, textureCoord);\n\t\t\t\t\t//System.out.println(\"put tex coord\");\n\t\t\t\t\tcount += 2;\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\tput(buffer, primNormals.get(i));\n\t\t\tcount += 3;\n\t\t\t//System.out.println(\"put normals\");\n\t\t\tif (material.getNumTextureLayers() > 0) {\n\t\t\t\tput(buffer, primTangents.get(i));\n\t\t\t\tcount += 4;\n\t\t\t\t//System.out.println(\"put tangent\");\n\t\t\t}\n\t\t\tif (material.hasBumpMap()) {\n\t\t\t\tput(buffer, primTexCoordLists.get(material.getBumpMapInd()).get(i));\n\t\t\t\tcount += 2;\n\t\t\t\t//System.out.println(\"put bm coord\");\n\t\t\t}\n\t\t\tput(buffer, primVertices.get(i));\n\t\t\tcount += 3;\n\t\t\t//System.out.println(\"put vertices\");\n\t\t\t\n\t\t\tif (count != JOGLRendererVBO.getValuesPerVertex(material)) {\n\t\t\t\tthrow new RuntimeException(\"put: \"+count +\" values:\" + JOGLRendererVBO.getValuesPerVertex(material));\n\t\t\t}\n\t\t\t//System.out.println(\"values per Material:\" + JOGLRendererVBO.getValuesPerVertex(material));\n\t\t}\n\t\t\n\t} \n #location 77 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tprotected void addPrimitiveToValueBuffer(BufferT buffer,\n\t\t\tPrimitive primitive) {\n\t\t\t\t\t\n\t\t/*\n\t\t * rearrange the lists of vertices, normals and texture coordinates\n\t\t * to turn triangle strips and triangle fans into separate triangles\n\t\t */\n\n\t\tList primVertices = primitive.vertices;\n\t\tList primNormals = primitive.normals;\n\t\tList> primTexCoordLists = primitive.texCoordLists;\n\t\t\n\t\tif (primitive.type == Type.TRIANGLE_STRIP) {\n\t\t\t\n\t\t\tprimVertices = triangleVertexListFromTriangleStrip(primVertices);\n\t\t\tprimNormals = triangleNormalListFromTriangleStrip(primNormals);\n\t\t\t\n\t\t\tif (primTexCoordLists != null) {\n\t\t\t\tList> newPrimTexCoordLists = new ArrayList>();\n\t\t\t\tfor (List primTexCoordList : primTexCoordLists) {\n\t\t\t\t\tnewPrimTexCoordLists.add(triangleVertexListFromTriangleStrip(primTexCoordList));\n\t\t\t\t}\n\t\t\t\tprimTexCoordLists = newPrimTexCoordLists;\n\t\t\t}\n\t\t\t\n\t\t} else if (primitive.type == Type.TRIANGLE_FAN) {\n\t\t\t\n\t\t\tprimVertices = triangleVertexListFromTriangleFan(primVertices);\n\t\t\tprimNormals = triangleVertexListFromTriangleFan(primNormals);\n\t\t\t\n\t\t\tif (primTexCoordLists != null) {\n\t\t\t\tList> newPrimTexCoordLists = new ArrayList>();\n\t\t\t\tfor (List primTexCoordList : primTexCoordLists) {\n\t\t\t\t\tnewPrimTexCoordLists.add(triangleVertexListFromTriangleFan(primTexCoordList));\n\t\t\t\t}\n\t\t\t\tprimTexCoordLists = newPrimTexCoordLists;\n\t\t\t}\n\t\t\t\n\t\t}\n\t\t\n\t\tList primTangents = null;\n\t\tif (material.hasBumpMap()) {\n\t\t\tprimTangents = calculateTangentVectorsForTexLayer(primVertices, primNormals, primTexCoordLists.get(material.getBumpMapInd()));\n\t\t}\n\t\t\t\n\t\t/* put the values into the buffer, in the right order */\n\t\t\n\t\tfor (int i = 0; i < primVertices.size(); i++) {\n\t\t\t\n\t\t\tint count = 0;\n\t\t\tassert (primTexCoordLists == null\n\t\t\t\t\t&& material.getNumTextureLayers() == 0)\n\t\t\t\t|| (primTexCoordLists != null\n\t\t\t\t\t&& primTexCoordLists.size() == material.getNumTextureLayers())\n\t\t\t\t: \"WorldModules need to provide the correct number of tex coords\";\n\t\t\t\n\t\t\tif (primTexCoordLists == null && material.getNumTextureLayers() > 0) {\n\t\t\t\tSystem.out.println(material);\n\t\t\t}\n\t\t\t\t\n\t\t\tfor (int t = 0; t < material.getNumTextureLayers(); t++) {\n\t\t\t\tif (!material.hasBumpMap() || t != material.getBumpMapInd()) {\n\t\t\t\t\tVectorXZ textureCoord =\tprimTexCoordLists.get(t).get(i);\n\t\t\t\t\tput(buffer, textureCoord);\n\t\t\t\t\t//System.out.println(\"put tex coord\");\n\t\t\t\t\tcount += 2;\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\tput(buffer, primNormals.get(i));\n\t\t\tcount += 3;\n\t\t\tif (material.hasBumpMap()) {\n\t\t\t\tput(buffer, primTangents.get(i));\n\t\t\t\tcount += 4;\n\t\t\t\tput(buffer, primTexCoordLists.get(material.getBumpMapInd()).get(i));\n\t\t\t\tcount += 2;\n\t\t\t}\n\t\t\tput(buffer, primVertices.get(i));\n\t\t\tcount += 3;\n\t\t\t\n\t\t\tif (count != JOGLRendererVBO.getValuesPerVertex(material)) {\n\t\t\t\tthrow new RuntimeException(\"put: \"+count +\" values:\" + JOGLRendererVBO.getValuesPerVertex(material));\n\t\t\t}\n\t\t}\n\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] unparsedArgs) {\n\t\t\n\t\tProgramMode programMode;\n\t\tCLIArguments args = null;\n\t\t\n\t\tif (unparsedArgs.length > 0) {\n\t\t\t\n\t\t\ttry {\n\t\t\t\targs = CliFactory.parseArguments(CLIArguments.class, unparsedArgs);\n\t\t\t} catch (ArgumentValidationException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tif (!CLIArgumentsUtil.isValid(args)) {\n\t\t\t\tSystem.err.println(CLIArgumentsUtil.getErrorString(args));\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tprogramMode = CLIArgumentsUtil.getProgramMode(args);\n\t\t\t\n\t\t} else {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\tprogramMode = ProgramMode.GUI;\n\t\t\t\n\t\t}\n\t\t\n\t\tswitch (programMode) {\n\t\t\n\t\tcase HELP:\n\t\t\t//parser.printHelp();\n\t\t\tSystem.out.println(\n\t\t\t\t\tCliFactory.createCli(CLIArguments.class).getHelpMessage()\n\t\t\t\t\t+ \"\\n\\nFor more information, see \" + GlobalValues.WIKI_URI);\n\t\t\tbreak;\n\t\t\t\n\t\tcase VERSION:\n\t\t\tSystem.out.println(\"OSM2World \" + VERSION_STRING);\n\t\t\tbreak;\n\t\t\n\t\tcase GUI:\n\t\t\ttry {\n\t\t\t\tUIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());\n\t\t\t} catch(Exception e) {\n\t\t\t\tSystem.out.println(\"Error setting native look and feel: \" + e);\n\t\t\t}\n\t\t\tnew ViewerFrame(new Data(), new MessageManager(), new RenderOptions())\n\t\t\t\t.setVisible(true);\n\t\t\tbreak;\n\t\t\t\n\t\tcase CONVERT:\n\t\t\ttry {\n\t\t\t\tOutput.output(args);\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t\tbreak;\n\t\t\t\n\t\t}\n\t\t\n\t} \n #location 56 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static void main(String[] unparsedArgs) {\n\t\t\n\t\tProgramMode programMode;\n\t\tCLIArguments args = null;\n\t\t\n\t\t/* parse command line arguments */\n\t\t\n\t\tif (unparsedArgs.length > 0) {\n\t\t\t\n\t\t\ttry {\n\t\t\t\targs = CliFactory.parseArguments(CLIArguments.class, unparsedArgs);\n\t\t\t} catch (ArgumentValidationException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tif (!CLIArgumentsUtil.isValid(args)) {\n\t\t\t\tSystem.err.println(CLIArgumentsUtil.getErrorString(args));\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tprogramMode = CLIArgumentsUtil.getProgramMode(args);\n\t\t\t\n\t\t} else {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\tprogramMode = ProgramMode.GUI;\n\t\t\t\n\t\t}\n\t\t\n\t\t/* load configuration file */\n\n\t\tConfiguration config = new BaseConfiguration();\n\t\t\n\t\tif (args.isConfig()) {\n\t\t\ttry {\n\t\t\t\tconfig = new PropertiesConfiguration(args.getConfig());\n\t\t\t} catch (ConfigurationException e) {\n\t\t\t\tSystem.err.println(\"could not read config, ignoring it: \");\n\t\t\t\tSystem.err.println(e);\n\t\t\t}\n\t\t}\n\t\t\n\t\t/* run selected mode */\n\t\t\n\t\tswitch (programMode) {\n\t\t\n\t\tcase HELP:\n\t\t\t//parser.printHelp();\n\t\t\tSystem.out.println(\n\t\t\t\t\tCliFactory.createCli(CLIArguments.class).getHelpMessage()\n\t\t\t\t\t+ \"\\n\\nFor more information, see \" + GlobalValues.WIKI_URI);\n\t\t\tbreak;\n\t\t\t\n\t\tcase VERSION:\n\t\t\tSystem.out.println(\"OSM2World \" + VERSION_STRING);\n\t\t\tbreak;\n\t\t\n\t\tcase GUI:\n\t\t\ttry {\n\t\t\t\tUIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());\n\t\t\t} catch(Exception e) {\n\t\t\t\tSystem.out.println(\"Error setting native look and feel: \" + e);\n\t\t\t}\n\t\t\tnew ViewerFrame(new Data(), new MessageManager(),\n\t\t\t\t\tnew RenderOptions(), config).setVisible(true);\n\t\t\tbreak;\n\t\t\t\n\t\tcase CONVERT:\n\t\t\ttry {\n\t\t\t\tOutput.output(config, args);\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t\tbreak;\n\t\t\t\n\t\t}\n\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void beginObject(WorldObject object) {\n\n\t\t/* build the previous object (if it's inside the bounding box) */\n\n\t\tboolean isInsideBbox = true;\n\n\t\tif (currentObject != null && currentObject.getPrimaryMapElement() != null) {\n\n\t\t\tMapElement mapElement = currentObject.getPrimaryMapElement();\n\n\t\t\tVectorXZ center = null;\n\n\t\t\tif (mapElement instanceof MapNode) {\n\t\t\t\tcenter = ((MapNode) mapElement).getPos();\n\t\t\t} else if (mapElement instanceof MapWaySegment) {\n\t\t\t\tcenter = ((MapWaySegment) mapElement).getCenter();\n\t\t\t} else if (mapElement instanceof MapArea) {\n\t\t\t\tcenter = ((MapArea) mapElement).getOuterPolygon().getCenter();\n\t\t\t}\n\n\t\t\tisInsideBbox = bbox.contains(center);\n\n\t\t}\n\n\t\tif (!currentTriangles.isEmpty() && isInsideBbox) {\n\t\t\tobjects.add(buildCurrentObject());\n\t\t}\n\n\t\t/* start a new object */\n\n\t\tcurrentObject = object;\n\t\tcurrentTriangles = new HashMap();\n\n\t} \n #location 22 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic void beginObject(WorldObject object) {\n\n\t\tfinishCurrentObject();\n\n\t\t/* start a new object */\n\n\t\tcurrentObject = object;\n\t\tcurrentTriangles = new HashMap();\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static final boolean isJOSMGenerated(File file) {\n\t\t\n\t\ttry {\n\t\t\t\n\t\t\tBufferedReader reader = new BufferedReader(new FileReader(file));\n\t\t\t\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\treader.close();\n\t\t\t\n\t\t} catch (IOException e) { }\n\t\t\n\t\treturn false;\n\t\t\n\t} \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static final boolean isJOSMGenerated(File file) {\n\t\t\n\t\ttry {\n\t\t\t\n\t\t\tBufferedReader reader = new BufferedReader(new FileReader(file));\n\t\t\t\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treader.close();\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\treader.close();\n\t\t\t\n\t\t} catch (IOException e) { }\n\t\t\n\t\treturn false;\n\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static int createFragmentShader(GL3 gl, String filename) {\n\n\t\tint fragShader = gl.glCreateShader(GL3.GL_FRAGMENT_SHADER);\n\t\tif (fragShader == 0)\n\t\t\treturn 0;\n\n\t\tString[] fragCode = new String[1];\n\t\tfragCode[0] = \"\";\n\t\tString line;\n\n\t\tInputStream stream = loadShaderFile(filename);\n\t\tif (stream == null) {\n\t\t\tthrow new RuntimeException(\"Fragment shader not found in classpath: \\\"\"+ filename +\"\\\"\");\n\t\t}\n\t\tBufferedReader reader = new BufferedReader(new InputStreamReader(stream));\n\t\ttry {\n\t\t\twhile ((line = reader.readLine()) != null) {\n\t\t\t\tfragCode[0] += line + \"\\n\";\n\t\t\t}\n\t\t} catch (IOException e) {\n\t\t\tthrow new RuntimeException(\"Failed reading fragment shader \\\"\" + filename + \"\\\".\",e);\n\t\t}\n\n\t\tgl.glShaderSource(fragShader, 1, fragCode, null);\n\t\tgl.glCompileShader(fragShader);\n\n\t\t// acquire compilation status\n\t\tIntBuffer shaderStatus = IntBuffer.allocate(1);\n\t\tgl.glGetShaderiv(fragShader, GL3.GL_COMPILE_STATUS, shaderStatus);\n\n\t\t// check whether compilation was successful\n\t\tif (shaderStatus.get() == GL.GL_FALSE) {\n\t\t\tprintShaderInfoLog(gl, fragShader);\n\t\t\tthrow new IllegalStateException(\"compilation error for shader [\"\n\t\t\t\t\t+ filename + \"].\");\n\t\t}\n\t\tprintShaderInfoLog(gl, fragShader);\n\n\t\treturn fragShader;\n\t} \n #location 20 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static int createFragmentShader(GL3 gl, String filename) {\n\n\t\tint fragShader = gl.glCreateShader(GL3.GL_FRAGMENT_SHADER);\n\t\tif (fragShader == 0)\n\t\t\treturn 0;\n\n\t\tString[] fragCode = new String[1];\n\t\tfragCode[0] = \"\";\n\t\tString line;\n\n\t\tInputStream stream = loadShaderFile(filename);\n\t\tif (stream == null) {\n\t\t\tthrow new RuntimeException(\"Fragment shader not found in classpath: \\\"\"+ filename +\"\\\"\");\n\t\t}\n\n\t\ttry (BufferedReader reader = new BufferedReader(new InputStreamReader(stream))) {\n\n\t\t\twhile ((line = reader.readLine()) != null) {\n\t\t\t\tfragCode[0] += line + \"\\n\";\n\t\t\t}\n\n\t\t\tgl.glShaderSource(fragShader, 1, fragCode, null);\n\t\t\tgl.glCompileShader(fragShader);\n\n\t\t\t// acquire compilation status\n\t\t\tIntBuffer shaderStatus = IntBuffer.allocate(1);\n\t\t\tgl.glGetShaderiv(fragShader, GL3.GL_COMPILE_STATUS, shaderStatus);\n\n\t\t\t// check whether compilation was successful\n\t\t\tif (shaderStatus.get() == GL.GL_FALSE) {\n\t\t\t\tprintShaderInfoLog(gl, fragShader);\n\t\t\t\tthrow new IllegalStateException(\"compilation error for shader [\"\n\t\t\t\t\t\t+ filename + \"].\");\n\t\t\t}\n\t\t\tprintShaderInfoLog(gl, fragShader);\n\n\t\t\treturn fragShader;\n\n\t\t} catch (IOException e) {\n\t\t\tthrow new RuntimeException(\"Failed reading fragment shader \\\"\" + filename + \"\\\".\",e);\n\t\t}\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void createComponents(){\n\n for (MapElement element : elements){\n\n switch (element.getTags().getValue(\"indoor\")){\n\n case \"wall\":\n\n walls.add(new IndoorWall(buildingPart, element));\n break;\n\n case \"room\":\n\n rooms.add(new IndoorRoom((MapArea) element, buildingPart));\n break;\n\n case \"area\":\n\n areas.add(new IndoorArea(buildingPart, (MapArea) element));\n break;\n\n case \"corridor\":\n\n corridors.add(new Corridor(buildingPart, (MapArea) element));\n break;\n\n }\n\n\n }\n\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void createComponents(){\n\n for (MapElement element : elements){\n\n IndoorObjectData data = new IndoorObjectData(buildingPart, element);\n\n switch (element.getTags().getValue(\"indoor\")){\n\n case \"wall\":\n\n walls.add(new IndoorWall(data));\n break;\n\n case \"room\":\n\n rooms.add(new IndoorRoom(data));\n break;\n\n case \"area\":\n\n areas.add(new IndoorArea(data));\n break;\n\n case \"corridor\":\n\n corridors.add(new Corridor(data));\n break;\n\n }\n\n\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static final boolean isJOSMGenerated(File file) {\n\n\t\ttry {\n\n\t\t\tBufferedReader reader = new BufferedReader(new FileReader(file));\n\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\treader.close();\n\n\t\t} catch (IOException e) { }\n\n\t\treturn false;\n\n\t} \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static final boolean isJOSMGenerated(File file) {\n\n\t\ttry (BufferedReader reader = new BufferedReader(new FileReader(file))) {\n\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t} catch (IOException e) { }\n\n\t\treturn false;\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static int createVertexShader(GL3 gl, String filename) {\n\n\t\t// get the unique id\n\t\tint vertShader = gl.glCreateShader(GL3.GL_VERTEX_SHADER);\n\t\tif (vertShader == 0)\n\t\t\tthrow new RuntimeException(\"Unable to create vertex shader.\");\n\n\t\t// create a single String array index to hold the shader code\n\t\tString[] vertCode = new String[1];\n\t\tvertCode[0] = \"\";\n\t\tString line;\n\n\t\t// open the file and read the contents into the String array.\n\t\tInputStream stream = loadShaderFile(filename);\n\t\tif (stream == null) {\n\t\t\tthrow new RuntimeException(\"Vertex shader not found in classpath: \\\"\"+ filename +\"\\\"\");\n\t\t}\n\t\tBufferedReader reader = new BufferedReader(new InputStreamReader(stream));\n\t\ttry {\n\t\t\twhile ((line = reader.readLine()) != null) {\n\t\t\t\tvertCode[0] += line + \"\\n\";\n\t\t\t}\n\t\t} catch (IOException e) {\n\t\t\tthrow new RuntimeException(\"Failed reading vertex shader \\\"\" + filename + \"\\\".\",e);\n\t\t}\n\n\t\t// Associate the code string with the unique id\n\t\tgl.glShaderSource(vertShader, 1, vertCode, null);\n\t\t// compile the vertex shader\n\t\tgl.glCompileShader(vertShader);\n\n\t\t// acquire compilation status\n\t\tIntBuffer shaderStatus = IntBuffer.allocate(1);\n\t\tgl.glGetShaderiv(vertShader, GL3.GL_COMPILE_STATUS, shaderStatus);\n\n\t\t// check whether compilation was successful\n\t\tif (shaderStatus.get() == GL.GL_FALSE) {\n\t\t\tprintShaderInfoLog(gl, vertShader);\n\t\t\tthrow new IllegalStateException(\"compilation error for shader [\"\n\t\t\t\t\t+ filename + \"].\");\n\t\t}\n\t\tprintShaderInfoLog(gl, vertShader);\n\n\t\t// the int returned is now associated with the compiled shader\n\t\treturn vertShader;\n\t} \n #location 23 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static int createVertexShader(GL3 gl, String filename) {\n\n\t\t// get the unique id\n\t\tint vertShader = gl.glCreateShader(GL3.GL_VERTEX_SHADER);\n\t\tif (vertShader == 0)\n\t\t\tthrow new RuntimeException(\"Unable to create vertex shader.\");\n\n\t\t// create a single String array index to hold the shader code\n\t\tString[] vertCode = new String[1];\n\t\tvertCode[0] = \"\";\n\t\tString line;\n\n\t\t// open the file and read the contents into the String array.\n\t\tInputStream stream = loadShaderFile(filename);\n\t\tif (stream == null) {\n\t\t\tthrow new RuntimeException(\"Vertex shader not found in classpath: \\\"\"+ filename +\"\\\"\");\n\t\t}\n\n\t\ttry (BufferedReader reader = new BufferedReader(new InputStreamReader(stream))) {\n\n\t\t\twhile ((line = reader.readLine()) != null) {\n\t\t\t\tvertCode[0] += line + \"\\n\";\n\t\t\t}\n\n\t\t\t// Associate the code string with the unique id\n\t\t\tgl.glShaderSource(vertShader, 1, vertCode, null);\n\t\t\t// compile the vertex shader\n\t\t\tgl.glCompileShader(vertShader);\n\n\t\t\t// acquire compilation status\n\t\t\tIntBuffer shaderStatus = IntBuffer.allocate(1);\n\t\t\tgl.glGetShaderiv(vertShader, GL3.GL_COMPILE_STATUS, shaderStatus);\n\n\t\t\t// check whether compilation was successful\n\t\t\tif (shaderStatus.get() == GL.GL_FALSE) {\n\t\t\t\tprintShaderInfoLog(gl, vertShader);\n\t\t\t\tthrow new IllegalStateException(\"compilation error for shader [\" + filename + \"].\");\n\t\t\t}\n\t\t\tprintShaderInfoLog(gl, vertShader);\n\n\t\t\t// the int returned is now associated with the compiled shader\n\t\t\treturn vertShader;\n\n\t\t} catch (IOException e) {\n\t\t\tthrow new RuntimeException(\"Failed reading vertex shader \\\"\" + filename + \"\\\".\",e);\n\t\t}\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static final List getUnparsedParameterGroups(\n\t\t\tFile parameterFile) throws IOException {\n\n\t\tList result = new ArrayList();\n\n\t\tBufferedReader in = new BufferedReader(new FileReader(parameterFile));\n\n\t\tString line;\n\n\t\twhile ((line = in.readLine()) != null) {\n\n\t\t\tif (line.startsWith(\"#\")) continue;\n\t\t\tif (line.trim().isEmpty()) continue;\n\n\t\t\tList argList = new ArrayList();\n\n\t\t\tPattern regex = Pattern.compile(\"[^\\\\s\\\"']+|\\\"([^\\\"]*)\\\"|'([^']*)'\");\n\t\t\tMatcher matcher = regex.matcher(line);\n\n\t\t\twhile (matcher.find()) {\n\t\t\t if (matcher.group(1) != null) {\n\t\t\t // Add double-quoted string without the quotes\n\t\t\t \targList.add(matcher.group(1));\n\t\t\t } else if (matcher.group(2) != null) {\n\t\t\t // Add single-quoted string without the quotes\n\t\t\t \targList.add(matcher.group(2));\n\t\t\t } else {\n\t\t\t // Add unquoted word\n\t\t\t \targList.add(matcher.group());\n\t\t\t }\n\t\t\t}\n\n\t\t\tresult.add(argList.toArray(new String[argList.size()]));\n\n\t\t}\n\t\tin.close();\n\n\t\treturn result;\n\n\t} \n #location 38 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static final List getUnparsedParameterGroups(\n\t\t\tFile parameterFile) throws IOException {\n\n\t\ttry (BufferedReader in = new BufferedReader(new FileReader(parameterFile))) {\n\n\t\t\tList result = new ArrayList<>();\n\n\t\t\tString line;\n\n\t\t\twhile ((line = in.readLine()) != null) {\n\n\t\t\t\tif (line.startsWith(\"#\")) continue;\n\t\t\t\tif (line.trim().isEmpty()) continue;\n\n\t\t\t\tList argList = new ArrayList<>();\n\n\t\t\t\tPattern regex = Pattern.compile(\"[^\\\\s\\\"']+|\\\"([^\\\"]*)\\\"|'([^']*)'\");\n\t\t\t\tMatcher matcher = regex.matcher(line);\n\n\t\t\t\twhile (matcher.find()) {\n\t\t\t\t if (matcher.group(1) != null) {\n\t\t\t\t // Add double-quoted string without the quotes\n\t\t\t\t \targList.add(matcher.group(1));\n\t\t\t\t } else if (matcher.group(2) != null) {\n\t\t\t\t // Add single-quoted string without the quotes\n\t\t\t\t \targList.add(matcher.group(2));\n\t\t\t\t } else {\n\t\t\t\t // Add unquoted word\n\t\t\t\t \targList.add(matcher.group());\n\t\t\t\t }\n\t\t\t\t}\n\n\t\t\t\tresult.add(argList.toArray(new String[argList.size()]));\n\n\t\t\t}\n\n\t\t\treturn result;\n\n\t\t}\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static final boolean isJOSMGenerated(File file) {\n\n\t\ttry {\n\n\t\t\tBufferedReader reader = new BufferedReader(new FileReader(file));\n\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\treader.close();\n\n\t\t} catch (IOException e) { }\n\n\t\treturn false;\n\n\t} \n #location 18 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static final boolean isJOSMGenerated(File file) {\n\n\t\ttry (BufferedReader reader = new BufferedReader(new FileReader(file))) {\n\n\t\t\tfor (int i=0; i<100; i++) {\n\t\t\t\tString line = reader.readLine();\n\t\t\t\tif (line != null) {\n\t\t\t\t\tif (line.contains(\"generator='JOSM'\")) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t} catch (IOException e) { }\n\n\t\treturn false;\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] unparsedArgs) {\n\t\t\n\t\tProgramMode programMode;\n\t\tCLIArguments args = null;\n\t\t\n\t\t/* parse command line arguments */\n\t\t\n\t\tif (unparsedArgs.length > 0) {\n\t\t\t\n\t\t\ttry {\n\t\t\t\targs = CliFactory.parseArguments(CLIArguments.class, unparsedArgs);\n\t\t\t} catch (ArgumentValidationException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tif (!CLIArgumentsUtil.isValid(args)) {\n\t\t\t\tSystem.err.println(CLIArgumentsUtil.getErrorString(args));\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tprogramMode = CLIArgumentsUtil.getProgramMode(args);\n\t\t\t\n\t\t} else {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\tprogramMode = ProgramMode.GUI;\n\t\t\t\n\t\t}\n\t\t\n\t\t/* load configuration file */\n\n\t\tConfiguration config = new BaseConfiguration();\n\t\t\n\t\tif (args.isConfig()) {\n\t\t\ttry {\n\t\t\t\tconfig = new PropertiesConfiguration(args.getConfig());\n\t\t\t} catch (ConfigurationException e) {\n\t\t\t\tSystem.err.println(\"could not read config, ignoring it: \");\n\t\t\t\tSystem.err.println(e);\n\t\t\t}\n\t\t}\n\t\t\n\t\t/* run selected mode */\n\t\t\n\t\tswitch (programMode) {\n\t\t\n\t\tcase HELP:\n\t\t\t//parser.printHelp();\n\t\t\tSystem.out.println(\n\t\t\t\t\tCliFactory.createCli(CLIArguments.class).getHelpMessage()\n\t\t\t\t\t+ \"\\n\\nFor more information, see \" + GlobalValues.WIKI_URI);\n\t\t\tbreak;\n\t\t\t\n\t\tcase VERSION:\n\t\t\tSystem.out.println(\"OSM2World \" + VERSION_STRING);\n\t\t\tbreak;\n\t\t\n\t\tcase GUI:\n\t\t\ttry {\n\t\t\t\tUIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());\n\t\t\t} catch(Exception e) {\n\t\t\t\tSystem.out.println(\"Error setting native look and feel: \" + e);\n\t\t\t}\n\t\t\tnew ViewerFrame(new Data(), new MessageManager(),\n\t\t\t\t\tnew RenderOptions(), config).setVisible(true);\n\t\t\tbreak;\n\t\t\t\n\t\tcase CONVERT:\n\t\t\ttry {\n\t\t\t\tOutput.output(config, args);\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t\tbreak;\n\t\t\t\n\t\t}\n\t\t\n\t} \n #location 37 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public static void main(String[] unparsedArgs) {\n\t\t\n\t\tProgramMode programMode;\n\t\tCLIArguments args = null;\n\t\t\n\t\t/* parse command line arguments */\n\t\t\n\t\tif (unparsedArgs.length > 0) {\n\t\t\t\n\t\t\ttry {\n\t\t\t\targs = CliFactory.parseArguments(CLIArguments.class, unparsedArgs);\n\t\t\t} catch (ArgumentValidationException e) {\n\t\t\t\tSystem.err.println(e.getMessage());\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tif (!CLIArgumentsUtil.isValid(args)) {\n\t\t\t\tSystem.err.println(CLIArgumentsUtil.getErrorString(args));\n\t\t\t\tSystem.exit(1);\n\t\t\t}\n\t\t\t\n\t\t\tprogramMode = CLIArgumentsUtil.getProgramMode(args);\n\t\t\t\n\t\t} else {\n\t\t \n\t\t\tSystem.out.println(\"No parameters, running graphical interface.\\n\"\n\t\t\t\t\t+ \"If you want to use the command line, use the --help\"\n\t\t\t\t\t+ \" parameter for a list of available parameters.\");\n\t\t\tprogramMode = ProgramMode.GUI;\n\t\t\t\n\t\t}\n\t\t\n\t\t/* load configuration file */\n\n\t\tConfiguration config = new BaseConfiguration();\n\t\t\n\t\tif (args != null && args.isConfig()) {\n\t\t\ttry {\n\t\t\t\tconfig = new PropertiesConfiguration(args.getConfig());\n\t\t\t} catch (ConfigurationException e) {\n\t\t\t\tSystem.err.println(\"could not read config, ignoring it: \");\n\t\t\t\tSystem.err.println(e);\n\t\t\t}\n\t\t}\n\t\t\n\t\t/* run selected mode */\n\t\t\n\t\tswitch (programMode) {\n\t\t\n\t\tcase HELP:\n\t\t\t//parser.printHelp();\n\t\t\tSystem.out.println(\n\t\t\t\t\tCliFactory.createCli(CLIArguments.class).getHelpMessage()\n\t\t\t\t\t+ \"\\n\\nFor more information, see \" + GlobalValues.WIKI_URI);\n\t\t\tbreak;\n\t\t\t\n\t\tcase VERSION:\n\t\t\tSystem.out.println(\"OSM2World \" + VERSION_STRING);\n\t\t\tbreak;\n\t\t\n\t\tcase GUI:\n\t\t\ttry {\n\t\t\t\tUIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());\n\t\t\t} catch(Exception e) {\n\t\t\t\tSystem.out.println(\"Error setting native look and feel: \" + e);\n\t\t\t}\n\t\t\tnew ViewerFrame(new Data(), new MessageManager(),\n\t\t\t\t\tnew RenderOptions(), config).setVisible(true);\n\t\t\tbreak;\n\t\t\t\n\t\tcase CONVERT:\n\t\t\ttry {\n\t\t\t\tOutput.output(config, args);\n\t\t\t} catch (IOException e) {\n\t\t\t\te.printStackTrace();\n\t\t\t}\n\t\t\tbreak;\n\t\t\t\n\t\t}\n\t\t\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void slaveDown(ClusterSlotRange slotRange, String host, int port) {\n Collection allPubSubConnections = getEntry(slotRange).slaveDown(host, port);\n\n // reattach listeners to other channels\n for (Entry mapEntry : name2PubSubConnection.entrySet()) {\n for (RedisPubSubConnection redisPubSubConnection : allPubSubConnections) {\n PubSubConnectionEntry entry = mapEntry.getValue();\n final String channelName = mapEntry.getKey();\n\n if (!entry.getConnection().equals(redisPubSubConnection)) {\n continue;\n }\n\n synchronized (entry) {\n entry.close();\n\n final Collection listeners = entry.getListeners(channelName);\n if (entry.getConnection().getPatternChannels().get(channelName) != null) {\n Codec subscribeCodec = punsubscribe(channelName);\n if (!listeners.isEmpty()) {\n Future future = psubscribe(channelName, subscribeCodec);\n future.addListener(new FutureListener() {\n @Override\n public void operationComplete(Future future)\n throws Exception {\n PubSubConnectionEntry newEntry = future.getNow();\n for (RedisPubSubListener redisPubSubListener : listeners) {\n newEntry.addListener(channelName, redisPubSubListener);\n }\n log.debug(\"resubscribed listeners for '{}' channel-pattern\", channelName);\n }\n });\n }\n } else {\n Codec subscribeCodec = unsubscribe(channelName);\n if (!listeners.isEmpty()) {\n Future future = subscribe(channelName, subscribeCodec);\n future.addListener(new FutureListener() {\n\n @Override\n public void operationComplete(Future future)\n throws Exception {\n PubSubConnectionEntry newEntry = future.getNow();\n for (RedisPubSubListener redisPubSubListener : listeners) {\n newEntry.addListener(channelName, redisPubSubListener);\n }\n log.debug(\"resubscribed listeners for '{}' channel\", channelName);\n }\n });\n }\n }\n }\n }\n }\n } \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected void slaveDown(ClusterSlotRange slotRange, String host, int port) {\n MasterSlaveEntry entry = getEntry(slotRange);\n slaveDown(entry, host, port);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public boolean compareAndSet(long expect, long update) {\n RedisConnection conn = connectionManager.connection();\n try {\n while (true) {\n conn.watch(getName());\n Long value = (Long) conn.get(getName());\n if (value != expect) {\n conn.discard();\n return false;\n }\n conn.multi();\n conn.set(getName(), update);\n if (conn.exec().size() == 1) {\n return true;\n }\n }\n } finally {\n connectionManager.release(conn);\n }\n } \n #location 8 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public boolean compareAndSet(long expect, long update) {\n RedisConnection conn = connectionManager.connection();\n try {\n while (true) {\n conn.watch(getName());\n Long value = ((Number) conn.get(getName())).longValue();\n if (value != expect) {\n conn.discard();\n return false;\n }\n conn.multi();\n conn.set(getName(), update);\n if (conn.exec().size() == 1) {\n return true;\n }\n }\n } finally {\n connectionManager.release(conn);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public boolean remove(Object o) {\n RedisConnection connection = connectionManager.connectionWriteOp();\n try {\n return connection.lrem(getName(), 1, o) > 0;\n } finally {\n connectionManager.release(connection);\n }\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public boolean remove(Object o) {\n return remove(o, 1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReplaceDepartments(){\n List departments = Departments.defaultDepartments().list();\n\n File tmpDir = Files.createTempDir();\n File groups = new File(tmpDir, \"departments.csv\");\n\n try {\n PrintWriter groupPrintWriter = new PrintWriter(new BufferedWriter(new FileWriter(groups, false)));\n groupPrintWriter.append(\"\u90e8\u95e8\u540d\u79f0,\u90e8\u95e8ID,\u7236\u90e8\u95e8ID,\u6392\u5e8f\").append(\"\\n\");\n\n for (Department department : departments) {\n groupPrintWriter.append(csv(department));\n }\n groupPrintWriter.close();\n\n String job = Jobs.defaultJobs().replaceDepartments(groups);\n while (true) {\n JobResult jobResult = Jobs.defaultJobs().getResult(job);\n if (3 == jobResult.getStatus()) {\n if (100 == jobResult.getPercentage()) {\n Assert.assertTrue(true);\n }\n break;\n } else {\n System.out.println(\"\u6b63\u5728\u540c\u6b65:\" + jobResult.getPercentage());\n sleep(100);\n }\n }\n } catch(Exception e) {\n e.printStackTrace();\n Assert.fail(\"test failed.\");\n } finally {\n try {\n FileUtils.forceDelete(tmpDir);\n } catch (IOException e) {\n }\n }\n } \n #location 30 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testReplaceDepartments(){\n List departments = Departments.defaultDepartments().list();\n\n File tmpDir = Files.createTempDir();\n File groups = new File(tmpDir, \"departments.csv\");\n\n try {\n PrintWriter groupPrintWriter = new PrintWriter(new BufferedWriter(new FileWriter(groups, false)));\n groupPrintWriter.println(\"\u90e8\u95e8\u540d\u79f0,\u90e8\u95e8ID,\u7236\u90e8\u95e8ID,\u6392\u5e8f\");\n\n for (Department department : departments) {\n groupPrintWriter.print(csv(department));\n }\n groupPrintWriter.close();\n\n String job = Jobs.defaultJobs().replaceDepartments(groups);\n while (true) {\n JobResult jobResult = Jobs.defaultJobs().getResult(job);\n if (3 == jobResult.getStatus()) {\n if (100 == jobResult.getPercentage()) {\n Assert.assertTrue(true);\n }\n break;\n } else {\n System.out.println(\"\u6b63\u5728\u540c\u6b65:\" + jobResult.getPercentage());\n sleep(100);\n }\n }\n } catch(Exception e) {\n e.printStackTrace();\n Assert.fail(\"test failed.\");\n } finally {\n try {\n FileUtils.forceDelete(tmpDir);\n } catch (IOException e) {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testReplaceUsers(){\n List allUsers = Users.defaultUsers().list();\n\n File tmpDir = Files.createTempDir();\n File users = new File(tmpDir, \"users.csv\");\n\n try {\n PrintWriter userPrintWriter = new PrintWriter(new BufferedWriter(new FileWriter(users, false)));\n userPrintWriter.append(\"\u59d3\u540d,\u5e10\u53f7,\u5fae\u4fe1\u53f7,\u624b\u673a\u53f7,\u90ae\u7bb1,\u6240\u5728\u90e8\u95e8,\u804c\u4f4d\").append(\"\\n\");\n\n for(ReadUser user: allUsers) {\n CreateUser createUser = new CreateUser();\n createUser.setName(user.getName());\n createUser.setMobile(user.getMobile());\n createUser.setUserId(user.getUserId());\n createUser.setPosition(user.getPosition());\n createUser.setWeixinId(user.getWeixinId());\n createUser.setDepartment(user.getDepartment());\n createUser.setEmail(user.getEmail());\n userPrintWriter.append(csv(createUser));\n }\n\n userPrintWriter.close();\n\n String job = Jobs.defaultJobs().replaceUsers(users);\n while (true) {\n JobResult jobResult = Jobs.defaultJobs().getResult(job);\n if (3 == jobResult.getStatus()) {\n if (100 == jobResult.getPercentage()) {\n Assert.assertTrue(true);\n }\n break;\n } else {\n System.out.println(\"\u6b63\u5728\u540c\u6b65:\" + jobResult.getPercentage());\n sleep(10);\n }\n }\n } catch(Exception e) {\n e.printStackTrace();\n Assert.fail(\"test failed.\");\n } finally {\n try {\n FileUtils.forceDelete(tmpDir);\n } catch (IOException e) {\n }\n }\n } \n #location 39 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testReplaceUsers(){\n List allUsers = Users.defaultUsers().list();\n\n File tmpDir = Files.createTempDir();\n File users = new File(tmpDir, \"users.csv\");\n\n try {\n PrintWriter userPrintWriter = new PrintWriter(new BufferedWriter(new FileWriter(users, false)));\n userPrintWriter.println(\"\u59d3\u540d,\u5e10\u53f7,\u5fae\u4fe1\u53f7,\u624b\u673a\u53f7,\u90ae\u7bb1,\u6240\u5728\u90e8\u95e8,\u804c\u4f4d\");\n\n for(ReadUser user: allUsers) {\n CreateUser createUser = new CreateUser();\n createUser.setName(user.getName());\n createUser.setMobile(user.getMobile());\n createUser.setUserId(user.getUserId());\n createUser.setPosition(user.getPosition());\n createUser.setWeixinId(user.getWeixinId());\n createUser.setDepartment(user.getDepartment());\n createUser.setEmail(user.getEmail());\n userPrintWriter.print(csv(createUser));\n }\n\n userPrintWriter.close();\n\n String job = Jobs.defaultJobs().replaceUsers(users);\n while (true) {\n JobResult jobResult = Jobs.defaultJobs().getResult(job);\n if (3 == jobResult.getStatus()) {\n if (100 == jobResult.getPercentage()) {\n Assert.assertTrue(true);\n }\n break;\n } else {\n System.out.println(\"\u6b63\u5728\u540c\u6b65:\" + jobResult.getPercentage());\n sleep(10);\n }\n }\n } catch(Exception e) {\n e.printStackTrace();\n Assert.fail(\"test failed.\");\n } finally {\n try {\n FileUtils.forceDelete(tmpDir);\n } catch (IOException e) {\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadMainDict() {\n //\u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _MainDict = new DictSegment((char) 0);\n //\u8bfb\u53d6\u4e3b\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getMainDictionary());\n if (is == null) {\n throw new RuntimeException(\"Main Dictionary not found!!!\");\n }\n\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, \"UTF-8\"), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Main Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n //\u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\n this.loadExtDict();\n } \n #location 20 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadMainDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _MainDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u4e3b\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getMainDictionary());\n if (is == null) {\n throw new RuntimeException(\"Main Dictionary not found!!!\");\n }\n\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Main Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\n this.loadExtDict();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadStopWordDict() {\n //\u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _StopWordDict = new DictSegment((char) 0);\n //\u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\n List extStopWordDictFiles = cfg.getExtStopWordDictionarys();\n if (extStopWordDictFiles != null) {\n InputStream is;\n for (String extStopWordDictName : extStopWordDictFiles) {\n System.out.println(\"\u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\uff1a\" + extStopWordDictName);\n //\u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n is = this.getClass().getClassLoader().getResourceAsStream(extStopWordDictName);\n //\u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, \"UTF-8\"), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n //System.out.println(theWord);\n //\u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\u6570\u636e\u5230\u5185\u5b58\u4e2d\n _StopWordDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Stop word Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadStopWordDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _StopWordDict = new DictSegment((char) 0);\n // \u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\n List extStopWordDictFiles = cfg.getExtStopWordDictionarys();\n if (extStopWordDictFiles != null) {\n InputStream is;\n for (String extStopWordDictName : extStopWordDictFiles) {\n System.out.println(\"\u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\uff1a\" + extStopWordDictName);\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n is = this.getClass().getClassLoader().getResourceAsStream(extStopWordDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n // System.out.println(theWord);\n // \u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\u6570\u636e\u5230\u5185\u5b58\u4e2d\n _StopWordDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Stop word Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static UpdateKeeper getInstance() {\n if (singleton == null) {\n synchronized (UpdateKeeper.class) {\n if (singleton == null) {\n singleton = new UpdateKeeper();\n return singleton;\n }\n }\n }\n return singleton;\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n static UpdateKeeper getInstance() {\n return UpdateKeeper.Builder.singleton;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadExtDict() {\n //\u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u914d\u7f6e\n List extDictFiles = cfg.getExtDictionarys();\n if (extDictFiles != null) {\n InputStream is;\n for (String extDictName : extDictFiles) {\n //\u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n System.out.println(\"\u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\uff1a\" + extDictName);\n is = this.getClass().getClassLoader().getResourceAsStream(extDictName);\n //\u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, \"UTF-8\"), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n //\u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u6570\u636e\u5230\u4e3b\u5185\u5b58\u8bcd\u5178\u4e2d\n //System.out.println(theWord);\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n } \n #location 26 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadExtDict() {\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u914d\u7f6e\n List extDictFiles = cfg.getExtDictionarys();\n if (extDictFiles != null) {\n InputStream is;\n for (String extDictName : extDictFiles) {\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n System.out.println(\"\u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\uff1a\" + extDictName);\n is = this.getClass().getClassLoader().getResourceAsStream(extDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u6570\u636e\u5230\u4e3b\u5185\u5b58\u8bcd\u5178\u4e2d\n // System.out.println(theWord);\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadQuantifierDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u91cf\u8bcd\u5178\u5b9e\u4f8b\n _QuantifierDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u91cf\u8bcd\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getQuantifierDicionary());\n if (is == null) {\n throw new RuntimeException(\"Quantifier Dictionary not found!!!\");\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _QuantifierDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Quantifier Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n } \n #location 19 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadQuantifierDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u91cf\u8bcd\u5178\u5b9e\u4f8b\n _QuantifierDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u91cf\u8bcd\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getQuantifierDicionary());\n if (is == null) {\n throw new RuntimeException(\"Quantifier Dictionary not found!!!\");\n }\n try {\n readDict(is, _QuantifierDict);\n } catch (IOException ioe) {\n System.err.println(\"Quantifier Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadMainDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _MainDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u4e3b\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getMainDictionary());\n if (is == null) {\n throw new RuntimeException(\"Main Dictionary not found!!!\");\n }\n\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Main Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\n this.loadExtDict();\n } \n #location 20 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadMainDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _MainDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u4e3b\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getMainDictionary());\n if (is == null) {\n throw new RuntimeException(\"Main Dictionary not found!!!\");\n }\n\n try {\n readDict(is, _MainDict);\n } catch (IOException ioe) {\n System.err.println(\"Main Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\n this.loadExtDict();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadStopWordDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _StopWordDict = new DictSegment((char) 0);\n // \u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\n List extStopWordDictFiles = cfg.getExtStopWordDictionarys();\n if (extStopWordDictFiles != null) {\n InputStream is;\n for (String extStopWordDictName : extStopWordDictFiles) {\n System.out.println(\"Load stopwords dictionary:\" + extStopWordDictName);\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n is = this.getClass().getClassLoader().getResourceAsStream(extStopWordDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n // System.out.println(theWord);\n // \u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\u6570\u636e\u5230\u5185\u5b58\u4e2d\n _StopWordDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Stop word Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadStopWordDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u4e3b\u8bcd\u5178\u5b9e\u4f8b\n _StopWordDict = new DictSegment((char) 0);\n // \u52a0\u8f7d\u6269\u5c55\u505c\u6b62\u8bcd\u5178\n List extStopWordDictFiles = cfg.getExtStopWordDictionarys();\n if (extStopWordDictFiles != null) {\n InputStream is;\n for (String extStopWordDictName : extStopWordDictFiles) {\n System.out.println(\"Load stopwords dictionary:\" + extStopWordDictName);\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n is = this.getClass().getClassLoader().getResourceAsStream(extStopWordDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n readDict(is, _StopWordDict);\n } catch (IOException ioe) {\n System.err.println(\"Extension Stop word Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadQuantifierDict() {\n //\u5efa\u7acb\u4e00\u4e2a\u91cf\u8bcd\u5178\u5b9e\u4f8b\n _QuantifierDict = new DictSegment((char) 0);\n //\u8bfb\u53d6\u91cf\u8bcd\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getQuantifierDicionary());\n if (is == null) {\n throw new RuntimeException(\"Quantifier Dictionary not found!!!\");\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, \"UTF-8\"), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _QuantifierDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Quantifier Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n } \n #location 19 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadQuantifierDict() {\n // \u5efa\u7acb\u4e00\u4e2a\u91cf\u8bcd\u5178\u5b9e\u4f8b\n _QuantifierDict = new DictSegment((char) 0);\n // \u8bfb\u53d6\u91cf\u8bcd\u8bcd\u5178\u6587\u4ef6\n InputStream is = this.getClass().getClassLoader().getResourceAsStream(cfg.getQuantifierDicionary());\n if (is == null) {\n throw new RuntimeException(\"Quantifier Dictionary not found!!!\");\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n _QuantifierDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Quantifier Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void loadExtDict() {\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u914d\u7f6e\n List extDictFiles = cfg.getExtDictionarys();\n if (extDictFiles != null) {\n InputStream is;\n for (String extDictName : extDictFiles) {\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n System.out.println(\"Load extended dictionary:\" + extDictName);\n is = this.getClass().getClassLoader().getResourceAsStream(extDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u6570\u636e\u5230\u4e3b\u5185\u5b58\u8bcd\u5178\u4e2d\n // System.out.println(theWord);\n _MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n\n } catch (IOException ioe) {\n System.err.println(\"Extension Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n } \n #location 26 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void loadExtDict() {\n // \u52a0\u8f7d\u6269\u5c55\u8bcd\u5178\u914d\u7f6e\n List extDictFiles = cfg.getExtDictionarys();\n if (extDictFiles != null) {\n InputStream is;\n for (String extDictName : extDictFiles) {\n // \u8bfb\u53d6\u6269\u5c55\u8bcd\u5178\u6587\u4ef6\n System.out.println(\"Load extended dictionary:\" + extDictName);\n is = this.getClass().getClassLoader().getResourceAsStream(extDictName);\n // \u5982\u679c\u627e\u4e0d\u5230\u6269\u5c55\u7684\u5b57\u5178\uff0c\u5219\u5ffd\u7565\n if (is == null) {\n continue;\n }\n try {\n readDict(is, _MainDict);\n } catch (IOException ioe) {\n System.err.println(\"Extension Dictionary loading exception.\");\n ioe.printStackTrace();\n\n } finally {\n try {\n is.close();\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void reloadDic(List inputStreamList) {\n if (singleton == null) {\n Configuration cfg = DefaultConfig.getInstance();\n initial(cfg);\n }\n for (InputStream is : inputStreamList) {\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, \"UTF-8\"), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n singleton._MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n } catch (IOException ioe) {\n System.err.println(\"Other Dictionary loading exception.\");\n ioe.printStackTrace();\n } finally {\n try {\n if (is != null) {\n is.close();\n }\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n } \n #location 16 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void reloadDic(List inputStreamList) {\n // \u5982\u679c\u672c\u7c7b\u5355\u4f8b\u5c1a\u672a\u5b9e\u4f8b\u5316\uff0c\u5219\u5148\u8fdb\u884c\u521d\u59cb\u5316\u64cd\u4f5c\n if (singleton == null) {\n Configuration cfg = DefaultConfig.getInstance();\n initial(cfg);\n }\n // \u5bf9\u8bcd\u5178\u6d41\u96c6\u5408\u8fdb\u884c\u5faa\u73af\u8bfb\u53d6\uff0c\u5c06\u8bfb\u53d6\u5230\u7684\u8bcd\u8bed\u52a0\u8f7d\u5230\u4e3b\u8bcd\u5178\u4e2d\n for (InputStream is : inputStreamList) {\n try {\n BufferedReader br = new BufferedReader(new InputStreamReader(is, StandardCharsets.UTF_8), 512);\n String theWord;\n do {\n theWord = br.readLine();\n if (theWord != null && !\"\".equals(theWord.trim())) {\n singleton._MainDict.fillSegment(theWord.trim().toLowerCase().toCharArray());\n }\n } while (theWord != null);\n } catch (IOException ioe) {\n System.err.println(\"Other Dictionary loading exception.\");\n ioe.printStackTrace();\n } finally {\n try {\n if (is != null) {\n is.close();\n }\n } catch (IOException e) {\n e.printStackTrace();\n }\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List buildDynamicNodes() {\n if (refreshInterval.millis() != 0) {\n if (cachedDiscoNodes != null &&\n (refreshInterval.millis() < 0 || (System.currentTimeMillis() - lastRefresh) < refreshInterval.millis())) {\n if (logger.isTraceEnabled()) logger.trace(\"using cache to retrieve node list\");\n return cachedDiscoNodes;\n }\n lastRefresh = System.currentTimeMillis();\n }\n logger.debug(\"start building nodes list using GCE API\");\n\n cachedDiscoNodes = Lists.newArrayList();\n String ipAddress = null;\n try {\n InetAddress inetAddress = networkService.resolvePublishHostAddress(null);\n if (inetAddress != null) {\n ipAddress = inetAddress.getHostAddress();\n }\n } catch (IOException e) {\n // We can't find the publish host address... Hmmm. Too bad :-(\n // We won't simply filter it\n }\n\n try {\n Collection instances = gceComputeService.instances();\n\n for (Instance instance : instances) {\n String name = instance.getName();\n String type = instance.getMachineType();\n String image = instance.getImage();\n\n String status = instance.getStatus();\n\n // We don't want to connect to TERMINATED status instances\n // See https://github.com/elasticsearch/elasticsearch-cloud-gce/issues/3\n if (Status.TERMINATED.equals(status)) {\n logger.debug(\"node {} is TERMINATED. Ignoring\", name);\n continue;\n }\n\n // see if we need to filter by tag\n boolean filterByTag = false;\n if (tags.length > 0) {\n if (instance.getTags() == null || instance.getTags().isEmpty()) {\n // If this instance have no tag, we filter it\n filterByTag = true;\n } else {\n // check that all tags listed are there on the instance\n for (String tag : tags) {\n boolean found = false;\n for (String instancetag : instance.getTags().getItems()) {\n if (instancetag.equals(tag)) {\n found = true;\n break;\n }\n }\n if (!found) {\n filterByTag = true;\n break;\n }\n }\n }\n }\n if (filterByTag) {\n logger.trace(\"filtering out instance {} based tags {}, not part of {}\", name, tags,\n instance.getTags().getItems());\n continue;\n }\n\n String ip_public = null;\n String ip_private = null;\n\n List interfaces = instance.getNetworkInterfaces();\n\n for (NetworkInterface networkInterface : interfaces) {\n if (ip_public == null) {\n // Trying to get Public IP Address (For future use)\n for (AccessConfig accessConfig : networkInterface.getAccessConfigs()) {\n if (Strings.hasText(accessConfig.getNatIP())) {\n ip_public = accessConfig.getNatIP();\n break;\n }\n }\n }\n\n if (ip_private == null) {\n ip_private = networkInterface.getNetworkIP();\n }\n\n // If we have both public and private, we can stop here\n if (ip_private != null && ip_public != null) break;\n }\n\n try {\n if (ip_private.equals(ipAddress)) {\n // We found the current node.\n // We can ignore it in the list of DiscoveryNode\n logger.trace(\"current node found. Ignoring {} - {}\", name, ip_private);\n } else {\n TransportAddress[] addresses = transportService.addressesFromString(ip_private);\n // we only limit to 1 addresses, makes no sense to ping 100 ports\n for (int i = 0; (i < addresses.length && i < UnicastZenPing.LIMIT_PORTS_COUNT); i++) {\n logger.trace(\"adding {}, type {}, image {}, address {}, transport_address {}, status {}\", name, type,\n image, ip_private, addresses[i], status);\n cachedDiscoNodes.add(new DiscoveryNode(\"#cloud-\" + name + \"-\" + i, addresses[i]));\n }\n }\n } catch (Exception e) {\n logger.warn(\"failed to add {}, address {}\", e, name, ip_private);\n }\n\n }\n } catch (Throwable e) {\n logger.warn(\"Exception caught during discovery {} : {}\", e.getClass().getName(), e.getMessage());\n logger.trace(\"Exception caught during discovery\", e);\n }\n\n logger.debug(\"using dynamic discovery nodes {}\", cachedDiscoNodes);\n return cachedDiscoNodes;\n } \n #location 67 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List buildDynamicNodes() {\n if (refreshInterval.millis() != 0) {\n if (cachedDiscoNodes != null &&\n (refreshInterval.millis() < 0 || (System.currentTimeMillis() - lastRefresh) < refreshInterval.millis())) {\n if (logger.isTraceEnabled()) logger.trace(\"using cache to retrieve node list\");\n return cachedDiscoNodes;\n }\n lastRefresh = System.currentTimeMillis();\n }\n logger.debug(\"start building nodes list using GCE API\");\n\n cachedDiscoNodes = Lists.newArrayList();\n String ipAddress = null;\n try {\n InetAddress inetAddress = networkService.resolvePublishHostAddress(null);\n if (inetAddress != null) {\n ipAddress = inetAddress.getHostAddress();\n }\n } catch (IOException e) {\n // We can't find the publish host address... Hmmm. Too bad :-(\n // We won't simply filter it\n }\n\n try {\n Collection instances = gceComputeService.instances();\n\n for (Instance instance : instances) {\n String name = instance.getName();\n String type = instance.getMachineType();\n String image = instance.getImage();\n\n String status = instance.getStatus();\n logger.trace(\"gce instance {} with status {} found.\", name, status);\n\n // We don't want to connect to TERMINATED status instances\n // See https://github.com/elasticsearch/elasticsearch-cloud-gce/issues/3\n if (Status.TERMINATED.equals(status)) {\n logger.debug(\"node {} is TERMINATED. Ignoring\", name);\n continue;\n }\n\n // see if we need to filter by tag\n boolean filterByTag = false;\n if (tags.length > 0) {\n logger.trace(\"start filtering instance {} with tags {}.\", name, tags);\n if (instance.getTags() == null || instance.getTags().isEmpty()) {\n // If this instance have no tag, we filter it\n logger.trace(\"no tags for this instance but we asked for tags. {} won't be part of the cluster.\", name);\n filterByTag = true;\n } else {\n // check that all tags listed are there on the instance\n logger.trace(\"comparing instance tags {} with tags filter {}.\", instance.getTags().getItems(), tags);\n for (String tag : tags) {\n boolean found = false;\n for (String instancetag : instance.getTags().getItems()) {\n if (instancetag.equals(tag)) {\n found = true;\n break;\n }\n }\n if (!found) {\n filterByTag = true;\n break;\n }\n }\n }\n }\n if (filterByTag) {\n logger.trace(\"*** filtering out instance {} based tags {}, not part of {}\", name, tags,\n instance.getTags() == null ? \"\" : instance.getTags().getItems());\n continue;\n } else {\n logger.trace(\"*** instance {} with tags {} is added to discovery\", name, tags);\n }\n\n String ip_public = null;\n String ip_private = null;\n\n List interfaces = instance.getNetworkInterfaces();\n\n for (NetworkInterface networkInterface : interfaces) {\n if (ip_public == null) {\n // Trying to get Public IP Address (For future use)\n if (networkInterface.getAccessConfigs() != null) {\n for (AccessConfig accessConfig : networkInterface.getAccessConfigs()) {\n if (Strings.hasText(accessConfig.getNatIP())) {\n ip_public = accessConfig.getNatIP();\n break;\n }\n }\n }\n }\n\n if (ip_private == null) {\n ip_private = networkInterface.getNetworkIP();\n }\n\n // If we have both public and private, we can stop here\n if (ip_private != null && ip_public != null) break;\n }\n\n try {\n if (ip_private.equals(ipAddress)) {\n // We found the current node.\n // We can ignore it in the list of DiscoveryNode\n logger.trace(\"current node found. Ignoring {} - {}\", name, ip_private);\n } else {\n TransportAddress[] addresses = transportService.addressesFromString(ip_private);\n // we only limit to 1 addresses, makes no sense to ping 100 ports\n for (int i = 0; (i < addresses.length && i < UnicastZenPing.LIMIT_PORTS_COUNT); i++) {\n logger.trace(\"adding {}, type {}, image {}, address {}, transport_address {}, status {}\", name, type,\n image, ip_private, addresses[i], status);\n cachedDiscoNodes.add(new DiscoveryNode(\"#cloud-\" + name + \"-\" + i, addresses[i]));\n }\n }\n } catch (Exception e) {\n logger.warn(\"failed to add {}, address {}\", e, name, ip_private);\n }\n\n }\n } catch (Throwable e) {\n logger.warn(\"Exception caught during discovery {} : {}\", e.getClass().getName(), e.getMessage());\n logger.trace(\"Exception caught during discovery\", e);\n }\n\n logger.debug(\"using dynamic discovery nodes {}\", cachedDiscoNodes);\n return cachedDiscoNodes;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 19 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void harvest(IceMediaStream mediaStream, PortManager portManager, Selector selector) throws HarvestException, NoCandidatesGatheredException {\n\t\t// Safe copy of currently registered harvesters\n\t\tMap copy;\n\t\tsynchronized (this.harvesters) {\n\t\t\tcopy = new HashMap(this.harvesters);\n\t\t}\n\n\t\t// Ask each harvester to gather candidates for the media stream\n\t\t// HOST candidates take precedence and are mandatory\n\t\tCandidateHarvester hostHarvester = copy.get(CandidateType.HOST);\n\t\tif (hostHarvester != null) {\n\t\t\thostHarvester.harvest(portManager, mediaStream, selector);\n\t\t} else {\n\t\t\tthrow new HarvestException(\"No HOST harvester registered!\");\n\t\t}\n\t\t// Then comes the SRFLX, which depends on HOST candidates\n\t\tCandidateHarvester srflxHarvester = copy.get(CandidateType.SRFLX);\n\t\tif (srflxHarvester != null) {\n\t\t\tsrflxHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\t\t// RELAY candidates come last\n\t\tCandidateHarvester relayHarvester = copy.get(CandidateType.RELAY);\n\t\tif (relayHarvester != null) {\n\t\t\trelayHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\n\t\t// Verify at least one candidate was gathered\n\t\tif (!mediaStream.hasLocalRtpCandidates()) {\n\t\t\tthrow new NoCandidatesGatheredException(\"No RTP candidates were gathered for \" + mediaStream.getName() + \" stream\");\n\t\t}\n\n\t\t// After harvesting all possible candidates, ask the media stream to\n\t\t// select its default local candidates\n\t\tmediaStream.getRtpComponent().selectDefaultLocalCandidate();\n\t\tif (mediaStream.supportsRtcp() && !mediaStream.isRtcpMux()) {\n\t\t\tmediaStream.getRtcpComponent().selectDefaultLocalCandidate();\n\t\t}\n\t} \n #location 34 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void harvest(IceMediaStream mediaStream, PortManager portManager, Selector selector) throws HarvestException, NoCandidatesGatheredException {\n\t\t// Ask each harvester to gather candidates for the media stream\n\t\t// HOST candidates take precedence and are mandatory\n\t\tCandidateHarvester hostHarvester = harvesters.get(CandidateType.HOST);\n\t\tif (hostHarvester != null) {\n\t\t\thostHarvester.harvest(portManager, mediaStream, selector);\n\t\t} else {\n\t\t\tthrow new HarvestException(\"No HOST harvester registered!\");\n\t\t}\n\t\t// Then comes the SRFLX, which depends on HOST candidates\n\t\tCandidateHarvester srflxHarvester = harvesters.get(CandidateType.SRFLX);\n\t\tif (srflxHarvester != null) {\n\t\t\tsrflxHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\t\t// RELAY candidates come last\n\t\tCandidateHarvester relayHarvester = harvesters.get(CandidateType.RELAY);\n\t\tif (relayHarvester != null) {\n\t\t\trelayHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\n\t\t// Verify at least one candidate was gathered\n\t\tif (!mediaStream.hasLocalRtpCandidates()) {\n\t\t\tthrow new NoCandidatesGatheredException(\"No RTP candidates were gathered for \" + mediaStream.getName() + \" stream\");\n\t\t}\n\n\t\t// After harvesting all possible candidates, ask the media stream to\n\t\t// select its default local candidates\n\t\tmediaStream.getRtpComponent().selectDefaultLocalCandidate();\n\t\tif (mediaStream.supportsRtcp() && !mediaStream.isRtcpMux()) {\n\t\t\tmediaStream.getRtcpComponent().selectDefaultLocalCandidate();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void leaveRtpSession() {\n if (this.joined.get()) {\n this.joined.set(false);\n\n /*\n * When the participant decides to leave the system, tp is reset to tc, the current time, members and pmembers are\n * initialized to 1, initial is set to 1, we_sent is set to false, senders is set to 0, and avg_rtcp_size is set to\n * the size of the compound BYE packet.\n * \n * The calculated interval T is computed. The BYE packet is then scheduled for time tn = tc + T.\n */\n this.tp = this.statistics.getCurrentTime();\n this.statistics.resetMembers();\n this.initial.set(true);\n this.statistics.clearSenders();\n\n // XXX Sending the BYE packet NOW, since channel will be closed - hrosa\n // long t = this.statistics.rtcpInterval(initial);\n // this.tn = resolveDelay(t);\n // this.scheduleRtcp(this.tn, RtcpPacketType.RTCP_BYE);\n\n // cancel scheduled task and schedule BYE now\n if(this.reportTaskFuture != null) {\n this.reportTaskFuture.cancel(true);\n }\n scheduleNow(RtcpPacketType.RTCP_BYE);\n }\n } \n #location 26 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void leaveRtpSession() {\n if (this.joined.get()) {\n this.joined.set(false);\n\n /*\n * When the participant decides to leave the system, tp is reset to tc, the current time, members and pmembers are\n * initialized to 1, initial is set to 1, we_sent is set to false, senders is set to 0, and avg_rtcp_size is set to\n * the size of the compound BYE packet.\n * \n * The calculated interval T is computed. The BYE packet is then scheduled for time tn = tc + T.\n */\n this.tp = this.statistics.getCurrentTime();\n this.statistics.resetMembers();\n this.initial.set(true);\n this.statistics.clearSenders();\n\n // XXX Sending the BYE packet NOW, since channel will be closed - hrosa\n // long t = this.statistics.rtcpInterval(initial);\n // this.tn = resolveDelay(t);\n // this.scheduleRtcp(this.tn, RtcpPacketType.RTCP_BYE);\n\n // cancel scheduled task and schedule BYE now\n if(this.reportTaskFuture != null) {\n this.reportTaskFuture.cancel(true);\n }\n \n // Send BYE\n // Do not run in separate thread so channel can be properly closed by the owner of this handler\n this.statistics.setRtcpPacketType(RtcpPacketType.RTCP_BYE);\n this.scheduledTask = new TxTask(RtcpPacketType.RTCP_BYE);\n this.scheduledTask.run();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void startMixer() {\n if (!started) {\n started = true;\n output.buffer.clear();\n scheduler.submit(mixer,scheduler.MIXER_MIX_QUEUE);\n mixCount = 0;\n Iterator activeInputs=inputs.iterator();\n while(activeInputs.hasNext())\n \tactiveInputs.next().start(); \n }\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void startMixer() {\n if (!started) {\n started = true;\n output.resetBuffer(); \n mixCount = 0;\n Iterator activeInputs=inputs.iterator();\n Input currInput;\n while(activeInputs.hasNext())\n {\n \tcurrInput=activeInputs.next();\n \tcurrInput.resetBuffer();\n \tcurrInput.start();\n } \t \n scheduler.submit(mixer,scheduler.MIXER_MIX_QUEUE);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 17 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testCodec() throws Exception {\n \t\n \tboolean testPassed = false;\n \t\n \ttry {\n \t\tfinal int packetSize = 480;\n \t\tFile outputFile = File.createTempFile(\"opustest\", \".tmp\");\n\t FileInputStream inputStream = new FileInputStream(\"src\\\\test\\\\resources\\\\test_sound_mono_48.pcm\");\n\t FileOutputStream outputStream = new FileOutputStream(outputFile, false);\n\t \t\n\t \tOpusJni opus = new OpusJni();\n\t \topus.initNative();\n\n\t try {\n\t \tbyte[] input = new byte[packetSize];\n\t \tshort[] inputData = new short[packetSize];\n \t\tbyte[] output = new byte[2 * packetSize];\n\t \twhile (inputStream.read(input) == 2 * packetSize) {\n\t \t\tByteBuffer.wrap(input).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().get(inputData);\n\t \t\tbyte[] encodedData = opus.encodeNative(inputData);\n\t \t\tshort[] decodedData = opus.decodeNative(encodedData);\n\t \t\tByteBuffer.wrap(output).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().put(decodedData);\n\t \t\toutputStream.write(output);\n\t \t}\n \t\ttestPassed = true;\n\t } finally {\n\t \tinputStream.close();\n\t \toutputStream.close();\n\t \topus.closeNative();\n\t \toutputFile.delete();\n\t }\n \t} catch (IOException exc) {\n \t\tlog.error(\"IOException: \" + exc.getMessage());\n \tfail(\"Opus test file access error\");\n \t}\n \t\n \tassertTrue(testPassed);\n } \n #location 33 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testCodec() throws Exception {\n \t\n \tboolean testPassed = false;\n \t\n \ttry {\t \t\n\t \tOpusJni opus = new OpusJni();\n\t \topus.initNative();\n\n \t\tfinal int packetSize = 480;\n \t\tFile outputFile = File.createTempFile(\"opustest\", \".tmp\");\n \t\tbyte[] output = new byte[2 * packetSize];\n\t try (FileInputStream inputStream = new FileInputStream(\"src\\\\test\\\\resources\\\\test_sound_mono_48.pcm\");\n\t \t\tFileOutputStream outputStream = new FileOutputStream(outputFile, false)) {\n\t \tbyte[] input = new byte[packetSize];\n\t \tshort[] inputData = new short[packetSize];\n\t \twhile (inputStream.read(input) == 2 * packetSize) {\n\t \t\tByteBuffer.wrap(input).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().get(inputData);\n\t \t\tbyte[] encodedData = opus.encodeNative(inputData);\n\t \t\tshort[] decodedData = opus.decodeNative(encodedData);\n\t \t\tByteBuffer.wrap(output).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().put(decodedData);\n\t \t\toutputStream.write(output);\n\t \t}\n \t\ttestPassed = true;\n\t }\n\t \n \topus.closeNative();\n \toutputFile.delete();\n \t} catch (IOException exc) {\n \t\tlog.error(\"IOException: \" + exc.getMessage());\n \tfail(\"Opus test file access error\");\n \t}\n \t\n \tassertTrue(testPassed);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void harvest(IceMediaStream mediaStream, PortManager portManager, Selector selector) throws HarvestException, NoCandidatesGatheredException {\n\t\t// Safe copy of currently registered harvesters\n\t\tMap copy;\n\t\tsynchronized (this.harvesters) {\n\t\t\tcopy = new HashMap(this.harvesters);\n\t\t}\n\n\t\t// Ask each harvester to gather candidates for the media stream\n\t\t// HOST candidates take precedence and are mandatory\n\t\tCandidateHarvester hostHarvester = copy.get(CandidateType.HOST);\n\t\tif (hostHarvester != null) {\n\t\t\thostHarvester.harvest(portManager, mediaStream, selector);\n\t\t} else {\n\t\t\tthrow new HarvestException(\"No HOST harvester registered!\");\n\t\t}\n\t\t// Then comes the SRFLX, which depends on HOST candidates\n\t\tCandidateHarvester srflxHarvester = copy.get(CandidateType.SRFLX);\n\t\tif (srflxHarvester != null) {\n\t\t\tsrflxHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\t\t// RELAY candidates come last\n\t\tCandidateHarvester relayHarvester = copy.get(CandidateType.RELAY);\n\t\tif (relayHarvester != null) {\n\t\t\trelayHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\n\t\t// Verify at least one candidate was gathered\n\t\tif (!mediaStream.hasLocalRtpCandidates()) {\n\t\t\tthrow new NoCandidatesGatheredException(\"No RTP candidates were gathered for \" + mediaStream.getName() + \" stream\");\n\t\t}\n\n\t\t// After harvesting all possible candidates, ask the media stream to\n\t\t// select its default local candidates\n\t\tmediaStream.getRtpComponent().selectDefaultLocalCandidate();\n\t\tif (mediaStream.supportsRtcp() && !mediaStream.isRtcpMux()) {\n\t\t\tmediaStream.getRtcpComponent().selectDefaultLocalCandidate();\n\t\t}\n\t} \n #location 36 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void harvest(IceMediaStream mediaStream, PortManager portManager, Selector selector) throws HarvestException, NoCandidatesGatheredException {\n\t\t// Ask each harvester to gather candidates for the media stream\n\t\t// HOST candidates take precedence and are mandatory\n\t\tCandidateHarvester hostHarvester = harvesters.get(CandidateType.HOST);\n\t\tif (hostHarvester != null) {\n\t\t\thostHarvester.harvest(portManager, mediaStream, selector);\n\t\t} else {\n\t\t\tthrow new HarvestException(\"No HOST harvester registered!\");\n\t\t}\n\t\t// Then comes the SRFLX, which depends on HOST candidates\n\t\tCandidateHarvester srflxHarvester = harvesters.get(CandidateType.SRFLX);\n\t\tif (srflxHarvester != null) {\n\t\t\tsrflxHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\t\t// RELAY candidates come last\n\t\tCandidateHarvester relayHarvester = harvesters.get(CandidateType.RELAY);\n\t\tif (relayHarvester != null) {\n\t\t\trelayHarvester.harvest(portManager, mediaStream, selector);\n\t\t}\n\n\t\t// Verify at least one candidate was gathered\n\t\tif (!mediaStream.hasLocalRtpCandidates()) {\n\t\t\tthrow new NoCandidatesGatheredException(\"No RTP candidates were gathered for \" + mediaStream.getName() + \" stream\");\n\t\t}\n\n\t\t// After harvesting all possible candidates, ask the media stream to\n\t\t// select its default local candidates\n\t\tmediaStream.getRtpComponent().selectDefaultLocalCandidate();\n\t\tif (mediaStream.supportsRtcp() && !mediaStream.isRtcpMux()) {\n\t\t\tmediaStream.getRtcpComponent().selectDefaultLocalCandidate();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 16 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 35 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 23 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Frame read(long timestamp) {\n\t\ttry {\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\treturn null;\n\t\t\t}\n\n\n\t\t\t//extract packet\n\t\t\tFrame frame = queue.remove(0);\n\n\t\t\t//buffer empty now? - change ready flag.\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\t//arrivalDeadLine = 0;\n\t\t\t\t//set it as 1 ms since otherwise will be dropped by pipe\n\t\t\t\tframe.setDuration(1);\n\t\t\t}\n\n\n\t\t\tarrivalDeadLine = rtpClock.convertToRtpTime(frame.getTimestamp() + frame.getDuration());\n\n\t\t\t//convert duration to nanoseconds\n\t\t\tframe.setDuration(frame.getDuration() * 1000000L);\n\t\t\tframe.setTimestamp(frame.getTimestamp() * 1000000L);\n\n\t\t\treturn frame;\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n } \n #location 21 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Frame read(long timestamp) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\treturn null;\n\t\t\t}\n\n\n\t\t\t//extract packet\n\t\t\tFrame frame = queue.remove(0);\n\n\t\t\t//buffer empty now? - change ready flag.\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\t//arrivalDeadLine = 0;\n\t\t\t\t//set it as 1 ms since otherwise will be dropped by pipe\n\t\t\t\tframe.setDuration(1);\n\t\t\t}\n\n\n\t\t\tarrivalDeadLine = rtpClock.convertToRtpTime(frame.getTimestamp() + frame.getDuration());\n\n\t\t\t//convert duration to nanoseconds\n\t\t\tframe.setDuration(frame.getDuration() * 1000000L);\n\t\t\tframe.setTimestamp(frame.getTimestamp() * 1000000L);\n\n\t\t\treturn frame;\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 109 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 33 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 9 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private byte[] processRequest(StunRequest request, InetSocketAddress localPeer, InetSocketAddress remotePeer)\n throws IOException {\n\n // Produce Binding Response\n TransportAddress transportAddress = new TransportAddress(remotePeer.getAddress(), remotePeer.getPort(), TransportProtocol.UDP);\n StunResponse response = StunMessageFactory.createBindingResponse(request, transportAddress);\n byte[] transactionID = request.getTransactionId();\n try {\n response.setTransactionID(transactionID);\n } catch (StunException e) {\n throw new IOException(\"Illegal STUN Transaction ID: \" + new String(transactionID), e);\n }\n\n // The agent MUST use a short-term credential to authenticate the request and perform a message integrity check.\n UsernameAttribute remoteUnameAttribute;\n String remoteUsername;\n // Send binding error response if username is null\n try {\n remoteUnameAttribute = (UsernameAttribute) request.getAttribute(StunAttribute.USERNAME);\n remoteUsername = new String(remoteUnameAttribute.getUsername());\n }\n catch(NullPointerException nullPointer) {\n response.setMessageType(StunMessage.BINDING_ERROR_RESPONSE);\n response.addAttribute(StunAttributeFactory.createErrorCodeAttribute(ErrorCodeAttribute.BAD_REQUEST,\n ErrorCodeAttribute.getDefaultReasonPhrase(ErrorCodeAttribute.BAD_REQUEST)));\n return response.encode();\n } \n\n // The agent MUST consider the username to be valid if it consists of two values separated by a colon, where the first\n // value is equal to the username fragment generated by the agent in an offer or answer for a session in-progress.\n if (!this.authenticator.validateUsername(remoteUsername)) {\n // TODO return error response\n throw new IOException(\"Invalid username \" + remoteUsername);\n }\n\n // The username for the credential is formed by concatenating the username fragment provided by the peer with the\n // username fragment of the agent sending the request, separated by a colon (\":\").\n int colon = remoteUsername.indexOf(\":\");\n String localUFrag = remoteUsername.substring(0, colon);\n String remoteUfrag = remoteUsername.substring(colon + 1);\n\n // Add USERNAME and MESSAGE-INTEGRITY attribute in the response.\n // The responses utilize the same usernames and passwords as the requests.\n String localUsername = remoteUfrag.concat(\":\").concat(localUFrag);\n StunAttribute unameAttribute = StunAttributeFactory.createUsernameAttribute(localUsername);\n response.addAttribute(unameAttribute);\n\n byte[] localKey = this.authenticator.getLocalKey(localUFrag);\n MessageIntegrityAttribute integrityAttribute = StunAttributeFactory.createMessageIntegrityAttribute(remoteUsername,\n localKey);\n response.addAttribute(integrityAttribute);\n\n // If the client issues a USE-CANDIDATE, tell ICE Agent to select the candidate\n if (request.containsAttribute(StunAttribute.USE_CANDIDATE)) {\n if (!this.candidateSelected.get()) {\n this.candidateSelected.set(true);\n if (logger.isDebugEnabled()) {\n logger.debug(\"Selected candidate \" + remotePeer.toString());\n }\n this.iceListener.onSelectedCandidates(new SelectedCandidatesEvent(remotePeer));\n }\n }\n\n // Pass response to the server\n return response.encode();\n } \n #location 20 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private byte[] processRequest(StunRequest request, InetSocketAddress localPeer, InetSocketAddress remotePeer)\n throws IOException {\n\n // Produce Binding Response\n TransportAddress transportAddress = new TransportAddress(remotePeer.getAddress(), remotePeer.getPort(), TransportProtocol.UDP);\n StunResponse response = StunMessageFactory.createBindingResponse(request, transportAddress);\n byte[] transactionID = request.getTransactionId();\n try {\n response.setTransactionID(transactionID);\n } catch (StunException e) {\n throw new IOException(\"Illegal STUN Transaction ID: \" + new String(transactionID), e);\n }\n\n // The agent MUST use a short-term credential to authenticate the request and perform a message integrity check.\n UsernameAttribute remoteUnameAttribute = (UsernameAttribute) request.getAttribute(StunAttribute.USERNAME);;\n\n // Send binding error response if username is null\n if (remoteUnameAttribute.getUsername()==null) {\n response.setMessageType(StunMessage.BINDING_ERROR_RESPONSE);\n response.addAttribute(StunAttributeFactory.createErrorCodeAttribute(ErrorCodeAttribute.BAD_REQUEST,\n ErrorCodeAttribute.getDefaultReasonPhrase(ErrorCodeAttribute.BAD_REQUEST)));\n return response.encode();\n }\n String remoteUsername = new String(remoteUnameAttribute.getUsername());\n\n // The agent MUST consider the username to be valid if it consists of two values separated by a colon, where the first\n // value is equal to the username fragment generated by the agent in an offer or answer for a session in-progress.\n if (!this.authenticator.validateUsername(remoteUsername)) {\n // TODO return error response\n throw new IOException(\"Invalid username \" + remoteUsername);\n }\n\n // The username for the credential is formed by concatenating the username fragment provided by the peer with the\n // username fragment of the agent sending the request, separated by a colon (\":\").\n int colon = remoteUsername.indexOf(\":\");\n String localUFrag = remoteUsername.substring(0, colon);\n String remoteUfrag = remoteUsername.substring(colon + 1);\n\n // Add USERNAME and MESSAGE-INTEGRITY attribute in the response.\n // The responses utilize the same usernames and passwords as the requests.\n String localUsername = remoteUfrag.concat(\":\").concat(localUFrag);\n StunAttribute unameAttribute = StunAttributeFactory.createUsernameAttribute(localUsername);\n response.addAttribute(unameAttribute);\n\n byte[] localKey = this.authenticator.getLocalKey(localUFrag);\n MessageIntegrityAttribute integrityAttribute = StunAttributeFactory.createMessageIntegrityAttribute(remoteUsername,\n localKey);\n response.addAttribute(integrityAttribute);\n\n // If the client issues a USE-CANDIDATE, tell ICE Agent to select the candidate\n if (request.containsAttribute(StunAttribute.USE_CANDIDATE)) {\n if (!this.candidateSelected.get()) {\n this.candidateSelected.set(true);\n if (logger.isDebugEnabled()) {\n logger.debug(\"Selected candidate \" + remotePeer.toString());\n }\n this.iceListener.onSelectedCandidates(new SelectedCandidatesEvent(remotePeer));\n }\n }\n\n // Pass response to the server\n return response.encode();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 52 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 29 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public String open(String sdp) throws MgcpConnectionException {\n synchronized (this.stateLock) {\n switch (this.state) {\n case CLOSED:\n case HALF_OPEN:\n // Update state\n this.state = MgcpConnectionState.OPEN;\n\n // Parse remote SDP\n try {\n this.remoteSdp = SessionDescriptionParser.parse(sdp);\n } catch (SdpException e) {\n throw new MgcpConnectionException(e.getMessage(), e);\n }\n\n // Open connection\n openConnection();\n \n if(log.isDebugEnabled()) {\n log.debug(\"Connection \" + getHexIdentifier() + \" state is \" + this.state.name());\n }\n \n // Submit timer\n if (this.timeout > 0) {\n expireIn(this.timeout);\n }\n break;\n\n default:\n throw new MgcpConnectionException(\n \"Cannot open connection \" + this.getHexIdentifier() + \" because state is \" + this.state.name());\n }\n }\n return this.localSdp.toString();\n } \n #location 35 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public String open(String sdp) throws MgcpConnectionException {\n synchronized (this.stateLock) {\n switch (this.state) {\n case CLOSED:\n case HALF_OPEN:\n // Update state\n this.state = MgcpConnectionState.OPEN;\n\n // Parse remote SDP\n try {\n this.remoteSdp = SessionDescriptionParser.parse(sdp);\n } catch (SdpException e) {\n throw new MgcpConnectionException(e.getMessage(), e);\n }\n\n // Open connection\n openConnection();\n \n if(log.isDebugEnabled()) {\n log.debug(\"Connection \" + getHexIdentifier() + \" state is \" + this.state.name());\n }\n \n // Submit timer\n if (this.timeout > 0) {\n expireIn(this.timeout);\n }\n break;\n\n default:\n throw new MgcpConnectionException(\"Cannot open connection \" + this.getHexIdentifier() + \" because state is \" + this.state.name());\n }\n }\n return this.localSdp.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 34 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 15 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testCodec() throws Exception {\n \t\n \tboolean testPassed = false;\n \t\n \ttry {\n \t\tfinal int packetSize = 480;\n \t\tFile outputFile = File.createTempFile(\"opustest\", \".tmp\");\n\t FileInputStream inputStream = new FileInputStream(\"src\\\\test\\\\resources\\\\test_sound_mono_48.pcm\");\n\t FileOutputStream outputStream = new FileOutputStream(outputFile, false);\n\t \t\n\t \tOpusJni opus = new OpusJni();\n\t \topus.initNative();\n\n\t try {\n\t \tbyte[] input = new byte[packetSize];\n\t \tshort[] inputData = new short[packetSize];\n \t\tbyte[] output = new byte[2 * packetSize];\n\t \twhile (inputStream.read(input) == 2 * packetSize) {\n\t \t\tByteBuffer.wrap(input).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().get(inputData);\n\t \t\tbyte[] encodedData = opus.encodeNative(inputData);\n\t \t\tshort[] decodedData = opus.decodeNative(encodedData);\n\t \t\tByteBuffer.wrap(output).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().put(decodedData);\n\t \t\toutputStream.write(output);\n\t \t}\n \t\ttestPassed = true;\n\t } finally {\n\t \tinputStream.close();\n\t \toutputStream.close();\n\t \topus.closeNative();\n\t \toutputFile.delete();\n\t }\n \t} catch (IOException exc) {\n \t\tlog.error(\"IOException: \" + exc.getMessage());\n \tfail(\"Opus test file access error\");\n \t}\n \t\n \tassertTrue(testPassed);\n } \n #location 33 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testCodec() throws Exception {\n \t\n \tboolean testPassed = false;\n \t\n \ttry {\t \t\n\t \tOpusJni opus = new OpusJni();\n\t \topus.initNative();\n\n \t\tfinal int packetSize = 480;\n \t\tFile outputFile = File.createTempFile(\"opustest\", \".tmp\");\n \t\tbyte[] output = new byte[2 * packetSize];\n\t try (FileInputStream inputStream = new FileInputStream(\"src\\\\test\\\\resources\\\\test_sound_mono_48.pcm\");\n\t \t\tFileOutputStream outputStream = new FileOutputStream(outputFile, false)) {\n\t \tbyte[] input = new byte[packetSize];\n\t \tshort[] inputData = new short[packetSize];\n\t \twhile (inputStream.read(input) == 2 * packetSize) {\n\t \t\tByteBuffer.wrap(input).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().get(inputData);\n\t \t\tbyte[] encodedData = opus.encodeNative(inputData);\n\t \t\tshort[] decodedData = opus.decodeNative(encodedData);\n\t \t\tByteBuffer.wrap(output).order(ByteOrder.LITTLE_ENDIAN).asShortBuffer().put(decodedData);\n\t \t\toutputStream.write(output);\n\t \t}\n \t\ttestPassed = true;\n\t }\n\t \n \topus.closeNative();\n \toutputFile.delete();\n \t} catch (IOException exc) {\n \t\tlog.error(\"IOException: \" + exc.getMessage());\n \tfail(\"Opus test file access error\");\n \t}\n \t\n \tassertTrue(testPassed);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Frame read(long timestamp) {\n\t\ttry {\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\treturn null;\n\t\t\t}\n\n\n\t\t\t//extract packet\n\t\t\tFrame frame = queue.remove(0);\n\n\t\t\t//buffer empty now? - change ready flag.\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\t//arrivalDeadLine = 0;\n\t\t\t\t//set it as 1 ms since otherwise will be dropped by pipe\n\t\t\t\tframe.setDuration(1);\n\t\t\t}\n\n\n\t\t\tarrivalDeadLine = rtpClock.convertToRtpTime(frame.getTimestamp() + frame.getDuration());\n\n\t\t\t//convert duration to nanoseconds\n\t\t\tframe.setDuration(frame.getDuration() * 1000000L);\n\t\t\tframe.setTimestamp(frame.getTimestamp() * 1000000L);\n\n\t\t\treturn frame;\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n } \n #location 21 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public Frame read(long timestamp) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\treturn null;\n\t\t\t}\n\n\n\t\t\t//extract packet\n\t\t\tFrame frame = queue.remove(0);\n\n\t\t\t//buffer empty now? - change ready flag.\n\t\t\tif (queue.size() == 0) {\n\t\t\t\tthis.ready = false;\n\t\t\t\t//arrivalDeadLine = 0;\n\t\t\t\t//set it as 1 ms since otherwise will be dropped by pipe\n\t\t\t\tframe.setDuration(1);\n\t\t\t}\n\n\n\t\t\tarrivalDeadLine = rtpClock.convertToRtpTime(frame.getTimestamp() + frame.getDuration());\n\n\t\t\t//convert duration to nanoseconds\n\t\t\tframe.setDuration(frame.getDuration() * 1000000L);\n\t\t\tframe.setTimestamp(frame.getTimestamp() * 1000000L);\n\n\t\t\treturn frame;\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void stop() {\n\t\twhile (buffer.size() > 0) {\n\t\t\tbuffer.poll().recycle();\n\t\t}\n\t\tsuper.stop();\n\t} \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic void stop() {\n\t\twhile (buffer.size() > 0) {\n\t\t\tFrame frame = buffer.poll();\n\t\t\tif(frame != null) {\n\t\t\t frame.recycle();\n\t\t\t}\n\t\t}\n\t\tsuper.stop();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 46 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 30 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 14 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 41 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void write(RtpPacket packet, RTPFormat format) {\n\t\t// checking format\n\t\tif (format == null) {\n\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\treturn;\n\t\t}\n\n\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\tthis.format = format;\n\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t}\n\n\t\t// if this is first packet then synchronize clock\n\t\tif (isn == -1) {\n\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\tisn = packet.getSeqNumber();\n\t\t\tinitJitter(packet);\n\t\t} else {\n\t\t\testimateJitter(packet);\n\t\t}\n\n\t\t// update clock rate\n\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t// drop outstanding packets\n\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t// then consumer media time\n\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\tdropCount++;\n\n\t\t\t// checking if not dropping too much\n\t\t\tdroppedInRaw++;\n\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\tarrivalDeadLine = 0;\n\t\t\t} else {\n\t\t\t\treturn;\n\t\t\t}\n\t\t}\n\n\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t// put packet into buffer irrespective of its sequence number\n\t\tf.setHeader(null);\n\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t// here time is in milliseconds\n\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\tf.setOffset(0);\n\t\tf.setLength(packet.getPayloadLength());\n\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t// set format\n\t\tf.setFormat(this.format.getFormat());\n\t\t\n\t\t// make checks only if have packet\n\t\tif (f != null) {\n\t\t LOCK.lock();\n\n\t\t droppedInRaw = 0;\n\n\t\t\t// find correct position to insert a packet\n\t\t\t// use timestamp since its always positive\n\t\t\tint currIndex = queue.size() - 1;\n\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\tcurrIndex--;\n\t\t\t}\n\n\t\t\t// check for duplicate packet\n\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t LOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\tduration = 0;\n\t\t\tif (queue.size() > 1) {\n\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t}\n\n\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t// duration measured by wall clock\n\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t}\n\n\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t// reset\n\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\treset();\n\t\t\t\tLOCK.unlock();\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// overflow?\n\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\tdropCount++;\n\t\t\t\tqueue.remove(0).recycle();\n\t\t\t}\n\t\t\tLOCK.unlock();\n\n\t\t\t// check if this buffer already full\n\t\t\tif (!ready) {\n\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\tlistener.onFill();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 111 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void write(RtpPacket packet, RTPFormat format) {\n\t\ttry {\n\t\t\tLOCK.lock();\n\t\t\t// checking format\n\t\t\tif (format == null) {\n\t\t\t\tlogger.warn(\"No format specified. Packet dropped!\");\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tif (this.format == null || this.format.getID() != format.getID()) {\n\t\t\t\tthis.format = format;\n\t\t\t\tlogger.info(\"Format has been changed: \" + this.format.toString());\n\t\t\t}\n\n\t\t\t// if this is first packet then synchronize clock\n\t\t\tif (isn == -1) {\n\t\t\t\trtpClock.synchronize(packet.getTimestamp());\n\t\t\t\tisn = packet.getSeqNumber();\n\t\t\t\tinitJitter(packet);\n\t\t\t} else {\n\t\t\t\testimateJitter(packet);\n\t\t\t}\n\n\t\t\t// update clock rate\n\t\t\trtpClock.setClockRate(this.format.getClockRate());\n\n\t\t\t// drop outstanding packets\n\t\t\t// packet is outstanding if its timestamp of arrived packet is less\n\t\t\t// then consumer media time\n\t\t\tif (packet.getTimestamp() < this.arrivalDeadLine) {\n\t\t\t\tlogger.warn(\"drop packet: dead line=\" + arrivalDeadLine + \", packet time=\" + packet.getTimestamp() + \", seq=\" + packet.getSeqNumber() + \", payload length=\" + packet.getPayloadLength() + \", format=\" + this.format.toString());\n\t\t\t\tdropCount++;\n\n\t\t\t\t// checking if not dropping too much\n\t\t\t\tdroppedInRaw++;\n\t\t\t\tif (droppedInRaw == QUEUE_SIZE / 2 || queue.size() == 0) {\n\t\t\t\t\tarrivalDeadLine = 0;\n\t\t\t\t} else {\n\t\t\t\t\treturn;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tFrame f = Memory.allocate(packet.getPayloadLength());\n\t\t\t// put packet into buffer irrespective of its sequence number\n\t\t\tf.setHeader(null);\n\t\t\tf.setSequenceNumber(packet.getSeqNumber());\n\t\t\t// here time is in milliseconds\n\t\t\tf.setTimestamp(rtpClock.convertToAbsoluteTime(packet.getTimestamp()));\n\t\t\tf.setOffset(0);\n\t\t\tf.setLength(packet.getPayloadLength());\n\t\t\tpacket.getPayload(f.getData(), 0);\n\n\t\t\t// set format\n\t\t\tf.setFormat(this.format.getFormat());\n\n\t\t\t// make checks only if have packet\n\t\t\tif (f != null) {\n\n\t\t\t\tdroppedInRaw = 0;\n\n\t\t\t\t// find correct position to insert a packet\n\t\t\t\t// use timestamp since its always positive\n\t\t\t\tint currIndex = queue.size() - 1;\n\t\t\t\twhile (currIndex >= 0 && queue.get(currIndex).getTimestamp() > f.getTimestamp()) {\n\t\t\t\t\tcurrIndex--;\n\t\t\t\t}\n\n\t\t\t\t// check for duplicate packet\n\t\t\t\tif (currIndex >= 0 && queue.get(currIndex).getSequenceNumber() == f.getSequenceNumber()) {\n\t\t\t\t\tLOCK.unlock();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\tqueue.add(currIndex + 1, f);\n\n\t\t\t\t// recalculate duration of each frame in queue and overall duration\n\t\t\t\t// since we could insert the frame in the middle of the queue\n\t\t\t\tduration = 0;\n\t\t\t\tif (queue.size() > 1) {\n\t\t\t\t\tduration = queue.get(queue.size() - 1).getTimestamp() - queue.get(0).getTimestamp();\n\t\t\t\t}\n\n\t\t\t\tfor (int i = 0; i < queue.size() - 1; i++) {\n\t\t\t\t\t// duration measured by wall clock\n\t\t\t\t\tlong d = queue.get(i + 1).getTimestamp() - queue.get(i).getTimestamp();\n\t\t\t\t\t// in case of RFC2833 event timestamp remains same\n\t\t\t\t\tqueue.get(i).setDuration(d > 0 ? d : 0);\n\t\t\t\t}\n\n\t\t\t\t// if overall duration is negative we have some mess here,try to\n\t\t\t\t// reset\n\t\t\t\tif (duration < 0 && queue.size() > 1) {\n\t\t\t\t\tlogger.warn(\"Something messy happened. Reseting jitter buffer!\");\n\t\t\t\t\treset();\n\t\t\t\t\treturn;\n\t\t\t\t}\n\n\t\t\t\t// overflow?\n\t\t\t\t// only now remove packet if overflow , possibly the same packet we just received\n\t\t\t\tif (queue.size() > QUEUE_SIZE) {\n\t\t\t\t\tlogger.warn(\"Buffer overflow!\");\n\t\t\t\t\tdropCount++;\n\t\t\t\t\tqueue.remove(0).recycle();\n\t\t\t\t}\n\n\t\t\t\t// check if this buffer already full\n\t\t\t\tif (!ready) {\n\t\t\t\t\tready = !useBuffer || (duration >= jitterBufferSize && queue.size() > 1);\n\t\t\t\t\tif (ready && listener != null) {\n\t\t\t\t\t\tlistener.onFill();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} finally {\n\t\t\tLOCK.unlock();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public int count() {\n\t\treturn this.count;\n\t} \n #location 2 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public int count() {\n return this.count;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private byte[] processRequest(StunRequest request, InetSocketAddress localPeer, InetSocketAddress remotePeer) throws IOException {\n\t\t/*\n\t\t * The agent MUST use a short-term credential to authenticate the\n\t\t * request and perform a message integrity check.\n\t\t */\n\n\t\t// Produce Binding Response\n\t\tTransportAddress transportAddress = new TransportAddress(remotePeer.getAddress(), remotePeer.getPort(), TransportProtocol.UDP);\n\t\tStunResponse response = StunMessageFactory.createBindingResponse(request, transportAddress);\n\t\tbyte[] transactionID = request.getTransactionId();\n\t\ttry {\n\t\t\tresponse.setTransactionID(transactionID);\n\t\t} catch (StunException e) {\n\t\t\tthrow new IOException(\"Illegal STUN Transaction ID: \" + new String(transactionID), e);\n\t\t}\n\n\t\tUsernameAttribute remoteUnameAttribute;\n\t\tString remoteUsername;\n\t\t// Send binding error response if username is null\n\t\ttry {\n\t\t\tremoteUnameAttribute = (UsernameAttribute) request.getAttribute(StunAttribute.USERNAME);\n\t\t\tremoteUsername = new String(remoteUnameAttribute.getUsername());\n\t\t}\n\t\tcatch(NullPointerException nullPointer) {\n\t\t\tresponse.setMessageType(StunMessage.BINDING_ERROR_RESPONSE);\n\t\t\tresponse.addAttribute(StunAttributeFactory.createErrorCodeAttribute(ErrorCodeAttribute.BAD_REQUEST,\n\t\t\t\t\tErrorCodeAttribute.getDefaultReasonPhrase(ErrorCodeAttribute.BAD_REQUEST)));\n\t\t\treturn response.encode();\n\t\t}\n\t\t\n\t\t/*\n\t\t * The agent MUST consider the username to be valid if it consists of\n\t\t * two values separated by a colon, where the first value is equal to\n\t\t * the username fragment generated by the agent in an offer or answer\n\t\t * for a session in-progress.\n\t\t */\n\t\tif(!this.iceAuthenticator.validateUsername(remoteUsername)) {\n\t\t\t// TODO return error response\n\t\t\tthrow new IOException(\"Invalid username \"+ remoteUsername);\n\t\t}\n\t\t\n\t\t/*\n\t\t * The username for the credential is formed by concatenating the\n\t\t * username fragment provided by the peer with the username fragment of\n\t\t * the agent sending the request, separated by a colon (\":\").\n\t\t */\n\t\tint colon = remoteUsername.indexOf(\":\");\n\t\tString localUFrag = remoteUsername.substring(0, colon);\n\t\tString remoteUfrag = remoteUsername.substring(colon);\n\t\t\n\t\t/*\n\t\t * An agent MUST include the PRIORITY attribute in its Binding request.\n\t\t * This priority value will be computed identically to how the priority\n\t\t * for the local candidate of the pair was computed, except that the\n\t\t * type preference is set to the value for peer reflexive candidate\n\t\t * types\n\t\t */\n\t\tlong priority = extractPriority(request);\n\n\t\t/*\n\t\t * Add USERNAME and MESSAGE-INTEGRITY attribute in the response. The\n\t\t * responses utilize the same usernames and passwords as the requests\n\t\t */\n\t\tString localUsername = remoteUfrag.concat(\":\").concat(localUFrag);\n\t\tStunAttribute unameAttribute = StunAttributeFactory.createUsernameAttribute(localUsername);\n\t\tresponse.addAttribute(unameAttribute);\n\n\t\tbyte[] localKey = this.iceAuthenticator.getLocalKey(localUFrag);\n\t\tMessageIntegrityAttribute messageIntegrityAttribute = StunAttributeFactory.createMessageIntegrityAttribute(remoteUsername, localKey);\n\t\tresponse.addAttribute(messageIntegrityAttribute);\n\t\t\n\t\t// If the client issues a USE-CANDIDATE, tell ICE Agent to select the candidate\n\t\tif (request.containsAttribute(StunAttribute.USE_CANDIDATE)) {\n\t\t\tfireStunBindingEvent(localPeer, remotePeer);\n\t\t}\n\n\t\t// Pass response to the server\n\t\treturn response.encode();\n\t} \n #location 22 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private byte[] processRequest(StunRequest request, InetSocketAddress localPeer, InetSocketAddress remotePeer) throws IOException {\n\t\t/*\n\t\t * The agent MUST use a short-term credential to authenticate the\n\t\t * request and perform a message integrity check.\n\t\t */\n\n\t\t// Produce Binding Response\n\t\tTransportAddress transportAddress = new TransportAddress(remotePeer.getAddress(), remotePeer.getPort(), TransportProtocol.UDP);\n\t\tStunResponse response = StunMessageFactory.createBindingResponse(request, transportAddress);\n\t\tbyte[] transactionID = request.getTransactionId();\n\t\ttry {\n\t\t\tresponse.setTransactionID(transactionID);\n\t\t} catch (StunException e) {\n\t\t\tthrow new IOException(\"Illegal STUN Transaction ID: \" + new String(transactionID), e);\n\t\t}\n\n\t\tUsernameAttribute remoteUnameAttribute = (UsernameAttribute) request.getAttribute(StunAttribute.USERNAME);\n\n\t\t// Send binding error response if username is null\n\t\tif (remoteUnameAttribute.getUsername()== null)\t{\n\t\t\tresponse.setMessageType(StunMessage.BINDING_ERROR_RESPONSE);\n\t\t\tresponse.addAttribute(StunAttributeFactory.createErrorCodeAttribute(ErrorCodeAttribute.BAD_REQUEST,\n\t\t\t\t\tErrorCodeAttribute.getDefaultReasonPhrase(ErrorCodeAttribute.BAD_REQUEST)));\n\t\t\treturn response.encode();\n\t\t}\n\t\tString remoteUsername = new String(remoteUnameAttribute.getUsername());\n\t\t\n\t\t/*\n\t\t * The agent MUST consider the username to be valid if it consists of\n\t\t * two values separated by a colon, where the first value is equal to\n\t\t * the username fragment generated by the agent in an offer or answer\n\t\t * for a session in-progress.\n\t\t */\n\t\tif(!this.iceAuthenticator.validateUsername(remoteUsername)) {\n\t\t\t// TODO return error response\n\t\t\tthrow new IOException(\"Invalid username \"+ remoteUsername);\n\t\t}\n\t\t\n\t\t/*\n\t\t * The username for the credential is formed by concatenating the\n\t\t * username fragment provided by the peer with the username fragment of\n\t\t * the agent sending the request, separated by a colon (\":\").\n\t\t */\n\t\tint colon = remoteUsername.indexOf(\":\");\n\t\tString localUFrag = remoteUsername.substring(0, colon);\n\t\tString remoteUfrag = remoteUsername.substring(colon);\n\t\t\n\t\t/*\n\t\t * An agent MUST include the PRIORITY attribute in its Binding request.\n\t\t * This priority value will be computed identically to how the priority\n\t\t * for the local candidate of the pair was computed, except that the\n\t\t * type preference is set to the value for peer reflexive candidate\n\t\t * types\n\t\t */\n\t\tlong priority = extractPriority(request);\n\n\t\t/*\n\t\t * Add USERNAME and MESSAGE-INTEGRITY attribute in the response. The\n\t\t * responses utilize the same usernames and passwords as the requests\n\t\t */\n\t\tString localUsername = remoteUfrag.concat(\":\").concat(localUFrag);\n\t\tStunAttribute unameAttribute = StunAttributeFactory.createUsernameAttribute(localUsername);\n\t\tresponse.addAttribute(unameAttribute);\n\n\t\tbyte[] localKey = this.iceAuthenticator.getLocalKey(localUFrag);\n\t\tMessageIntegrityAttribute messageIntegrityAttribute = StunAttributeFactory.createMessageIntegrityAttribute(remoteUsername, localKey);\n\t\tresponse.addAttribute(messageIntegrityAttribute);\n\t\t\n\t\t// If the client issues a USE-CANDIDATE, tell ICE Agent to select the candidate\n\t\tif (request.containsAttribute(StunAttribute.USE_CANDIDATE)) {\n\t\t\tfireStunBindingEvent(localPeer, remotePeer);\n\t\t}\n\n\t\t// Pass response to the server\n\t\treturn response.encode();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void train(String dataFile, int maxite, float c) throws IOException {\n\n\t\tfp = File.createTempFile(\"train-features\", null, new File(\"./tmp/\"));\n\n\t\tbuildInstanceList(dataFile);\n\n\t\tLabelAlphabet postagAlphabet = factory.buildLabelAlphabet(\"postag\");\n\n\t\tIFeatureAlphabet features = factory.DefaultFeatureAlphabet();\n\n\t\tSFGenerator generator = new SFGenerator();\n\t\tLinear[] models = new Linear[postagAlphabet.size()];\n\t\tint fsize = features.size();\n\n\t\tfor (int i = 0; i < postagAlphabet.size(); i++) {\n\t\t\tString pos = postagAlphabet.lookupString(i);\n\t\t\tInstanceSet instset = readInstanceSet(pos);\n\t\t\tLabelAlphabet alphabet = factory.buildLabelAlphabet(pos);\n\t\t\tint ysize = alphabet.size();\n\t\t\tSystem.out.printf(\"Training with data: %s\\n\", pos);\n\t\t\tSystem.out.printf(\"Number of labels: %d\\n\", ysize);\n\t\t\tLinearMax solver = new LinearMax(generator, ysize);\n\t\t\tZeroOneLoss loss = new ZeroOneLoss();\n\t\t\tUpdate update = new LinearMaxPAUpdate(loss);\n\t\t\tOnlineTrainer trainer = new OnlineTrainer(solver, update, loss,\n\t\t\t\t\tfsize, maxite, c);\n\t\t\tmodels[i] = trainer.train(instset, null);\n\t\t\tinstset = null;\n\t\t\tsolver = null;\n\t\t\tloss = null;\n\t\t\ttrainer = null;\n\t\t\tSystem.out.println();\n\t\t}\n\t\tfactory.setStopIncrement(true);\n\t\tsaveModels(modelfile, models,factory);\n\n\t\tfp.delete();\n\t\tfp = null;\n\t} \n #location 13 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void train(String dataFile, int maxite, float c) throws IOException {\n\n\t\tfp = File.createTempFile(\"train-features\", null, new File(\"./tmp/\"));\n\n\t\tbuildInstanceList(dataFile);\n\n\t\tLabelAlphabet postagAlphabet = factory.buildLabelAlphabet(\"postag\");\n\n\n\t\tSFGenerator generator = new SFGenerator();\n\t\tLinear[] models = new Linear[postagAlphabet.size()];\n\n\t\tfor (int i = 0; i < postagAlphabet.size(); i++) {\n\t\t\tString pos = postagAlphabet.lookupString(i);\n\t\t\tInstanceSet instset = readInstanceSet(pos);\n\t\t\tLabelAlphabet alphabet = factory.buildLabelAlphabet(pos);\n\t\t\tint ysize = alphabet.size();\n\t\t\tSystem.out.printf(\"Training with data: %s\\n\", pos);\n\t\t\tSystem.out.printf(\"Number of labels: %d\\n\", ysize);\n\t\t\tLinearMax solver = new LinearMax(generator, ysize);\n\t\t\tZeroOneLoss loss = new ZeroOneLoss();\n\t\t\tUpdate update = new LinearMaxPAUpdate(loss);\n\t\t\tOnlineTrainer trainer = new OnlineTrainer(solver, update, loss,\n\t\t\t\t\tfactory, maxite, c);\n\t\t\tmodels[i] = trainer.train(instset, null);\n\t\t\tinstset = null;\n\t\t\tsolver = null;\n\t\t\tloss = null;\n\t\t\ttrainer = null;\n\t\t\tSystem.out.println();\n\t\t}\n\t\tfactory.setStopIncrement(true);\n\t\tsaveModels(modelfile, models,factory);\n\n\t\tfp.delete();\n\t\tfp = null;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] args)\n\t{\n\t\ttry\n\t\t{\n\t\t\tString ls_1;\n\t\t\tProcess process =null;\n\t\t\tFile handle = new File(\"./tmpdata/ctb/data3\");\n\t\t\tBufferedWriter bout = new BufferedWriter(new OutputStreamWriter(\n\t\t\t\t\tnew FileOutputStream(\"./tmpdata/malt.train\"), \"UTF-8\"));\n\t\t\tfor (File sub : Arrays.asList(handle.listFiles())){\n\t\t\t\tString str = sub.getAbsolutePath();\n\t\t\t\tprocess = Runtime.getRuntime().exec(\"cmd /c java -jar ./tmpdata/ctb/Penn2Malt.jar \"+str+\" ./tmpdata/ctb/headrules.txt 3 2 chtb\");\t\t\t\n\t\t\t\tBufferedReader bufferedReader = new BufferedReader(\n\t\t\t\t\tnew InputStreamReader(process.getInputStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t}\t\t\t\n\t\t}\n\t\tcatch(IOException e)\n\t\t{\n\t\t\tSystem.err.println(e);\n\t\t}\n\t} \n #location 21 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void main(String[] args)\n\t{\n\t\ttry\n\t\t{\n\t\t\tString ls_1;\n\t\t\tProcess process =null;\n//\t\t\tFile handle = new File(\"../tmp/ctb_v1/data\");\n\t\t\tFile handle = new File(\"../tmp/ctb_v6/data/bracketed\");\n\t\t\t\n\t\t\tBufferedWriter bout = new BufferedWriter(new OutputStreamWriter(\n\t\t\t\t\tnew FileOutputStream(\"../tmp/malt.train\"), \"UTF-8\"));\n\t\t\tfor (File sub : Arrays.asList(handle.listFiles())){\n\t\t\t\tString file = sub.getAbsolutePath();\n\t\t\t\tif(!file.endsWith(\".fid\"))\n\t\t\t\t\tcontinue;\n\t\t\t\tclean(file);\n\t\t\t\tprocess = Runtime.getRuntime().exec(\"cmd /c java -jar ../tmp/Penn2Malt.jar \"+file+\" ../tmp/headrules.txt 3 2 chtb\");\t\t\t\n\t\t\t\tBufferedReader bufferedReader = new BufferedReader(\n\t\t\t\t\t\tnew InputStreamReader(process.getInputStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t\tbufferedReader = new BufferedReader(\n\t\t\t\t\t\tnew InputStreamReader(process.getErrorStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t}\t\t\t\n\t\t}\n\t\tcatch(IOException e)\n\t\t{\n\t\t\tSystem.err.println(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private InstanceSet buildInstanceList(String file) throws IOException {\n\n\t\tSystem.out.print(\"\u751f\u6210\u8bad\u7ec3\u6570\u636e ...\");\n\n\t\tFNLPReader reader = new FNLPReader(file);\n\t\tInstanceSet instset = new InstanceSet();\n\t\t\n\t\tLabelAlphabet la = factory.DefaultLabelAlphabet();\n\t\tint count = 0;\n\t\twhile (reader.hasNext()) {\n\t\t\tSentence sent = (Sentence) reader.next();\n\t\t\t//\tint[] heads = (int[]) instance.getTarget();\n\t\t\tString depClass = null;\n\t\t\tTarget targets = (Target)sent.getTarget();\n\t\t\tJointParsingState state = new JointParsingState(sent);\n\t\t\t\n\t\t\twhile (!state.isFinalState()) {\n\t\t\t\t// \u5de6\u53f3\u7126\u70b9\u8bcd\u5728\u53e5\u5b50\u4e2d\u7684\u4f4d\u7f6e\n\t\t\t\tint[] lr = state.getFocusIndices();\n\n\t\t\t\tArrayList features = state.getFeatures();\n\t\t\t\tJointParsingState.Action action = getAction(lr[0], lr[1],\n\t\t\t\t\t\ttargets);\n\t\t\t\tswitch (action) {\n\t\t\t\tcase LEFT:\n\t\t\t\t\tdepClass = targets.getDepClass(lr[1]);\n\t\t\t\t\tbreak;\n\t\t\t\tcase RIGHT:\n\t\t\t\t\tdepClass = targets.getDepClass(lr[0]);\n\t\t\t\t\tbreak;\n\t\t\t\tdefault:\n\n\t\t\t\t}\n\t\t\t\tstate.next(action,depClass);\n\t\t\t\tif (action == JointParsingState.Action.LEFT)\n\t\t\t\t\ttargets.setHeads(lr[1],-1);\n\t\t\t\tif (action == JointParsingState.Action.RIGHT)\n\t\t\t\t\ttargets.setHeads(lr[0],-1);\n\t\t\t\tString label = \"\";\n\t\t\t\tswitch (action) {\n\t\t\t\tcase LEFT:\n\t\t\t\t\tlabel += \"L\"+sent.getDepClass(lr[1]);\t\t\n\t\t\t\t\tbreak;\n\t\t\t\tcase RIGHT:\n\t\t\t\t\tlabel+=\"R\"+sent.getDepClass(lr[0]);\n\t\t\t\t\tbreak;\n\t\t\t\tdefault:\n\t\t\t\t\tlabel = \"S\";\t\t\t\t\t\n\t\t\t\t}\n\t\t\t\tint id = la.lookupIndex(label);\t\t\t\t\n\t\t\t\tInstance inst = new Instance();\n\t\t\t\tinst.setTarget(id);\n\t\t\t\tinst.setData(features);\n\t\t\t\tinstset.add(inst);\n\t\t\t}\n\t\t\tcount++;\n//\t\t\tSystem.out.println(count);\n\t\t}\n\t\tla.setStopIncrement(true);\n\t\t\n\t\t//\u91cd\u65b0\u751f\u6210\u7279\u5f81\n\t\tint ysize = la.size();\t\t\n\t\tIFeatureAlphabet fa = factory.DefaultFeatureAlphabet();\n\t\t\n\t\tfor(Instance inst:instset){\n\t\t\tArrayList data = (ArrayList) inst.getData();\n\t\t\tint[] idx = JointParser.addFeature(fa, data, ysize);\n\t\t\tinst.setData(idx);\n\t\t}\n\t\tinstset.setAlphabetFactory(factory);\n\t\tSystem.out.printf(\"\u5171\u751f\u6210\u5b9e\u4f8b:%d\u4e2a\\n\", count);\n\t\treturn instset;\n\t} \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private InstanceSet buildInstanceList(String file) throws IOException {\n\n\t\tSystem.out.print(\"\u751f\u6210\u8bad\u7ec3\u6570\u636e ...\");\n\n\t\tFNLPReader reader = new FNLPReader(file);\n\t\tFNLPReader preReader = new FNLPReader(file);\n\t\tInstanceSet instset = new InstanceSet();\n\t\t\n\t\tLabelAlphabet la = factory.DefaultLabelAlphabet();\n\t\tIFeatureAlphabet fa = factory.DefaultFeatureAlphabet();\n\t\tint count = 0;\n\t\t\n\t\t//preReader\u4e3a\u4e86\u628aysize\u5b9a\u4e0b\u6765\n\t\tla.lookupIndex(\"S\");\n\t\twhile(preReader.hasNext()){\n\t\t\tSentence sent = (Sentence) preReader.next();\n\t\t\tTarget targets = (Target)sent.getTarget();\n\t\t\tfor(int i=0; i i){\n\t\t\t\t\telse{\n\t\t\t\t\t\tlabel = \"R\" + targets.getDepClass(i);\n\t\t\t\t\t}\n\t\t\t\t\tla.lookupIndex(label);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tint ysize = la.size();\n\t\tla.setStopIncrement(true);\n\t\t\t\t\n\t\twhile (reader.hasNext()) {\n\t\t\tSentence sent = (Sentence) reader.next();\n\t\t\t//\tint[] heads = (int[]) instance.getTarget();\n\t\t\tString depClass = null;\n\t\t\tTarget targets = (Target)sent.getTarget();\n\t\t\tJointParsingState state = new JointParsingState(sent);\n\t\t\t\n\t\t\twhile (!state.isFinalState()) {\n\t\t\t\t// \u5de6\u53f3\u7126\u70b9\u8bcd\u5728\u53e5\u5b50\u4e2d\u7684\u4f4d\u7f6e\n\t\t\t\tint[] lr = state.getFocusIndices();\n\n\t\t\t\tArrayList features = state.getFeatures();\n\t\t\t\tJointParsingState.Action action = getAction(lr[0], lr[1],\n\t\t\t\t\t\ttargets);\n\t\t\t\tswitch (action) {\n\t\t\t\tcase LEFT:\n\t\t\t\t\tdepClass = targets.getDepClass(lr[1]);\n\t\t\t\t\tbreak;\n\t\t\t\tcase RIGHT:\n\t\t\t\t\tdepClass = targets.getDepClass(lr[0]);\n\t\t\t\t\tbreak;\n\t\t\t\tdefault:\n\n\t\t\t\t}\n\t\t\t\tstate.next(action,depClass);\n\t\t\t\tif (action == JointParsingState.Action.LEFT)\n\t\t\t\t\ttargets.setHeads(lr[1],-1);\n\t\t\t\tif (action == JointParsingState.Action.RIGHT)\n\t\t\t\t\ttargets.setHeads(lr[0],-1);\n\t\t\t\tString label = \"\";\n\t\t\t\tswitch (action) {\n\t\t\t\tcase LEFT:\n\t\t\t\t\tlabel += \"L\"+sent.getDepClass(lr[1]);\t\t\n\t\t\t\t\tbreak;\n\t\t\t\tcase RIGHT:\n\t\t\t\t\tlabel+=\"R\"+sent.getDepClass(lr[0]);\n\t\t\t\t\tbreak;\n\t\t\t\tdefault:\n\t\t\t\t\tlabel = \"S\";\t\t\t\t\t\n\t\t\t\t}\n\t\t\t\tint id = la.lookupIndex(label);\t\t\t\t\n\t\t\t\tInstance inst = new Instance();\n\t\t\t\tinst.setTarget(id);\n\t\t\t\tint[] idx = JointParser.addFeature(fa, features, ysize);\n\t\t\t\tinst.setData(idx);\n\t\t\t\tinstset.add(inst);\n\t\t\t}\n\t\t\tcount++;\n//\t\t\tSystem.out.println(count);\n\t\t}\n\t\t\n\t\tinstset.setAlphabetFactory(factory);\n\t\tSystem.out.printf(\"\u5171\u751f\u6210\u5b9e\u4f8b:%d\u4e2a\\n\", count);\n\t\treturn instset;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] args)\n\t{\n\t\ttry\n\t\t{\n\t\t\tString ls_1;\n\t\t\tProcess process =null;\n\t\t\tFile handle = new File(\"./tmpdata/ctb/data3\");\n\t\t\tBufferedWriter bout = new BufferedWriter(new OutputStreamWriter(\n\t\t\t\t\tnew FileOutputStream(\"./tmpdata/malt.train\"), \"UTF-8\"));\n\t\t\tfor (File sub : Arrays.asList(handle.listFiles())){\n\t\t\t\tString str = sub.getAbsolutePath();\n\t\t\t\tprocess = Runtime.getRuntime().exec(\"cmd /c java -jar ./tmpdata/ctb/Penn2Malt.jar \"+str+\" ./tmpdata/ctb/headrules.txt 3 2 chtb\");\t\t\t\n\t\t\t\tBufferedReader bufferedReader = new BufferedReader(\n\t\t\t\t\tnew InputStreamReader(process.getInputStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t}\t\t\t\n\t\t}\n\t\tcatch(IOException e)\n\t\t{\n\t\t\tSystem.err.println(e);\n\t\t}\n\t} \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void main(String[] args)\n\t{\n\t\ttry\n\t\t{\n\t\t\tString ls_1;\n\t\t\tProcess process =null;\n//\t\t\tFile handle = new File(\"../tmp/ctb_v1/data\");\n\t\t\tFile handle = new File(\"../tmp/ctb_v6/data/bracketed\");\n\t\t\t\n\t\t\tBufferedWriter bout = new BufferedWriter(new OutputStreamWriter(\n\t\t\t\t\tnew FileOutputStream(\"../tmp/malt.train\"), \"UTF-8\"));\n\t\t\tfor (File sub : Arrays.asList(handle.listFiles())){\n\t\t\t\tString file = sub.getAbsolutePath();\n\t\t\t\tif(!file.endsWith(\".fid\"))\n\t\t\t\t\tcontinue;\n\t\t\t\tclean(file);\n\t\t\t\tprocess = Runtime.getRuntime().exec(\"cmd /c java -jar ../tmp/Penn2Malt.jar \"+file+\" ../tmp/headrules.txt 3 2 chtb\");\t\t\t\n\t\t\t\tBufferedReader bufferedReader = new BufferedReader(\n\t\t\t\t\t\tnew InputStreamReader(process.getInputStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t\tbufferedReader = new BufferedReader(\n\t\t\t\t\t\tnew InputStreamReader(process.getErrorStream()));\n\t\t\t\twhile ( (ls_1=bufferedReader.readLine()) != null)\n\t\t\t\t{\n\t\t\t\t\tSystem.out.println(ls_1);\n\t\t\t\t}\n\t\t\t}\t\t\t\n\t\t}\n\t\tcatch(IOException e)\n\t\t{\n\t\t\tSystem.err.println(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void train(String dataFile, int maxite, float c) throws IOException {\n\t\t\n\t\tInstanceSet instset = buildInstanceList(dataFile);\n\t\tIFeatureAlphabet features = factory.DefaultFeatureAlphabet();\n\n\t\tSFGenerator generator = new SFGenerator();\n\t\tint fsize = features.size();\n\t\t\n\t\tLabelAlphabet la = factory.DefaultLabelAlphabet();\n\t\tint ysize = la.size();\n\t\tSystem.out.printf(\"\u5f00\u59cb\u8bad\u7ec3\");\n\t\tLinearMax solver = new LinearMax(generator, ysize);\n\t\tZeroOneLoss loss = new ZeroOneLoss();\n\t\tUpdate update = new LinearMaxPAUpdate(loss);\n\t\tOnlineTrainer trainer = new OnlineTrainer(solver, update, loss,\n\t\t\t\tfsize, maxite, c);\n\t\tLinear models = trainer.train(instset, null);\n\t\tinstset = null;\n\t\tsolver = null;\n\t\tloss = null;\n\t\ttrainer = null;\n\t\tSystem.out.println();\n\t\tfactory.setStopIncrement(true);\n\t\tmodels.saveTo(modelfile);\n\n\t} \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void train(String dataFile, int maxite, float c) throws IOException {\n\t\t\n\t\tInstanceSet instset = buildInstanceList(dataFile);\n\n\t\tSFGenerator generator = new SFGenerator();\n\t\t\n\t\tLabelAlphabet la = factory.DefaultLabelAlphabet();\n\t\tint ysize = la.size();\n\t\tSystem.out.printf(\"\u5f00\u59cb\u8bad\u7ec3\");\n\t\tLinearMax solver = new LinearMax(generator, ysize);\n\t\tZeroOneLoss loss = new ZeroOneLoss();\n\t\tUpdate update = new LinearMaxPAUpdate(loss);\n\t\tOnlineTrainer trainer = new OnlineTrainer(solver, update, loss,\n\t\t\t\tfactory, maxite, c);\n\t\tLinear models = trainer.train(instset, null);\n\t\tinstset = null;\n\t\tsolver = null;\n\t\tloss = null;\n\t\ttrainer = null;\n\t\tSystem.out.println();\n\t\tfactory.setStopIncrement(true);\n\t\tmodels.saveTo(modelfile);\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testStartNewSpanSampleNullNotPartOfExistingSpan() {\n\n final ServerSpan mockServerSpan = mock(ServerSpan.class);\n when(mockServerSpan.getSpan()).thenReturn(null);\n when(mockState.sample()).thenReturn(null);\n when(mockState.getCurrentServerSpan()).thenReturn(mockServerSpan);\n when(mockRandom.nextLong()).thenReturn(1l).thenReturn(2l);\n\n final SpanId newSpanId = clientTracer.startNewSpan(REQUEST_NAME);\n assertNotNull(newSpanId);\n assertEquals(1l, newSpanId.getTraceId());\n assertEquals(1l, newSpanId.getSpanId());\n assertNull(newSpanId.getParentSpanId());\n\n final Span expectedSpan = new Span();\n expectedSpan.setTrace_id(1);\n expectedSpan.setId(1);\n expectedSpan.setName(REQUEST_NAME);\n\n verify(mockState).sample();\n verify(mockTraceFilter).trace(REQUEST_NAME);\n verify(mockTraceFilter2).trace(REQUEST_NAME);\n verify(mockRandom, times(1)).nextLong();\n verify(mockState).getCurrentServerSpan();\n verify(mockState).setCurrentClientSpan(expectedSpan);\n\n verifyNoMoreInteractions(mockState, mockRandom, mockCollector, mockTraceFilter, mockTraceFilter2);\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testStartNewSpanSampleNullNotPartOfExistingSpan() {\n\n final ServerSpan mockServerSpan = mock(ServerSpan.class);\n when(mockServerSpan.getSpan()).thenReturn(null);\n when(mockState.sample()).thenReturn(null);\n when(mockState.getCurrentServerSpan()).thenReturn(mockServerSpan);\n when(mockRandom.nextLong()).thenReturn(TRACE_ID).thenReturn(2l);\n\n final SpanId newSpanId = clientTracer.startNewSpan(REQUEST_NAME);\n assertNotNull(newSpanId);\n assertEquals(TRACE_ID, newSpanId.getTraceId());\n assertEquals(TRACE_ID, newSpanId.getSpanId());\n assertNull(newSpanId.getParentSpanId());\n\n final Span expectedSpan = new Span();\n expectedSpan.setTrace_id(TRACE_ID);\n expectedSpan.setId(TRACE_ID);\n expectedSpan.setName(REQUEST_NAME);\n\n verify(mockState).sample();\n verify(mockTraceFilter).trace(TRACE_ID, REQUEST_NAME);\n verify(mockTraceFilter2).trace(TRACE_ID, REQUEST_NAME);\n verify(mockRandom, times(1)).nextLong();\n verify(mockState).getCurrentServerSpan();\n verify(mockState).setCurrentClientSpan(expectedSpan);\n\n verifyNoMoreInteractions(mockState, mockRandom, mockCollector, mockTraceFilter, mockTraceFilter2);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void finishSpan() {\n Span finished = new Span().setTimestamp(1000L); // set in start span\n finished.startTick = 500000L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.nanoTime()).thenReturn(1000000L);\n\n localTracer.finishSpan();\n\n verify(mockCollector).collect(finished);\n verifyNoMoreInteractions(mockCollector);\n\n assertEquals(500L, finished.getDuration().longValue());\n } \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void finishSpan() {\n Span finished = new Span().setName(\"foo\").setTimestamp(1000L); // set in start span\n finished.startTick = 500000L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.nanoTime()).thenReturn(1000000L);\n\n localTracer.finishSpan();\n\n verify(mockReporter).report(finished.toZipkin());\n verifyNoMoreInteractions(mockReporter);\n\n assertEquals(500L, finished.getDuration().longValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public T call() throws Exception {\n serverSpanThreadBinder().setCurrentSpan(currentServerSpan());\n final long start = System.currentTimeMillis();\n try {\n return wrappedCallable().call();\n } finally {\n final long duration = System.currentTimeMillis() - start;\n currentServerSpan().incThreadDuration(duration);\n }\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public T call() throws Exception {\n serverSpanThreadBinder().setCurrentSpan(currentServerSpan());\n return wrappedCallable().call();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void recordClientSentAnnotations(Endpoint serverAddress) {\n if (serverAddress == null) {\n clientTracer.setClientSent();\n } else {\n clientTracer.setClientSent(serverAddress.ipv4, serverAddress.port, serverAddress.service_name);\n }\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void recordClientSentAnnotations(Endpoint serverAddress) {\n if (serverAddress == null) {\n clientTracer.setClientSent();\n } else {\n clientTracer.setClientSent(serverAddress);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void finishSpan_userSuppliedTimestamp() {\n Span finished = new Span().setTimestamp(1000L); // Set by user\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.currentTimeMillis()).thenReturn(2L);\n\n localTracer.finishSpan();\n\n verify(mockCollector).collect(finished);\n verifyNoMoreInteractions(mockCollector);\n\n assertEquals(1000L, finished.getDuration().longValue());\n } \n #location 13 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void finishSpan_userSuppliedTimestamp() {\n Span finished = new Span().setName(\"foo\").setTimestamp(1000L); // Set by user\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.currentTimeMillis()).thenReturn(2L);\n\n localTracer.finishSpan();\n\n verify(mockReporter).report(finished.toZipkin());\n verifyNoMoreInteractions(mockReporter);\n\n assertEquals(1000L, finished.getDuration().longValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void finishSpan_userSuppliedTimestampAndDuration() {\n Span finished = new Span().setTimestamp(1000L); // Set by user\n state.setCurrentLocalSpan(finished);\n\n localTracer.finishSpan(500L);\n\n verify(mockCollector).collect(finished);\n verifyNoMoreInteractions(mockCollector);\n\n assertEquals(500L, finished.getDuration().longValue());\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void finishSpan_userSuppliedTimestampAndDuration() {\n Span finished = new Span().setName(\"foo\").setTimestamp(1000L); // Set by user\n state.setCurrentLocalSpan(finished);\n\n localTracer.finishSpan(500L);\n\n verify(mockReporter).report(finished.toZipkin());\n verifyNoMoreInteractions(mockReporter);\n\n assertEquals(500L, finished.getDuration().longValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void finishSpan_lessThanMicrosRoundUp() {\n Span finished = new Span().setTimestamp(1000L); // set in start span\n finished.startTick = 500L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.nanoTime()).thenReturn(1000L);\n\n localTracer.finishSpan();\n\n verify(mockCollector).collect(finished);\n verifyNoMoreInteractions(mockCollector);\n\n assertEquals(1L, finished.getDuration().longValue());\n } \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void finishSpan_lessThanMicrosRoundUp() {\n Span finished = new Span().setName(\"foo\").setTimestamp(1000L); // set in start span\n finished.startTick = 500L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n PowerMockito.when(System.nanoTime()).thenReturn(1000L);\n\n localTracer.finishSpan();\n\n verify(mockReporter).report(finished.toZipkin());\n verifyNoMoreInteractions(mockReporter);\n\n assertEquals(1L, finished.getDuration().longValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void finishSpan_userSuppliedDuration() {\n Span finished = new Span().setTimestamp(1000L); // set in start span\n finished.startTick = 500L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n localTracer.finishSpan(500L);\n\n verify(mockCollector).collect(finished);\n verifyNoMoreInteractions(mockCollector);\n\n assertEquals(500L, finished.getDuration().longValue());\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void finishSpan_userSuppliedDuration() {\n Span finished = new Span().setName(\"foo\").setTimestamp(1000L); // set in start span\n finished.startTick = 500L; // set in start span\n state.setCurrentLocalSpan(finished);\n\n localTracer.finishSpan(500L);\n\n verify(mockReporter).report(finished.toZipkin());\n verifyNoMoreInteractions(mockReporter);\n\n assertEquals(500L, finished.getDuration().longValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void run() {\n serverSpanThreadBinder().setCurrentSpan(currentServerSpan());\n final long start = System.currentTimeMillis();\n try {\n wrappedRunnable().run();\n } finally {\n final long duration = System.currentTimeMillis() - start;\n currentServerSpan().incThreadDuration(duration);\n }\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void run() {\n serverSpanThreadBinder().setCurrentSpan(currentServerSpan());\n wrappedRunnable().run();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected boolean checkQuiesceLock() {\n\t\tfinal String methodName = \"checkQuiesceLock\";\n\t\t// if (quiescing && actualInFlight == 0 && pendingFlows.size() == 0 &&\n\t\t// inFlightPubRels == 0 && callback.isQuiesced()) {\n\t\tint tokC = tokenStore.count();\n\t\tif (quiescing && tokC == 0 && pendingFlows.size() == 0 && callback.isQuiesced()) {\n\t\t\t// @TRACE 626=quiescing={0} actualInFlight={1} pendingFlows={2}\n\t\t\t// inFlightPubRels={3} callbackQuiesce={4} tokens={5}\n\t\t\tlog.fine(CLASS_NAME, methodName, \"626\",\n\t\t\t\t\tnew Object[] { new Boolean(quiescing), Integer.valueOf(actualInFlight),\n\t\t\t\t\t\t\tInteger.valueOf(pendingFlows.size()), Integer.valueOf(inFlightPubRels),\n\t\t\t\t\t\t\tBoolean.valueOf(callback.isQuiesced()), Integer.valueOf(tokC) });\n\t\t\tsynchronized (quiesceLock) {\n\t\t\t\tquiesceLock.notifyAll();\n\t\t\t}\n\t\t\treturn true;\n\t\t}\n\t\treturn false;\n\t} \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n protected boolean checkQuiesceLock() {\n\t\tfinal String methodName = \"checkQuiesceLock\";\n\t\t// if (quiescing && actualInFlight == 0 && pendingFlows.size() == 0 &&\n\t\t// inFlightPubRels == 0 && callback.isQuiesced()) {\n\t\tint tokC = tokenStore.count();\n\t\tif (quiescing && tokC == 0 && pendingFlows.size() == 0 && callback.isQuiesced()) {\n\t\t\t// @TRACE 626=quiescing={0} actualInFlight={1} pendingFlows={2}\n\t\t\t// inFlightPubRels={3} callbackQuiesce={4} tokens={5}\n\t\t\tlog.fine(CLASS_NAME, methodName, \"626\",\n\t\t\t\t\tnew Object[] { Boolean.valueOf(quiescing), Integer.valueOf(actualInFlight),\n\t\t\t\t\t\t\tInteger.valueOf(pendingFlows.size()), Integer.valueOf(inFlightPubRels),\n\t\t\t\t\t\t\tBoolean.valueOf(callback.isQuiesced()), Integer.valueOf(tokC) });\n\t\t\tsynchronized (quiesceLock) {\n\t\t\t\tquiesceLock.notifyAll();\n\t\t\t}\n\t\t\treturn true;\n\t\t}\n\t\treturn false;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testGetStructure() {\n\t\ttry {\n\t\t\tSimpleFormatter sf = new SimpleFormatter();\n\t\t\tString delimiter = \"/\";\n\t\t\tString bucket = \"maven.kuali.org\";\n\t\t\tAmazonS3Client client = getClient();\n\t\t\tKualiMavenBucketBaseCase baseCase1 = new KualiMavenBucketBaseCase();\n\t\t\tbaseCase1.setDelimiter(delimiter);\n\t\t\tbaseCase1.setToken(\"latest\");\n\t\t\tJavaxServletOnlyBaseCase baseCase2 = new JavaxServletOnlyBaseCase();\n\t\t\tbaseCase2.setDelimiter(delimiter);\n\t\t\tbaseCase2.setToken(\"latest\");\n\n\t\t\tlong start = System.currentTimeMillis();\n\t\t\tList prefixes = new ArrayList();\n\t\t\tbuildPrefixList(client, bucket, prefixes, null, delimiter, baseCase2);\n\t\t\tlong elapsed = System.currentTimeMillis() - start;\n\t\t\tDefaultMutableTreeNode node = buildTree(prefixes, delimiter);\n\t\t\tList leaves = getLeaves(node);\n\t\t\tlog.info(\"Total Prefixes: \" + prefixes.size());\n\t\t\tlog.info(\"Total Time: \" + sf.getTime(elapsed));\n\t\t\tlog.info(\"Leaves: \" + leaves.size());\n\t\t} catch (Exception e) {\n\t\t\te.printStackTrace();\n\t\t}\n\t} \n #location 20 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n\tpublic void testGetStructure() {\n\t\ttry {\n\t\t\tlong now = System.currentTimeMillis();\n\t\t\tlong bytes = Long.MAX_VALUE;\n\t\t\tSimpleFormatter sf = new SimpleFormatter();\n\t\t\tlog.info(sf.getSize(bytes));\n\t\t\tlog.info(sf.getRate(now, bytes));\n\t\t\tlog.info(sf.getTime(now));\n\t\t\tString delimiter = \"/\";\n\t\t\tString bucket = \"maven.kuali.org\";\n\t\t\tAmazonS3Client client = getClient();\n\t\t\tKualiMavenBucketBaseCase baseCase1 = new KualiMavenBucketBaseCase();\n\t\t\tbaseCase1.setDelimiter(delimiter);\n\t\t\tbaseCase1.setToken(\"latest\");\n\t\t\tJavaxServletOnlyBaseCase baseCase2 = new JavaxServletOnlyBaseCase();\n\t\t\tbaseCase2.setDelimiter(delimiter);\n\t\t\tbaseCase2.setToken(\"latest\");\n\n\t\t\tlong start = System.currentTimeMillis();\n\t\t\tList prefixes = new ArrayList();\n\t\t\tbuildPrefixList(client, bucket, prefixes, null, delimiter, baseCase2);\n\t\t\tlong elapsed = System.currentTimeMillis() - start;\n\t\t\tDefaultMutableTreeNode node = buildTree(prefixes, delimiter);\n\t\t\tList leaves = getLeaves(node);\n\t\t\tlog.info(\"Total Prefixes: \" + prefixes.size());\n\t\t\tlog.info(\"Total Time: \" + sf.getTime(elapsed));\n\t\t\tlog.info(\"Leaves: \" + leaves.size());\n\t\t} catch (Exception e) {\n\t\t\te.printStackTrace();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void transitionInto(RunState state) {\n switch (state.state()) {\n case SUBMITTING:\n try {\n final String executionId = dockerRunnerStart(state);\n // this is racy\n final Event submitted = Event.submitted(state.workflowInstance(), executionId);\n try {\n stateManager.receive(submitted);\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Could not send 'created' event\", isClosed);\n }\n } catch (Exception e) {\n LOG.warn(\"Failed the docker starting procedure for \" + state.workflowInstance().toKey(), e);\n stateManager.receiveIgnoreClosed(Event.halt(state.workflowInstance()));\n }\n break;\n\n case TERMINATED:\n case FAILED:\n case ERROR:\n if (state.executionId().isPresent()) {\n final String executionId = state.executionId().get();\n LOG.info(\"Cleaning up {} pod: {}\", state.workflowInstance().toKey(), executionId);\n\n dockerRunner.cleanup(executionId);\n }\n break;\n\n default:\n // do nothing\n }\n } \n #location 15 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void transitionInto(RunState state) {\n switch (state.state()) {\n case SUBMITTING:\n try {\n final String executionId = dockerRunnerStart(state);\n // this is racy\n final Event submitted = Event.submitted(state.workflowInstance(), executionId);\n try {\n stateManager.receive(submitted);\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Could not send 'created' event\", isClosed);\n }\n } catch (ResourceNotFoundException e) {\n LOG.error(\"Unable to start docker procedure.\", e);\n stateManager.receiveIgnoreClosed(Event.halt(state.workflowInstance()));\n } catch (IOException e) {\n try {\n LOG.error(\"Failed the docker starting procedure for \" + state.workflowInstance().toKey(), e);\n stateManager.receive(Event.runError(state.workflowInstance(), e.getMessage()));\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Failed to send 'runError' event\", isClosed);\n }\n }\n break;\n\n case TERMINATED:\n case FAILED:\n case ERROR:\n if (state.executionId().isPresent()) {\n final String executionId = state.executionId().get();\n LOG.info(\"Cleaning up {} pod: {}\", state.workflowInstance().toKey(), executionId);\n\n dockerRunner.cleanup(executionId);\n }\n break;\n\n default:\n // do nothing\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public Map activeStates() {\n final ImmutableMap.Builder builder = ImmutableMap.builder();\n states.entrySet().forEach(entry -> builder.put(entry.getKey(), entry.getValue().runState));\n return builder.build();\n } \n #location 2 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n @Override\n public Map activeStates() {\n return states.entrySet().stream()\n .collect(Collectors.toMap(Map.Entry::getKey, (entry) -> entry.getValue().runState));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Map readActiveWorkflowInstances() throws IOException {\n final Table activeStatesTable = connection.getTable(ACTIVE_STATES_TABLE_NAME);\n final ImmutableMap.Builder map = ImmutableMap.builder();\n\n for (Result result : activeStatesTable.getScanner(STATE_CF, STATE_QUALIFIER)) {\n final WorkflowInstance workflowInstance =\n WorkflowInstance.parseKey(Bytes.toString(result.getRow()));\n final long counter = Long.parseLong(Bytes.toString(result.value()));\n\n map.put(workflowInstance, counter);\n }\n\n return map.build();\n } \n #location 1 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n BigtableStorage(Connection connection, Duration retryBaseDelay) {\n this.connection = Objects.requireNonNull(connection);\n this.retryBaseDelay = Objects.requireNonNull(retryBaseDelay);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static KubernetesClient getKubernetesClient(Config config, String id) {\n try {\n final HttpTransport httpTransport = GoogleNetHttpTransport.newTrustedTransport();\n final JsonFactory jsonFactory = Utils.getDefaultJsonFactory();\n final GoogleCredential credential =\n GoogleCredential.getApplicationDefault(httpTransport, jsonFactory)\n .createScoped(ContainerScopes.all());\n final Container gke = new Container.Builder(httpTransport, jsonFactory, credential)\n .setApplicationName(SERVICE_NAME)\n .build();\n\n final String projectKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_PROJECT_ID;\n final String zoneKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_ZONE;\n final String clusterIdKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_ID;\n\n final Cluster cluster = gke.projects().zones().clusters()\n .get(config.getString(projectKey),\n config.getString(zoneKey),\n config.getString(clusterIdKey)).execute();\n\n final io.fabric8.kubernetes.client.Config kubeConfig = new ConfigBuilder()\n .withMasterUrl(\"https://\" + cluster.getEndpoint())\n .withCaCertData(cluster.getMasterAuth().getClusterCaCertificate())\n .withClientCertData(cluster.getMasterAuth().getClientCertificate())\n .withClientKeyData(cluster.getMasterAuth().getClientKey())\n .build();\n\n return new AutoAdaptableKubernetesClient(kubeConfig).inNamespace(KUBERNETES_NAMESPACE);\n } catch (GeneralSecurityException | IOException e) {\n throw Throwables.propagate(e);\n }\n } \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static KubernetesClient getKubernetesClient(Config config, String id) {\n try {\n final HttpTransport httpTransport = GoogleNetHttpTransport.newTrustedTransport();\n final JsonFactory jsonFactory = Utils.getDefaultJsonFactory();\n final GoogleCredential credential =\n GoogleCredential.getApplicationDefault(httpTransport, jsonFactory)\n .createScoped(ContainerScopes.all());\n final Container gke = new Container.Builder(httpTransport, jsonFactory, credential)\n .setApplicationName(SERVICE_NAME)\n .build();\n\n final String projectKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_PROJECT_ID;\n final String zoneKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_ZONE;\n final String clusterIdKey = GKE_CLUSTER_PREFIX + id + GKE_CLUSTER_ID;\n\n final Cluster cluster = gke.projects().zones().clusters()\n .get(config.getString(projectKey),\n config.getString(zoneKey),\n config.getString(clusterIdKey)).execute();\n\n final io.fabric8.kubernetes.client.Config kubeConfig = new ConfigBuilder()\n .withMasterUrl(\"https://\" + cluster.getEndpoint())\n .withCaCertData(cluster.getMasterAuth().getClusterCaCertificate())\n .withClientCertData(cluster.getMasterAuth().getClientCertificate())\n .withClientKeyData(cluster.getMasterAuth().getClientKey())\n .build();\n\n return new DefaultKubernetesClient(kubeConfig);\n } catch (GeneralSecurityException | IOException e) {\n throw Throwables.propagate(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n List getBackfills() {\n final EntityQuery query = Query.entityQueryBuilder().kind(KIND_BACKFILL).build();\n final QueryResults results = datastore.run(query);\n final ImmutableList.Builder resources = ImmutableList.builder();\n while (results.hasNext()) {\n resources.add(entityToBackfill(results.next()));\n }\n return resources.build();\n } \n #location 1 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n DatastoreStorage(Datastore datastore, Duration retryBaseDelay) {\n this.datastore = Objects.requireNonNull(datastore);\n this.retryBaseDelay = Objects.requireNonNull(retryBaseDelay);\n\n this.componentKeyFactory = datastore.newKeyFactory().kind(KIND_COMPONENT);\n this.globalConfigKey = datastore.newKeyFactory().kind(KIND_STYX_CONFIG).newKey(KEY_GLOBAL_CONFIG);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void transitionInto(RunState state) {\n switch (state.state()) {\n case SUBMITTING:\n try {\n final String executionId = dockerRunnerStart(state);\n // this is racy\n final Event submitted = Event.submitted(state.workflowInstance(), executionId);\n try {\n stateManager.receive(submitted);\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Could not send 'created' event\", isClosed);\n }\n } catch (ResourceNotFoundException e) {\n LOG.error(\"Unable to start docker procedure.\", e);\n stateManager.receiveIgnoreClosed(Event.halt(state.workflowInstance()));\n } catch (Throwable e) {\n try {\n LOG.error(\"Failed the docker starting procedure for \" + state.workflowInstance().toKey(), e);\n stateManager.receive(Event.runError(state.workflowInstance(), e.getMessage()));\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Failed to send 'runError' event\", isClosed);\n }\n }\n break;\n\n case TERMINATED:\n case FAILED:\n case ERROR:\n if (state.data().executionId().isPresent()) {\n final String executionId = state.data().executionId().get();\n\n boolean debugEnabled = false;\n try {\n debugEnabled = storage.debugEnabled();\n } catch (IOException e) {\n LOG.info(\"Couldn't fetch debug flag. Will clean up pod anyway.\");\n }\n\n if (!debugEnabled) {\n LOG.info(\"Cleaning up {} pod: {}\", state.workflowInstance().toKey(), executionId);\n dockerRunner.cleanup(executionId);\n } else {\n LOG.info(\"Keeping {} pod: {}\", state.workflowInstance().toKey(), executionId);\n }\n }\n break;\n\n default:\n // do nothing\n }\n } \n #location 19 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void transitionInto(RunState state) {\n switch (state.state()) {\n case SUBMITTING:\n // Perform rate limited submission on a separate thread pool to avoid blocking the caller.\n executor.submit(() -> {\n rateLimiter.acquire();\n try {\n final String executionId = dockerRunnerStart(state);\n // this is racy\n final Event submitted = Event.submitted(state.workflowInstance(), executionId);\n try {\n stateManager.receive(submitted);\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Could not send 'created' event\", isClosed);\n }\n } catch (ResourceNotFoundException e) {\n LOG.error(\"Unable to start docker procedure.\", e);\n stateManager.receiveIgnoreClosed(Event.halt(state.workflowInstance()));\n } catch (Throwable e) {\n try {\n LOG.error(\"Failed the docker starting procedure for \" + state.workflowInstance().toKey(), e);\n stateManager.receive(Event.runError(state.workflowInstance(), e.getMessage()));\n } catch (StateManager.IsClosed isClosed) {\n LOG.warn(\"Failed to send 'runError' event\", isClosed);\n }\n }\n });\n break;\n\n case TERMINATED:\n case FAILED:\n case ERROR:\n if (state.data().executionId().isPresent()) {\n final String executionId = state.data().executionId().get();\n\n boolean debugEnabled = false;\n try {\n debugEnabled = storage.debugEnabled();\n } catch (IOException e) {\n LOG.info(\"Couldn't fetch debug flag. Will clean up pod anyway.\");\n }\n\n if (!debugEnabled) {\n LOG.info(\"Cleaning up {} pod: {}\", state.workflowInstance().toKey(), executionId);\n dockerRunner.cleanup(executionId);\n } else {\n LOG.info(\"Keeping {} pod: {}\", state.workflowInstance().toKey(), executionId);\n }\n }\n break;\n\n default:\n // do nothing\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Map allActiveStates() throws IOException {\n final EntityQuery activeStatesQuery = Query.entityQueryBuilder()\n .kind(KIND_ACTIVE_STATE)\n .build();\n\n final ImmutableMap.Builder mapBuilder = ImmutableMap.builder();\n\n final QueryResults results = datastore.run(activeStatesQuery);\n while (results.hasNext()) {\n final Entity activeState = results.next();\n final WorkflowInstance instance = parseWorkflowInstance(activeState);\n final long counter = activeState.getLong(PROPERTY_ACTIVE_STATE_COUNTER);\n\n mapBuilder.put(instance, counter);\n }\n\n return mapBuilder.build();\n } \n #location 1 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n DatastoreStorage(Datastore datastore, Duration retryBaseDelay) {\n this.datastore = Objects.requireNonNull(datastore);\n this.retryBaseDelay = Objects.requireNonNull(retryBaseDelay);\n\n this.componentKeyFactory = datastore.newKeyFactory().kind(KIND_COMPONENT);\n this.globalConfigKey = datastore.newKeyFactory().kind(KIND_STYX_CONFIG).newKey(KEY_GLOBAL_CONFIG);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void doRequest(ServletTransaction transaction)\n\t\t\tthrows ServletException {\n\t\ttry {\n\t\t\tHttpServletRequest request = transaction.getServletRequest();\n\t\t\tClient client = ClientCatalog\n\t\t\t\t\t.getClient(request.getParameter(\"use\"));\n\t\t\tString report = request.getParameter(\"report\");\n\t\t\tString emails = request.getParameter(\"emails\");\n\t\t\tif (emails == null)\n\t\t\t\treturn;\n\t\t\tHtmlEmail htmlEmail = client.getMailer().getHtmlEmail(emails, null);\n\t\t\tStringWriter sw = new StringWriter();\n\t\t\tPrintWriter pw = new PrintWriter(sw);\n\t\t\tif (\"statistics\".equals(report)) {\n\t\t\t\thtmlEmail.setSubject(\"OpenSearchServer statistics report\");\n\t\t\t\tdoStatistics(client, request.getParameter(\"stat\"), request\n\t\t\t\t\t\t.getParameter(\"period\"), pw);\n\t\t\t}\n\t\t\thtmlEmail.setHtmlMsg(sw.toString());\n\t\t\thtmlEmail.send();\n\t\t\ttransaction.addXmlResponse(\"MailSent\", emails);\n\t\t} catch (Exception e) {\n\t\t\tthrow new ServletException(e);\n\t\t}\n\t} \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n\tprotected void doRequest(ServletTransaction transaction)\n\t\t\tthrows ServletException {\n\t\ttry {\n\t\t\tHttpServletRequest request = transaction.getServletRequest();\n\t\t\tClient client = ClientCatalog\n\t\t\t\t\t.getClient(request.getParameter(\"use\"));\n\t\t\tString report = request.getParameter(\"report\");\n\t\t\tString emails = request.getParameter(\"emails\");\n\t\t\tif (emails == null)\n\t\t\t\treturn;\n\t\t\tHtmlEmail htmlEmail = client.getMailer().getHtmlEmail(emails, null);\n\t\t\tStringWriter sw = new StringWriter();\n\t\t\tPrintWriter pw = new PrintWriter(sw);\n\t\t\tif (\"statistics\".equals(report)) {\n\t\t\t\thtmlEmail.setSubject(\"OpenSearchServer statistics report\");\n\t\t\t\tdoStatistics(client, request.getParameter(\"stat\"), request\n\t\t\t\t\t\t.getParameter(\"period\"), pw);\n\t\t\t}\n\t\t\tpw.close();\n\t\t\tsw.close();\n\t\t\tString html = sw.toString();\n\t\t\tif (html == null || html.length() == 0) {\n\t\t\t\ttransaction.addXmlResponse(\"Result\", \"Nothing to send\");\n\t\t\t} else {\n\t\t\t\thtmlEmail.setHtmlMsg(sw.toString());\n\t\t\t\thtmlEmail\n\t\t\t\t\t\t.setTextMsg(\"Your email client does not support HTML messages\");\n\t\t\t\thtmlEmail.send();\n\t\t\t}\n\t\t\ttransaction.addXmlResponse(\"MailSent\", emails);\n\t\t} catch (Exception e) {\n\t\t\tthrow new ServletException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void deleteUrl(String sUrl) throws SearchLibException {\n\t\ttry {\n\t\t\tclient.deleteDocument(sUrl);\n\t\t} catch (CorruptIndexException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (LockObtainFailedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t} \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void deleteUrl(String sUrl) throws SearchLibException {\n\t\ttry {\n\t\t\ttargetClient.deleteDocument(sUrl);\n\t\t\turlDbClient.deleteDocument(sUrl);\n\t\t} catch (CorruptIndexException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (LockObtainFailedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\tfieldLeft = null;\n\t\tselectedFacet = null;\n\t\tsuper.reloadPage();\n\t} \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\tfieldLeft = null;\n\t\t\tselectedFacet = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\thighlightFieldLeft = null;\n\t\tselectedHighlight = null;\n\t\tsuper.reloadPage();\n\t} \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\thighlightFieldLeft = null;\n\t\t\tselectedHighlight = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void readExternal(ObjectInput in) throws IOException,\n\t\t\tClassNotFoundException {\n\t\tsuper.readExternal(in);\n\t\tfragmenter = External.readObject(in);\n\t\ttag = External.readUTF(in);\n\t\tmaxDocChar = in.readInt();\n\t\tseparator = External.readUTF(in);\n\t\tmaxSnippetSize = in.readInt();\n\t\tmaxSnippetNumber = in.readInt();\n\t\tint l = in.readInt();\n\t\tif (l > 0) {\n\t\t\tsearchTerms = new String[l];\n\t\t\tExternal.readArray(in, searchTerms);\n\t\t} else\n\t\t\tsearchTerms = null;\n\t} \n #location 13 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void readExternal(ObjectInput in) throws IOException,\n\t\t\tClassNotFoundException {\n\t\tsuper.readExternal(in);\n\t\tfragmenter = External.readObject(in);\n\t\ttag = External.readUTF(in);\n\t\tmaxDocChar = in.readInt();\n\t\tseparator = External.readUTF(in);\n\t\tmaxSnippetSize = in.readInt();\n\t\tmaxSnippetNumber = in.readInt();\n\t\tsearchTerms = External.readStringArray(in);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void onUpload() throws InterruptedException,\n\t\t\tXPathExpressionException, NoSuchAlgorithmException,\n\t\t\tParserConfigurationException, SAXException, IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tMedia media = Fileupload.get();\n\t\tif (media == null)\n\t\t\treturn;\n\t\tsetCurrentDocument(null);\n\t\tParserSelector parserSelector = getClient().getParserSelector();\n\t\tParser parser = null;\n\t\tString contentType = media.getContentType();\n\t\tif (contentType != null)\n\t\t\tparser = parserSelector.getParserFromMimeType(contentType);\n\t\tif (parser == null) {\n\t\t\tString extension = FileUtils.getFileNameExtension(media.getName());\n\t\t\tparser = parserSelector.getParserFromExtension(extension);\n\t\t}\n\t\tif (parser == null) {\n\t\t\tMessagebox.show(\"No parser found for that document type (\"\n\t\t\t\t\t+ contentType + \" - \" + media.getName() + ')');\n\t\t\treturn;\n\t\t}\n\n\t\tBasketDocument basketDocument = parser.getBasketDocument();\n\t\tsetCurrentDocument(basketDocument);\n\t\tbasketDocument.addIfNoEmpty(\"filename\", media.getName());\n\t\tbasketDocument.addIfNoEmpty(\"content_type\", contentType);\n\n\t\tsynchronized (this) {\n\t\t\tif (media.inMemory()) {\n\t\t\t\tif (media.isBinary())\n\t\t\t\t\tparser.parseContent(media.getByteData());\n\t\t\t\telse\n\t\t\t\t\tparser.parseContent(media.getStringData());\n\t\t\t} else {\n\t\t\t\tif (media.isBinary())\n\t\t\t\t\tparser.parseContent(media.getStreamData());\n\t\t\t\telse\n\t\t\t\t\tparser.parseContent(media.getReaderData());\n\t\t\t}\n\t\t\treloadPage();\n\t\t}\n\t} \n #location 28 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void onUpload() throws InterruptedException,\n\t\t\tXPathExpressionException, NoSuchAlgorithmException,\n\t\t\tParserConfigurationException, SAXException, IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tMedia media = Fileupload.get();\n\t\tif (media == null)\n\t\t\treturn;\n\t\tsynchronized (this) {\n\t\t\tsetCurrentDocument(null);\n\t\t\tParserSelector parserSelector = getClient().getParserSelector();\n\t\t\tParser parser = null;\n\t\t\tString contentType = media.getContentType();\n\t\t\tif (contentType != null)\n\t\t\t\tparser = parserSelector.getParserFromMimeType(contentType);\n\t\t\tif (parser == null) {\n\t\t\t\tString extension = FileUtils.getFileNameExtension(media\n\t\t\t\t\t\t.getName());\n\t\t\t\tparser = parserSelector.getParserFromExtension(extension);\n\t\t\t}\n\t\t\tif (parser == null) {\n\t\t\t\tMessagebox.show(\"No parser found for that document type (\"\n\t\t\t\t\t\t+ contentType + \" - \" + media.getName() + ')');\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\tBasketDocument basketDocument = parser.getBasketDocument();\n\t\t\tbasketDocument.addIfNoEmpty(\"filename\", media.getName());\n\t\t\tbasketDocument.addIfNoEmpty(\"content_type\", contentType);\n\n\t\t\tif (media.inMemory()) {\n\t\t\t\tif (media.isBinary())\n\t\t\t\t\tparser.parseContent(media.getByteData());\n\t\t\t\telse\n\t\t\t\t\tparser.parseContent(media.getStringData());\n\t\t\t} else {\n\t\t\t\tif (media.isBinary())\n\t\t\t\t\tparser.parseContent(media.getStreamData());\n\t\t\t\telse\n\t\t\t\t\tparser.parseContent(media.getReaderData());\n\t\t\t}\n\t\t\tsetCurrentDocument(basketDocument);\n\t\t\treloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\tfieldLeft = null;\n\t\tselectedFacet = null;\n\t\tsuper.reloadPage();\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\tfieldLeft = null;\n\t\t\tselectedFacet = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void doRequest(ServletTransaction transaction)\n\t\t\tthrows ServletException {\n\t\ttry {\n\t\t\tClient client = Client.getWebAppInstance();\n\t\t\tHttpServletRequest request = transaction.getServletRequest();\n\t\t\tString indexName = request.getParameter(\"index\");\n\t\t\tString uniq = request.getParameter(\"uniq\");\n\t\t\tObject result = null;\n\t\t\tif (uniq != null)\n\t\t\t\tresult = deleteDoc(client, indexName, uniq);\n\t\t\telse\n\t\t\t\tresult = doObjectRequest(request, indexName);\n\t\t\tPrintWriter pw = transaction.getWriter(\"UTF-8\");\n\t\t\tpw.println(result);\n\t\t} catch (Exception e) {\n\t\t\tthrow new ServletException(e);\n\t\t}\n\t} \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tprotected void doRequest(ServletTransaction transaction)\n\t\t\tthrows ServletException {\n\t\ttry {\n\t\t\tClient client = Client.getWebAppInstance();\n\t\t\tHttpServletRequest request = transaction.getServletRequest();\n\t\t\tString indexName = request.getParameter(\"index\");\n\t\t\tString uniq = request.getParameter(\"uniq\");\n\t\t\tString docId = request.getParameter(\"docId\");\n\t\t\tboolean byId = request.getParameter(\"byId\") != null;\n\t\t\tObject result = null;\n\t\t\tif (uniq != null)\n\t\t\t\tresult = deleteUniqDoc(client, indexName, uniq);\n\t\t\telse if (docId != null)\n\t\t\t\tresult = deleteDocById(client, indexName, Integer\n\t\t\t\t\t\t.parseInt(docId));\n\t\t\telse\n\t\t\t\tresult = doObjectRequest(request, indexName, byId);\n\t\t\tPrintWriter pw = transaction.getWriter(\"UTF-8\");\n\t\t\tpw.println(result);\n\t\t} catch (Exception e) {\n\t\t\tthrow new ServletException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void reload(boolean optimize) throws IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tif (optimize) {\n\t\t\tclient.reload(null);\n\t\t\tclient.getIndex().optimize(null);\n\t\t}\n\t\tclient.reload(null);\n\t} \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void reload(boolean optimize) throws IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tif (optimize) {\n\t\t\turlDbClient.reload(null);\n\t\t\turlDbClient.getIndex().optimize(null);\n\t\t\ttargetClient.reload(null);\n\t\t\ttargetClient.getIndex().optimize(null);\n\t\t}\n\t\turlDbClient.reload(null);\n\t\ttargetClient.reload(null);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void deleteUrls(Collection workDeleteUrlList)\n\t\t\tthrows SearchLibException {\n\t\ttry {\n\t\t\tclient.deleteDocuments(workDeleteUrlList);\n\t\t} catch (CorruptIndexException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (LockObtainFailedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void deleteUrls(Collection workDeleteUrlList)\n\t\t\tthrows SearchLibException {\n\t\ttry {\n\t\t\ttargetClient.deleteDocuments(workDeleteUrlList);\n\t\t\turlDbClient.deleteDocuments(workDeleteUrlList);\n\t\t} catch (CorruptIndexException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (LockObtainFailedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void writeXmlConfig(XmlWriter xmlWriter) throws SAXException,\n\t\t\tSearchLibException {\n\t\txmlWriter.startElement(\"system\");\n\n\t\txmlWriter.startElement(\"availableProcessors\", \"value\", Integer\n\t\t\t\t.toString(getAvailableProcessors()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"freeMemory\", \"value\", Long\n\t\t\t\t.toString(getFreeMemory()), \"rate\", Double\n\t\t\t\t.toString(getMemoryRate()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"maxMemory\", \"value\", Long\n\t\t\t\t.toString(getMaxMemory()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"totalMemory\", \"value\", Long\n\t\t\t\t.toString(getTotalMemory()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"indexCount\", \"value\", Integer\n\t\t\t\t.toString(getIndexCount()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"freeDiskSpace\", \"value\", getFreeDiskSpace()\n\t\t\t\t.toString());\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"dataDirectoryPath\", \"value\",\n\t\t\t\tgetDataDirectoryPath());\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"properties\");\n\n\t\tfor (Entry prop : getProperties()) {\n\t\t\txmlWriter.startElement(\"property\", \"name\",\n\t\t\t\t\tprop.getKey().toString(), \"value\", prop.getValue()\n\t\t\t\t\t\t\t.toString());\n\t\t\txmlWriter.endElement();\n\t\t}\n\n\t\txmlWriter.endElement();\n\t} \n #location 27 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void writeXmlConfig(XmlWriter xmlWriter) throws SAXException,\n\t\t\tSearchLibException, SecurityException, IOException {\n\t\txmlWriter.startElement(\"system\");\n\n\t\txmlWriter.startElement(\"availableProcessors\", \"value\", Integer\n\t\t\t\t.toString(getAvailableProcessors()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"freeMemory\", \"value\", Long\n\t\t\t\t.toString(getFreeMemory()), \"rate\", Double\n\t\t\t\t.toString(getMemoryRate()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"maxMemory\", \"value\", Long\n\t\t\t\t.toString(getMaxMemory()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"totalMemory\", \"value\", Long\n\t\t\t\t.toString(getTotalMemory()));\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"indexCount\", \"value\", Integer\n\t\t\t\t.toString(getIndexCount()));\n\t\txmlWriter.endElement();\n\n\t\tDouble rate = getDiskRate();\n\t\tif (rate == null)\n\t\t\txmlWriter.startElement(\"freeDiskSpace\", \"value\", getFreeDiskSpace()\n\t\t\t\t\t.toString());\n\t\telse\n\t\t\txmlWriter.startElement(\"freeDiskSpace\", \"value\", getFreeDiskSpace()\n\t\t\t\t\t.toString(), \"rate\", rate.toString());\n\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"dataDirectoryPath\", \"value\",\n\t\t\t\tgetDataDirectoryPath());\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.endElement();\n\n\t\txmlWriter.startElement(\"properties\");\n\n\t\tfor (Entry prop : getProperties()) {\n\t\t\txmlWriter.startElement(\"property\", \"name\",\n\t\t\t\t\tprop.getKey().toString(), \"value\", prop.getValue()\n\t\t\t\t\t\t\t.toString());\n\t\t\txmlWriter.endElement();\n\t\t}\n\n\t\txmlWriter.endElement();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void onAdd() throws SearchLibException,\n\t\t\tUnsupportedEncodingException, ParseException, InterruptedException {\n\t\tsynchronized (this) {\n\t\t\tif (getSelectedFile() != null) {\n\t\t\t\t// Already In\n\t\t\t\tif (getClient().getFilePathManager().getStrictPaths(\n\t\t\t\t\t\tgetSelectedFile().getPath(), 0, 0, null) > 0) {\n\t\t\t\t\tMessagebox\n\t\t\t\t\t\t\t.show(\"Already In.\", \"Jaeksoft OpenSearchServer\",\n\t\t\t\t\t\t\t\t\tMessagebox.OK,\n\t\t\t\t\t\t\t\t\torg.zkoss.zul.Messagebox.INFORMATION);\n\t\t\t\t} else {\n\t\t\t\t\tList list = FilePathManager.addPath(\n\t\t\t\t\t\t\tgetSelectedFile().getPath(), getSelectedFile()\n\t\t\t\t\t\t\t\t\t.isDirectory()\n\t\t\t\t\t\t\t\t\t&& isSelectedFileCheck());\n\n\t\t\t\t\tif (list.size() > 0) {\n\t\t\t\t\t\tgetClient().getFilePathManager().addList(list, false);\n\t\t\t\t\t}\n\n\t\t\t\t\tpathList = null;\n\t\t\t\t\tsetSelectedFileCheck(false);\n\t\t\t\t\tsetSelectedFilePath(null);\n\t\t\t\t\treloadPage();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} \n #location 18 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void onAdd() throws SearchLibException,\n\t\t\tUnsupportedEncodingException, ParseException, InterruptedException {\n\t\tsynchronized (this) {\n\t\t\tif (getSelectedFile() != null) {\n\t\t\t\t// Already In\n\t\t\t\tif (getClient().getFilePathManager().getFilePaths(\n\t\t\t\t\t\tgetSelectedFile().getPath(), 0, 0, null) > 0) {\n\t\t\t\t\tMessagebox\n\t\t\t\t\t\t\t.show(\"Already In.\", \"Jaeksoft OpenSearchServer\",\n\t\t\t\t\t\t\t\t\tMessagebox.OK,\n\t\t\t\t\t\t\t\t\torg.zkoss.zul.Messagebox.INFORMATION);\n\t\t\t\t} else {\n\t\t\t\t\t/*\n\t\t\t\t\t * List list = FilePathManager(\n\t\t\t\t\t * getSelectedFile().getPath(), getSelectedFile()\n\t\t\t\t\t * .isDirectory() && isSelectedFileCheck());\n\t\t\t\t\t * \n\t\t\t\t\t * if (list.size() > 0) {\n\t\t\t\t\t * getClient().getFilePathManager().addList(list, false); }\n\t\t\t\t\t */\n\t\t\t\t\tpathList = null;\n\t\t\t\t\tsetSelectedFileCheck(false);\n\t\t\t\t\tsetSelectedFilePath(null);\n\t\t\t\t\treloadPage();\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void getNewUrlToFetch(NamedItem host, long limit,\n\t\t\tList urlList) throws SearchLibException, ParseException,\n\t\t\tIOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = client.getNewSearchRequest(\"urlSearch\");\n\t\tsearchRequest.addFilter(\"host:\\\"\"\n\t\t\t\t+ SearchRequest.escapeQuery(host.getName()) + \"\\\"\");\n\t\tsearchRequest.setQueryString(\"*:*\");\n\t\tfilterQueryToFetchNew(searchRequest);\n\t\tsearchRequest.setRows((int) limit);\n\t\tResult result = client.search(searchRequest);\n\t\tfor (ResultDocument item : result)\n\t\t\turlList.add(new UrlItem(item));\n\t} \n #location 12 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void getNewUrlToFetch(NamedItem host, long limit,\n\t\t\tList urlList) throws SearchLibException, ParseException,\n\t\t\tIOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = urlDbClient\n\t\t\t\t.getNewSearchRequest(\"urlSearch\");\n\t\tsearchRequest.addFilter(\"host:\\\"\"\n\t\t\t\t+ SearchRequest.escapeQuery(host.getName()) + \"\\\"\");\n\t\tsearchRequest.setQueryString(\"*:*\");\n\t\tfilterQueryToFetchNew(searchRequest);\n\t\tsearchRequest.setRows((int) limit);\n\t\tResult result = urlDbClient.search(searchRequest);\n\t\tfor (ResultDocument item : result)\n\t\t\turlList.add(new UrlItem(item));\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\tselectedSort = null;\n\t\tsortFieldLeft = null;\n\t\tsuper.reloadPage();\n\t} \n #location 3 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\tselectedSort = null;\n\t\t\tsortFieldLeft = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void updateUrlItems(List urlItems)\n\t\t\tthrows SearchLibException {\n\t\ttry {\n\t\t\tList documents = new ArrayList(\n\t\t\t\t\turlItems.size());\n\t\t\tfor (UrlItem urlItem : urlItems) {\n\t\t\t\tIndexDocument indexDocument = new IndexDocument();\n\t\t\t\turlItem.populate(indexDocument);\n\t\t\t\tdocuments.add(indexDocument);\n\t\t\t}\n\t\t\tclient.updateDocuments(documents);\n\t\t} catch (NoSuchAlgorithmException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t} \n #location 11 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void updateUrlItems(List urlItems)\n\t\t\tthrows SearchLibException {\n\t\ttry {\n\t\t\tList documents = new ArrayList(\n\t\t\t\t\turlItems.size());\n\t\t\tfor (UrlItem urlItem : urlItems) {\n\t\t\t\tIndexDocument indexDocument = new IndexDocument();\n\t\t\t\turlItem.populate(indexDocument);\n\t\t\t\tdocuments.add(indexDocument);\n\t\t\t}\n\t\t\turlDbClient.updateDocuments(documents);\n\t\t} catch (NoSuchAlgorithmException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void getStartingWith(String queryString, Field field, String start,\n\t\t\tint limit, List list) throws ParseException,\n\t\t\tIOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException, SearchLibException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = client.getNewSearchRequest(field\n\t\t\t\t+ \"Facet\");\n\t\tsearchRequest.setQueryString(queryString);\n\t\tsearchRequest.getFilterList().add(field + \":\" + start + \"*\",\n\t\t\t\tSource.REQUEST);\n\t\tgetFacetLimit(field, searchRequest, limit, list);\n\t} \n #location 11 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void getStartingWith(String queryString, Field field, String start,\n\t\t\tint limit, List list) throws ParseException,\n\t\t\tIOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException, SearchLibException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = urlDbClient.getNewSearchRequest(field\n\t\t\t\t+ \"Facet\");\n\t\tsearchRequest.setQueryString(queryString);\n\t\tsearchRequest.getFilterList().add(field + \":\" + start + \"*\",\n\t\t\t\tSource.REQUEST);\n\t\tgetFacetLimit(field, searchRequest, limit, list);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public long getUrls(SearchRequest searchRequest, Field orderBy,\n\t\t\tboolean orderAsc, long start, long rows, List list)\n\t\t\tthrows SearchLibException {\n\t\tsearchRequest.setStart((int) start);\n\t\tsearchRequest.setRows((int) rows);\n\t\ttry {\n\t\t\tif (orderBy != null)\n\t\t\t\tsearchRequest.addSort(orderBy.name, !orderAsc);\n\t\t\tResult result = client.search(searchRequest);\n\t\t\tif (list != null)\n\t\t\t\tfor (ResultDocument doc : result)\n\t\t\t\t\tlist.add(new UrlItem(doc));\n\t\t\treturn result.getNumFound();\n\t\t} catch (ParseException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (RuntimeException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (SyntaxError e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InterruptedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t} \n #location 9 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public long getUrls(SearchRequest searchRequest, Field orderBy,\n\t\t\tboolean orderAsc, long start, long rows, List list)\n\t\t\tthrows SearchLibException {\n\t\tsearchRequest.setStart((int) start);\n\t\tsearchRequest.setRows((int) rows);\n\t\ttry {\n\t\t\tif (orderBy != null)\n\t\t\t\tsearchRequest.addSort(orderBy.name, !orderAsc);\n\t\t\tResult result = urlDbClient.search(searchRequest);\n\t\t\tif (list != null)\n\t\t\t\tfor (ResultDocument doc : result)\n\t\t\t\t\tlist.add(new UrlItem(doc));\n\t\t\treturn result.getNumFound();\n\t\t} catch (ParseException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (RuntimeException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (SyntaxError e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InterruptedException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void renderDocument(int pos) throws CorruptIndexException,\n\t\t\tIOException, ParseException, SyntaxError {\n\t\twriter.print(\"\\t\");\n\t\tResultDocument doc = result.getDocument(pos);\n\t\tfor (Field field : searchRequest.getReturnFieldList())\n\t\t\trenderField(doc, field);\n\t\tfor (HighlightField field : searchRequest.getHighlightFieldList())\n\t\t\trenderHighlightValue(doc, field);\n\n\t\tint cc = result.getCollapseCount(pos);\n\t\tif (cc > 0) {\n\t\t\twriter.print(\"\\t\\t\");\n\t\t\twriter.print(cc);\n\t\t\twriter.println(\"\");\n\t\t}\n\t\twriter.println(\"\\t\");\n\t} \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void renderDocument(int pos) throws CorruptIndexException,\n\t\t\tIOException, ParseException, SyntaxError {\n\t\twriter.print(\"\\t\");\n\t\tResultDocument doc = result.getDocument(pos);\n\t\tfor (Field field : searchRequest.getReturnFieldList())\n\t\t\trenderField(doc, field);\n\t\tfor (HighlightField field : searchRequest.getHighlightFieldList())\n\t\t\trenderHighlightValue(doc, field);\n\n\t\tint cc = result.getCollapseCount(pos);\n\t\tif (cc > 0) {\n\t\t\twriter.print(\"\\t\\t\");\n\t\t\twriter.print(cc);\n\t\t\twriter.println(\"\");\n\t\t}\n\t\twriter.println(\"\\t\");\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\thighlightFieldLeft = null;\n\t\tselectedHighlight = null;\n\t\tsuper.reloadPage();\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\thighlightFieldLeft = null;\n\t\t\tselectedHighlight = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void updateCrawls(List crawls) throws SearchLibException {\n\t\ttry {\n\t\t\tList documents = new ArrayList(crawls\n\t\t\t\t\t.size());\n\t\t\tfor (Crawl crawl : crawls) {\n\t\t\t\tIndexDocument indexDocument = new IndexDocument();\n\t\t\t\tcrawl.getUrlItem().populate(indexDocument);\n\t\t\t\tdocuments.add(indexDocument);\n\t\t\t}\n\t\t\tclient.updateDocuments(documents);\n\t\t} catch (NoSuchAlgorithmException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t} \n #location 10 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void updateCrawls(List crawls) throws SearchLibException {\n\t\ttry {\n\t\t\t// Update target index\n\t\t\tList documents = new ArrayList(crawls\n\t\t\t\t\t.size());\n\t\t\tfor (Crawl crawl : crawls) {\n\t\t\t\tIndexDocument indexDocument = crawl.getTargetIndexDocument();\n\t\t\t\tdocuments.add(indexDocument);\n\t\t\t}\n\t\t\ttargetClient.updateDocuments(documents);\n\n\t\t\t// Update URL DB\n\t\t\tdocuments.clear();\n\t\t\tfor (Crawl crawl : crawls) {\n\t\t\t\tIndexDocument indexDocument = new IndexDocument();\n\t\t\t\tcrawl.getUrlItem().populate(indexDocument);\n\t\t\t\tdocuments.add(indexDocument);\n\t\t\t}\n\t\t\turlDbClient.updateDocuments(documents);\n\n\t\t} catch (NoSuchAlgorithmException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IOException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (URISyntaxException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (InstantiationException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (IllegalAccessException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t} catch (ClassNotFoundException e) {\n\t\t\tthrow new SearchLibException(e);\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void getOldUrlToFetch(NamedItem host, Date fetchIntervalDate,\n\t\t\tlong limit, List urlList) throws SearchLibException,\n\t\t\tParseException, IOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = client.getNewSearchRequest(\"urlSearch\");\n\t\tsearchRequest.addFilter(\"host:\\\"\"\n\t\t\t\t+ SearchRequest.escapeQuery(host.getName()) + \"\\\"\");\n\t\tsearchRequest.setQueryString(\"*:*\");\n\t\tfilterQueryToFetchOld(searchRequest, fetchIntervalDate);\n\t\tsearchRequest.setRows((int) limit);\n\t\tResult result = client.search(searchRequest);\n\t\tfor (ResultDocument item : result)\n\t\t\turlList.add(new UrlItem(item));\n\t} \n #location 12 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void getOldUrlToFetch(NamedItem host, Date fetchIntervalDate,\n\t\t\tlong limit, List urlList) throws SearchLibException,\n\t\t\tParseException, IOException, SyntaxError, URISyntaxException,\n\t\t\tClassNotFoundException, InterruptedException,\n\t\t\tInstantiationException, IllegalAccessException {\n\t\tSearchRequest searchRequest = urlDbClient\n\t\t\t\t.getNewSearchRequest(\"urlSearch\");\n\t\tsearchRequest.addFilter(\"host:\\\"\"\n\t\t\t\t+ SearchRequest.escapeQuery(host.getName()) + \"\\\"\");\n\t\tsearchRequest.setQueryString(\"*:*\");\n\t\tfilterQueryToFetchOld(searchRequest, fetchIntervalDate);\n\t\tsearchRequest.setRows((int) limit);\n\t\tResult result = urlDbClient.search(searchRequest);\n\t\tfor (ResultDocument item : result)\n\t\t\turlList.add(new UrlItem(item));\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected void reloadPage() {\n\t\tselectedSort = null;\n\t\tsortFieldLeft = null;\n\t\tsuper.reloadPage();\n\t} \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n\tprotected void reloadPage() {\n\t\tsynchronized (this) {\n\t\t\tselectedSort = null;\n\t\t\tsortFieldLeft = null;\n\t\t\tsuper.reloadPage();\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void reload(boolean optimize) throws IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tif (optimize) {\n\t\t\tclient.reload(null);\n\t\t\tclient.getIndex().optimize(null);\n\t\t}\n\t\tclient.reload(null);\n\t} \n #location 5 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n public void reload(boolean optimize) throws IOException,\n\t\t\tURISyntaxException, SearchLibException, InstantiationException,\n\t\t\tIllegalAccessException, ClassNotFoundException {\n\t\tif (optimize) {\n\t\t\turlDbClient.reload(null);\n\t\t\turlDbClient.getIndex().optimize(null);\n\t\t\ttargetClient.reload(null);\n\t\t\ttargetClient.getIndex().optimize(null);\n\t\t}\n\t\turlDbClient.reload(null);\n\t\ttargetClient.reload(null);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void run(ResultScoreDoc[] fetchedDocs, int fetchLength)\n\t\t\tthrows IOException {\n\n\t\tcollapsedDoc = null;\n\n\t\tif (fetchedDocs == null)\n\t\t\treturn;\n\n\t\tif (fetchLength > fetchedDocs.length)\n\t\t\tfetchLength = fetchedDocs.length;\n\n\t\tOpenBitSet collapsedSet = new OpenBitSet(fetchLength);\n\n\t\tString lastTerm = null;\n\t\tint adjacent = 0;\n\t\tcollapsedDocCount = 0;\n\t\tfor (int i = 0; i < fetchLength; i++) {\n\t\t\tString term = fetchedDocs[i].collapseTerm;\n\t\t\tif (term != null && term.equals(lastTerm)) {\n\t\t\t\tif (++adjacent >= collapseMax)\n\t\t\t\t\tcollapsedSet.set(i);\n\t\t\t} else {\n\t\t\t\tlastTerm = term;\n\t\t\t\tadjacent = 0;\n\t\t\t}\n\t\t}\n\t\tcollapsedDocCount = (int) collapsedSet.cardinality();\n\n\t\tcollapsedDoc = new ResultScoreDoc[fetchLength - collapsedDocCount];\n\n\t\tint currentPos = 0;\n\t\tResultScoreDoc collapseDoc = null;\n\t\tfor (int i = 0; i < fetchLength; i++) {\n\t\t\tif (!collapsedSet.get(i)) {\n\t\t\t\tcollapseDoc = fetchedDocs[i];\n\t\t\t\tcollapseDoc.collapseCount = 0;\n\t\t\t\tcollapsedDoc[currentPos++] = collapseDoc;\n\t\t\t} else {\n\t\t\t\tcollapseDoc.collapseCount++;\n\t\t\t}\n\t\t}\n\t} \n #location 39 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void run(ResultScoreDoc[] fetchedDocs, int fetchLength)\n\t\t\tthrows IOException {\n\n\t\tcollapsedDoc = null;\n\n\t\tif (fetchedDocs == null)\n\t\t\treturn;\n\n\t\tif (fetchLength > fetchedDocs.length)\n\t\t\tfetchLength = fetchedDocs.length;\n\n\t\tcollapse(fetchedDocs, fetchLength);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n final protected void getFragments(String originalText,\n\t\t\tFragmentList fragments, int vectorOffset) {\n\t\toriginalTextLength = originalText.length();\n\t\tif (splitPos == null)\n\t\t\tsplitPos = new TreeSet();\n\t\tsplitPos.clear();\n\t\tcheck(originalText);\n\t\tIterator splitIterator = splitPos.iterator();\n\t\tint pos = 0;\n\t\tFragment lastFragment = null;\n\t\twhile (splitIterator.hasNext()) {\n\t\t\tint nextSplitPos = splitIterator.next();\n\t\t\tlastFragment = fragments.addOriginalText(originalText.substring(\n\t\t\t\t\tpos, nextSplitPos), vectorOffset, lastFragment == null);\n\t\t\tpos = nextSplitPos;\n\t\t}\n\t\tif (pos < originalText.length())\n\t\t\tlastFragment = fragments.addOriginalText(originalText\n\t\t\t\t\t.substring(pos), vectorOffset, lastFragment == null);\n\t\tlastFragment.setEdge(true);\n\t} \n #location 20 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n final protected void getFragments(String originalText,\n\t\t\tFragmentList fragments, int vectorOffset) {\n\t\toriginalTextLength = originalText.length();\n\t\tif (splitPos == null)\n\t\t\tsplitPos = new TreeSet();\n\t\tsplitPos.clear();\n\t\tcheck(originalText);\n\t\tIterator splitIterator = splitPos.iterator();\n\t\tint pos = 0;\n\t\tFragment lastFragment = null;\n\t\twhile (splitIterator.hasNext()) {\n\t\t\tint nextSplitPos = splitIterator.next();\n\t\t\tlastFragment = fragments.addOriginalText(originalText.substring(\n\t\t\t\t\tpos, nextSplitPos), vectorOffset, lastFragment == null);\n\t\t\tpos = nextSplitPos;\n\t\t}\n\t\tif (pos < originalText.length())\n\t\t\tlastFragment = fragments.addOriginalText(originalText\n\t\t\t\t\t.substring(pos), vectorOffset, lastFragment == null);\n\t\tif (lastFragment != null)\n\t\t\tlastFragment.setEdge(true);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static HTMLDocument fetch(final URL url) throws IOException {\n\t\tfinal URLConnection conn = url.openConnection();\n\t\tfinal String charset = conn.getContentEncoding();\n\n\t\tCharset cs = Charset.forName(\"Cp1252\");\n\t\tif (charset != null) {\n\t\t\ttry {\n\t\t\t\tcs = Charset.forName(charset);\n\t\t\t} catch (UnsupportedCharsetException e) {\n\t\t\t\t// keep default\n\t\t\t}\n\t\t}\n\t\t\n\t\tInputStream in = conn.getInputStream();\n\n\t\tfinal String encoding = conn.getContentEncoding();\n\t\tif(encoding != null) {\n\t\t\tif(\"gzip\".equalsIgnoreCase(encoding)) {\n\t\t\t\tin = new GZIPInputStream(in);\n\t\t\t} else {\n\t\t\t\tSystem.err.println(\"WARN: unsupported Content-Encoding: \"+encoding);\n\t\t\t}\n\t\t}\n\n\t\tByteArrayOutputStream bos = new ByteArrayOutputStream();\n\t\tbyte[] buf = new byte[4096];\n\t\tint r;\n\t\twhile ((r = in.read(buf)) != -1) {\n\t\t\tbos.write(buf, 0, r);\n\t\t}\n\t\tin.close();\n\n\t\tfinal byte[] data = bos.toByteArray();\n\t\t\n\t\treturn new HTMLDocument(data, cs);\n\t} \n #location 35 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static HTMLDocument fetch(final URL url) throws IOException {\n\t\tfinal URLConnection conn = url.openConnection();\n\t\tfinal String ct = conn.getContentType();\n\n\t\tCharset cs = Charset.forName(\"Cp1252\");\n\t\tif (ct != null) {\n\t\t\tMatcher m = PAT_CHARSET.matcher(ct);\n\t\t\tif(m.find()) {\n\t\t\t\tfinal String charset = m.group(1);\n\t\t\t\ttry {\n\t\t\t\t\tcs = Charset.forName(charset);\n\t\t\t\t} catch (UnsupportedCharsetException e) {\n\t\t\t\t\t// keep default\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t\n\t\tInputStream in = conn.getInputStream();\n\n\t\tfinal String encoding = conn.getContentEncoding();\n\t\tif(encoding != null) {\n\t\t\tif(\"gzip\".equalsIgnoreCase(encoding)) {\n\t\t\t\tin = new GZIPInputStream(in);\n\t\t\t} else {\n\t\t\t\tSystem.err.println(\"WARN: unsupported Content-Encoding: \"+encoding);\n\t\t\t}\n\t\t}\n\n\t\tByteArrayOutputStream bos = new ByteArrayOutputStream();\n\t\tbyte[] buf = new byte[4096];\n\t\tint r;\n\t\twhile ((r = in.read(buf)) != -1) {\n\t\t\tbos.write(buf, 0, r);\n\t\t}\n\t\tin.close();\n\n\t\tfinal byte[] data = bos.toByteArray();\n\t\t\n\t\treturn new HTMLDocument(data, cs);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String getText(final URL url) throws BoilerpipeProcessingException {\n try {\n final URLConnection conn = url.openConnection();\n final String encoding = conn.getContentEncoding();\n\n Charset cs = Charset.forName(\"Cp1252\");\n if (encoding != null) {\n try {\n cs = Charset.forName(encoding);\n } catch (UnsupportedCharsetException e) {\n // keep default\n }\n }\n\n final InputStream in = conn.getInputStream();\n \n InputSource is = new InputSource(in);\n if(cs != null) {\n is.setEncoding(cs.name());\n }\n \n final String text = getText(is);\n in.close();\n return text;\n } catch (IOException e) {\n throw new BoilerpipeProcessingException(e);\n }\n } \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public String getText(final URL url) throws BoilerpipeProcessingException {\n try {\n \treturn getText(HTMLFetcher.fetch(url).toInputSource());\n } catch (IOException e) {\n throw new BoilerpipeProcessingException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static HTMLDocument fetch(final URL url) throws IOException {\n\t\tfinal URLConnection conn = url.openConnection();\n\t\tfinal String charset = conn.getContentEncoding();\n\n\t\tCharset cs = Charset.forName(\"Cp1252\");\n\t\tif (charset != null) {\n\t\t\ttry {\n\t\t\t\tcs = Charset.forName(charset);\n\t\t\t} catch (UnsupportedCharsetException e) {\n\t\t\t\t// keep default\n\t\t\t}\n\t\t}\n\t\t\n\t\tInputStream in = conn.getInputStream();\n\n\t\tfinal String encoding = conn.getContentEncoding();\n\t\tif(encoding != null) {\n\t\t\tif(\"gzip\".equalsIgnoreCase(encoding)) {\n\t\t\t\tin = new GZIPInputStream(in);\n\t\t\t} else {\n\t\t\t\tSystem.err.println(\"WARN: unsupported Content-Encoding: \"+encoding);\n\t\t\t}\n\t\t}\n\n\t\tByteArrayOutputStream bos = new ByteArrayOutputStream();\n\t\tbyte[] buf = new byte[4096];\n\t\tint r;\n\t\twhile ((r = in.read(buf)) != -1) {\n\t\t\tbos.write(buf, 0, r);\n\t\t}\n\t\tin.close();\n\n\t\tfinal byte[] data = bos.toByteArray();\n\t\t\n\t\treturn new HTMLDocument(data, cs);\n\t} \n #location 35 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static HTMLDocument fetch(final URL url) throws IOException {\n\t\tfinal URLConnection conn = url.openConnection();\n\t\tfinal String ct = conn.getContentType();\n\n\t\tCharset cs = Charset.forName(\"Cp1252\");\n\t\tif (ct != null) {\n\t\t\tMatcher m = PAT_CHARSET.matcher(ct);\n\t\t\tif(m.find()) {\n\t\t\t\tfinal String charset = m.group(1);\n\t\t\t\ttry {\n\t\t\t\t\tcs = Charset.forName(charset);\n\t\t\t\t} catch (UnsupportedCharsetException e) {\n\t\t\t\t\t// keep default\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t\n\t\tInputStream in = conn.getInputStream();\n\n\t\tfinal String encoding = conn.getContentEncoding();\n\t\tif(encoding != null) {\n\t\t\tif(\"gzip\".equalsIgnoreCase(encoding)) {\n\t\t\t\tin = new GZIPInputStream(in);\n\t\t\t} else {\n\t\t\t\tSystem.err.println(\"WARN: unsupported Content-Encoding: \"+encoding);\n\t\t\t}\n\t\t}\n\n\t\tByteArrayOutputStream bos = new ByteArrayOutputStream();\n\t\tbyte[] buf = new byte[4096];\n\t\tint r;\n\t\twhile ((r = in.read(buf)) != -1) {\n\t\t\tbos.write(buf, 0, r);\n\t\t}\n\t\tin.close();\n\n\t\tfinal byte[] data = bos.toByteArray();\n\t\t\n\t\treturn new HTMLDocument(data, cs);\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void insertLoginLog(String username) {\n UmsAdmin admin = getAdminByUsername(username);\n UmsAdminLoginLog loginLog = new UmsAdminLoginLog();\n loginLog.setAdminId(admin.getId());\n loginLog.setCreateTime(new Date());\n ServletRequestAttributes attributes = (ServletRequestAttributes) RequestContextHolder.getRequestAttributes();\n HttpServletRequest request = attributes.getRequest();\n loginLog.setIp(request.getRemoteAddr());\n loginLogMapper.insert(loginLog);\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void insertLoginLog(String username) {\n UmsAdmin admin = getAdminByUsername(username);\n if(admin==null) return;\n UmsAdminLoginLog loginLog = new UmsAdminLoginLog();\n loginLog.setAdminId(admin.getId());\n loginLog.setCreateTime(new Date());\n ServletRequestAttributes attributes = (ServletRequestAttributes) RequestContextHolder.getRequestAttributes();\n HttpServletRequest request = attributes.getRequest();\n loginLog.setIp(request.getRemoteAddr());\n loginLogMapper.insert(loginLog);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String getUserNameFromToken(String token) {\n String username;\n try {\n Claims claims = getClaimsFromToken(token);\n username = claims.getSubject();\n } catch (Exception e) {\n e.printStackTrace();\n username = null;\n }\n return username;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public String getUserNameFromToken(String token) {\n String username;\n try {\n Claims claims = getClaimsFromToken(token);\n username = claims.getSubject();\n } catch (Exception e) {\n username = null;\n }\n return username;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private Date getExpiredDateFromToken(String token) {\n Date expiredDate = null;\n try {\n Claims claims = getClaimsFromToken(token);\n expiredDate = claims.getExpiration();\n } catch (Exception e) {\n e.printStackTrace();\n }\n return expiredDate;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private Date getExpiredDateFromToken(String token) {\n Claims claims = getClaimsFromToken(token);\n return claims.getExpiration();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic void onHttpFinish(QQHttpResponse response) {\n\t\ttry {\n\t\t\tLOG.debug(response.getContentType());\n\t\t\tString type = response.getContentType();\n\t\t\tif((type.startsWith(\"application/x-javascript\")\n\t\t\t\t\t|| type.startsWith(\"application/json\")\n\t\t\t\t\t|| type.indexOf(\"text\") >= 0\n\t\t\t\t\t) && response.getContentLength() > 0){\n\t\t\t\tLOG.debug(response.getResponseString());\n\t\t\t}\n\n\t\t\tif(response.getResponseCode() == QQHttpResponse.S_OK){\n\t\t\t\tonHttpStatusOK(response);\n\t\t\t}else{\n\t\t\t\tonHttpStatusError(response);\n\t\t\t}\n\t\t} catch (QQException e) {\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, e);\n\t\t} catch (JSONException e) {\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, new QQException(QQErrorCode.JSON_ERROR, e));\n\t\t} catch (Throwable e){\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, new QQException(QQErrorCode.UNKNOWN_ERROR, e));\n\t\t}\n\t} \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic void onHttpFinish(QQHttpResponse response) {\n\t\ttry {\n\t\t\tLOG.debug(response.getContentType());\n\t\t\tString type = response.getContentType();\n\t\t\tif(type!=null && (type.startsWith(\"application/x-javascript\")\n\t\t\t\t\t|| type.startsWith(\"application/json\")\n\t\t\t\t\t|| type.indexOf(\"text\") >= 0\n\t\t\t\t\t) && response.getContentLength() > 0){\n\t\t\t\tLOG.debug(response.getResponseString());\n\t\t\t}\n\n\t\t\tif(response.getResponseCode() == QQHttpResponse.S_OK){\n\t\t\t\tonHttpStatusOK(response);\n\t\t\t}else{\n\t\t\t\tonHttpStatusError(response);\n\t\t\t}\n\t\t} catch (QQException e) {\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, e);\n\t\t} catch (JSONException e) {\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, new QQException(QQErrorCode.JSON_ERROR, e));\n\t\t} catch (Throwable e){\n\t\t\tnotifyActionEvent(QQActionEvent.Type.EVT_ERROR, new QQException(QQErrorCode.UNKNOWN_ERROR, e));\n\t\t}\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void progressCallbackSend() throws Exception {\n final AtomicReference body = new AtomicReference();\n handler = new RequestHandler() {\n\n @Override\n public void handle(Request request, HttpServletResponse response) {\n body.set(new String(read()));\n response.setStatus(HTTP_OK);\n }\n };\n final File file = File.createTempFile(\"post\", \".txt\");\n new FileWriter(file).append(\"hello\").close();\n\n final AtomicInteger tx = new AtomicInteger(0);\n ProgressCallback progress = new ProgressCallback() {\n public void onProgress(int transferred, int total) {\n assertEquals(file.length(), total);\n assertEquals(tx.incrementAndGet(), transferred);\n }\n };\n post(url).bufferSize(1).progress(progress).send(file);\n assertEquals(file.length(), tx.get());\n } \n #location 22 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void progressCallbackSend() throws Exception {\n final AtomicReference body = new AtomicReference();\n handler = new RequestHandler() {\n\n @Override\n public void handle(Request request, HttpServletResponse response) {\n body.set(new String(read()));\n response.setStatus(HTTP_OK);\n }\n };\n final File file = File.createTempFile(\"post\", \".txt\");\n new FileWriter(file).append(\"hello\").close();\n\n final AtomicInteger tx = new AtomicInteger(0);\n ProgressCallback progress = new ProgressCallback() {\n public void onProgress(int transferred, int total) {\n assertEquals(file.length(), total);\n assertEquals(tx.incrementAndGet(), transferred);\n }\n };\n post(url).bufferSize(1).progress(progress).send(file).code();\n assertEquals(file.length(), tx.get());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void progressCallbackSendInputStream() throws Exception {\n final AtomicReference body = new AtomicReference();\n handler = new RequestHandler() {\n\n @Override\n public void handle(Request request, HttpServletResponse response) {\n body.set(new String(read()));\n response.setStatus(HTTP_OK);\n }\n };\n File file = File.createTempFile(\"post\", \".txt\");\n new FileWriter(file).append(\"hello\").close();\n InputStream input = new FileInputStream(file);\n final AtomicInteger tx = new AtomicInteger(0);\n ProgressCallback progress = new ProgressCallback() {\n public void onProgress(int transferred, int total) {\n assertEquals(0, total);\n assertEquals(tx.incrementAndGet(), transferred);\n }\n };\n post(url).bufferSize(1).progress(progress).send(input);\n assertEquals(file.length(), tx.get());\n } \n #location 22 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void progressCallbackSendInputStream() throws Exception {\n final AtomicReference body = new AtomicReference();\n handler = new RequestHandler() {\n\n @Override\n public void handle(Request request, HttpServletResponse response) {\n body.set(new String(read()));\n response.setStatus(HTTP_OK);\n }\n };\n File file = File.createTempFile(\"post\", \".txt\");\n new FileWriter(file).append(\"hello\").close();\n InputStream input = new FileInputStream(file);\n final AtomicInteger tx = new AtomicInteger(0);\n ProgressCallback progress = new ProgressCallback() {\n public void onProgress(int transferred, int total) {\n assertEquals(0, total);\n assertEquals(tx.incrementAndGet(), transferred);\n }\n };\n post(url).bufferSize(1).progress(progress).send(input).code();\n assertEquals(file.length(), tx.get());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(new Configuration(\"com.zuoxiaolong.niubi.job.jobs\"), \"localhost:2181,localhost:3181,localhost:4181\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode();\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(\"localhost:2181,localhost:3181,localhost:4181\", \"http://localhost:8080/job\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(\"localhost:2181,localhost:3181,localhost:4181\", \"http://localhost:8080/job\", StringHelper.emptyArray());\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new MasterSlaveNode(new Configuration(\"com.zuoxiaolong.niubi.job.jobs\"), \"localhost:2181,localhost:3181,localhost:4181\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new MasterSlaveNode();\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(new Configuration(\"com.zuoxiaolong.niubi.job.jobs\"), \"localhost:2181,localhost:3181,localhost:4181\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode();\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List getAllNodes() {\n List childDataList = getChildren(PathHelper.getParentPath(getMasterSlavePathApi().getNodePath()));\n List masterSlaveNodeDataList = childDataList.stream().map(MasterSlaveNodeData::new).collect(Collectors.toList());\n return masterSlaveNodeDataList;\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List getAllNodes() {\n List childDataList = getChildren(PathHelper.getParentPath(getMasterSlavePathApi().getNodePath()));\n if (ListHelper.isEmpty(childDataList)) {\n return null;\n }\n List masterSlaveNodeDataList = childDataList.stream().map(MasterSlaveNodeData::new).collect(Collectors.toList());\n return masterSlaveNodeDataList;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(\"localhost:2181,localhost:3181,localhost:4181\", \"http://localhost:8080/job\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new StandbyNode(\"localhost:2181,localhost:3181,localhost:4181\", \"http://localhost:8080/job\", StringHelper.emptyArray());\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List getAllNodes() {\n List childDataList = getChildren(PathHelper.getParentPath(getStandbyPathApi().getNodePath()));\n List standbyNodeDataList = childDataList.stream().map(StandbyNodeData::new).collect(Collectors.toList());\n return standbyNodeDataList;\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List getAllNodes() {\n List childDataList = getChildren(PathHelper.getParentPath(getStandbyPathApi().getNodePath()));\n if (ListHelper.isEmpty(childDataList)) {\n return null;\n }\n List standbyNodeDataList = childDataList.stream().map(StandbyNodeData::new).collect(Collectors.toList());\n return standbyNodeDataList;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new MasterSlaveNode(new Configuration(\"com.zuoxiaolong.niubi.job.jobs\"), \"localhost:2181,localhost:3181,localhost:4181\");\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @org.junit.Test\n public void test() throws InterruptedException, IOException {\n Node node = new MasterSlaveNode();\n node.join();\n new BufferedReader(new InputStreamReader(System.in)).readLine();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List> getColumns(String schema, String table) throws VerdictDBDbmsException {\n List> columns = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getColumnsCommand(schema, table));\n JdbcResultSet jdbcResultSet = new JdbcResultSet(queryResult);\n try {\n while (queryResult.next()) {\n String type = jdbcResultSet.getString(syntax.getColumnTypeColumnIndex()+1);\n type = type.toLowerCase();\n\n// // remove the size of type\n// type = type.replaceAll(\"\\\\(.*\\\\)\", \"\");\n\n columns.add(\n new ImmutablePair<>(jdbcResultSet.getString(syntax.getColumnNameColumnIndex()+1), type));\n }\n } catch (SQLException e) {\n throw new VerdictDBDbmsException(e);\n } finally {\n jdbcResultSet.close();\n }\n return columns;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List> getColumns(String schema, String table) throws VerdictDBDbmsException {\n List> columns = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getColumnsCommand(schema, table));\n while (queryResult.next()) {\n String type = (String) queryResult.getValue(syntax.getColumnTypeColumnIndex());\n type = type.toLowerCase();\n\n columns.add(\n new ImmutablePair<>((String) queryResult.getValue(syntax.getColumnNameColumnIndex()), type));\n }\n\n return columns;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getSchemas() throws SQLException {\n if (!schemaCache.isEmpty()){\n return schemaCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getSchemaCommand());\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n schemaCache.add(jdbcQueryResult.getString(syntax.getSchemaNameColumnIndex()));\n }\n return schemaCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getSchemas() throws SQLException {\n if (!schemaCache.isEmpty()){\n return schemaCache;\n }\n schemaCache.addAll(connection.getSchemas());\n return schemaCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public ApproxRelation approx() throws VerdictException {\n\t\tList exprs = exprsInSelectElems(elems);\n\t\t\n\t\t// for each expression, we obtain pairs of sample candidates and the costs of using them. \n\t\tList, List>, SelectElem>> candidates_list = new ArrayList, List>, SelectElem>>();\n\t\tfor (int i = 0; i < exprs.size(); i++) {\n\t\t\tMap, List> candidates = source.findSample(exprs.get(i));\n\t\t\tcandidates_list.add(Pair.of(candidates, elems.get(i)));\n\t\t}\n\t\t\n\t\t// We test if we can consolidate those sample candidates so that the number of select statements is less than\n\t\t// the number of the expressions. In the worst case (e.g., all count-distinct), the number of select statements\n\t\t// will be equal to the number of the expressions. If the cost of running those select statements individually\n\t\t// is higher than the cost of running a single select statement using the original tables, we do not use samples.\n\t\tList, List>> consolidated = consolidate(candidates_list);\n\t\tList individuals = new ArrayList();\n\t\t\n\t\tfor (Pair, List> p : consolidated) {\n\t\t\tList elemsPart = p.getRight();\n\t\t\tSet samplesPart = p.getLeft();\n\t\t\tindividuals.add(new ApproxAggregatedRelation(vc, source.approxWith(attachTableMapping(samplesPart)), elemsPart));\n\t\t}\n\t\t\n\t\t// join the results from those multiple relations (if there are more than one)\n\t\tApproxRelation r = null;\n\t\tfor (ApproxAggregatedRelation r1 : individuals) {\n\t\t\tif (r == null) {\n\t\t\t\tr = r1;\n\t\t\t} else {\n\t\t\t\tString ln = Relation.genTableAlias();\n\t\t\t\tString rn = Relation.genTableAlias();\n\t\t\t\tr.setAliasName(ln);\n\t\t\t\tr1.setAliasName(rn);\n\t\t\t\tif (r1.getSource() instanceof ApproxGroupedRelation) {\n\t\t\t\t\tList groupby = ((ApproxGroupedRelation) r1.getSource()).getGroupby();\n\t\t\t\t\tList> joincols = new ArrayList>();\n\t\t\t\t\tfor (ColNameExpr col : groupby) {\n\t\t\t\t\t\tjoincols.add(Pair.of((Expr) new ColNameExpr(col.getCol(), ln), (Expr) new ColNameExpr(col.getCol(), rn)));\n\t\t\t\t\t}\n\t\t\t\t\tr = new ApproxJoinedRelation(vc, r, r1, joincols);\n\t\t\t\t} else {\n\t\t\t\t\tr = new ApproxJoinedRelation(vc, r, r1, null);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tr.setAliasName(getAliasName());\n\t\treturn r;\n\t} \n #location 46 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public ApproxRelation approx() throws VerdictException {\n\t\t// for each expression, we obtain pairs of sample candidates and the costs of using them. \n\t\tList> candidates_list = new ArrayList>();\n\t\tfor (int i = 0; i < elems.size(); i++) {\n\t\t\tList candidates = source.findSample(elems.get(i));\n\t\t\tcandidates_list.add(candidates);\n\t\t}\n\t\t\n\t\t// We test if we can consolidate those sample candidates so that the number of select statements is less than\n\t\t// the number of the expressions. In the worst case (e.g., all count-distinct), the number of select statements\n\t\t// will be equal to the number of the expressions. If the cost of running those select statements individually\n\t\t// is higher than the cost of running a single select statement using the original tables, we do not use samples.\n\t\tSamplePlan plan = consolidate(candidates_list);\n\t\tList individuals = new ArrayList();\n\t\t\n\t\tfor (SampleGroup group : plan.getSampleGroups()) {\n\t\t\tList elems = group.getElems();\n\t\t\tSet samplesPart = group.sampleSet();\n\t\t\tindividuals.add(new ApproxAggregatedRelation(vc, source.approxWith(attachTableMapping(samplesPart)), elems));\n\t\t}\n\t\t\n\t\t// join the results from those multiple relations (if there are more than one)\n\t\tApproxRelation r = null;\n\t\tfor (ApproxAggregatedRelation r1 : individuals) {\n\t\t\tif (r == null) {\n\t\t\t\tr = r1;\n\t\t\t} else {\n\t\t\t\tString ln = Relation.genTableAlias();\n\t\t\t\tString rn = Relation.genTableAlias();\n\t\t\t\tr.setAliasName(ln);\n\t\t\t\tr1.setAliasName(rn);\n\t\t\t\tif (r1.getSource() instanceof ApproxGroupedRelation) {\n\t\t\t\t\tList groupby = ((ApproxGroupedRelation) r1.getSource()).getGroupby();\n\t\t\t\t\tList> joincols = new ArrayList>();\n\t\t\t\t\tfor (ColNameExpr col : groupby) {\n\t\t\t\t\t\tjoincols.add(Pair.of((Expr) new ColNameExpr(col.getCol(), ln), (Expr) new ColNameExpr(col.getCol(), rn)));\n\t\t\t\t\t}\n\t\t\t\t\tr = new ApproxJoinedRelation(vc, r, r1, joincols);\n\t\t\t\t} else {\n\t\t\t\t\tr = new ApproxJoinedRelation(vc, r, r1, null);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tr.setAliasName(getAliasName());\n\t\treturn r;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic ExactRelation rewriteWithSubsampledErrorBounds() {\n\t\tExactRelation newSource = source.rewriteWithSubsampledErrorBounds();\n\t\tList sourceElems = null; // newSource.getSelectList();\n\t\tSet colAliases = new HashSet();\n\t\tfor (SelectElem e : sourceElems) {\n\t\t\tif (e.aliasPresent()) {\n\t\t\t\t// we're only interested in the columns for which aliases are present.\n\t\t\t\t// note that every column with aggregate function must have an alias (enforced by ColNameExpr class).\n\t\t\t\tcolAliases.add(e.getAlias());\n\t\t\t}\n\t\t}\n\t\t\n\t\t// we search for error bound columns based on the assumption that the error bound columns have the suffix attached\n\t\t// to the original agg columns. The suffix is obtained from the ApproxRelation#errColSuffix() method.\n\t\t// ApproxAggregatedRelation#rewriteWithSubsampledErrorBounds() method is responsible for having those columns. \n\t\tList elemsWithErr = new ArrayList();\n\t\tfor (SelectElem e : elems) {\n\t\t\telemsWithErr.add(e);\n\t\t\tString errColName = errColName(e.getExpr().getText());\n\t\t\tif (colAliases.contains(errColName)) {\n\t\t\t\telemsWithErr.add(new SelectElem(new ColNameExpr(errColName), errColName));\n\t\t\t}\n\t\t}\n\t\t\n\t\tExactRelation r = new ProjectedRelation(vc, newSource, elemsWithErr);\n\t\tr.setAliasName(getAliasName());\n\t\treturn r;\n\t} \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic ExactRelation rewriteWithSubsampledErrorBounds() {\n\t\tExactRelation r = rewriteWithPartition(true);\n\t\t\n\t\t// construct a new list of select elements. the last element is __vpart, which should be omitted.\n\t\t// newElems and newAggs hold almost the same info; just replicate them to follow the structure\n\t\t// of AggregatedRelation-ProjectedRelation.\n\t\tList newElems = new ArrayList();\n\t\tList newAggs = new ArrayList();\n\t\tList elems = ((ProjectedRelation) r).getSelectElems();\n\t\tfor (int i = 0; i < elems.size() - 1; i++) {\n\t\t\tSelectElem elem = elems.get(i);\n\t\t\tif (!elem.isagg()) {\n\t\t\t\tnewElems.add(new SelectElem(ColNameExpr.from(elem.getAlias()), elem.getAlias()));\n\t\t\t} else {\n\t\t\t\tif (elem.getAlias().equals(partitionSizeAlias)) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\t\n\t\t\t\tColNameExpr est = new ColNameExpr(elem.getAlias(), r.getAliasName());\n\t\t\t\tColNameExpr psize = new ColNameExpr(partitionSizeAlias, r.getAliasName());\n\t\t\t\t\n\t\t\t\t// average estimate\n\t\t\t\tExpr averaged = null;\n\t\t\t\tif (elem.getExpr().isCountDistinct()) {\n\t\t\t\t\t// for count-distinct (i.e., universe samples), weighted average should not be used.\n\t\t\t\t\taveraged = FuncExpr.round(FuncExpr.avg(est));\n\t\t\t\t} else {\n\t\t\t\t\t// weighted average\n\t\t\t\t\taveraged = BinaryOpExpr.from(FuncExpr.sum(BinaryOpExpr.from(est, psize, \"*\")),\n\t\t \t\t\t\t\t FuncExpr.sum(psize), \"/\");\n\t\t\t\t\tif (elem.getExpr().isCount()) {\n\t\t\t\t\t\taveraged = FuncExpr.round(averaged);\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tnewElems.add(new SelectElem(averaged, elem.getAlias()));\n\t\t\t\tnewAggs.add(averaged);\n\t\t\t\t\n\t\t\t\t// error estimation\n\t\t\t\t// scale by sqrt(subsample size) / sqrt(sample size)\n\t\t\t\tExpr error = BinaryOpExpr.from(\n\t\t\t\t\t\t\t\tBinaryOpExpr.from(FuncExpr.stddev(est), FuncExpr.sqrt(FuncExpr.avg(psize)), \"*\"),\n\t\t\t\t\t\t\t\tFuncExpr.sqrt(FuncExpr.sum(psize)),\n\t\t\t\t\t\t\t\t\"/\");\n\t\t\t\terror = BinaryOpExpr.from(error, ConstantExpr.from(confidenceIntervalMultiplier()), \"*\");\n\t\t\t\tnewElems.add(new SelectElem(error, Relation.errorBoundColumn(elem.getAlias())));\n\t\t\t\tnewAggs.add(error);\n\t\t\t}\n\t\t}\n\t\t\n\t\t// this extra aggregation stage should be grouped by non-agg elements except for __vpart\n\t\tList newGroupby = new ArrayList();\n\t\tfor (SelectElem elem : elems) {\n\t\t\tif (!elem.isagg() && !elem.getAlias().equals(partitionColumnName())) {\n\t\t\t\tnewGroupby.add(ColNameExpr.from(elem.getAlias()));\n\t\t\t}\n\t\t}\n\t\tr = new GroupedRelation(vc, r, newGroupby);\n\t\tr = new AggregatedRelation(vc, r, newAggs);\n\t\tr = new ProjectedRelation(vc, r, newElems);\n\t\t\n\t\treturn r;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic String visitQuery_specification(VerdictSQLParser.Query_specificationContext ctx) {\n\t\tList> subqueryColName2Aliases = null;\n\t\tBootstrapSelectStatementRewriter singleRewriter = null;\n\t\t\n\t\tStringBuilder unionedFrom = new StringBuilder(2000);\n\t\tint trialNum = vc.getConf().getInt(\"bootstrap_trial_num\");\n\t\tfor (int i = 0; i < trialNum; i++) {\n\t\t\tsingleRewriter = new BootstrapSelectStatementRewriter(vc, queryString);\n\t\t\tsingleRewriter.setIndentLevel(2);\n\t\t\tsingleRewriter.setDepth(1);\n\t\t\tString singleTrialQuery = singleRewriter.visitQuery_specificationForSingleTrial(ctx);\n\t\t\tif (i == 0) {\n\t\t\t\tsubqueryColName2Aliases = singleRewriter.getColName2Aliases();\n\t\t\t}\n\t\t\tif (i > 0) unionedFrom.append(\"\\n UNION\\n\");\n\t\t\tunionedFrom.append(singleTrialQuery);\n\t\t}\n\t\t\n\t\tStringBuilder sql = new StringBuilder(2000);\n\t\tsql.append(\"SELECT\");\n\t\tint selectElemIndex = 0;\n\t\tfor (Pair e : subqueryColName2Aliases) {\n\t\t\tselectElemIndex++;\n\t\t\tsql.append((selectElemIndex > 1)? \", \" : \" \");\n\t\t\tif (singleRewriter.isAggregateColumn(selectElemIndex)) {\n\t\t\t\tString alias = genAlias();\n\t\t\t\tsql.append(String.format(\"AVG(%s) AS %s\",\n\t\t\t\t\t\te.getRight(), alias));\n\t\t\t\tcolName2Aliases.add(Pair.of(e.getLeft(), alias));\n\t\t\t} else {\n\t\t\t\tif (e.getLeft().equals(e.getRight())) sql.append(e.getLeft());\n\t\t\t\telse sql.append(String.format(\"%s AS %s\", e.getLeft(), e.getRight()));\n\t\t\t\tcolName2Aliases.add(Pair.of(e.getLeft(), e.getRight()));\n\t\t\t}\n\t\t}\n\t\tsql.append(\"\\nFROM (\\n\");\n\t\tsql.append(unionedFrom.toString());\n\t\tsql.append(\"\\n) AS t\");\n\t\tsql.append(\"\\nGROUP BY\");\n\t\tfor (int colIndex = 1; colIndex <= subqueryColName2Aliases.size(); colIndex++) {\n\t\t\tif (!singleRewriter.isAggregateColumn(colIndex)) {\n\t\t\t\tif (colIndex > 1) {\n\t\t\t\t\tsql.append(String.format(\", %s\", subqueryColName2Aliases.get(colIndex-1).getRight()));\n\t\t\t\t} else {\n\t\t\t\t\tsql.append(String.format(\" %s\", subqueryColName2Aliases.get(colIndex-1).getRight()));\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t\n\t\treturn sql.toString();\n\t} \n #location 23 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic String visitQuery_specification(VerdictSQLParser.Query_specificationContext ctx) {\n\t\tStringBuilder sql = new StringBuilder(2000);\n\t\t\n\t\t// this statement computes the mean value\n\t\tAnalyticSelectStatementRewriter meanRewriter = new AnalyticSelectStatementRewriter(vc, queryString);\n\t\tmeanRewriter.setDepth(depth+1);\n\t\tmeanRewriter.setIndentLevel(defaultIndent + 6);\n\t\tString mainSql = meanRewriter.visit(ctx);\n\t\tcumulativeReplacedTableSources.putAll(meanRewriter.getCumulativeSampleTables());\n\t\t\n\t\t// this statement computes the standard deviation\n\t\tBootstrapSelectStatementRewriter varianceRewriter = new BootstrapSelectStatementRewriter(vc, queryString);\n\t\tvarianceRewriter.setDepth(depth+1);\n\t\tvarianceRewriter.setIndentLevel(defaultIndent + 6);\n\t\tString subSql = varianceRewriter.varianceComputationStatement(ctx);\n\t\t\n\t\tString leftAlias = genAlias();\n\t\tString rightAlias = genAlias();\n\t\t\n\t\t// we combine those two statements using join.\n\t\tList> thisColumnName2Aliases = new ArrayList>();\n\t\t\n\t\tList> leftColName2Aliases = meanRewriter.getColName2Aliases();\n//\t\tList leftAggColIndicator = meanRewriter.getAggregateColumnIndicator();\n\t\t\n\t\tList> rightColName2Aliases = varianceRewriter.getColName2Aliases();\n//\t\tList rightAggColIndicator = varianceRewriter.getAggregateColumnIndicator();\n\t\t\n\t\tsql.append(String.format(\"%sSELECT\", indentString));\n\t\tint leftSelectElemIndex = 0;\n\t\tint totalSelectElemIndex = 0;\n\t\tfor (Pair colName2Alias : leftColName2Aliases) {\n\t\t\tleftSelectElemIndex++;\n\t\t\tif (leftSelectElemIndex == 1) sql.append(\" \");\n\t\t\telse sql.append(\", \");\n\t\t\t\n\t\t\tif (meanRewriter.isAggregateColumn(leftSelectElemIndex)) {\n\t\t\t\t// mean\n\t\t\t\ttotalSelectElemIndex++;\n\t\t\t\tString alias = genAlias();\n\t\t\t\tsql.append(String.format(\"%s.%s AS %s\", leftAlias, colName2Alias.getRight(), alias));\n\t\t\t\tthisColumnName2Aliases.add(Pair.of(colName2Alias.getLeft(), alias));\n\t\t\t\t\n\t\t\t\t// error (standard deviation * 1.96 (for 95% confidence interval))\n\t\t\t\ttotalSelectElemIndex++;\n\t\t\t\talias = genAlias();\n\t\t\t\tString matchingAliasName = null;\n\t\t\t\tfor (Pair r : rightColName2Aliases) {\n\t\t\t\t\tif (colName2Alias.getLeft().equals(r.getLeft())) {\n\t\t\t\t\t\tmatchingAliasName = r.getRight();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tsql.append(String.format(\", %s.%s AS %s\", rightAlias, matchingAliasName, alias));\n\t\t\t\tthisColumnName2Aliases.add(Pair.of(colName2Alias.getLeft(), alias));\n\t\t\t\t\n\t\t\t\tmeanColIndex2ErrColIndex.put(totalSelectElemIndex-1, totalSelectElemIndex);\n\t\t\t} else {\n\t\t\t\ttotalSelectElemIndex++;\n\t\t\t\tsql.append(String.format(\"%s.%s AS %s\", leftAlias, colName2Alias.getRight(), colName2Alias.getRight()));\n\t\t\t\tthisColumnName2Aliases.add(Pair.of(colName2Alias.getLeft(), colName2Alias.getRight()));\n\t\t\t}\n\t\t}\n\t\tcolName2Aliases = thisColumnName2Aliases;\n\t\t\n\t\tsql.append(String.format(\"\\n%sFROM (\\n\", indentString));\n\t\tsql.append(mainSql);\n\t\tsql.append(String.format(\"\\n%s ) AS %s\", indentString, leftAlias));\n\t\tsql.append(\" LEFT JOIN (\\n\");\n\t\tsql.append(subSql);\n\t\tsql.append(String.format(\"%s) AS %s\", indentString, rightAlias));\n\t\tsql.append(String.format(\" ON %s.l_shipmode = %s.l_shipmode\", leftAlias, rightAlias));\n\t\t\n\t\treturn sql.toString();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getPartitionColumns(String schema, String table) throws SQLException {\n if (!syntax.doesSupportTablePartitioning()) {\n throw new SQLException(\"Database does not support table partitioning\");\n }\n if (!partitionCache.isEmpty()){\n return partitionCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getPartitionCommand(schema, table));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n partitionCache.add(jdbcQueryResult.getString(0));\n }\n return partitionCache;\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getPartitionColumns(String schema, String table) throws SQLException {\n if (!syntax.doesSupportTablePartitioning()) {\n throw new SQLException(\"Database does not support table partitioning\");\n }\n if (!partitionCache.isEmpty()){\n return partitionCache;\n }\n partitionCache.addAll(getPartitionColumns(schema, table));\n return partitionCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic ExactRelation rewriteWithSubsampledErrorBounds() {\n\t\tExactRelation r = rewriteWithPartition();\n//\t\tList selectElems = r.selectElemsWithAggregateSource();\n\t\tList selectElems = ((AggregatedRelation) r).getAggList();\n\t\t\n\t\t// another wrapper to combine all subsampled aggregations.\n\t\tList finalAgg = new ArrayList();\n\t\t\n\t\tfor (int i = 0; i < selectElems.size() - 1; i++) {\t// excluding the last one which is psize\n\t\t\tSelectElem e = selectElems.get(i);\n\t\t\tColNameExpr est = new ColNameExpr(e.getAlias(), r.getAliasName());\n\t\t\tColNameExpr psize = new ColNameExpr(partitionSizeAlias, r.getAliasName());\n\t\t\t\n\t\t\t// average estimate\n//\t\t\tExpr meanEst = BinaryOpExpr.from(\n//\t\t\t\t\t\t\tFuncExpr.sum(BinaryOpExpr.from(est, psize, \"*\")),\n//\t\t\t\t\t\t\tFuncExpr.sum(psize), \"/\");\n\t\t\tExpr meanEst = FuncExpr.avg(est);\n\t\t\tExpr originalAggExpr = elems.get(i).getExpr(); \n\t\t\tif (originalAggExpr instanceof FuncExpr) {\n\t\t\t\tif (((FuncExpr) originalAggExpr).getFuncName().equals(FuncExpr.FuncName.COUNT)\n\t\t\t\t\t|| ((FuncExpr) originalAggExpr).getFuncName().equals(FuncExpr.FuncName.COUNT_DISTINCT)) {\n\t\t\t\t\tmeanEst = FuncExpr.round(meanEst);\n\t\t\t\t}\n\t\t\t}\n\t\t\tfinalAgg.add(new SelectElem(meanEst, e.getAlias()));\n\n\t\t\t// error estimation\n\t\t\tfinalAgg.add(new SelectElem(\n\t\t\t\t\tBinaryOpExpr.from(\n\t\t\t\t\t\t\tBinaryOpExpr.from(FuncExpr.stddev(est), FuncExpr.sqrt(FuncExpr.avg(psize)), \"*\"),\n\t\t\t\t\t\t\tFuncExpr.sqrt(FuncExpr.sum(psize)),\n\t\t\t\t\t\t\t\"/\"),\n\t\t\t\t\te.getAlias() + errColSuffix()));\n\t\t}\n\t\t\n\t\t/*\n\t\t * Example input query:\n\t\t * select category, avg(col)\n\t\t * from t\n\t\t * group by category\n\t\t * \n\t\t * Transformed query:\n\t\t * select category, sum(est * psize) / sum(psize) AS final_est\n\t\t * from (\n\t\t * select category, avg(col) AS est, count(*) as psize\n\t\t * from t\n\t\t * group by category, verdict_partition) AS vt1\n\t\t * group by category\n\t\t * \n\t\t * where t1 was obtained by rewriteWithPartition().\n\t\t */ \n\t\tif (source instanceof ApproxGroupedRelation) {\n\t\t\tList groupby = ((ApproxGroupedRelation) source).getGroupby();\n\t\t\tList groupbyInNewSource = new ArrayList();\n\t\t\tfor (ColNameExpr g : groupby) {\n\t\t\t\tgroupbyInNewSource.add(new ColNameExpr(g.getCol(), r.getAliasName()));\n\t\t\t}\n\t\t\tr = new GroupedRelation(vc, r, groupbyInNewSource);\n\t\t}\n\t\t\n\t\tr = new AggregatedRelation(vc, r, finalAgg);\n\t\tr.setAliasName(getAliasName());\n\t\treturn r;\n\t} \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic ExactRelation rewriteWithSubsampledErrorBounds() {\n\t\tExactRelation r = rewriteWithPartition();\n//\t\tList selectElems = r.selectElemsWithAggregateSource();\n\t\tList selectElems = ((AggregatedRelation) r).getAggList();\n\t\t\n\t\t// another wrapper to combine all subsampled aggregations.\n\t\tList finalAgg = new ArrayList();\n\t\t\n\t\tfor (int i = 0; i < selectElems.size() - 1; i++) {\t// excluding the last one which is psize\n\t\t\t// odd columns are for mean estimation\n\t\t\t// even columns are for err estimation\n\t\t\tif (i%2 == 1) continue;\n\t\t\t\n\t\t\tSelectElem meanElem = selectElems.get(i);\n\t\t\tSelectElem errElem = selectElems.get(i+1);\n\t\t\tColNameExpr est = new ColNameExpr(meanElem.getAlias(), r.getAliasName());\n\t\t\tColNameExpr errEst = new ColNameExpr(errElem.getAlias(), r.getAliasName());\n\t\t\tColNameExpr psize = new ColNameExpr(partitionSizeAlias, r.getAliasName());\n\t\t\t\n\t\t\tExpr originalAggExpr = elems.get(i/2).getExpr();\n\t\t\t\n\t\t\t// average estimate\n\t\t\tExpr meanEstExpr = null;\n\t\t\tif (originalAggExpr.isCountDistinct()) {\n\t\t\t\tmeanEstExpr = FuncExpr.round(FuncExpr.avg(est));\n\t\t\t} else {\n\t\t\t\tmeanEstExpr = BinaryOpExpr.from(FuncExpr.sum(BinaryOpExpr.from(est, psize, \"*\")),\n\t \t\t\t\t\tFuncExpr.sum(psize), \"/\");\n\t\t\t\tif (originalAggExpr.isCount()) {\n\t\t\t\t\tmeanEstExpr = FuncExpr.round(meanEstExpr);\n\t\t\t\t}\n\t\t\t}\n\t\t\tfinalAgg.add(new SelectElem(meanEstExpr, meanElem.getAlias()));\n\n\t\t\t// error estimation\n\t\t\tExpr errEstExpr = BinaryOpExpr.from(\n\t\t\t\t\tBinaryOpExpr.from(FuncExpr.stddev(errEst), FuncExpr.sqrt(FuncExpr.avg(psize)), \"*\"),\n\t\t\t\t\tFuncExpr.sqrt(FuncExpr.sum(psize)),\n\t\t\t\t\t\"/\");\n\t\t\tfinalAgg.add(new SelectElem(errEstExpr, errElem.getAlias()));\n\t\t}\n\t\t\n\t\t/*\n\t\t * Example input query:\n\t\t * select category, avg(col)\n\t\t * from t\n\t\t * group by category\n\t\t * \n\t\t * Transformed query:\n\t\t * select category, sum(est * psize) / sum(psize) AS final_est\n\t\t * from (\n\t\t * select category, avg(col) AS est, count(*) as psize\n\t\t * from t\n\t\t * group by category, verdict_partition) AS vt1\n\t\t * group by category\n\t\t * \n\t\t * where t1 was obtained by rewriteWithPartition().\n\t\t */ \n\t\tif (source instanceof ApproxGroupedRelation) {\n\t\t\tList groupby = ((ApproxGroupedRelation) source).getGroupby();\n\t\t\tList groupbyInNewSource = new ArrayList();\n\t\t\tfor (ColNameExpr g : groupby) {\n\t\t\t\tgroupbyInNewSource.add(new ColNameExpr(g.getCol(), r.getAliasName()));\n\t\t\t}\n\t\t\tr = new GroupedRelation(vc, r, groupbyInNewSource);\n\t\t}\n\t\t\n\t\tr = new AggregatedRelation(vc, r, finalAgg);\n\t\tr.setAliasName(getAliasName());\n\t\treturn r;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List> getColumns(String schema, String table) throws SQLException {\n if (!columnsCache.isEmpty()){\n return columnsCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getColumnsCommand(schema, table));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n String type = jdbcQueryResult.getString(syntax.getColumnTypeColumnIndex());\n // remove the size of type\n type = type.replaceAll(\"\\\\(.*\\\\)\", \"\");\n columnsCache.add(new ImmutablePair<>(jdbcQueryResult.getString(syntax.getColumnNameColumnIndex()),\n DataTypeConverter.typeInt(type)));\n }\n return columnsCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List> getColumns(String schema, String table) throws SQLException {\n if (!columnsCache.isEmpty()){\n return columnsCache;\n }\n columnsCache.addAll(connection.getColumns(schema, table));\n return columnsCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void print(int indentSpace) {\n StringBuilder builder = new StringBuilder();\n for (int i = 0; i < indentSpace; i++) {\n builder.append(\" \");\n }\n builder.append(this.toString());\n System.out.println(builder.toString());\n \n for (QueryExecutionNode dep : dependents) {\n dep.print(indentSpace + 2);\n }\n } \n #location 6 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n void addParent(QueryExecutionNode parent) {\n parents.add(parent);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getTables(String schema) throws SQLException {\n if (!tablesCache.isEmpty()){\n return tablesCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getTableCommand(schema));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n tablesCache.add(jdbcQueryResult.getString(syntax.getTableNameColumnIndex()));\n }\n return tablesCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getTables(String schema) throws SQLException {\n if (!tablesCache.isEmpty()){\n return tablesCache;\n }\n tablesCache.addAll(connection.getTables(schema));\n return tablesCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List getPartitionColumns(String schema, String table) throws VerdictDBDbmsException {\n List partition = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getPartitionCommand(schema, table));\n JdbcResultSet jdbcResultSet = new JdbcResultSet(queryResult);\n // the result of postgresql is a vector of column index\n\n try {\n if (syntax instanceof PostgresqlSyntax) {\n queryResult.next();\n Object o = jdbcResultSet.getObject(1);\n String[] arr = o.toString().split(\" \");\n List> columns = getColumns(schema, table);\n for (int i=0; i getPartitionColumns(String schema, String table) throws VerdictDBDbmsException {\n List partition = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getPartitionCommand(schema, table));\n while (queryResult.next()) {\n partition.add((String) queryResult.getValue(0));\n }\n\n return partition;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testConvertFlatToProgressiveAgg() throws VerdictDBValueException {\n SelectQuery aggQuery = SelectQuery.create(\n ColumnOp.count(),\n new BaseTable(\"myschema\", \"mytable\", \"t\"));\n AggExecutionNode aggnode = AggExecutionNode.create(aggQuery, \"myschema\");\n AggExecutionNodeBlock block = new AggExecutionNodeBlock(aggnode);\n ScrambleMeta scrambleMeta = generateTestScrambleMeta();\n QueryExecutionNode converted = block.convertToProgressiveAgg(scrambleMeta);\n converted.print();\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testConvertFlatToProgressiveAgg() throws VerdictDBValueException {\n SelectQuery aggQuery = SelectQuery.create(\n new AliasedColumn(ColumnOp.count(), \"agg\"),\n new BaseTable(newSchema, newTable, \"t\"));\n AggExecutionNode aggnode = AggExecutionNode.create(aggQuery, newSchema);\n AggExecutionNodeBlock block = new AggExecutionNodeBlock(aggnode);\n QueryExecutionNode converted = block.convertToProgressiveAgg(newSchema, scrambleMeta);\n converted.print();\n converted.execute(new JdbcConnection(conn, new H2Syntax()));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public ExactRelation rewriteWithSubsampledErrorBounds() {\n // if this is not an approximate relation effectively, we don't need any special rewriting.\n if (!doesIncludeSample()) {\n return getOriginalRelation();\n }\n \n ExactRelation r = rewriteWithPartition(true);\n// String newAlias = genTableAlias();\n \n // put another layer to combine per-partition aggregates\n List newElems = new ArrayList();\n List oldElems = ((AggregatedRelation) r).getElemList();\n List newGroupby = new ArrayList();\n \n for (int i = 0; i < oldElems.size(); i++) {\n SelectElem elem = oldElems.get(i);\n \n // used to identify the original aggregation type\n Optional originalElem = Optional.absent();\n if (i < this.elems.size()) {\n originalElem = Optional.fromNullable(this.elems.get(i));\n }\n \n if (!elem.isagg()) {\n // skip the partition number\n if (elem.aliasPresent() && elem.getAlias().equals(partitionColumnName())) {\n continue;\n }\n \n SelectElem newElem = null;\n Expr newExpr = null;\n if (elem.getAlias() == null) {\n newExpr = elem.getExpr().withTableSubstituted(r.getAlias());\n newElem = new SelectElem(vc, newExpr, elem.getAlias());\n } else {\n newExpr = new ColNameExpr(vc, elem.getAlias(), r.getAlias());\n newElem = new SelectElem(vc, newExpr, elem.getAlias());\n }\n \n // groupby element may not be present in the select list.\n if (originalElem.isPresent()) {\n newElems.add(newElem);\n }\n newGroupby.add(newExpr);\n }\n else {\n // skip the partition size column\n if (elem.getAlias().equals(partitionSizeAlias)) {\n continue;\n }\n \n // skip the extra columns inserted\n if (!originalElem.isPresent()) {\n continue;\n }\n\n ColNameExpr est = new ColNameExpr(vc, elem.getAlias(), r.getAlias());\n ColNameExpr psize = new ColNameExpr(vc, partitionSizeAlias, r.getAlias());\n\n // average estimate\n Expr averaged = null;\n Expr originalExpr = originalElem.get().getExpr();\n if (originalExpr.isCountDistinct()) {\n // for count-distinct (i.e., universe samples), weighted average should not be used.\n averaged = FuncExpr.round(FuncExpr.avg(est));\n } else if (originalExpr.isMax()) {\n averaged = FuncExpr.max(est);\n } else if (originalExpr.isMin()) {\n averaged = FuncExpr.min(est);\n } else {\n // weighted average\n averaged = BinaryOpExpr.from(vc, FuncExpr.sum(BinaryOpExpr.from(vc, est, psize, \"*\")),\n FuncExpr.sum(psize), \"/\");\n if (originalElem.get().getExpr().isCount()) {\n averaged = FuncExpr.round(averaged);\n }\n }\n newElems.add(new SelectElem(vc, averaged, elem.getAlias()));\n\n // error estimation\n // scale by sqrt(subsample size) / sqrt(sample size)\n if (originalExpr.isMax() || originalExpr.isMin()) {\n // no error estimations for extreme statistics\n } else {\n Expr error = BinaryOpExpr.from(vc,\n BinaryOpExpr.from(vc, FuncExpr.stddev(est), FuncExpr.sqrt(FuncExpr.avg(psize)), \"*\"),\n FuncExpr.sqrt(FuncExpr.sum(psize)),\n \"/\");\n error = BinaryOpExpr.from(vc, error, ConstantExpr.from(vc, confidenceIntervalMultiplier()), \"*\");\n newElems.add(new SelectElem(vc, error, Relation.errorBoundColumn(elem.getAlias())));\n }\n }\n }\n \n // this extra aggregation stage should be grouped by non-agg elements except for __vpart\n// List newGroupby = new ArrayList();\n// if (source instanceof ApproxGroupedRelation) {\n// for (Expr g : ((ApproxGroupedRelation) source).getGroupby()) {\n// if (g instanceof ColNameExpr && ((ColNameExpr) g).getCol().equals(partitionColumnName())) {\n// continue;\n// } else {\n// newGroupby.add(g.withTableSubstituted(r.getAlias()));\n// }\n// }\n// }\n \n for (SelectElem elem : elems) {\n if (!elem.isagg()) {\n if (elem.aliasPresent()) {\n if (!elem.getAlias().equals(partitionColumnName())) {\n newGroupby.add(new ColNameExpr(vc, elem.getAlias(), r.getAlias()));\n }\n } else {\n if (!elem.getExpr().toString().equals(partitionColumnName())) {\n newGroupby.add(elem.getExpr().withTableSubstituted(r.getAlias()));\n }\n }\n }\n }\n if (newGroupby.size() > 0) {\n r = new GroupedRelation(vc, r, newGroupby);\n }\n \n r = new AggregatedRelation(vc, r, newElems);\n r.setAlias(getAlias());\n return r;\n } \n #location 112 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public ExactRelation rewriteWithSubsampledErrorBounds() {\n // if this is not an approximate relation effectively, we don't need any special rewriting.\n if (!doesIncludeSample()) {\n return getOriginalRelation();\n }\n \n ExactRelation r = rewriteWithPartition(true);\n// String newAlias = genTableAlias();\n \n // put another layer to combine per-partition aggregates\n List newElems = new ArrayList();\n List oldElems = ((AggregatedRelation) r).getElemList();\n List newGroupby = new ArrayList();\n \n for (int i = 0; i < oldElems.size(); i++) {\n SelectElem elem = oldElems.get(i);\n \n // used to identify the original aggregation type\n Optional originalElem = Optional.absent();\n if (i < this.elems.size()) {\n originalElem = Optional.fromNullable(this.elems.get(i));\n }\n \n if (!elem.isagg()) {\n // skip the partition number\n if (elem.aliasPresent() && elem.getAlias().equals(partitionColumnName())) {\n continue;\n }\n \n SelectElem newElem = null;\n Expr newExpr = null;\n if (elem.getAlias() == null) {\n newExpr = elem.getExpr().withTableSubstituted(r.getAlias());\n newElem = new SelectElem(vc, newExpr, elem.getAlias());\n } else {\n newExpr = new ColNameExpr(vc, elem.getAlias(), r.getAlias());\n newElem = new SelectElem(vc, newExpr, elem.getAlias());\n }\n \n // groupby element may not be present in the select list.\n if (originalElem.isPresent()) {\n newElems.add(newElem);\n }\n newGroupby.add(newExpr);\n }\n else {\n // skip the partition size column\n if (elem.getAlias().equals(partitionSizeAlias)) {\n continue;\n }\n \n // skip the extra columns inserted\n if (!originalElem.isPresent()) {\n continue;\n }\n\n ColNameExpr est = new ColNameExpr(vc, elem.getAlias(), r.getAlias());\n ColNameExpr psize = new ColNameExpr(vc, partitionSizeAlias, r.getAlias());\n\n // average estimate\n Expr averaged = null;\n Expr originalExpr = originalElem.get().getExpr();\n if (originalExpr.isCountDistinct()) {\n // for count-distinct (i.e., universe samples), weighted average should not be used.\n averaged = FuncExpr.round(FuncExpr.avg(est));\n } else if (originalExpr.isMax()) {\n averaged = FuncExpr.max(est);\n } else if (originalExpr.isMin()) {\n averaged = FuncExpr.min(est);\n } else {\n // weighted average\n averaged = BinaryOpExpr.from(vc, FuncExpr.sum(BinaryOpExpr.from(vc, est, psize, \"*\")),\n FuncExpr.sum(psize), \"/\");\n if (originalElem.get().getExpr().isCount()) {\n averaged = FuncExpr.round(averaged);\n }\n }\n newElems.add(new SelectElem(vc, averaged, elem.getAlias()));\n\n // error estimation\n // scale by sqrt(subsample size) / sqrt(sample size)\n if (originalExpr.isMax() || originalExpr.isMin()) {\n // no error estimations for extreme statistics\n } else {\n Expr error = BinaryOpExpr.from(vc,\n BinaryOpExpr.from(vc, FuncExpr.stddev(est), FuncExpr.sqrt(FuncExpr.avg(psize)), \"*\"),\n FuncExpr.sqrt(FuncExpr.sum(psize)),\n \"/\");\n error = BinaryOpExpr.from(vc, error, ConstantExpr.from(vc, confidenceIntervalMultiplier()), \"*\");\n newElems.add(new SelectElem(vc, error, Relation.errorBoundColumn(elem.getAlias())));\n }\n }\n }\n \n // this extra aggregation stage should be grouped by non-agg elements except for __vpart\n// List newGroupby = new ArrayList();\n// if (source instanceof ApproxGroupedRelation) {\n// for (Expr g : ((ApproxGroupedRelation) source).getGroupby()) {\n// if (g instanceof ColNameExpr && ((ColNameExpr) g).getCol().equals(partitionColumnName())) {\n// continue;\n// } else {\n// newGroupby.add(g.withTableSubstituted(r.getAlias()));\n// }\n// }\n// }\n \n// for (SelectElem elem : elems) {\n// if (!elem.isagg()) {\n// if (elem.aliasPresent()) {\n// if (!elem.getAlias().equals(partitionColumnName())) {\n// newGroupby.add(new ColNameExpr(vc, elem.getAlias(), r.getAlias()));\n// }\n// } else { // does not happen\n// if (!elem.getExpr().toString().equals(partitionColumnName())) {\n// newGroupby.add(elem.getExpr().withTableSubstituted(r.getAlias()));\n// }\n// }\n// }\n// }\n if (newGroupby.size() > 0) {\n r = new GroupedRelation(vc, r, newGroupby);\n }\n \n r = new AggregatedRelation(vc, r, newElems);\n r.setAlias(getAlias());\n return r;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List getTables(String schema) throws VerdictDBDbmsException {\n List tables = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getTableCommand(schema));\n JdbcResultSet jdbcResultSet = new JdbcResultSet(queryResult);\n try {\n while (queryResult.next()) {\n tables.add(jdbcResultSet.getString(syntax.getTableNameColumnIndex()+1));\n }\n } catch (SQLException e) {\n throw new VerdictDBDbmsException(e);\n } finally {\n jdbcResultSet.close();\n }\n return tables;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List getTables(String schema) throws VerdictDBDbmsException {\n List tables = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getTableCommand(schema));\n while (queryResult.next()) {\n tables.add((String) queryResult.getValue(syntax.getTableNameColumnIndex()));\n }\n return tables;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List> getColumns(String schema, String table) throws SQLException {\n if (!columnsCache.isEmpty()){\n return columnsCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getColumnsCommand(schema, table));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n String type = jdbcQueryResult.getString(syntax.getColumnTypeColumnIndex());\n // remove the size of type\n type = type.replaceAll(\"\\\\(.*\\\\)\", \"\");\n columnsCache.add(new ImmutablePair<>(jdbcQueryResult.getString(syntax.getColumnNameColumnIndex()),\n DataTypeConverter.typeInt(type)));\n }\n return columnsCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List> getColumns(String schema, String table) throws SQLException {\n if (!columnsCache.isEmpty()){\n return columnsCache;\n }\n columnsCache.addAll(connection.getColumns(schema, table));\n return columnsCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testExecuteNode() throws VerdictDBException {\n BaseTable base = new BaseTable(originalSchema, originalTable, \"t\");\n SelectQuery query = SelectQuery.create(Arrays.asList(new AsteriskColumn()), base);\n QueryExecutionNode root = CreateTableAsSelectExecutionNode.create(query, \"newschema\");\n// LinkedBlockingDeque resultQueue = new LinkedBlockingDeque<>();\n root.executeNode(conn, null); // no information to pass\n conn.executeUpdate(String.format(\"DROP TABLE \\\"%s\\\".\\\"%s\\\"\", newSchema, \"verdictdbtemptable_0\"));\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testExecuteNode() throws VerdictDBException {\n BaseTable base = new BaseTable(originalSchema, originalTable, \"t\");\n SelectQuery query = SelectQuery.create(Arrays.asList(new AsteriskColumn()), base);\n QueryExecutionNode root = CreateTableAsSelectExecutionNode.create(query, \"newschema\");\n// ExecutionInfoToken token = new ExecutionInfoToken();\n ExecutionInfoToken newTableName = root.executeNode(conn, Arrays.asList()); // no information to pass\n \n String schemaName = (String) newTableName.getValue(\"schemaName\");\n String tableName = (String) newTableName.getValue(\"tableName\");\n conn.executeUpdate(String.format(\"DROP TABLE \\\"%s\\\".\\\"%s\\\"\", schemaName, tableName));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getTables(String schema) throws SQLException {\n if (!tablesCache.isEmpty()){\n return tablesCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getTableCommand(schema));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n tablesCache.add(jdbcQueryResult.getString(syntax.getTableNameColumnIndex()));\n }\n return tablesCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getTables(String schema) throws SQLException {\n if (!tablesCache.isEmpty()){\n return tablesCache;\n }\n tablesCache.addAll(connection.getTables(schema));\n return tablesCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tprotected Map tableSubstitution() {\n\t\treturn ImmutableMap.of();\n\t} \n #location 2 \n #vulnerability type CHECKERS_IMMUTABLE_CAST", "output": "#fixed code\n @Override\n\tprotected Map tableSubstitution() {\n\t\treturn source.tableSubstitution();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public List getSchemas() throws VerdictDBDbmsException {\n List schemas = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getSchemaCommand());\n JdbcResultSet jdbcResultSet = new JdbcResultSet(queryResult);\n try {\n while (queryResult.next()) {\n schemas.add(jdbcResultSet.getString(syntax.getSchemaNameColumnIndex()+1));\n }\n } catch (SQLException e) {\n throw new VerdictDBDbmsException(e);\n } finally {\n jdbcResultSet.close();\n }\n return schemas;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public List getSchemas() throws VerdictDBDbmsException {\n List schemas = new ArrayList<>();\n DbmsQueryResult queryResult = execute(syntax.getSchemaCommand());\n while (queryResult.next()) {\n schemas.add((String) queryResult.getValue(syntax.getSchemaNameColumnIndex()));\n }\n return schemas;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getPartitionColumns(String schema, String table) throws SQLException {\n if (!syntax.doesSupportTablePartitioning()) {\n throw new SQLException(\"Database does not support table partitioning\");\n }\n if (!partitionCache.isEmpty()){\n return partitionCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getPartitionCommand(schema, table));\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n partitionCache.add(jdbcQueryResult.getString(0));\n }\n return partitionCache;\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getPartitionColumns(String schema, String table) throws SQLException {\n if (!syntax.doesSupportTablePartitioning()) {\n throw new SQLException(\"Database does not support table partitioning\");\n }\n if (!partitionCache.isEmpty()){\n return partitionCache;\n }\n partitionCache.addAll(getPartitionColumns(schema, table));\n return partitionCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public List getSchemas() throws SQLException {\n if (!schemaCache.isEmpty()){\n return schemaCache;\n }\n DbmsQueryResult queryResult = connection.executeQuery(syntax.getSchemaCommand());\n JdbcResultSet jdbcQueryResult = new JdbcResultSet(queryResult);\n while (queryResult.next()) {\n schemaCache.add(jdbcQueryResult.getString(syntax.getSchemaNameColumnIndex()));\n }\n return schemaCache;\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public List getSchemas() throws SQLException {\n if (!schemaCache.isEmpty()){\n return schemaCache;\n }\n schemaCache.addAll(connection.getSchemas());\n return schemaCache;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testSingleAggCombiningWithH2() throws VerdictDBDbmsException, VerdictDBException {\n QueryExecutionPlan plan = new QueryExecutionPlan(\"newschema\");\n \n BaseTable base = new BaseTable(originalSchema, originalTable, \"t\");\n SelectQuery leftQuery = SelectQuery.create(new AliasedColumn(ColumnOp.count(), \"mycount\"), base);\n leftQuery.addFilterByAnd(ColumnOp.lessequal(new BaseColumn(\"t\", \"value\"), ConstantColumn.valueOf(5.0)));\n SelectQuery rightQuery = SelectQuery.create(new AliasedColumn(ColumnOp.count(), \"mycount\"), base);\n rightQuery.addFilterByAnd(ColumnOp.greater(new BaseColumn(\"t\", \"value\"), ConstantColumn.valueOf(5.0)));\n \n AggExecutionNode leftNode = AggExecutionNode.create(plan, leftQuery);\n AggExecutionNode rightNode = AggExecutionNode.create(plan, rightQuery);\n \n// ExecutionTokenQueue queue = new ExecutionTokenQueue();\n AggCombinerExecutionNode combiner = AggCombinerExecutionNode.create(plan, leftNode, rightNode);\n combiner.print();\n ExecutionTokenReader reader = ExecutablePlanRunner.getTokenReader(\n conn, \n new SimpleTreePlan(combiner));\n \n// combiner.addBroadcastingQueue(queue);\n// combiner.executeAndWaitForTermination(conn);\n \n ExecutionInfoToken token = reader.next();\n String schemaName = (String) token.getValue(\"schemaName\");\n String tableName = (String) token.getValue(\"tableName\");\n \n conn.execute(QueryToSql.convert(\n new H2Syntax(),\n SelectQuery.create(ColumnOp.count(), base)));\n DbmsQueryResult result = conn.getResult();\n result.next();\n int expectedCount = Integer.valueOf(result.getValue(0).toString());\n \n conn.execute(QueryToSql.convert(\n new H2Syntax(),\n SelectQuery.create(new AsteriskColumn(), new BaseTable(schemaName, tableName, \"t\"))));\n DbmsQueryResult result2 = conn.getResult();\n result2.next();\n int actualCount = Integer.valueOf(result2.getValue(0).toString());\n assertEquals(expectedCount, actualCount);\n conn.execute(QueryToSql.convert(\n new H2Syntax(),\n DropTableQuery.create(schemaName, tableName)));\n } \n #location 25 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testSingleAggCombiningWithH2() throws VerdictDBDbmsException, VerdictDBException {\n QueryExecutionPlan plan = new QueryExecutionPlan(\"newschema\");\n \n BaseTable base = new BaseTable(originalSchema, originalTable, \"t\");\n SelectQuery leftQuery = SelectQuery.create(new AliasedColumn(ColumnOp.count(), \"mycount\"), base);\n leftQuery.addFilterByAnd(ColumnOp.lessequal(new BaseColumn(\"t\", \"value\"), ConstantColumn.valueOf(5.0)));\n SelectQuery rightQuery = SelectQuery.create(new AliasedColumn(ColumnOp.count(), \"mycount\"), base);\n rightQuery.addFilterByAnd(ColumnOp.greater(new BaseColumn(\"t\", \"value\"), ConstantColumn.valueOf(5.0)));\n \n AggExecutionNode leftNode = AggExecutionNode.create(plan, leftQuery);\n AggExecutionNode rightNode = AggExecutionNode.create(plan, rightQuery);\n \n// ExecutionTokenQueue queue = new ExecutionTokenQueue();\n AggCombinerExecutionNode combiner = AggCombinerExecutionNode.create(plan, leftNode, rightNode);\n combiner.print();\n ExecutionTokenReader reader = ExecutablePlanRunner.getTokenReader(\n conn, \n new SimpleTreePlan(combiner));\n \n// combiner.addBroadcastingQueue(queue);\n// combiner.executeAndWaitForTermination(conn);\n \n ExecutionInfoToken token = reader.next();\n String schemaName = (String) token.getValue(\"schemaName\");\n String tableName = (String) token.getValue(\"tableName\");\n \n DbmsQueryResult result = conn.execute(QueryToSql.convert(\n new H2Syntax(),\n SelectQuery.create(ColumnOp.count(), base)));\n result.next();\n int expectedCount = Integer.valueOf(result.getValue(0).toString());\n \n DbmsQueryResult result2 = conn.execute(QueryToSql.convert(\n new H2Syntax(),\n SelectQuery.create(new AsteriskColumn(), new BaseTable(schemaName, tableName, \"t\"))));\n result2.next();\n int actualCount = Integer.valueOf(result2.getValue(0).toString());\n assertEquals(expectedCount, actualCount);\n conn.execute(QueryToSql.convert(\n new H2Syntax(),\n DropTableQuery.create(schemaName, tableName)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n\tpublic String visitSelect_list_elem(VerdictSQLParser.Select_list_elemContext ctx) {\n\t\tselect_list_elem_num++;\n\t\tString newSelectListElem = null;\n\t\tPair colName2Alias = null;\n\t\t\n\t\tif (ctx.getText().equals(\"*\")) {\n\t\t\t// TODO: replace * with all columns in the (joined) source table.\n\t\t\tnewSelectListElem = \"*\";\n\t\t} else {\n\t\t\tStringBuilder elem = new StringBuilder();\n\t\t\telem.append(visit(ctx.expression()));\n\t\t\t\n\t\t\tSelectStatementBaseRewriter baseRewriter = new SelectStatementBaseRewriter(queryString);\n\t\t\tString colName = baseRewriter.visit(ctx.expression());\n\t\t\t\n\t\t\tif (ctx.column_alias() != null) {\n\t\t\t\tAlias alias = new Alias(colName, ctx.column_alias().getText());\n\t\t\t\telem.append(String.format(\" AS %s\", alias));\n\t\t\t\tcolName2Alias = Pair.of(colName, alias);\n\t\t\t} else {\n\t\t\t\t// We add a pseudo column alias\n\t\t\t\tAlias alias = Alias.genAlias(depth, colName);\n\t\t\t\telem.append(String.format(\" AS %s\", alias));\n\t\t\t\tcolName2Alias = Pair.of(baseRewriter.visit(ctx.expression()), alias);\n\t\t\t}\n\t\t\t\n\t\t\tnewSelectListElem = elem.toString();\n\t\t}\n\t\t\n\t\tcolName2Aliases.add(Pair.of(colName2Alias.getKey(), colName2Alias.getValue()));\n\t\treturn newSelectListElem;\n\t} \n #location 31 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n\tpublic String visitSelect_list_elem(VerdictSQLParser.Select_list_elemContext ctx) {\n\t\tselect_list_elem_num++;\n\t\tString newSelectListElem = null;\n\t\tPair colName2Alias = null;\n\t\t\n\t\tif (ctx.getText().equals(\"*\")) {\n\t\t\t// TODO: replace * with all columns in the (joined) source table.\n\t\t\tnewSelectListElem = \"*\";\n\t\t} else {\n\t\t\tStringBuilder elem = new StringBuilder();\n\t\t\t\n\t\t\t// We use a baseRewriter to prevent that \"COUNT(*)\" is rewritten to \"COUNT(*) * (1/sample_ratio)\"\n\t\t\tSelectStatementBaseRewriter baseRewriter = new SelectStatementBaseRewriter(queryString);\n\t\t\tString tabColName = baseRewriter.visit(ctx.expression());\n\t\t\tString tabName = NameHelpers.tabNameOfColName(tabColName);\n\t\t\tTableUniqueName tabUniqueName = NameHelpers.tabUniqueNameOfColName(vc, tabColName);\n\t\t\tString colName = NameHelpers.colNameOfColName(tabColName);\n\t\t\t\n\t\t\t// if a table name is specified, we change it to its alias name.\n\t\t\tif (tableAliases.containsKey(tabUniqueName)) {\n\t\t\t\ttabName = tableAliases.get(tabUniqueName).toString();\n\t\t\t}\n\t\t\t\n\t\t\t// if there was derived table(s), we may need to substitute aliased name for the colName.\n\t\t\tfor (Map.Entry> e : derivedTableColName2Aliases.entrySet()) {\n\t\t\t\tString derivedTabName = e.getKey();\n\t\t\t\t\n\t\t\t\tif (tabName.length() > 0 && !tabName.equals(derivedTabName)) {\n\t\t\t\t\t// this is the case where there are more than one derived tables, and a user specifically referencing\n\t\t\t\t\t// a column in one of those derived tables.\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\t\t\t\tif (e.getValue().containsKey(colName)) {\n\t\t\t\t\tAlias alias = e.getValue().get(colName);\n\t\t\t\t\tif (alias.autoGenerated()) {\n\t\t\t\t\t\tcolName = alias.toString();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\t\n\t\t\tif (tabName.length() > 0) {\n\t\t\t\telem.append(String.format(\"%s.%s\", tabName, colName));\n\t\t\t} else {\n\t\t\t\telem.append(colName);\n\t\t\t}\n\t\t\t\n\t\t\tif (ctx.column_alias() != null) {\n\t\t\t\tAlias alias = new Alias(colName, ctx.column_alias().getText());\n\t\t\t\telem.append(String.format(\" AS %s\", alias));\n\t\t\t\tcolName2Alias = Pair.of(colName, alias);\n\t\t\t} else {\n\t\t\t\t// We add a pseudo column alias\n\t\t\t\tAlias alias = Alias.genAlias(depth, colName);\n\t\t\t\telem.append(String.format(\" AS %s\", alias));\n\t\t\t\tcolName2Alias = Pair.of(baseRewriter.visit(ctx.expression()), alias);\n\t\t\t}\n\t\t\t\n\t\t\tnewSelectListElem = elem.toString();\n\t\t}\n\t\t\n\t\tcolName2Aliases.add(Pair.of(colName2Alias.getKey(), colName2Alias.getValue()));\n\t\treturn newSelectListElem;\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] a) throws Exception {\n PropertyConfigurator.configure(FoxCfg.LOG_FILE);\n\n String in = \"University of Leipzig in Leipzig..\";\n\n String query = \"select * from search.termextract where context=\";\n\n URIBuilder builder = new URIBuilder();\n builder.setScheme(\"http\").setHost(\"query.yahooapis.com\").setPath(\"/v1/public/yql\").setParameter(\"diagnostics\", \"false\").setParameter(\"q\", query + \"'\" + in + \"'\");\n HttpGet httpget = new HttpGet(builder.build());\n System.out.println(httpget.getURI());\n\n HttpClient httpclient = new DefaultHttpClient();\n HttpResponse response = httpclient.execute(httpget);\n HttpEntity entity = response.getEntity();\n if (entity != null) {\n InputStream instream = entity.getContent();\n try {\n String myString = IOUtils.toString(instream, \"UTF-8\");\n System.out.println(myString);\n } finally {\n instream.close();\n }\n }\n } \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static void main(String[] a) throws Exception {\n PropertyConfigurator.configure(FoxCfg.LOG_FILE);\n\n String in = \"University of Leipzig in Leipzig..\";\n\n String query = \"select * from search.termextract where context=\";\n\n URIBuilder builder = new URIBuilder();\n builder.setScheme(\"http\").setHost(\"query.yahooapis.com\").setPath(\"/v1/public/yql\").setParameter(\"diagnostics\", \"false\").setParameter(\"q\", query + \"'\" + in + \"'\");\n HttpGet httpget = new HttpGet(builder.build());\n System.out.println(httpget.getURI());\n \n HttpClient httpclient = HttpClientBuilder.create().build();\n HttpResponse response = httpclient.execute(httpget);\n\t\tHttpEntity entity = response.getEntity();\n\t\t\n if (entity != null) {\n InputStream instream = entity.getContent();\n try {\n String myString = IOUtils.toString(instream, \"UTF-8\");\n System.out.println(myString);\n } finally {\n instream.close();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public Swagger read(Set> classes) throws GenerateException {\n //relate all methods to one base request mapping if multiple controllers exist for that mapping\n //get all methods from each controller & find their request mapping\n //create map - resource string (after first slash) as key, new SpringResource as value\n Map resourceMap = generateResourceMap(classes);\n for (String str : resourceMap.keySet()) {\n SpringResource resource = resourceMap.get(str);\n swagger = read(resource);\n }\n\n return swagger;\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public Swagger read(Set> classes) throws GenerateException {\n //relate all methods to one base request mapping if multiple controllers exist for that mapping\n //get all methods from each controller & find their request mapping\n //create map - resource string (after first slash) as key, new SpringResource as value\n Map resourceMap = generateResourceMap(classes);\n for (String str : resourceMap.keySet()) {\n SpringResource resource = resourceMap.get(str);\n read(resource);\n }\n\n return swagger;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected List getParameters(Type type, List annotations) {\n // look for path, query\n Iterator chain = SwaggerExtensions.chain();\n List parameters = null;\n\n LOG.info(\"getParameters for \" + type.getClass().getName());\n Set typesToSkip = new HashSet();\n if (chain.hasNext()) {\n SwaggerExtension extension = chain.next();\n LOG.info(\"trying extension \" + extension);\n parameters = extension.extractParameters(annotations, type, typesToSkip, chain);\n }\n\n if (parameters.size() > 0) {\n for (Parameter parameter : parameters) {\n\n ParameterProcessor.applyAnnotations(swagger, parameter, type, annotations);\n }\n } else {\n LOG.info(\"no parameter found, looking at body params\");\n if (typesToSkip.contains(type) == false) {\n Parameter param = null;\n param = ParameterProcessor.applyAnnotations(swagger, null, type, annotations);\n if (param != null) {\n for (Annotation annotation : annotations) {\n if (annotation instanceof ApiParam) {\n ApiParam apiParam = (ApiParam) annotation;\n param.setRequired(apiParam.required());\n break;\n }\n }\n parameters.add(param);\n }\n\n\n }\n }\n return parameters;\n } \n #location 14 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected List getParameters(Type type, List annotations) {\n Iterator chain = SwaggerExtensions.chain();\n List parameters = new ArrayList();\n\n LOG.info(\"Looking for path/query/header/form/cookie params in\" + type.getClass().getName());\n Set typesToSkip = new HashSet();\n if (chain.hasNext()) {\n SwaggerExtension extension = chain.next();\n LOG.info(\"trying extension \" + extension);\n parameters = extension.extractParameters(annotations, type, typesToSkip, chain);\n }\n\n if (parameters.size() > 0) {\n for (Parameter parameter : parameters) {\n ParameterProcessor.applyAnnotations(swagger, parameter, type, annotations);\n }\n } else {\n // look for body parameters\n LOG.info(\"Looking for body params in\" + type.getClass().getName());\n if (typesToSkip.contains(type) == false) {\n Parameter param = ParameterProcessor.applyAnnotations(swagger, null, type, annotations);\n if (param != null) {\n parameters.add(param);\n }\n }\n }\n return parameters;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void toDocuments() throws GenerateException {\n if (outputTemplate == null) {\n prepareMustacheTemplate();\n }\n if (outputTemplate.getApiDocuments().isEmpty()) {\n LOG.warn(\"nothing to write.\");\n return;\n }\n LOG.info(\"Writing doc to \" + outputPath + \"...\");\n\n FileOutputStream fileOutputStream = null;\n try {\n fileOutputStream = new FileOutputStream(outputPath);\n } catch (FileNotFoundException e) {\n throw new GenerateException(e);\n }\n OutputStreamWriter writer = new OutputStreamWriter(fileOutputStream, Charset.forName(\"UTF-8\"));\n\n try {\n URL url = getTemplateUri().toURL();\n InputStreamReader reader = new InputStreamReader(url.openStream(), Charset.forName(\"UTF-8\"));\n Mustache mustache = getMustacheFactory().compile(reader, templatePath);\n\n mustache.execute(writer, outputTemplate).flush();\n writer.close();\n LOG.info(\"Done!\");\n } catch (MalformedURLException e) {\n throw new GenerateException(e);\n } catch (IOException e) {\n throw new GenerateException(e);\n }\n } \n #location 27 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void toDocuments() throws GenerateException {\n if (outputTemplate == null) {\n prepareMustacheTemplate();\n }\n if (outputTemplate.getApiDocuments().isEmpty()) {\n LOG.warn(\"nothing to write.\");\n return;\n }\n LOG.info(\"Writing doc to \" + outputPath + \"...\");\n\n FileOutputStream fileOutputStream = null;\n try {\n fileOutputStream = new FileOutputStream(outputPath);\n } catch (FileNotFoundException e) {\n throw new GenerateException(e);\n }\n OutputStreamWriter writer = new OutputStreamWriter(fileOutputStream, Charset.forName(\"UTF-8\"));\n MustacheFactory mf = new DefaultMustacheFactory();\n\n\n URI uri = null;\n try {\n uri = new URI(templatePath);\n } catch (URISyntaxException e) {\n throw new GenerateException(e);\n }\n if (!uri.isAbsolute()) {\n File file = new File(templatePath);\n if (!file.exists()) {\n throw new GenerateException(\"Template \" + file.getAbsoluteFile()\n + \" not found. You can go to https://github.com/kongchen/api-doc-template to get templates.\");\n } else {\n uri = new File(templatePath).toURI();\n }\n }\n\n URL url = null;\n try {\n url = uri.toURL();\n InputStreamReader reader = new InputStreamReader(url.openStream(), Charset.forName(\"UTF-8\"));\n Mustache mustache = mf.compile(reader, templatePath);\n\n mustache.execute(writer, outputTemplate).flush();\n writer.close();\n LOG.info(\"Done!\");\n } catch (MalformedURLException e) {\n throw new GenerateException(e);\n } catch (IOException e) {\n throw new GenerateException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Swagger read(SpringResource resource) {\n if (swagger == null) {\n swagger = new Swagger();\n }\n List methods = resource.getMethods();\n Map tags = new HashMap();\n\n List resourceSecurities = new ArrayList();\n\n // Add the description from the controller api\n Class controller = resource.getControllerClass();\n RequestMapping apiPath = controller.getAnnotation(RequestMapping.class);\n\n\n if (controller != null && controller.isAnnotationPresent(Api.class)) {\n Api api = controller.getAnnotation(Api.class);\n if (!canReadApi(false, api)) {\n return null;\n }\n tags = updateTagsForApi(null, api);\n\n resourceSecurities = getSecurityRequirements(api);\n\n// description = api.description();\n// position = api.position();\n }\n\n resourcePath = resource.getControllerMapping();\n\n Map> apiMethodMap = new HashMap>();\n\n //collect api from method with @RequestMapping\n collectApisByRequestMapping(methods, apiMethodMap);\n\n for (String p : apiMethodMap.keySet()) {\n List operations = new ArrayList();\n\n for (Method method : apiMethodMap.get(p)) {\n\n RequestMapping requestMapping = method.getAnnotation(RequestMapping.class);\n ApiOperation apiOperation = method.getAnnotation(ApiOperation.class);\n\n String operationPath = p;\n //getPath(apiPath, requestMapping, \"\");\n String operationId;\n String httpMethod = null;\n\n if (operationPath != null && apiOperation != null) {\n\n\n Map regexMap = new HashMap();\n operationPath = parseOperationPath(operationPath, regexMap);\n\n //http method\n if (requestMapping.method() != null && requestMapping.method().length != 0) {\n httpMethod = requestMapping.method()[0].toString().toLowerCase();\n }\n\n Operation operation = parseMethod(method);\n\n updateOperationParameters(new ArrayList(), regexMap, operation);\n\n updateOperationProtocols(apiOperation, operation);\n\n String[] apiConsumes = new String[0];\n String[] apiProduces = new String[0];\n RequestMapping rm = controller.getAnnotation(RequestMapping.class);\n\n String[] pps = new String[0];\n String[] pcs = new String[0];\n if (rm != null) {\n pcs = rm.consumes();\n pps = rm.produces();\n }\n\n apiConsumes = updateOperationConsumes(method, pcs, apiConsumes, operation);\n apiProduces = updateOperationProduces(method, pps, apiProduces, operation);\n\n // can't continue without a valid http method\n// httpMethod = httpMethod == null ? parentMethod : httpMethod;\n ApiOperation op = method.getAnnotation(ApiOperation.class);\n updateTagsForOperation(operation, op);\n updateOperation(apiConsumes, apiProduces, tags, resourceSecurities, operation);\n updatePath(operationPath, httpMethod, operation);\n }\n\n\n }\n\n }\n return swagger;\n } \n #location 38 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Swagger read(SpringResource resource) {\n if (swagger == null) {\n swagger = new Swagger();\n }\n String description;\n List methods = resource.getMethods();\n Map tags = new HashMap();\n\n List resourceSecurities = new ArrayList();\n\n // Add the description from the controller api\n Class controller = resource.getControllerClass();\n RequestMapping controllerRM = controller.getAnnotation(RequestMapping.class);\n\n\n String[] controllerProduces = new String[0];\n String[] controllerConsumes = new String[0];\n if (controllerRM != null) {\n controllerConsumes = controllerRM.consumes();\n controllerProduces = controllerRM.produces();\n }\n\n if (controller != null && controller.isAnnotationPresent(Api.class)) {\n Api api = controller.getAnnotation(Api.class);\n if (!canReadApi(false, api)) {\n return swagger;\n }\n tags = updateTagsForApi(null, api);\n resourceSecurities = getSecurityRequirements(api);\n description = api.description();\n }\n\n resourcePath = resource.getControllerMapping();\n\n //collect api from method with @RequestMapping\n Map> apiMethodMap = collectApisByRequestMapping(methods);\n\n for (String path : apiMethodMap.keySet()) {\n for (Method method : apiMethodMap.get(path)) {\n\n RequestMapping requestMapping = method.getAnnotation(RequestMapping.class);\n if (requestMapping == null) {\n continue;\n }\n ApiOperation apiOperation = method.getAnnotation(ApiOperation.class);\n if (apiOperation == null) {\n continue;\n }\n String httpMethod = null;\n\n\n Map regexMap = new HashMap();\n String operationPath = parseOperationPath(path, regexMap);\n\n //http method\n if (requestMapping.method() != null && requestMapping.method().length != 0) {\n httpMethod = requestMapping.method()[0].toString().toLowerCase();\n if (httpMethod == null) {\n continue;\n }\n }\n\n Operation operation = parseMethod(method);\n\n updateOperationParameters(new ArrayList(), regexMap, operation);\n\n updateOperationProtocols(apiOperation, operation);\n\n String[] apiProduces = requestMapping.produces();\n String[] apiConsumes = requestMapping.consumes();\n\n apiProduces = (apiProduces == null || apiProduces.length == 0 ) ? controllerProduces : apiProduces;\n apiConsumes = (apiConsumes == null || apiProduces.length == 0 ) ? controllerConsumes : apiConsumes;\n\n apiConsumes = updateOperationConsumes(new String[0], apiConsumes, operation);\n apiProduces = updateOperationProduces(new String[0], apiProduces, operation);\n\n ApiOperation op = method.getAnnotation(ApiOperation.class);\n updateTagsForOperation(operation, op);\n updateOperation(apiConsumes, apiProduces, tags, resourceSecurities, operation);\n updatePath(operationPath, httpMethod, operation);\n\n\n }\n\n }\n return swagger;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private Map> collectApisByRequestMapping(List methods) {\n Map> apiMethodMap = new HashMap>();\n for (Method method : methods) {\n if (method.isAnnotationPresent(RequestMapping.class)) {\n RequestMapping requestMapping = Annotations.get(method, RequestMapping.class);\n String path = \"\";\n if (requestMapping.value() != null && requestMapping.value().length != 0) {\n path = generateFullPath(requestMapping.value()[0]);\n } else {\n path = resourcePath;\n }\n if (apiMethodMap.containsKey(path)) {\n apiMethodMap.get(path).add(method);\n } else {\n List ms = new ArrayList();\n ms.add(method);\n apiMethodMap.put(path, ms);\n }\n }\n }\n\n return apiMethodMap;\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private Map> collectApisByRequestMapping(List methods) {\n Map> apiMethodMap = new HashMap>();\n for (Method method : methods) {\n if (method.isAnnotationPresent(RequestMapping.class)) {\n RequestMapping requestMapping = AnnotationUtils.findAnnotation(method, RequestMapping.class);\n String path = \"\";\n if (requestMapping.value() != null && requestMapping.value().length != 0) {\n path = generateFullPath(requestMapping.value()[0]);\n } else {\n path = resourcePath;\n }\n if (apiMethodMap.containsKey(path)) {\n apiMethodMap.get(path).add(method);\n } else {\n List ms = new ArrayList();\n ms.add(method);\n apiMethodMap.put(path, ms);\n }\n }\n }\n\n return apiMethodMap;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Operation parseMethod(String httpMethod, Method method) {\n int responseCode = 200;\n Operation operation = new Operation();\n ApiOperation apiOperation = AnnotationUtils.findAnnotation(method, ApiOperation.class);\n\n String operationId = getOperationId(method, httpMethod);\n\n String responseContainer = null;\n\n Type responseClassType = null;\n Map defaultResponseHeaders = null;\n\n if (apiOperation != null) {\n if (apiOperation.hidden()) {\n return null;\n }\n if (!apiOperation.nickname().isEmpty()) {\n operationId = apiOperation.nickname();\n }\n\n defaultResponseHeaders = parseResponseHeaders(apiOperation.responseHeaders());\n operation.summary(apiOperation.value()).description(apiOperation.notes());\n\n Map customExtensions = BaseReaderUtils.parseExtensions(apiOperation.extensions());\n operation.setVendorExtensions(customExtensions);\n\n if (!apiOperation.response().equals(Void.class) && !apiOperation.response().equals(void.class)) {\n responseClassType = apiOperation.response();\n }\n if (!apiOperation.responseContainer().isEmpty()) {\n responseContainer = apiOperation.responseContainer();\n }\n List securities = new ArrayList<>();\n for (Authorization auth : apiOperation.authorizations()) {\n if (!auth.value().isEmpty()) {\n SecurityRequirement security = new SecurityRequirement();\n security.setName(auth.value());\n for (AuthorizationScope scope : auth.scopes()) {\n if (!scope.scope().isEmpty()) {\n security.addScope(scope.scope());\n }\n }\n securities.add(security);\n }\n }\n\n for (SecurityRequirement sec : securities) {\n operation.security(sec);\n }\n }\n operation.operationId(operationId);\n\n if (responseClassType == null) {\n // pick out response from method declaration\n LOGGER.debug(\"picking up response class from method \" + method);\n responseClassType = method.getGenericReturnType();\n }\n boolean hasApiAnnotation = false;\n if (responseClassType instanceof Class) {\n hasApiAnnotation = AnnotationUtils.findAnnotation((Class) responseClassType, Api.class) != null;\n }\n if ((responseClassType != null)\n && !responseClassType.equals(Void.class)\n && !responseClassType.equals(void.class)\n && !responseClassType.equals(javax.ws.rs.core.Response.class)\n && !hasApiAnnotation\n && !isSubResource(httpMethod, method)) {\n if (isPrimitive(responseClassType)) {\n Property property = ModelConverters.getInstance().readAsProperty(responseClassType);\n if (property != null) {\n Property responseProperty = RESPONSE_CONTAINER_CONVERTER.withResponseContainer(responseContainer, property);\n\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n }\n } else if (!responseClassType.equals(Void.class) && !responseClassType.equals(void.class)) {\n Map models = readModels(responseClassType);\n if (models.isEmpty()) {\n Property p = ModelConverters.getInstance().readAsProperty(responseClassType);\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(p)\n .headers(defaultResponseHeaders));\n }\n for (String key : models.keySet()) {\n Property responseProperty = RESPONSE_CONTAINER_CONVERTER.withResponseContainer(responseContainer, new RefProperty().asDefault(key));\n\n\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n swagger.model(key, models.get(key));\n }\n }\n Map models = readAllModels(responseClassType);\n for (Map.Entry entry : models.entrySet()) {\n swagger.model(entry.getKey(), entry.getValue());\n }\n }\n\n Consumes consumes = AnnotationUtils.findAnnotation(method, Consumes.class);\n if (consumes != null) {\n for (String mediaType : consumes.value()) {\n operation.consumes(mediaType);\n }\n }\n\n Produces produces = AnnotationUtils.findAnnotation(method, Produces.class);\n if (produces != null) {\n for (String mediaType : produces.value()) {\n operation.produces(mediaType);\n }\n }\n\n ApiResponses responseAnnotation = AnnotationUtils.findAnnotation(method, ApiResponses.class);\n if (responseAnnotation != null) {\n updateApiResponse(operation, responseAnnotation);\n }\n\n if (AnnotationUtils.findAnnotation(method, Deprecated.class) != null) {\n operation.deprecated(true);\n }\n\n // process parameters\n Class[] parameterTypes = method.getParameterTypes();\n Type[] genericParameterTypes = method.getGenericParameterTypes();\n Annotation[][] paramAnnotations = findParamAnnotations(method);\n\n for (int i = 0; i < parameterTypes.length; i++) {\n Type type = genericParameterTypes[i];\n List annotations = Arrays.asList(paramAnnotations[i]);\n List parameters = getParameters(type, annotations);\n\n for (Parameter parameter : parameters) {\n if (hasCommonParameter(parameter)) {\n Parameter refParameter = new RefParameter(RefType.PARAMETER.getInternalPrefix() + parameter.getName());\n operation.parameter(refParameter);\n } else {\n parameter = replaceArrayModelForOctetStream(operation, parameter);\n operation.parameter(parameter);\n }\n }\n }\n if (operation.getResponses() == null) {\n operation.defaultResponse(new Response().description(\"successful operation\"));\n }\n\n // Process @ApiImplicitParams\n this.readImplicitParameters(method, operation);\n\n processOperationDecorator(operation, method);\n\n return operation;\n } \n #location 80 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Operation parseMethod(String httpMethod, Method method) {\n int responseCode = 200;\n Operation operation = new Operation();\n ApiOperation apiOperation = AnnotationUtils.findAnnotation(method, ApiOperation.class);\n\n String operationId = getOperationId(method, httpMethod);\n\n String responseContainer = null;\n\n Type responseClassType = null;\n Map defaultResponseHeaders = null;\n\n if (apiOperation != null) {\n if (apiOperation.hidden()) {\n return null;\n }\n if (!apiOperation.nickname().isEmpty()) {\n operationId = apiOperation.nickname();\n }\n\n defaultResponseHeaders = parseResponseHeaders(apiOperation.responseHeaders());\n operation.summary(apiOperation.value()).description(apiOperation.notes());\n\n Map customExtensions = BaseReaderUtils.parseExtensions(apiOperation.extensions());\n operation.setVendorExtensions(customExtensions);\n\n if (!apiOperation.response().equals(Void.class) && !apiOperation.response().equals(void.class)) {\n responseClassType = apiOperation.response();\n }\n if (!apiOperation.responseContainer().isEmpty()) {\n responseContainer = apiOperation.responseContainer();\n }\n List securities = new ArrayList<>();\n for (Authorization auth : apiOperation.authorizations()) {\n if (!auth.value().isEmpty()) {\n SecurityRequirement security = new SecurityRequirement();\n security.setName(auth.value());\n for (AuthorizationScope scope : auth.scopes()) {\n if (!scope.scope().isEmpty()) {\n security.addScope(scope.scope());\n }\n }\n securities.add(security);\n }\n }\n\n for (SecurityRequirement sec : securities) {\n operation.security(sec);\n }\n }\n operation.operationId(operationId);\n\n if (responseClassType == null) {\n // pick out response from method declaration\n LOGGER.debug(\"picking up response class from method \" + method);\n responseClassType = method.getGenericReturnType();\n }\n boolean hasApiAnnotation = false;\n if (responseClassType instanceof Class) {\n hasApiAnnotation = AnnotationUtils.findAnnotation((Class) responseClassType, Api.class) != null;\n }\n if ((responseClassType != null)\n && !responseClassType.equals(Void.class)\n && !responseClassType.equals(void.class)\n && !responseClassType.equals(javax.ws.rs.core.Response.class)\n && !hasApiAnnotation\n && !isSubResource(httpMethod, method)) {\n if (isPrimitive(responseClassType)) {\n Property property = ModelConverters.getInstance().readAsProperty(responseClassType);\n if (property != null) {\n Property responseProperty = RESPONSE_CONTAINER_CONVERTER.withResponseContainer(responseContainer, property);\n\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n }\n } else if (!responseClassType.equals(Void.class) && !responseClassType.equals(void.class)) {\n Map models = ModelConverters.getInstance().read(responseClassType);\n if (models.isEmpty()) {\n Property p = ModelConverters.getInstance().readAsProperty(responseClassType);\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(p)\n .headers(defaultResponseHeaders));\n }\n for (String key : models.keySet()) {\n Property responseProperty = RESPONSE_CONTAINER_CONVERTER.withResponseContainer(responseContainer, new RefProperty().asDefault(key));\n\n\n operation.response(responseCode, new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n swagger.model(key, models.get(key));\n }\n }\n Map models = readAllModels(responseClassType);\n for (Map.Entry entry : models.entrySet()) {\n swagger.model(entry.getKey(), entry.getValue());\n }\n }\n\n Consumes consumes = AnnotationUtils.findAnnotation(method, Consumes.class);\n if (consumes != null) {\n for (String mediaType : consumes.value()) {\n operation.consumes(mediaType);\n }\n }\n\n Produces produces = AnnotationUtils.findAnnotation(method, Produces.class);\n if (produces != null) {\n for (String mediaType : produces.value()) {\n operation.produces(mediaType);\n }\n }\n\n ApiResponses responseAnnotation = AnnotationUtils.findAnnotation(method, ApiResponses.class);\n if (responseAnnotation != null) {\n updateApiResponse(operation, responseAnnotation);\n }\n\n if (AnnotationUtils.findAnnotation(method, Deprecated.class) != null) {\n operation.deprecated(true);\n }\n\n // process parameters\n Class[] parameterTypes = method.getParameterTypes();\n Type[] genericParameterTypes = method.getGenericParameterTypes();\n Annotation[][] paramAnnotations = findParamAnnotations(method);\n\n for (int i = 0; i < parameterTypes.length; i++) {\n Type type = genericParameterTypes[i];\n List annotations = Arrays.asList(paramAnnotations[i]);\n List parameters = getParameters(type, annotations);\n\n for (Parameter parameter : parameters) {\n if (hasCommonParameter(parameter)) {\n Parameter refParameter = new RefParameter(RefType.PARAMETER.getInternalPrefix() + parameter.getName());\n operation.parameter(refParameter);\n } else {\n parameter = replaceArrayModelForOctetStream(operation, parameter);\n operation.parameter(parameter);\n }\n }\n }\n if (operation.getResponses() == null) {\n operation.defaultResponse(new Response().description(\"successful operation\"));\n }\n\n // Process @ApiImplicitParams\n this.readImplicitParameters(method, operation);\n\n processOperationDecorator(operation, method);\n\n return operation;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private Operation parseMethod(Method method) {\n Operation operation = new Operation();\n\n RequestMapping requestMapping = Annotations.get(method, RequestMapping.class);\n Class responseClass = null;\n List produces = new ArrayList();\n List consumes = new ArrayList();\n String responseContainer = null;\n String operationId = method.getName();\n Map defaultResponseHeaders = null;\n Set> customExtensions = null;\n\n ApiOperation apiOperation = Annotations.get(method, ApiOperation.class);\n\n if (apiOperation.hidden())\n return null;\n if (!\"\".equals(apiOperation.nickname()))\n operationId = apiOperation.nickname();\n\n defaultResponseHeaders = parseResponseHeaders(apiOperation.responseHeaders());\n\n operation.summary(apiOperation.value()).description(apiOperation.notes());\n\n customExtensions = parseCustomExtensions(apiOperation.extensions());\n if (customExtensions != null) {\n for (Map extension : customExtensions) {\n if (extension != null) {\n for (Map.Entry map : extension.entrySet()) {\n operation.setVendorExtension(map.getKey().startsWith(\"x-\") ? map.getKey() : \"x-\" + map.getKey(), map.getValue());\n }\n }\n }\n }\n\n if (apiOperation.response() != null && !Void.class.equals(apiOperation.response()))\n responseClass = apiOperation.response();\n if (!\"\".equals(apiOperation.responseContainer()))\n responseContainer = apiOperation.responseContainer();\n\n ///security\n if (apiOperation.authorizations() != null) {\n List securities = new ArrayList();\n for (Authorization auth : apiOperation.authorizations()) {\n if (auth.value() != null && !\"\".equals(auth.value())) {\n SecurityRequirement security = new SecurityRequirement();\n security.setName(auth.value());\n AuthorizationScope[] scopes = auth.scopes();\n for (AuthorizationScope scope : scopes) {\n if (scope.scope() != null && !\"\".equals(scope.scope())) {\n security.addScope(scope.scope());\n }\n }\n securities.add(security);\n }\n }\n if (securities.size() > 0) {\n for (SecurityRequirement sec : securities)\n operation.security(sec);\n }\n }\n\n if (responseClass == null) {\n // pick out response from method declaration\n LOG.info(\"picking up response class from method \" + method);\n Type t = method.getGenericReturnType();\n responseClass = method.getReturnType();\n if (responseClass.equals(ResponseEntity.class)) {\n responseClass = getGenericSubtype(method.getReturnType(), method.getGenericReturnType());\n }\n if (!responseClass.equals(Void.class) && !\"void\".equals(responseClass.toString()) && Annotations.get(responseClass, Api.class) == null) {\n LOG.info(\"reading model \" + responseClass);\n Map models = ModelConverters.getInstance().readAll(t);\n }\n }\n if (responseClass != null\n && !responseClass.equals(Void.class)\n && !responseClass.equals(ResponseEntity.class)\n && Annotations.get(responseClass, Api.class) == null) {\n if (isPrimitive(responseClass)) {\n Property responseProperty = null;\n Property property = ModelConverters.getInstance().readAsProperty(responseClass);\n if (property != null) {\n if (\"list\".equalsIgnoreCase(responseContainer))\n responseProperty = new ArrayProperty(property);\n else if (\"map\".equalsIgnoreCase(responseContainer))\n responseProperty = new MapProperty(property);\n else\n responseProperty = property;\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n }\n } else if (!responseClass.equals(Void.class) && !\"void\".equals(responseClass.toString())) {\n Map models = ModelConverters.getInstance().read(responseClass);\n if (models.size() == 0) {\n Property pp = ModelConverters.getInstance().readAsProperty(responseClass);\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(pp)\n .headers(defaultResponseHeaders));\n }\n for (String key : models.keySet()) {\n Property responseProperty = null;\n\n if (\"list\".equalsIgnoreCase(responseContainer))\n responseProperty = new ArrayProperty(new RefProperty().asDefault(key));\n else if (\"map\".equalsIgnoreCase(responseContainer))\n responseProperty = new MapProperty(new RefProperty().asDefault(key));\n else\n responseProperty = new RefProperty().asDefault(key);\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n swagger.model(key, models.get(key));\n }\n models = ModelConverters.getInstance().readAll(responseClass);\n for (String key : models.keySet()) {\n swagger.model(key, models.get(key));\n }\n }\n }\n\n operation.operationId(operationId);\n\n if (requestMapping.produces() != null) {\n for (String str : Arrays.asList(requestMapping.produces())) {\n if (!produces.contains(str)) {\n produces.add(str);\n }\n }\n }\n if (requestMapping.consumes() != null) {\n for (String str : Arrays.asList(requestMapping.consumes())) {\n if (!consumes.contains(str)) {\n consumes.add(str);\n }\n }\n }\n\n ApiResponses responseAnnotation = Annotations.get(method, ApiResponses.class);\n if (responseAnnotation != null) {\n updateApiResponse(operation, responseAnnotation);\n } else {\n ResponseStatus responseStatus = Annotations.get(method, ResponseStatus.class);\n if (responseStatus != null) {\n operation.response(responseStatus.value().value(), new Response().description(responseStatus.reason()));\n }\n }\n\n Deprecated annotation = Annotations.get(method, Deprecated.class);\n if (annotation != null)\n operation.deprecated(true);\n\n // FIXME `hidden` is never used\n boolean hidden = false;\n if (apiOperation != null)\n hidden = apiOperation.hidden();\n\n // process parameters\n Class[] parameterTypes = method.getParameterTypes();\n Type[] genericParameterTypes = method.getGenericParameterTypes();\n Annotation[][] paramAnnotations = method.getParameterAnnotations();\n // paramTypes = method.getParameterTypes\n // genericParamTypes = method.getGenericParameterTypes\n for (int i = 0; i < parameterTypes.length; i++) {\n Type type = genericParameterTypes[i];\n List annotations = Arrays.asList(paramAnnotations[i]);\n List parameters = getParameters(type, annotations);\n\n for (Parameter parameter : parameters) {\n operation.parameter(parameter);\n }\n }\n\n if (operation.getResponses() == null) {\n operation.defaultResponse(new Response().description(\"successful operation\"));\n }\n\n // Process @ApiImplicitParams\n this.readImplicitParameters(method, operation);\n\n return operation;\n\n } \n #location 15 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private Operation parseMethod(Method method) {\n Operation operation = new Operation();\n\n RequestMapping requestMapping = AnnotationUtils.findAnnotation(method, RequestMapping.class);\n Class responseClass = null;\n List produces = new ArrayList();\n List consumes = new ArrayList();\n String responseContainer = null;\n String operationId = method.getName();\n Map defaultResponseHeaders = null;\n Set> customExtensions = null;\n\n ApiOperation apiOperation = AnnotationUtils.findAnnotation(method, ApiOperation.class);\n\n if (apiOperation.hidden())\n return null;\n if (!\"\".equals(apiOperation.nickname()))\n operationId = apiOperation.nickname();\n\n defaultResponseHeaders = parseResponseHeaders(apiOperation.responseHeaders());\n\n operation.summary(apiOperation.value()).description(apiOperation.notes());\n\n customExtensions = parseCustomExtensions(apiOperation.extensions());\n if (customExtensions != null) {\n for (Map extension : customExtensions) {\n if (extension != null) {\n for (Map.Entry map : extension.entrySet()) {\n operation.setVendorExtension(map.getKey().startsWith(\"x-\") ? map.getKey() : \"x-\" + map.getKey(), map.getValue());\n }\n }\n }\n }\n\n if (apiOperation.response() != null && !Void.class.equals(apiOperation.response()))\n responseClass = apiOperation.response();\n if (!\"\".equals(apiOperation.responseContainer()))\n responseContainer = apiOperation.responseContainer();\n\n ///security\n if (apiOperation.authorizations() != null) {\n List securities = new ArrayList();\n for (Authorization auth : apiOperation.authorizations()) {\n if (auth.value() != null && !\"\".equals(auth.value())) {\n SecurityRequirement security = new SecurityRequirement();\n security.setName(auth.value());\n AuthorizationScope[] scopes = auth.scopes();\n for (AuthorizationScope scope : scopes) {\n if (scope.scope() != null && !\"\".equals(scope.scope())) {\n security.addScope(scope.scope());\n }\n }\n securities.add(security);\n }\n }\n if (securities.size() > 0) {\n for (SecurityRequirement sec : securities)\n operation.security(sec);\n }\n }\n\n if (responseClass == null) {\n // pick out response from method declaration\n LOG.info(\"picking up response class from method \" + method);\n Type t = method.getGenericReturnType();\n responseClass = method.getReturnType();\n if (responseClass.equals(ResponseEntity.class)) {\n responseClass = getGenericSubtype(method.getReturnType(), method.getGenericReturnType());\n }\n if (!responseClass.equals(Void.class) && !\"void\".equals(responseClass.toString())\n && AnnotationUtils.findAnnotation(responseClass, Api.class) == null) {\n LOG.info(\"reading model \" + responseClass);\n Map models = ModelConverters.getInstance().readAll(t);\n }\n }\n if (responseClass != null\n && !responseClass.equals(Void.class)\n && !responseClass.equals(ResponseEntity.class)\n && AnnotationUtils.findAnnotation(responseClass, Api.class) == null) {\n if (isPrimitive(responseClass)) {\n Property responseProperty = null;\n Property property = ModelConverters.getInstance().readAsProperty(responseClass);\n if (property != null) {\n if (\"list\".equalsIgnoreCase(responseContainer))\n responseProperty = new ArrayProperty(property);\n else if (\"map\".equalsIgnoreCase(responseContainer))\n responseProperty = new MapProperty(property);\n else\n responseProperty = property;\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n }\n } else if (!responseClass.equals(Void.class) && !\"void\".equals(responseClass.toString())) {\n Map models = ModelConverters.getInstance().read(responseClass);\n if (models.size() == 0) {\n Property pp = ModelConverters.getInstance().readAsProperty(responseClass);\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(pp)\n .headers(defaultResponseHeaders));\n }\n for (String key : models.keySet()) {\n Property responseProperty = null;\n\n if (\"list\".equalsIgnoreCase(responseContainer))\n responseProperty = new ArrayProperty(new RefProperty().asDefault(key));\n else if (\"map\".equalsIgnoreCase(responseContainer))\n responseProperty = new MapProperty(new RefProperty().asDefault(key));\n else\n responseProperty = new RefProperty().asDefault(key);\n operation.response(apiOperation.code(), new Response()\n .description(\"successful operation\")\n .schema(responseProperty)\n .headers(defaultResponseHeaders));\n swagger.model(key, models.get(key));\n }\n models = ModelConverters.getInstance().readAll(responseClass);\n for (String key : models.keySet()) {\n swagger.model(key, models.get(key));\n }\n }\n }\n\n operation.operationId(operationId);\n\n if (requestMapping.produces() != null) {\n for (String str : Arrays.asList(requestMapping.produces())) {\n if (!produces.contains(str)) {\n produces.add(str);\n }\n }\n }\n if (requestMapping.consumes() != null) {\n for (String str : Arrays.asList(requestMapping.consumes())) {\n if (!consumes.contains(str)) {\n consumes.add(str);\n }\n }\n }\n\n ApiResponses responseAnnotation = AnnotationUtils.findAnnotation(method, ApiResponses.class);\n if (responseAnnotation != null) {\n updateApiResponse(operation, responseAnnotation);\n } else {\n ResponseStatus responseStatus = AnnotationUtils.findAnnotation(method, ResponseStatus.class);\n if (responseStatus != null) {\n operation.response(responseStatus.value().value(), new Response().description(responseStatus.reason()));\n }\n }\n\n Deprecated annotation = AnnotationUtils.findAnnotation(method, Deprecated.class);\n if (annotation != null)\n operation.deprecated(true);\n\n // FIXME `hidden` is never used\n boolean hidden = false;\n if (apiOperation != null)\n hidden = apiOperation.hidden();\n\n // process parameters\n Class[] parameterTypes = method.getParameterTypes();\n Type[] genericParameterTypes = method.getGenericParameterTypes();\n Annotation[][] paramAnnotations = method.getParameterAnnotations();\n // paramTypes = method.getParameterTypes\n // genericParamTypes = method.getGenericParameterTypes\n for (int i = 0; i < parameterTypes.length; i++) {\n Type type = genericParameterTypes[i];\n List annotations = Arrays.asList(paramAnnotations[i]);\n List parameters = getParameters(type, annotations);\n\n for (Parameter parameter : parameters) {\n operation.parameter(parameter);\n }\n }\n\n if (operation.getResponses() == null) {\n operation.defaultResponse(new Response().description(\"successful operation\"));\n }\n\n // Process @ApiImplicitParams\n this.readImplicitParameters(method, operation);\n\n return operation;\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testGeneratedDoc() throws Exception {\n mojo.execute();\n\n BufferedReader actualReader = null;\n BufferedReader expectReader = null;\n FileInputStream swaggerJson = null;\n BufferedReader swaggerReader = null;\n\n try {\n File actual = docOutput;\n File expected = new File(this.getClass().getResource(\"/sample-springmvc.html\").getFile());\n FileAssert.assertEquals(expected, actual);\n\n swaggerJson = new FileInputStream(new File(swaggerOutputDir, \"swagger.json\"));\n swaggerReader = new BufferedReader(new InputStreamReader(swaggerJson));\n String s = swaggerReader.readLine();\n while (s != null) {\n if (s.contains(\"\\\"parameters\\\" : [ ],\")) {\n assertFalse(\"should not have null parameters\", true);\n }\n s = swaggerReader.readLine();\n }\n\n } finally {\n if (actualReader != null) {\n actualReader.close();\n }\n if (expectReader != null) {\n expectReader.close();\n }\n if (swaggerJson != null) {\n swaggerJson.close();\n }\n if (swaggerReader != null) {\n swaggerReader.close();\n }\n }\n\n } \n #location 21 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testGeneratedDoc() throws Exception {\n mojo.execute();\n\n FileInputStream swaggerJson = null;\n BufferedReader swaggerReader = null;\n\n try {\n File actual = docOutput;\n File expected = new File(this.getClass().getResource(\"/sample-springmvc.html\").getFile());\n String exptectedFileContent = CharMatcher.breakingWhitespace().removeFrom(Files.toString(expected, Charset.forName(\"UTF-8\")));\n String actualFileContent = CharMatcher.breakingWhitespace().removeFrom(Files.toString(actual, Charset.forName(\"UTF-8\")));\n assertEquals(exptectedFileContent, actualFileContent);\n\n swaggerJson = new FileInputStream(new File(swaggerOutputDir, \"swagger.json\"));\n swaggerReader = new BufferedReader(new InputStreamReader(swaggerJson));\n String s = swaggerReader.readLine();\n while (s != null) {\n if (s.contains(\"\\\"parameters\\\" : [ ],\")) {\n fail(\"should not have null parameters\");\n }\n s = swaggerReader.readLine();\n }\n\n } finally {\n if (swaggerJson != null) {\n swaggerJson.close();\n }\n if (swaggerReader != null) {\n swaggerReader.close();\n }\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void toDocuments() throws GenerateException {\n if (outputTemplate == null) {\n prepareMustacheTemplate();\n }\n if (outputTemplate.getApiDocuments().isEmpty()) {\n LOG.warn(\"nothing to write.\");\n return;\n }\n LOG.info(\"Writing doc to \" + outputPath + \"...\");\n\n FileOutputStream fileOutputStream = null;\n try {\n fileOutputStream = new FileOutputStream(outputPath);\n } catch (FileNotFoundException e) {\n throw new GenerateException(e);\n }\n OutputStreamWriter writer = new OutputStreamWriter(fileOutputStream, Charset.forName(\"UTF-8\"));\n MustacheFactory mf = new DefaultMustacheFactory();\n\n\n URI uri = null;\n try {\n uri = new URI(templatePath);\n } catch (URISyntaxException e) {\n throw new GenerateException(e);\n }\n if (!uri.isAbsolute()) {\n File file = new File(templatePath);\n if (!file.exists()) {\n throw new GenerateException(\"Template \" + file.getAbsoluteFile()\n + \" not found. You can go to https://github.com/kongchen/api-doc-template to get templates.\");\n } else {\n uri = new File(templatePath).toURI();\n }\n }\n\n URL url = null;\n try {\n url = uri.toURL();\n InputStreamReader reader = new InputStreamReader(url.openStream(), Charset.forName(\"UTF-8\"));\n Mustache mustache = mf.compile(reader, templatePath);\n\n mustache.execute(writer, outputTemplate).flush();\n writer.close();\n LOG.info(\"Done!\");\n } catch (MalformedURLException e) {\n throw new GenerateException(e);\n } catch (IOException e) {\n throw new GenerateException(e);\n }\n } \n #location 30 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void toDocuments() throws GenerateException {\n if (outputTemplate == null) {\n prepareMustacheTemplate();\n }\n if (outputTemplate.getApiDocuments().isEmpty()) {\n LOG.warn(\"nothing to write.\");\n return;\n }\n LOG.info(\"Writing doc to \" + outputPath + \"...\");\n\n FileOutputStream fileOutputStream = null;\n try {\n fileOutputStream = new FileOutputStream(outputPath);\n } catch (FileNotFoundException e) {\n throw new GenerateException(e);\n }\n OutputStreamWriter writer = new OutputStreamWriter(fileOutputStream, Charset.forName(\"UTF-8\"));\n\n try {\n URL url = getTemplateUri().toURL();\n InputStreamReader reader = new InputStreamReader(url.openStream(), Charset.forName(\"UTF-8\"));\n Mustache mustache = getMustacheFactory().compile(reader, templatePath);\n\n mustache.execute(writer, outputTemplate).flush();\n writer.close();\n LOG.info(\"Done!\");\n } catch (MalformedURLException e) {\n throw new GenerateException(e);\n } catch (IOException e) {\n throw new GenerateException(e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\n \"'Can't connect to MySQL server on 'localhost'\",\n Platform.detect() == Windows ? \"mysqld.exe: Shutdown complete\" : \"mysqld: Shutdown complete\");\n\n try {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(getRuntimeConfig().getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdOut, stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n } \n #location 39 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\n \"'Can't connect to MySQL server on 'localhost'\",\n Platform.detect() == Windows ? \"mysqld.exe: Shutdown complete\" : \"mysqld: Shutdown complete\");\n\n try {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(getRuntimeConfig().getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n String errOutput = CharStreams.toString(stdErr);\n\n if (errOutput.contains(\"Can't connect to MySQL server on\")) {\n logger.warn(\"mysql was already shutdown - no need to add extra shutdown hook - process does it out of the box.\");\n retValue = true;\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdOut, stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = Runtime.getRuntime().exec(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n \"-e\",\n command,\n schemaName});\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n } \n #location 18 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = new ProcessBuilder(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n schemaName}).start();\n\n IOUtils.copy(new StringReader(sql), p.getOutputStream(), Charset.defaultCharset());\n p.getOutputStream().close();\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\"'Can't connect to MySQL server on 'localhost'\");\n\n try {\n Process p;\n\n if (Platform.detect() == Platform.Windows) {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin.exe\").toString();\n successPatterns.add(\"mysqld.exe: Shutdown complete\");\n\n p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n } else {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n successPatterns.add(\"mysqld: Shutdown complete\");\n\n p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n //String.format(\"--socket=%s\", sockFile(getExecutable().executable)),\n \"shutdown\"});\n }\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(unsafeRuntimeConfig.getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseable(stdOut);\n closeCloseable(stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n } \n #location 59 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\n \"'Can't connect to MySQL server on 'localhost'\",\n Platform.detect() == Windows ? \"mysqld.exe: Shutdown complete\" : \"mysqld: Shutdown complete\");\n\n try {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(getRuntimeConfig().getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdOut, stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\n \"'Can't connect to MySQL server on 'localhost'\",\n Platform.detect() == Windows ? \"mysqld.exe: Shutdown complete\" : \"mysqld: Shutdown complete\");\n\n try {\n String cmd = Paths.get(getExecutable().getFile().baseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n format(\"--port=%s\", getConfig().getPort()),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(successPatterns, \"[ERROR]\",\n StreamToLineProcessor.wrap(getRuntimeConfig().getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().getBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n String errOutput = CharStreams.toString(stdErr);\n\n if (errOutput.contains(\"Can't connect to MySQL server on\")) {\n logger.warn(\"mysql was already shutdown - no need to add extra shutdown hook - process does it out of the box.\");\n retValue = true;\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n }\n\n } catch (InterruptedException | IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdOut, stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n } \n #location 51 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private boolean stopUsingMysqldadmin() {\n ResultMatchingListener shutdownListener = outputWatch.addListener(new ResultMatchingListener(\": Shutdown complete\"));\n boolean retValue = false;\n Reader stdErr = null;\n\n try {\n String cmd = Paths.get(getExecutable().getFile().baseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[]{\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n format(\"--port=%s\", getConfig().getPort()),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n shutdownListener.waitForResult(getConfig().getTimeout());\n\n if (!shutdownListener.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + shutdownListener.getFailureFound());\n retValue = false;\n } else {\n retValue = true;\n }\n\n } else {\n String errOutput = CharStreams.toString(stdErr);\n\n if (errOutput.contains(\"Can't connect to MySQL server on\")) {\n logger.warn(\"mysql was already shutdown - no need to add extra shutdown hook - process does it out of the box.\");\n retValue = true;\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + errOutput);\n }\n }\n\n } catch (InterruptedException | IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdErr);\n }\n\n return retValue;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = Runtime.getRuntime().exec(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n \"-e\",\n command,\n schemaName});\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n } \n #location 21 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = new ProcessBuilder(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n schemaName}).start();\n\n IOUtils.copy(new StringReader(sql), p.getOutputStream(), Charset.defaultCharset());\n p.getOutputStream().close();\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = Runtime.getRuntime().exec(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n \"-e\",\n command,\n schemaName});\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n } \n #location 20 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private void execute(final String sql) {\n String command = (Platform.detect() == Windows) ? format(\"\\\"%s\\\"\", sql) : sql;\n try {\n Process p = new ProcessBuilder(new String[]{\n Paths.get(executable.getBaseDir().getAbsolutePath(), \"bin\", \"mysql\").toString(),\n \"--protocol=tcp\",\n format(\"--user=%s\", SystemDefaults.USERNAME),\n format(\"--port=%s\", config.getPort()),\n schemaName}).start();\n\n IOUtils.copy(new StringReader(sql), p.getOutputStream(), Charset.defaultCharset());\n p.getOutputStream().close();\n\n if (p.waitFor() != 0) {\n String out = IOUtils.toString(p.getInputStream());\n String err = IOUtils.toString(p.getErrorStream());\n\n if (isNullOrEmpty(out))\n throw new CommandFailedException(command, schemaName, p.waitFor(), err);\n else\n throw new CommandFailedException(command, schemaName, p.waitFor(), out);\n }\n\n } catch (IOException | InterruptedException e) {\n throw new CommandFailedException(command, schemaName, e.getMessage(), e);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\"'Can't connect to MySQL server on 'localhost'\");\n\n try {\n Process p;\n\n if (Platform.detect() == Platform.Windows) {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin.exe\").toString();\n successPatterns.add(\"mysqld.exe: Shutdown complete\");\n\n p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n } else {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n successPatterns.add(\"mysqld: Shutdown complete\");\n\n p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n //String.format(\"--socket=%s\", sockFile(getExecutable().executable)),\n \"shutdown\"});\n }\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(unsafeRuntimeConfig.getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseable(stdOut);\n closeCloseable(stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n } \n #location 60 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private boolean stopUsingMysqldadmin() {\n boolean retValue = false;\n\n Reader stdOut = null;\n Reader stdErr = null;\n LogFileProcessor processor = null;\n Set successPatterns = Sets.newHashSet(\n \"'Can't connect to MySQL server on 'localhost'\",\n Platform.detect() == Windows ? \"mysqld.exe: Shutdown complete\" : \"mysqld: Shutdown complete\");\n\n try {\n String cmd = Paths.get(getExecutable().getFile().generatedBaseDir().getAbsolutePath(), \"bin\", \"mysqladmin\").toString();\n\n Process p = Runtime.getRuntime().exec(new String[] {\n cmd, \"--no-defaults\", \"--protocol=tcp\",\n String.format(\"-u%s\", MysqldConfig.SystemDefaults.USERNAME),\n \"shutdown\"});\n\n retValue = p.waitFor() == 0;\n\n OutputWatchStreamProcessor outputWatch = new OutputWatchStreamProcessor(\n successPatterns,\n Sets.newHashSet(\"[ERROR]\"),\n StreamToLineProcessor.wrap(getRuntimeConfig().getProcessOutput().getOutput()));\n\n processor = new LogFileProcessor(new File(this.getExecutable().executable.generatedBaseDir() + \"/data/error.log\"), outputWatch);\n\n stdOut = new InputStreamReader(p.getInputStream());\n stdErr = new InputStreamReader(p.getErrorStream());\n\n if (retValue) {\n outputWatch.waitForResult(getConfig().getTimeout());\n\n if (!outputWatch.isInitWithSuccess()) {\n logger.error(\"mysql shutdown failed. Expected to find in output: 'Shutdown complete', got: \" + outputWatch.getFailureFound());\n retValue = false;\n }\n } else {\n logger.error(\"mysql shutdown failed with error code: \" + p.waitFor() + \" and message: \" + CharStreams.toString(stdErr));\n }\n\n } catch (InterruptedException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } catch (IOException e) {\n logger.warn(\"Encountered error why shutting down process.\", e);\n } finally {\n closeCloseables(stdOut, stdErr);\n if (processor != null) processor.shutdown();\n }\n\n return retValue;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected SettableBeanProperty _resolvedObjectIdProperty(DeserializationContext ctxt,\n SettableBeanProperty prop) throws JsonMappingException\n {\n ObjectIdInfo objectIdInfo = prop.getObjectIdInfo();\n JsonDeserializer valueDeser = prop.getValueDeserializer();\n ObjectIdReader objectIdReader = valueDeser.getObjectIdReader();\n if (objectIdInfo == null && objectIdReader == null) {\n return prop;\n }\n return new ObjectIdReferenceProperty(prop, objectIdInfo);\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected SettableBeanProperty _resolvedObjectIdProperty(DeserializationContext ctxt,\n SettableBeanProperty prop) throws JsonMappingException\n {\n ObjectIdInfo objectIdInfo = prop.getObjectIdInfo();\n JsonDeserializer valueDeser = prop.getValueDeserializer();\n ObjectIdReader objectIdReader = (valueDeser == null) ? null : valueDeser.getObjectIdReader();\n if (objectIdInfo == null && objectIdReader == null) {\n return prop;\n }\n return new ObjectIdReferenceProperty(prop, objectIdInfo);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void runOnce() throws Exception {\n final ObjectMapper mapper = getObjectMapper();\n Callable writeJson = new Callable() {\n @Override\n public String call() throws Exception {\n Wrapper wrapper = new Wrapper(new TypeOne(\"test\"));\n return mapper.writeValueAsString(wrapper);\n }\n };\n\n int numThreads = 4;\n ExecutorService executor = Executors.newFixedThreadPool(numThreads);\n List> jsonFutures = new ArrayList>();\n for (int i = 0; i < numThreads; i++) {\n jsonFutures.add(executor.submit(writeJson));\n }\n\n executor.shutdown();\n executor.awaitTermination(5, TimeUnit.SECONDS);\n\n for (Future jsonFuture : jsonFutures) {\n String json = jsonFuture.get();\n JsonNode tree = mapper.readTree(json);\n JsonNode wrapped = tree.get(\"hasSubTypes\");\n\n if (!wrapped.has(\"one\")) {\n throw new IllegalStateException(\"Missing 'one', source: \"+json);\n }\n }\n } \n #location 26 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n void runOnce(int round, int max) throws Exception {\n final ObjectMapper mapper = getObjectMapper();\n Callable writeJson = new Callable() {\n @Override\n public String call() throws Exception {\n Wrapper wrapper = new Wrapper(new TypeOne(\"test\"));\n return mapper.writeValueAsString(wrapper);\n }\n };\n\n int numThreads = 4;\n ExecutorService executor = Executors.newFixedThreadPool(numThreads);\n List> jsonFutures = new ArrayList>();\n for (int i = 0; i < numThreads; i++) {\n jsonFutures.add(executor.submit(writeJson));\n }\n\n executor.shutdown();\n executor.awaitTermination(5, TimeUnit.SECONDS);\n\n for (Future jsonFuture : jsonFutures) {\n String json = jsonFuture.get();\n JsonNode tree = mapper.readTree(json);\n JsonNode wrapped = tree.get(\"hasSubTypes\");\n\n if (!wrapped.has(\"one\")) {\nSystem.out.println(\"JSON wrong: \"+json);\n throw new IllegalStateException(\"Round #\"+round+\"/\"+max+\" ; missing property 'one', source: \"+json);\n }\nSystem.out.println(\"JSON fine: \"+json);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testDeepPrefixedUnwrappingDeserialize() throws Exception\n {\n DeepPrefixUnwrap bean = mapper.readValue(\"{\\\"u.name\\\":\\\"Bubba\\\",\\\"u._x\\\":2,\\\"u._y\\\":3}\",\n DeepPrefixUnwrap.class);\n assertNotNull(bean.unwrapped);\n assertNotNull(bean.unwrapped.location);\n assertEquals(2, bean.unwrapped.location.x);\n assertEquals(3, bean.unwrapped.location.y);\n assertEquals(\"Bubba\", bean.unwrapped.name);\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testDeepPrefixedUnwrappingDeserialize() throws Exception\n {\n DeepPrefixUnwrap bean = MAPPER.readValue(\"{\\\"u.name\\\":\\\"Bubba\\\",\\\"u._x\\\":2,\\\"u._y\\\":3}\",\n DeepPrefixUnwrap.class);\n assertNotNull(bean.unwrapped);\n assertNotNull(bean.unwrapped.location);\n assertEquals(2, bean.unwrapped.location.x);\n assertEquals(3, bean.unwrapped.location.y);\n assertEquals(\"Bubba\", bean.unwrapped.name);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testHierarchicConfigRoundTrip() throws Exception\n {\n ConfigAlternate input = new ConfigAlternate(123, \"Joe\", 42);\n String json = mapper.writeValueAsString(input);\n\n ConfigAlternate root = mapper.readValue(json, ConfigAlternate.class);\n assertEquals(123, root.id);\n assertNotNull(root.general);\n assertNotNull(root.general.names);\n assertNotNull(root.misc);\n assertEquals(\"Joe\", root.general.names.name);\n assertEquals(42, root.misc.value);\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testHierarchicConfigRoundTrip() throws Exception\n {\n ConfigAlternate input = new ConfigAlternate(123, \"Joe\", 42);\n String json = MAPPER.writeValueAsString(input);\n\n ConfigAlternate root = MAPPER.readValue(json, ConfigAlternate.class);\n assertEquals(123, root.id);\n assertNotNull(root.general);\n assertNotNull(root.general.names);\n assertNotNull(root.misc);\n assertEquals(\"Joe\", root.general.names.name);\n assertEquals(42, root.misc.value);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testBytestoCharArray() throws Exception\n {\n byte[] input = new byte[] { 1, 2, 3, 4, 5, 6, 7 };\n // first, do baseline encoding\n char[] expEncoded = mapper.convertValue(input, String.class).toCharArray();\n // then compare\n char[] actEncoded = mapper.convertValue(input, char[].class);\n assertArrayEquals(expEncoded, actEncoded);\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testBytestoCharArray() throws Exception\n {\n byte[] input = new byte[] { 1, 2, 3, 4, 5, 6, 7 };\n // first, do baseline encoding\n char[] expEncoded = MAPPER.convertValue(input, String.class).toCharArray();\n // then compare\n char[] actEncoded = MAPPER.convertValue(input, char[].class);\n assertArrayEquals(expEncoded, actEncoded);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testSimpleMapImitation() throws Exception\n {\n MapImitator mapHolder = MAPPER.readValue\n (\"{ \\\"a\\\" : 3, \\\"b\\\" : true }\", MapImitator.class);\n Map result = mapHolder._map;\n assertEquals(2, result.size());\n assertEquals(Integer.valueOf(3), result.get(\"a\"));\n assertEquals(Boolean.TRUE, result.get(\"b\"));\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testSimpleMapImitation() throws Exception\n {\n MapImitator mapHolder = MAPPER.readValue\n (\"{ \\\"a\\\" : 3, \\\"b\\\" : true, \\\"c\\\":[1,2,3] }\", MapImitator.class);\n Map result = mapHolder._map;\n assertEquals(3, result.size());\n assertEquals(Integer.valueOf(3), result.get(\"a\"));\n assertEquals(Boolean.TRUE, result.get(\"b\"));\n Object ob = result.get(\"c\");\n assertTrue(ob instanceof List);\n List l = (List)ob;\n assertEquals(3, l.size());\n assertEquals(Integer.valueOf(3), l.get(2));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testHierarchicConfigDeserialize() throws Exception\n {\n ConfigRoot root = mapper.readValue(\"{\\\"general.names.name\\\":\\\"Bob\\\",\\\"misc.value\\\":3}\",\n ConfigRoot.class);\n assertNotNull(root.general);\n assertNotNull(root.general.names);\n assertNotNull(root.misc);\n assertEquals(3, root.misc.value);\n assertEquals(\"Bob\", root.general.names.name);\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testHierarchicConfigDeserialize() throws Exception\n {\n ConfigRoot root = MAPPER.readValue(\"{\\\"general.names.name\\\":\\\"Bob\\\",\\\"misc.value\\\":3}\",\n ConfigRoot.class);\n assertNotNull(root.general);\n assertNotNull(root.general.names);\n assertNotNull(root.misc);\n assertEquals(3, root.misc.value);\n assertEquals(\"Bob\", root.general.names.name);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAtomicReference() throws Exception\n {\n ObjectMapper mapper = new ObjectMapper();\n AtomicReference value = mapper.readValue(\"[1,2]\",\n new com.fasterxml.jackson.core.type.TypeReference>() { });\n Object ob = value.get();\n assertNotNull(ob);\n assertEquals(long[].class, ob.getClass());\n long[] longs = (long[]) ob;\n assertNotNull(longs);\n assertEquals(2, longs.length);\n assertEquals(1, longs[0]);\n assertEquals(2, longs[1]);\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testAtomicReference() throws Exception\n {\n AtomicReference value = MAPPER.readValue(\"[1,2]\",\n new com.fasterxml.jackson.core.type.TypeReference>() { });\n Object ob = value.get();\n assertNotNull(ob);\n assertEquals(long[].class, ob.getClass());\n long[] longs = (long[]) ob;\n assertNotNull(longs);\n assertEquals(2, longs.length);\n assertEquals(1, longs[0]);\n assertEquals(2, longs[1]);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MappingIterator readValues(File src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(\n _dataFormatReaders.findFormat(_inputStream(src)), false);\n }\n return _bindAndReadValues(considerFilter(_parserFactory.createParser(src)));\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public MappingIterator readValues(File src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(\n _dataFormatReaders.findFormat(_inputStream(src)), false);\n }\n return _bindAndReadValues(_considerFilter(_parserFactory.createParser(src)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testRootBeans() throws Exception\n {\n final String JSON = aposToQuotes(\"{'a':3} {'b':5}\");\n MappingIterator it = MAPPER.readerFor(Bean.class).readValues(JSON);\n // First one should be fine\n assertTrue(it.hasNextValue());\n Bean bean = it.nextValue();\n assertEquals(3, bean.a);\n // but second one not\n try {\n bean = it.nextValue();\n fail(\"Should not have succeeded\");\n } catch (JsonMappingException e) {\n verifyException(e, \"Unrecognized field\");\n }\n // 24-Mar-2015, tatu: With 2.5, best we can do is to avoid infinite loop;\n // also, since the next token is END_OBJECT, will produce empty Object\n assertTrue(it.hasNextValue());\n bean = it.nextValue();\n assertEquals(0, bean.a);\n // and we should be done now\n assertFalse(it.hasNextValue());\n it.close();\n } \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testRootBeans() throws Exception\n {\n final String JSON = aposToQuotes(\"{'a':3} {'x':5}\");\n MappingIterator it = MAPPER.readerFor(Bean.class).readValues(JSON);\n // First one should be fine\n assertTrue(it.hasNextValue());\n Bean bean = it.nextValue();\n assertEquals(3, bean.a);\n // but second one not\n try {\n bean = it.nextValue();\n fail(\"Should not have succeeded\");\n } catch (JsonMappingException e) {\n verifyException(e, \"Unrecognized field \\\"x\\\"\");\n }\n // 21-May-2015, tatu: With [databind#734], recovery, we now know there's no more data!\n assertFalse(it.hasNextValue());\n\n it.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @SuppressWarnings(\"resource\")\n public MappingIterator readValues(Reader src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n _reportUndetectableSource(src);\n }\n JsonParser p = considerFilter(_parserFactory.createParser(src));\n _initForMultiRead(p);\n p.nextToken();\n DeserializationContext ctxt = createDeserializationContext(p);\n return _newIterator(p, ctxt, _findRootDeserializer(ctxt), true);\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @SuppressWarnings(\"resource\")\n public MappingIterator readValues(Reader src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n _reportUndetectableSource(src);\n }\n JsonParser p = _considerFilter(_parserFactory.createParser(src));\n _initForMultiRead(p);\n p.nextToken();\n DeserializationContext ctxt = createDeserializationContext(p);\n return _newIterator(p, ctxt, _findRootDeserializer(ctxt), true);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAtomicBoolean() throws Exception\n {\n ObjectMapper mapper = new ObjectMapper();\n AtomicBoolean b = mapper.readValue(\"true\", AtomicBoolean.class);\n assertTrue(b.get());\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testAtomicBoolean() throws Exception\n {\n AtomicBoolean b = MAPPER.readValue(\"true\", AtomicBoolean.class);\n assertTrue(b.get());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public PropertyMetadata getMetadata() {\n final Boolean b = _findRequired();\n final String desc = _findDescription();\n final Integer idx = _findIndex();\n final String def = _findDefaultValue();\n if (b == null && idx == null && def == null) {\n return (desc == null) ? PropertyMetadata.STD_REQUIRED_OR_OPTIONAL\n : PropertyMetadata.STD_REQUIRED_OR_OPTIONAL.withDescription(desc);\n }\n return PropertyMetadata.construct(b.booleanValue(), desc, idx, def);\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public PropertyMetadata getMetadata() {\n final Boolean b = _findRequired();\n final String desc = _findDescription();\n final Integer idx = _findIndex();\n final String def = _findDefaultValue();\n if (b == null && idx == null && def == null) {\n return (desc == null) ? PropertyMetadata.STD_REQUIRED_OR_OPTIONAL\n : PropertyMetadata.STD_REQUIRED_OR_OPTIONAL.withDescription(desc);\n }\n return PropertyMetadata.construct(b, desc, idx, def);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public String idFromValue(Object value)\n {\n Class cls = _typeFactory.constructType(value.getClass()).getRawClass();\n final String key = cls.getName();\n String name;\n synchronized (_typeToId) {\n name = _typeToId.get(key);\n if (name == null) {\n // 24-Feb-2011, tatu: As per [JACKSON-498], may need to dynamically look up name\n // can either throw an exception, or use default name...\n if (_config.isAnnotationProcessingEnabled()) {\n BeanDescription beanDesc = _config.introspectClassAnnotations(cls);\n name = _config.getAnnotationIntrospector().findTypeName(beanDesc.getClassInfo());\n }\n if (name == null) {\n // And if still not found, let's choose default?\n name = _defaultTypeId(cls);\n }\n _typeToId.put(key, name);\n }\n }\n return name;\n } \n #location 4 \n #vulnerability type THREAD_SAFETY_VIOLATION", "output": "#fixed code\n @Override\n public String idFromValue(Object value)\n {\n return idFromClass(value.getClass());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MappingIterator readValues(byte[] src, int offset, int length)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(_dataFormatReaders.findFormat(src, offset, length), false);\n }\n return _bindAndReadValues(considerFilter(_parserFactory.createParser(src)));\n } \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public MappingIterator readValues(byte[] src, int offset, int length)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(_dataFormatReaders.findFormat(src, offset, length), false);\n }\n return _bindAndReadValues(_considerFilter(_parserFactory.createParser(src)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAtomicLong() throws Exception\n {\n ObjectMapper mapper = new ObjectMapper();\n AtomicLong value = mapper.readValue(\"12345678901\", AtomicLong.class);\n assertEquals(12345678901L, value.get());\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testAtomicLong() throws Exception\n {\n AtomicLong value = MAPPER.readValue(\"12345678901\", AtomicLong.class);\n assertEquals(12345678901L, value.get());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testMapUnwrapDeserialize() throws Exception\n {\n MapUnwrap root = mapper.readValue(\"{\\\"map.test\\\": 6}\", MapUnwrap.class);\n\n assertEquals(1, root.map.size());\n assertEquals(6, ((Number)root.map.get(\"test\")).intValue());\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testMapUnwrapDeserialize() throws Exception\n {\n MapUnwrap root = MAPPER.readValue(\"{\\\"map.test\\\": 6}\", MapUnwrap.class);\n\n assertEquals(1, root.map.size());\n assertEquals(6, ((Number)root.map.get(\"test\")).intValue());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void withTree749() throws Exception\n {\n Map inputMap = new LinkedHashMap();\n Map> replacements = new LinkedHashMap>();\n Map reps = new LinkedHashMap();\n reps.put(\"1\", \"one\");\n replacements.put(TestEnum.GREEN, reps);\n inputMap.put(KeyEnum.replacements, replacements);\n ObjectMapper mapper = TestEnumModule.setupObjectMapper(new ObjectMapper());\n JsonNode tree = mapper.valueToTree(inputMap);\n ObjectNode ob = (ObjectNode) tree;\n JsonNode inner = ob.get(\"replacements\");\n String firstFieldName = inner.fieldNames().next();\n assertEquals(\"green\", firstFieldName);\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void withTree749() throws Exception\n {\n ObjectMapper mapper = new ObjectMapper().registerModule(new TestEnumModule());\n\n Map inputMap = new LinkedHashMap();\n Map> replacements = new LinkedHashMap>();\n Map reps = new LinkedHashMap();\n reps.put(\"1\", \"one\");\n replacements.put(TestEnum.GREEN, reps);\n inputMap.put(KeyEnum.replacements, replacements);\n\n JsonNode tree = mapper.valueToTree(inputMap);\n ObjectNode ob = (ObjectNode) tree;\n\n JsonNode inner = ob.get(\"replacements\");\n String firstFieldName = inner.fieldNames().next();\n assertEquals(\"green\", firstFieldName);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MappingIterator readValues(InputStream src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(_dataFormatReaders.findFormat(src), false);\n }\n \n return _bindAndReadValues(considerFilter(_parserFactory.createParser(src)));\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public MappingIterator readValues(InputStream src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(_dataFormatReaders.findFormat(src), false);\n }\n \n return _bindAndReadValues(_considerFilter(_parserFactory.createParser(src)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAtomicInt() throws Exception\n {\n ObjectMapper mapper = new ObjectMapper();\n AtomicInteger value = mapper.readValue(\"13\", AtomicInteger.class);\n assertEquals(13, value.get());\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testAtomicInt() throws Exception\n {\n AtomicInteger value = MAPPER.readValue(\"13\", AtomicInteger.class);\n assertEquals(13, value.get());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public MappingIterator readValues(URL src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(\n _dataFormatReaders.findFormat(_inputStream(src)), true);\n }\n return _bindAndReadValues(considerFilter(_parserFactory.createParser(src)));\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public MappingIterator readValues(URL src)\n throws IOException, JsonProcessingException\n {\n if (_dataFormatReaders != null) {\n return _detectBindAndReadValues(\n _dataFormatReaders.findFormat(_inputStream(src)), true);\n }\n return _bindAndReadValues(_considerFilter(_parserFactory.createParser(src)));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testPrefixedUnwrapping() throws Exception\n {\n PrefixUnwrap bean = mapper.readValue(\"{\\\"name\\\":\\\"Axel\\\",\\\"_x\\\":4,\\\"_y\\\":7}\", PrefixUnwrap.class);\n assertNotNull(bean);\n assertEquals(\"Axel\", bean.name);\n assertNotNull(bean.location);\n assertEquals(4, bean.location.x);\n assertEquals(7, bean.location.y);\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testPrefixedUnwrapping() throws Exception\n {\n PrefixUnwrap bean = MAPPER.readValue(\"{\\\"name\\\":\\\"Axel\\\",\\\"_x\\\":4,\\\"_y\\\":7}\", PrefixUnwrap.class);\n assertNotNull(bean);\n assertEquals(\"Axel\", bean.name);\n assertNotNull(bean.location);\n assertEquals(4, bean.location.x);\n assertEquals(7, bean.location.y);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected SiteMap processText(String sitemapUrl, byte[] content) throws IOException {\n LOG.debug(\"Processing textual Sitemap\");\n\n SiteMap textSiteMap = new SiteMap(sitemapUrl);\n textSiteMap.setType(SitemapType.TEXT);\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(content));\n @SuppressWarnings(\"resource\")\n BufferedReader reader = new BufferedReader(new InputStreamReader(bomIs, \"UTF-8\"));\n\n String line;\n int i = 1;\n while ((line = reader.readLine()) != null) {\n if (line.length() > 0 && i <= MAX_URLS) {\n addUrlIntoSitemap(line, textSiteMap, null, null, null, i++);\n }\n }\n textSiteMap.setProcessed(true);\n\n return textSiteMap;\n } \n #location 20 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected SiteMap processText(String sitemapUrl, byte[] content) throws IOException {\n LOG.debug(\"Processing textual Sitemap\");\n\n SiteMap textSiteMap = new SiteMap(sitemapUrl);\n textSiteMap.setType(SitemapType.TEXT);\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(content));\n @SuppressWarnings(\"resource\")\n BufferedReader reader = new BufferedReader(new InputStreamReader(bomIs, UTF_8));\n\n String line;\n int i = 1;\n while ((line = reader.readLine()) != null) {\n if (line.length() > 0 && i <= MAX_URLS) {\n addUrlIntoSitemap(line, textSiteMap, null, null, null, i++);\n }\n }\n textSiteMap.setProcessed(true);\n\n return textSiteMap;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private AbstractSiteMap processXml(URL sitemapUrl, byte[] xmlContent) throws UnknownFormatException {\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(xmlContent));\n InputSource is = new InputSource();\n is.setCharacterStream(new BufferedReader(new InputStreamReader(bomIs)));\n return processXml(sitemapUrl, is);\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private AbstractSiteMap processXml(URL sitemapUrl, byte[] xmlContent) throws UnknownFormatException {\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(xmlContent));\n InputSource is = new InputSource();\n try {\n is.setCharacterStream(new BufferedReader(new InputStreamReader(bomIs, \"UTF-8\")));\n } catch (UnsupportedEncodingException e) {\n IOUtils.closeQuietly(bomIs);\n throw new RuntimeException(\"Impossible exception\", e);\n }\n \n return processXml(sitemapUrl, is);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testVideosSitemap() throws UnknownFormatException, IOException {\n SiteMapParser parser = new SiteMapParser();\n parser.enableExtension(Extension.VIDEO);\n\n String contentType = \"text/xml\";\n byte[] content = SiteMapParserTest.getResourceAsBytes(\"src/test/resources/sitemaps/extension/sitemap-videos.xml\");\n\n URL url = new URL(\"http://www.example.com/sitemap-video.xml\");\n AbstractSiteMap asm = parser.parseSiteMap(contentType, content, url);\n assertEquals(false, asm.isIndex());\n assertEquals(true, asm instanceof SiteMap);\n SiteMap sm = (SiteMap) asm;\n assertEquals(1, sm.getSiteMapUrls().size());\n VideoAttributes expectedVideoAttributes = new VideoAttributes(new URL(\"http://www.example.com/thumbs/123.jpg\"), \"Grilling steaks for summer\",\n \"Alkis shows you how to get perfectly done steaks every time\", new URL(\"http://www.example.com/video123.flv\"), new URL(\"http://www.example.com/videoplayer.swf?video=123\"));\n expectedVideoAttributes.setDuration(600);\n ZonedDateTime dt = ZonedDateTime.parse(\"2009-11-05T19:20:30+08:00\");\n expectedVideoAttributes.setExpirationDate(dt);\n dt = ZonedDateTime.parse(\"2007-11-05T19:20:30+08:00\");\n expectedVideoAttributes.setPublicationDate(dt);\n expectedVideoAttributes.setRating(4.2f);\n expectedVideoAttributes.setViewCount(12345);\n expectedVideoAttributes.setFamilyFriendly(true);\n expectedVideoAttributes.setTags(new String[] { \"sample_tag1\", \"sample_tag2\" });\n expectedVideoAttributes.setAllowedCountries(new String[] { \"IE\", \"GB\", \"US\", \"CA\" });\n expectedVideoAttributes.setGalleryLoc(new URL(\"http://cooking.example.com\"));\n expectedVideoAttributes.setGalleryTitle(\"Cooking Videos\");\n expectedVideoAttributes.setPrices(new VideoAttributes.VideoPrice[] { new VideoAttributes.VideoPrice(\"EUR\", 1.99f, VideoAttributes.VideoPriceType.own) });\n expectedVideoAttributes.setRequiresSubscription(true);\n expectedVideoAttributes.setUploader(\"GrillyMcGrillerson\");\n expectedVideoAttributes.setUploaderInfo(new URL(\"http://www.example.com/users/grillymcgrillerson\"));\n expectedVideoAttributes.setLive(false);\n\n for (SiteMapURL su : sm.getSiteMapUrls()) {\n assertNotNull(su.getAttributesForExtension(Extension.VIDEO));\n VideoAttributes attr = (VideoAttributes) su.getAttributesForExtension(Extension.VIDEO)[0];\n assertEquals(expectedVideoAttributes, attr);\n }\n } \n #location 37 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testVideosSitemap() throws UnknownFormatException, IOException {\n SiteMapParser parser = new SiteMapParser();\n parser.enableExtension(Extension.VIDEO);\n\n String contentType = \"text/xml\";\n byte[] content = SiteMapParserTest.getResourceAsBytes(\"src/test/resources/sitemaps/extension/sitemap-videos.xml\");\n\n URL url = new URL(\"http://www.example.com/sitemap-video.xml\");\n AbstractSiteMap asm = parser.parseSiteMap(contentType, content, url);\n assertEquals(false, asm.isIndex());\n assertEquals(true, asm instanceof SiteMap);\n SiteMap sm = (SiteMap) asm;\n assertEquals(2, sm.getSiteMapUrls().size());\n Iterator siter = sm.getSiteMapUrls().iterator();\n\n // first element: nearly all video attributes\n VideoAttributes expectedVideoAttributes = new VideoAttributes(new URL(\"http://www.example.com/thumbs/123.jpg\"), \"Grilling steaks for summer\",\n \"Alkis shows you how to get perfectly done steaks every time\", new URL(\"http://www.example.com/video123.flv\"), new URL(\"http://www.example.com/videoplayer.swf?video=123\"));\n expectedVideoAttributes.setDuration(600);\n ZonedDateTime dt = ZonedDateTime.parse(\"2009-11-05T19:20:30+08:00\");\n expectedVideoAttributes.setExpirationDate(dt);\n dt = ZonedDateTime.parse(\"2007-11-05T19:20:30+08:00\");\n expectedVideoAttributes.setPublicationDate(dt);\n expectedVideoAttributes.setRating(4.2f);\n expectedVideoAttributes.setViewCount(12345);\n expectedVideoAttributes.setFamilyFriendly(true);\n expectedVideoAttributes.setTags(new String[] { \"sample_tag1\", \"sample_tag2\" });\n expectedVideoAttributes.setAllowedCountries(new String[] { \"IE\", \"GB\", \"US\", \"CA\" });\n expectedVideoAttributes.setGalleryLoc(new URL(\"http://cooking.example.com\"));\n expectedVideoAttributes.setGalleryTitle(\"Cooking Videos\");\n expectedVideoAttributes.setPrices(new VideoAttributes.VideoPrice[] { new VideoAttributes.VideoPrice(\"EUR\", 1.99f, VideoAttributes.VideoPriceType.own) });\n expectedVideoAttributes.setRequiresSubscription(true);\n expectedVideoAttributes.setUploader(\"GrillyMcGrillerson\");\n expectedVideoAttributes.setUploaderInfo(new URL(\"http://www.example.com/users/grillymcgrillerson\"));\n expectedVideoAttributes.setLive(false);\n VideoAttributes attr = (VideoAttributes) siter.next().getAttributesForExtension(Extension.VIDEO)[0];\n assertNotNull(attr);\n assertEquals(expectedVideoAttributes, attr);\n\n // locale-specific number format in , test #220\n expectedVideoAttributes = new VideoAttributes(new URL(\"http://www.example.com/thumbs/123-2.jpg\"), \"Grilling steaks for summer, episode 2\",\n \"Alkis shows you how to get perfectly done steaks every time\", new URL(\"http://www.example.com/video123-2.flv\"), null);\n expectedVideoAttributes.setPrices(new VideoAttributes.VideoPrice[] { new VideoAttributes.VideoPrice(\"EUR\", null, VideoAttributes.VideoPriceType.own) });\n attr = (VideoAttributes) siter.next().getAttributesForExtension(Extension.VIDEO)[0];\n assertNotNull(attr);\n assertEquals(expectedVideoAttributes, attr);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected AbstractSiteMap processXml(URL sitemapUrl, byte[] xmlContent) throws UnknownFormatException {\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(xmlContent));\n InputSource is = new InputSource();\n try {\n is.setCharacterStream(new BufferedReader(new InputStreamReader(bomIs, \"UTF-8\")));\n } catch (UnsupportedEncodingException e) {\n IOUtils.closeQuietly(bomIs);\n throw new RuntimeException(\"Impossible exception\", e);\n }\n\n return processXml(sitemapUrl, is);\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected AbstractSiteMap processXml(URL sitemapUrl, byte[] xmlContent) throws UnknownFormatException {\n\n BOMInputStream bomIs = new BOMInputStream(new ByteArrayInputStream(xmlContent));\n InputSource is = new InputSource();\n is.setCharacterStream(new BufferedReader(new InputStreamReader(bomIs, UTF_8)));\n\n return processXml(sitemapUrl, is);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public boolean validate(UserPersonalInfo info) {\n\t\t\n\t\tvalidator.validate(info);\n\t\t\n\t\tif(validator.hasErrors()){\n\t\t\treturn false;\n\t\t}\n\t\t\n\t\tif (info.getUser() == null) {\n\t\t validator.add(new ValidationMessage(\"user.errors.wrong\", \"error\"));\n\t\t}\n\t\t\n\t\tif(!info.getUser().getEmail().equals(info.getEmail())){\n\t\t\temailValidator.validate(info.getEmail());\n\t\t}\n\t\t\n\t\tif(info.getBirthDate().getYear() > DateTime.now().getYear()-12){\n\t\t\tvalidator.add(new ValidationMessage(\"user.errors.invalid_birth_date.min_age\", \"error\"));\n\t\t}\n\t\t\n\t\tif(!info.getUser().getName().equals(info.getName())){\n\t\t\tDateTime nameLastTouchedAt = info.getUser().getNameLastTouchedAt();\n\t\t\tif(nameLastTouchedAt.isAfter(new DateTime().minusDays(30))){\n\t\t\t\tvalidator.add(new ValidationMessage(\"user.errors.name.min_time\", \"error\", nameLastTouchedAt.plusDays(30).toString()));\n\t\t\t}\n\t\t}\n\t\t\n\t\treturn !validator.hasErrors();\n\t} \n #location 13 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public boolean validate(UserPersonalInfo info) {\n\t\t\n\t\tvalidator.validate(info);\n\t\t\n\t\tif(validator.hasErrors()){\n\t\t\treturn false;\n\t\t}\n\t\t\n\t\tif (info.getUser() == null) {\n\t\t validator.add(new ValidationMessage(\"user.errors.wrong\", \"error\"));\n\t\t}\n\t\t\n\t\tif (!info.getUser().getEmail().equals(info.getEmail())){\n\t\t\temailValidator.validate(info.getEmail());\n\t\t}\n\t\t\n\t\tif (info.getBirthDate() != null && info.getBirthDate().getYear() > DateTime.now().getYear()-12){\n\t\t\tvalidator.add(new ValidationMessage(\"user.errors.invalid_birth_date.min_age\", \"error\"));\n\t\t}\n\t\n\t\tif(!info.getUser().getName().equals(info.getName())){\n\t\t\tDateTime nameLastTouchedAt = info.getUser().getNameLastTouchedAt();\n\t\t\tif(nameLastTouchedAt.isAfter(new DateTime().minusDays(30))){\n\t\t\t\tvalidator.add(new ValidationMessage(\"user.errors.name.min_time\", \"error\", nameLastTouchedAt.plusDays(30).toString()));\n\t\t\t}\n\t\t}\n\t\t\n\t\treturn !validator.hasErrors();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void moderator_should_approve_question_information() throws Exception {\n Question question = question(\"question title\", \"question description\", author);\n Information approvedInfo = new QuestionInformation(\"edited title\", \"edited desc\", \n new LoggedUser(otherUser, null), new ArrayList(), \"comment\");\n \n moderator.approve(question, approvedInfo);\n \n assertEquals(approvedInfo, question.getInformation());\n assertTrue(question.getInformation().isModerated());\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void moderator_should_approve_question_information() throws Exception {\n Information approvedInfo = new QuestionInformation(\"edited title\", \"edited desc\", \n new LoggedUser(otherUser, null), new ArrayList(), \"comment\");\n \n moderator.approve(myQuestion, approvedInfo);\n \n assertEquals(approvedInfo, myQuestion.getInformation());\n assertTrue(myQuestion.getInformation().isModerated());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public boolean validate(UserPersonalInfo info) {\n\t\t\n\t\tvalidator.validate(info);\n\t\t\n\t\tif (info.getUser() == null) {\n\t\t validator.add(new ValidationMessage(\"error\",\"user.errors.wrong\"));\n\t\t}\n\t\t\n\t\tif(!info.getUser().getName().equals(info.getName())){\n\t\t\tuserNameValidator.validate(info.getName());\n\t\t}\n\t\t\n\t\tif (!info.getUser().getEmail().equals(info.getEmail())){\n\t\t\temailValidator.validate(info.getEmail());\n\t\t}\n\t\t\n\t\treturn !validator.hasErrors();\n\t} \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public boolean validate(UserPersonalInfo info) {\n\t\t\n\t\tvalidator.validate(info);\n\t\t\n\t\tif (info.getUser() == null) {\n\t\t validator.add(new ValidationMessage(\"user.errors.wrong\", \"error\"));\n\t\t}\n\t\t\n\t\tif(!info.getUser().getName().equals(info.getName())){\n\t\t\tuserNameValidator.validate(info.getName());\n\t\t}\n\t\t\n\t\tif(!info.getUser().getEmail().equals(info.getEmail())){\n\t\t\temailValidator.validate(info.getEmail());\n\t\t}\n\t\t\n\t\tif(info.getUser().getNameLastTouchedAt() != null){\n\t\t\tif(info.getUser().getNameLastTouchedAt().isAfter(new DateTime().minusDays(30))){\n\t\t\t\tvalidator.add(new ValidationMessage(\"user.errors.name.min_time\", \"error\"));\n\t\t\t}\n\t\t}\n\t\t\n\t\treturn !validator.hasErrors();\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAlternateDefaultEncoding(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String alternateEnc)\n throws Exception {\n try {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n XmlReader.setDefaultEncoding(alternateEnc);\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n final String enc;\n if (alternateEnc != null) {\n enc = alternateEnc;\n } else {\n enc = streamEnc;\n }\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } finally {\n XmlReader.setDefaultEncoding(null);\n }\n } \n #location 22 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testAlternateDefaultEncoding(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String alternateEnc)\n throws Exception {\n XmlReader xmlReader = null;\n try {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n XmlReader.setDefaultEncoding(alternateEnc);\n xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } finally {\n XmlReader.setDefaultEncoding(null);\n if (xmlReader != null) {\n xmlReader.close();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomValid(final String encoding) throws Exception {\n InputStream is = getXmlStream(\"no-bom\", XML1, encoding, encoding);\n XmlReader xmlReader = new XmlReader(is, false);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML2, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML4, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML5, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomValid(final String encoding) throws Exception {\n checkEncoding(XML1, encoding, \"UTF-8\");\n checkEncoding(XML2, encoding, \"UTF-8\");\n checkEncoding(XML3, encoding, encoding);\n checkEncoding(XML4, encoding, encoding);\n checkEncoding(XML5, encoding, encoding);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomValid(final String encoding) throws Exception {\n InputStream is = getXmlStream(\"no-bom\", XML1, encoding, encoding);\n XmlReader xmlReader = new XmlReader(is, false);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML2, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML4, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML5, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomValid(final String encoding) throws Exception {\n checkEncoding(XML1, encoding, \"UTF-8\");\n checkEncoding(XML2, encoding, \"UTF-8\");\n checkEncoding(XML3, encoding, encoding);\n checkEncoding(XML4, encoding, encoding);\n checkEncoding(XML5, encoding, encoding);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static Date parseUsingMask(final String[] masks, String sDate) {\n sDate = sDate != null ? sDate.trim() : null;\n ParsePosition pp = null;\n Date d = null;\n for (int i = 0; d == null && i < masks.length; i++) {\n final DateFormat df = new SimpleDateFormat(masks[i], Locale.US);\n // df.setLenient(false);\n df.setLenient(true);\n try {\n pp = new ParsePosition(0);\n d = df.parse(sDate, pp);\n if (pp.getIndex() != sDate.length()) {\n d = null;\n }\n // System.out.println(\"pp[\"+pp.getIndex()+\"] s[\"+sDate+\" m[\"+masks[i]+\"] d[\"+d+\"]\");\n } catch (final Exception ex1) {\n // System.out.println(\"s: \"+sDate+\" m: \"+masks[i]+\" d: \"+null);\n }\n }\n return d;\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private static Date parseUsingMask(final String[] masks, String sDate) {\n if (sDate != null) {\n sDate = sDate.trim();\n }\n ParsePosition pp = null;\n Date d = null;\n for (int i = 0; d == null && i < masks.length; i++) {\n final DateFormat df = new SimpleDateFormat(masks[i], Locale.US);\n // df.setLenient(false);\n df.setLenient(true);\n try {\n pp = new ParsePosition(0);\n d = df.parse(sDate, pp);\n if (pp.getIndex() != sDate.length()) {\n d = null;\n }\n // System.out.println(\"pp[\"+pp.getIndex()+\"] s[\"+sDate+\" m[\"+masks[i]+\"] d[\"+d+\"]\");\n } catch (final Exception ex1) {\n // System.out.println(\"s: \"+sDate+\" m: \"+masks[i]+\" d: \"+null);\n }\n }\n return d;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testAlternateDefaultEncoding(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String alternateEnc)\n throws Exception {\n try {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n XmlReader.setDefaultEncoding(alternateEnc);\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n final String enc;\n if (alternateEnc != null) {\n enc = alternateEnc;\n } else {\n enc = streamEnc;\n }\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } finally {\n XmlReader.setDefaultEncoding(null);\n }\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testAlternateDefaultEncoding(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String alternateEnc)\n throws Exception {\n XmlReader xmlReader = null;\n try {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n XmlReader.setDefaultEncoding(alternateEnc);\n xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } finally {\n XmlReader.setDefaultEncoding(null);\n if (xmlReader != null) {\n xmlReader.close();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomValid(final String encoding) throws Exception {\n InputStream is = getXmlStream(\"no-bom\", XML1, encoding, encoding);\n XmlReader xmlReader = new XmlReader(is, false);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML2, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML4, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML5, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomValid(final String encoding) throws Exception {\n checkEncoding(XML1, encoding, \"UTF-8\");\n checkEncoding(XML2, encoding, \"UTF-8\");\n checkEncoding(XML3, encoding, encoding);\n checkEncoding(XML4, encoding, encoding);\n checkEncoding(XML5, encoding, encoding);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawBomInvalid(final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n try {\n final XmlReader xmlReader = new XmlReader(is, false);\n fail(\"It should have failed for BOM \" + bomEnc + \", streamEnc \" + streamEnc + \" and prologEnc \" + prologEnc);\n } catch (final IOException ex) {\n assertTrue(ex.getMessage().indexOf(\"Invalid encoding,\") > -1);\n }\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawBomInvalid(final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n try {\n final XmlReader xmlReader = new XmlReader(is, false);\n fail(\"It should have failed for BOM \" + bomEnc + \", streamEnc \" + streamEnc + \" and prologEnc \" + prologEnc);\n xmlReader.close();\n } catch (final IOException ex) {\n assertTrue(ex.getMessage().indexOf(\"Invalid encoding,\") > -1);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public SyndFeedInfo remove(final URL url) {\n SyndFeedInfo info = null;\n final String fileName = cachePath + File.separator + \"feed_\" + replaceNonAlphanumeric(url.toString(), '_').trim();\n FileInputStream fis;\n try {\n fis = new FileInputStream(fileName);\n final ObjectInputStream ois = new ObjectInputStream(fis);\n info = (SyndFeedInfo) ois.readObject();\n fis.close();\n\n final File file = new File(fileName);\n if (file.exists()) {\n file.delete();\n }\n } catch (final FileNotFoundException fnfe) {\n // That's OK, we'l return null\n } catch (final ClassNotFoundException cnfe) {\n // Error writing to cahce is fatal\n throw new RuntimeException(\"Attempting to read from cache\", cnfe);\n } catch (final IOException fnfe) {\n // Error writing to cahce is fatal\n throw new RuntimeException(\"Attempting to read from cache\", fnfe);\n }\n return info;\n } \n #location 16 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n public SyndFeedInfo remove(final URL url) {\n SyndFeedInfo info = null;\n final String fileName = cachePath + File.separator + \"feed_\" + replaceNonAlphanumeric(url.toString(), '_').trim();\n FileInputStream fis = null;\n ObjectInputStream ois = null;\n try {\n fis = new FileInputStream(fileName);\n ois = new ObjectInputStream(fis);\n info = (SyndFeedInfo) ois.readObject();\n\n final File file = new File(fileName);\n if (file.exists()) {\n file.delete();\n }\n } catch (final FileNotFoundException fnfe) {\n // That's OK, we'l return null\n } catch (final ClassNotFoundException cnfe) {\n // Error writing to cahce is fatal\n throw new RuntimeException(\"Attempting to read from cache\", cnfe);\n } catch (final IOException fnfe) {\n // Error writing to cahce is fatal\n throw new RuntimeException(\"Attempting to read from cache\", fnfe);\n } finally {\n if (fis != null) {\n try {\n fis.close();\n } catch (final IOException e) {\n }\n }\n if (ois != null) {\n try {\n ois.close();\n } catch (final IOException e) {\n }\n }\n }\n return info;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testHttpValid(final String cT, final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testHttpValid(final String cT, final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testEncodingAttributeXML() throws Exception {\n final InputStream is = new ByteArrayInputStream(ENCODING_ATTRIBUTE_XML.getBytes());\n final XmlReader xmlReader = new XmlReader(is, \"\", true);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testEncodingAttributeXML() throws Exception {\n final InputStream is = new ByteArrayInputStream(ENCODING_ATTRIBUTE_XML.getBytes());\n final XmlReader xmlReader = new XmlReader(is, \"\", true);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomInvalid(final String encoding) throws Exception {\n final InputStream is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n try {\n final XmlReader xmlReader = new XmlReader(is, false);\n fail(\"It should have failed\");\n } catch (final IOException ex) {\n assertTrue(ex.getMessage().indexOf(\"Invalid encoding,\") > -1);\n }\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomInvalid(final String encoding) throws Exception {\n InputStream is = null;\n XmlReader xmlReader = null;\n try {\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is, false);\n fail(\"It should have failed\");\n } catch (final IOException ex) {\n assertTrue(ex.getMessage().indexOf(\"Invalid encoding,\") > -1);\n } finally {\n if (xmlReader != null) {\n xmlReader.close();\n }\n if (is != null) {\n is.close();\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testHttpValid(final String cT, final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n } \n #location 13 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void testHttpValid(final String cT, final String bomEnc, final String streamEnc, final String prologEnc) throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML1, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, false);\n if (!streamEnc.equals(\"UTF-16\")) {\n // we can not assert things here becuase UTF-8, US-ASCII and\n // ISO-8859-1 look alike for the chars used for detection\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, streamEnc.length()), streamEnc);\n }\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public SyndFeedInfo getFeedInfo(final URL url) {\n SyndFeedInfo info = null;\n final String fileName = cachePath + File.separator + \"feed_\" + replaceNonAlphanumeric(url.toString(), '_').trim();\n FileInputStream fis;\n try {\n fis = new FileInputStream(fileName);\n final ObjectInputStream ois = new ObjectInputStream(fis);\n info = (SyndFeedInfo) ois.readObject();\n fis.close();\n } catch (final FileNotFoundException fnfe) {\n // That's OK, we'l return null\n } catch (final ClassNotFoundException cnfe) {\n // Error writing to cache is fatal\n throw new RuntimeException(\"Attempting to read from cache\", cnfe);\n } catch (final IOException fnfe) {\n // Error writing to cache is fatal\n throw new RuntimeException(\"Attempting to read from cache\", fnfe);\n }\n return info;\n } \n #location 11 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Override\n public SyndFeedInfo getFeedInfo(final URL url) {\n SyndFeedInfo info = null;\n final String fileName = cachePath + File.separator + \"feed_\" + replaceNonAlphanumeric(url.toString(), '_').trim();\n FileInputStream fis = null;\n ObjectInputStream ois = null;\n try {\n fis = new FileInputStream(fileName);\n ois = new ObjectInputStream(fis);\n info = (SyndFeedInfo) ois.readObject();\n } catch (final FileNotFoundException e) {\n // That's OK, we'l return null\n } catch (final ClassNotFoundException e) {\n // Error writing to cache is fatal\n throw new RuntimeException(\"Attempting to read from cache\", e);\n } catch (final IOException e) {\n // Error writing to cache is fatal\n throw new RuntimeException(\"Attempting to read from cache\", e);\n } finally {\n if (fis != null) {\n try {\n fis.close();\n } catch (final IOException e) {\n }\n }\n if (ois != null) {\n try {\n ois.close();\n } catch (final IOException e) {\n }\n }\n }\n return info;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawBomValid(final String encoding) throws Exception {\n final InputStream is = getXmlStream(encoding + \"-bom\", XML3, encoding, encoding);\n final XmlReader xmlReader = new XmlReader(is, false);\n if (!encoding.equals(\"UTF-16\")) {\n assertEquals(xmlReader.getEncoding(), encoding);\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, encoding.length()), encoding);\n }\n } \n #location 7 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawBomValid(final String encoding) throws Exception {\n final InputStream is = getXmlStream(encoding + \"-bom\", XML3, encoding, encoding);\n final XmlReader xmlReader = new XmlReader(is, false);\n if (!encoding.equals(\"UTF-16\")) {\n assertEquals(xmlReader.getEncoding(), encoding);\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, encoding.length()), encoding);\n }\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomValid(final String encoding) throws Exception {\n InputStream is = getXmlStream(\"no-bom\", XML1, encoding, encoding);\n XmlReader xmlReader = new XmlReader(is, false);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML2, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML4, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML5, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomValid(final String encoding) throws Exception {\n checkEncoding(XML1, encoding, \"UTF-8\");\n checkEncoding(XML2, encoding, \"UTF-8\");\n checkEncoding(XML3, encoding, encoding);\n checkEncoding(XML4, encoding, encoding);\n checkEncoding(XML5, encoding, encoding);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testParse() {\n final Calendar cal = new GregorianCalendar();\n cal.setTimeZone(TimeZone.getTimeZone(\"GMT\"));\n\n // four-digit year\n String sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // four-digit year\n sDate = \"Tue, 19 Jul 2005 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // RFC822\n sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate));\n\n // RFC822\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate));\n\n final Calendar c = Calendar.getInstance(TimeZone.getTimeZone(\"GMT\"));\n c.set(2000, Calendar.JANUARY, 01, 0, 0, 0);\n final Date expectedDate = c.getTime();\n\n // W3C\n sDate = \"2000-01-01T00:00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01T00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // EXTRA\n sDate = \"18:10 2000/10/10\";\n assertNotNull(DateParser.parseDate(sDate));\n\n // INVALID\n sDate = \"X20:10 2000-10-10\";\n assertNull(DateParser.parseDate(sDate));\n\n } \n #location 67 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testParse() {\n final Calendar cal = new GregorianCalendar();\n cal.setTimeZone(TimeZone.getTimeZone(\"GMT\"));\n\n // four-digit year\n String sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // four-digit year\n sDate = \"Tue, 19 Jul 2005 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // RFC822\n sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n // RFC822\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n final Calendar c = Calendar.getInstance(TimeZone.getTimeZone(\"GMT\"));\n c.set(2000, Calendar.JANUARY, 01, 0, 0, 0);\n final Date expectedDate = c.getTime();\n\n // W3C\n sDate = \"2000-01-01T00:00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01T00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // EXTRA\n sDate = \"18:10 2000/10/10\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n // INVALID\n sDate = \"X20:10 2000-10-10\";\n assertNull(DateParser.parseDate(sDate, Locale.US));\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testHttpLenient(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String shouldbe)\n throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML2, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, true);\n assertEquals(xmlReader.getEncoding(), shouldbe);\n } \n #location 10 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testHttpLenient(final String cT, final String bomEnc, final String streamEnc, final String prologEnc, final String shouldbe)\n throws Exception {\n final InputStream is;\n if (prologEnc == null) {\n is = getXmlStream(bomEnc, XML2, streamEnc, prologEnc);\n } else {\n is = getXmlStream(bomEnc, XML3, streamEnc, prologEnc);\n }\n final XmlReader xmlReader = new XmlReader(is, cT, true);\n assertEquals(xmlReader.getEncoding(), shouldbe);\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawBomValid(final String encoding) throws Exception {\n final InputStream is = getXmlStream(encoding + \"-bom\", XML3, encoding, encoding);\n final XmlReader xmlReader = new XmlReader(is, false);\n if (!encoding.equals(\"UTF-16\")) {\n assertEquals(xmlReader.getEncoding(), encoding);\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, encoding.length()), encoding);\n }\n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawBomValid(final String encoding) throws Exception {\n final InputStream is = getXmlStream(encoding + \"-bom\", XML3, encoding, encoding);\n final XmlReader xmlReader = new XmlReader(is, false);\n if (!encoding.equals(\"UTF-16\")) {\n assertEquals(xmlReader.getEncoding(), encoding);\n } else {\n assertEquals(xmlReader.getEncoding().substring(0, encoding.length()), encoding);\n }\n xmlReader.close();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void testParse() {\n final Calendar cal = new GregorianCalendar();\n cal.setTimeZone(TimeZone.getTimeZone(\"GMT\"));\n\n // four-digit year\n String sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // four-digit year\n sDate = \"Tue, 19 Jul 2005 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // RFC822\n sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate));\n\n // RFC822\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate));\n\n final Calendar c = Calendar.getInstance(TimeZone.getTimeZone(\"GMT\"));\n c.set(2000, Calendar.JANUARY, 01, 0, 0, 0);\n final Date expectedDate = c.getTime();\n\n // W3C\n sDate = \"2000-01-01T00:00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01T00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // W3C\n sDate = \"2000\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate).getTime() / 1000);\n\n // EXTRA\n sDate = \"18:10 2000/10/10\";\n assertNotNull(DateParser.parseDate(sDate));\n\n // INVALID\n sDate = \"X20:10 2000-10-10\";\n assertNull(DateParser.parseDate(sDate));\n\n } \n #location 67 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void testParse() {\n final Calendar cal = new GregorianCalendar();\n cal.setTimeZone(TimeZone.getTimeZone(\"GMT\"));\n\n // four-digit year\n String sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // four-digit year\n sDate = \"Tue, 19 Jul 2005 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // two-digit year\n sDate = \"Tue, 19 Jul 05 23:00:51 UT\";\n cal.setTime(DateParser.parseRFC822(sDate, Locale.US));\n\n assertEquals(2005, cal.get(Calendar.YEAR));\n assertEquals(6, cal.get(Calendar.MONTH)); // month is zero-indexed\n assertEquals(19, cal.get(Calendar.DAY_OF_MONTH));\n assertEquals(3, cal.get(Calendar.DAY_OF_WEEK));\n assertEquals(23, cal.get(Calendar.HOUR_OF_DAY));\n assertEquals(0, cal.get(Calendar.MINUTE));\n assertEquals(51, cal.get(Calendar.SECOND));\n\n // RFC822\n sDate = \"Tue, 19 Jul 2005 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n // RFC822\n sDate = \"Tue, 19 Jul 05 23:00:51 GMT\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n final Calendar c = Calendar.getInstance(TimeZone.getTimeZone(\"GMT\"));\n c.set(2000, Calendar.JANUARY, 01, 0, 0, 0);\n final Date expectedDate = c.getTime();\n\n // W3C\n sDate = \"2000-01-01T00:00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01T00:00Z\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000-01\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // W3C\n sDate = \"2000\";\n assertEquals(expectedDate.getTime() / 1000, DateParser.parseDate(sDate, Locale.US).getTime() / 1000);\n\n // EXTRA\n sDate = \"18:10 2000/10/10\";\n assertNotNull(DateParser.parseDate(sDate, Locale.US));\n\n // INVALID\n sDate = \"X20:10 2000-10-10\";\n assertNull(DateParser.parseDate(sDate, Locale.US));\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void testRawNoBomValid(final String encoding) throws Exception {\n InputStream is = getXmlStream(\"no-bom\", XML1, encoding, encoding);\n XmlReader xmlReader = new XmlReader(is, false);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML2, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), \"UTF-8\");\n\n is = getXmlStream(\"no-bom\", XML3, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML4, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n\n is = getXmlStream(\"no-bom\", XML5, encoding, encoding);\n xmlReader = new XmlReader(is);\n assertEquals(xmlReader.getEncoding(), encoding);\n } \n #location 4 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n protected void testRawNoBomValid(final String encoding) throws Exception {\n checkEncoding(XML1, encoding, \"UTF-8\");\n checkEncoding(XML2, encoding, \"UTF-8\");\n checkEncoding(XML3, encoding, encoding);\n checkEncoding(XML4, encoding, encoding);\n checkEncoding(XML5, encoding, encoding);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Element pop() {\n // todo - dev, remove validation check\n if (stack.peekLast().nodeName().equals(\"td\") && !state.name().equals(\"InCell\"))\n Validate.isFalse(true, \"pop td not in cell\");\n if (stack.peekLast().nodeName().equals(\"html\"))\n Validate.isFalse(true, \"popping html!\");\n return stack.pollLast();\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n HtmlTreeBuilder() {}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static String readInputStream(InputStream inStream, String charsetName) throws IOException {\n char[] buffer = new char[0x20000]; // ~ 130K\n StringBuilder data = new StringBuilder(0x20000);\n Reader inReader = new InputStreamReader(inStream, charsetName);\n int read;\n do {\n read = inReader.read(buffer, 0, buffer.length);\n if (read > 0) {\n data.append(buffer, 0, read);\n }\n\n } while (read >= 0);\n\n return data.toString();\n } \n #location 14 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static String readInputStream(InputStream inStream, String charsetName) throws IOException {\n byte[] buffer = new byte[bufferSize];\n ByteArrayOutputStream outStream = new ByteArrayOutputStream(bufferSize);\n int read;\n while(true) {\n read = inStream.read(buffer);\n if (read == -1) break;\n outStream.write(buffer, 0, read);\n }\n ByteBuffer byteData = ByteBuffer.wrap(outStream.toByteArray());\n \n String docData;\n if (charsetName == null) { // determine from http-equiv. safe parse as UTF-8\n docData = Charset.forName(defaultCharset).decode(byteData).toString();\n Document doc = Jsoup.parse(docData);\n Element httpEquiv = doc.select(\"meta[http-equiv]\").first();\n if (httpEquiv != null) { // if not found, will keep utf-8 as best attempt\n String foundCharset = getCharsetFromContentType(httpEquiv.attr(\"content\"));\n if (foundCharset != null && !foundCharset.equals(defaultCharset)) { // need to re-decode\n byteData.rewind();\n docData = Charset.forName(foundCharset).decode(byteData).toString();\n }\n }\n } else { // specified by content type header (or by user on file load)\n docData = Charset.forName(charsetName).decode(byteData).toString();\n }\n return docData;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static String load(File in, String charsetName) throws IOException { \n char[] buffer = new char[0x20000]; // ~ 130K\n StringBuilder data = new StringBuilder(0x20000);\n InputStream inStream = new FileInputStream(in);\n Reader inReader = new InputStreamReader(inStream, charsetName);\n int read;\n do {\n read = inReader.read(buffer, 0, buffer.length);\n if (read > 0) {\n data.append(buffer, 0, read);\n }\n \n } while (read >= 0);\n \n return data.toString(); \n } \n #location 5 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n static String load(File in, String charsetName) throws IOException { \n InputStream inStream = new FileInputStream(in);\n String data = readInputStream(inStream, charsetName);\n inStream.close();\n return data;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Document normalise() {\n if (select(\"html\").isEmpty())\n appendElement(\"html\");\n if (head() == null)\n select(\"html\").first().prependElement(\"head\");\n if (body() == null)\n select(\"html\").first().appendElement(\"body\");\n\n normalise(this);\n normalise(select(\"html\").first());\n normalise(head());\n\n return this;\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Document normalise() {\n if (select(\"html\").isEmpty())\n appendElement(\"html\");\n if (head() == null)\n select(\"html\").first().prependElement(\"head\");\n if (body() == null)\n select(\"html\").first().appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(select(\"html\").first());\n normalise(this); \n\n return this;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Document parse() {\n // TODO: figure out implicit head & body elements\n Document doc = new Document();\n stack.add(doc);\n\n while (tokenStream.hasNext()) {\n Token token = tokenStream.next();\n\n if (token.isStartTag()) {\n Attributes attributes = attributeParser.parse(token.getAttributeString());\n Tag tag = Tag.valueOf(token.getTagName());\n StartTag startTag = new StartTag(tag, attributes);\n\n // if tag is \"html\", we already have it, so OK to ignore skip. todo: abstract this. and can there be attributes to set?\n if (doc.getTag().equals(tag)) continue;\n\n Element parent = popStackToSuitableContainer(tag);\n Validate.notNull(parent, \"Should always have a viable container\");\n Element node = new Element(parent, startTag);\n parent.addChild(node);\n stack.add(node);\n }\n\n if (token.isEndTag()) { // empty tags are both start and end tags\n stack.removeLast();\n }\n\n // TODO[must] handle comments\n\n else if (token.isTextNode()) {\n String text = token.getData();\n TextNode textNode = new TextNode(stack.peek(), text);\n stack.getLast().addChild(textNode);\n }\n }\n return doc;\n } \n #location 20 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Document parse() {\n // TODO: figure out implicit head & body elements\n Document doc = new Document();\n stack.add(doc);\n\n StringBuilder commentAccum = null;\n\n while (tokenStream.hasNext()) {\n Token token = tokenStream.next();\n\n if (token.isFullComment()) { // \n Comment comment = new Comment(stack.peek(), token.getCommentData());\n stack.getLast().addChild(comment);\n } else if (token.isStartComment()) { // \n commentAccum.append(token.getCommentData());\n Comment comment = new Comment(stack.peek(), commentAccum.toString());\n stack.getLast().addChild(comment);\n commentAccum = null;\n } else if (commentAccum != null) { // within a comment\n commentAccum.append(token.getData());\n }\n\n else if (token.isStartTag()) {\n Attributes attributes = attributeParser.parse(token.getAttributeString());\n Tag tag = Tag.valueOf(token.getTagName());\n StartTag startTag = new StartTag(tag, attributes);\n\n // if tag is \"html\", we already have it, so OK to ignore skip. todo: abstract this. and can there be attributes to set?\n if (doc.getTag().equals(tag)) continue;\n\n Element parent = popStackToSuitableContainer(tag);\n Validate.notNull(parent, \"Should always have a viable container\");\n Element node = new Element(parent, startTag);\n parent.addChild(node);\n stack.add(node);\n }\n\n if (token.isEndTag() && commentAccum == null) { // empty tags are both start and end tags\n stack.removeLast();\n }\n\n\n\n // TODO[must] handle comments\n\n else if (token.isTextNode()) {\n String text = token.getData();\n TextNode textNode = new TextNode(stack.peek(), text);\n stack.getLast().addChild(textNode);\n }\n }\n return doc;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Node previousSibling() {\n List siblings = parentNode.childNodes;\n Integer index = indexInList(this, siblings);\n Validate.notNull(index);\n if (index > 0)\n return siblings.get(index-1);\n else\n return null;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Node previousSibling() {\n List siblings = parentNode.childNodes;\n Integer index = siblingIndex();\n Validate.notNull(index);\n if (index > 0)\n return siblings.get(index-1);\n else\n return null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void insert(Token.Character characterToken) {\n Node node;\n // characters in script and style go in as datanodes, not text nodes\n final String tagName = currentElement().tagName();\n final String data = characterToken.getData();\n\n if (characterToken.isCData())\n node = new CDataNode(data);\n else if (tagName.equals(\"script\") || tagName.equals(\"style\"))\n node = new DataNode(data);\n else\n node = new TextNode(data);\n currentElement().appendChild(node); // doesn't use insertNode, because we don't foster these; and will always have a stack.\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n ParseSettings defaultSettings() {\n return ParseSettings.htmlDefault;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testPreviousElementSiblings() {\n Document doc = Jsoup.parse(\"
  • a
    • \" +\n \"
  • b
    • \" +\n \"
  • c
    • \");\n Element element = doc.getElementById(\"b\");\n List elementSiblings = element.previousElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(1, elementSiblings.size());\n\n Element element1 = doc.getElementById(\"a\");\n List elementSiblings1 = element1.previousElementSiblings();\n assertNull(elementSiblings1);\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testPreviousElementSiblings() {\n Document doc = Jsoup.parse(\"
      \" +\n \"
    • a
      • \" +\n \"
    • b
      • \" +\n \"
    • c
      • \" +\n \"
    \" +\n \"
    \" +\n \"
  • d
    • \" +\n \"
    \");\n\n Element element = doc.getElementById(\"b\");\n List elementSiblings = element.previousElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(1, elementSiblings.size());\n assertEquals(\"a\", elementSiblings.get(0).id());\n\n Element element1 = doc.getElementById(\"a\");\n List elementSiblings1 = element1.previousElementSiblings();\n assertEquals(0, elementSiblings1.size());\n\n Element element2 = doc.getElementById(\"c\");\n List elementSiblings2 = element2.previousElementSiblings();\n assertNotNull(elementSiblings2);\n assertEquals(2, elementSiblings2.size());\n assertEquals(\"a\", elementSiblings2.get(0).id());\n assertEquals(\"b\", elementSiblings2.get(1).id());\n\n Element ul = doc.getElementById(\"ul\");\n List elementSiblings3 = ul.previousElementSiblings();\n try {\n Element element3 = elementSiblings3.get(0);\n fail(\"This element should has no previous siblings\");\n } catch (IndexOutOfBoundsException e) {\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test public void forms() {\n Document doc = Jsoup.parse(\"
    \");\n Elements els = doc.select(\"*\");\n assertEquals(9, els.size());\n\n List forms = els.forms();\n assertEquals(2, forms.size());\n assertTrue(forms.get(0) != null);\n assertTrue(forms.get(1) != null);\n assertEquals(\"1\", forms.get(0).id());\n assertEquals(\"2\", forms.get(1).id());\n } \n #location 10 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test public void forms() {\n Document doc = Jsoup.parse(\"
    \");\n Elements els = doc.select(\"*\");\n assertEquals(9, els.size());\n\n List forms = els.forms();\n assertEquals(2, forms.size());\n assertNotNull(forms.get(0));\n assertNotNull(forms.get(1));\n assertEquals(\"1\", forms.get(0).id());\n assertEquals(\"2\", forms.get(1).id());\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static String load(File in, String charsetName) throws IOException { \n char[] buffer = new char[0x20000]; // ~ 130K\n StringBuilder data = new StringBuilder(0x20000);\n InputStream inStream = new FileInputStream(in);\n Reader inReader = new InputStreamReader(inStream, charsetName);\n int read;\n do {\n read = inReader.read(buffer, 0, buffer.length);\n if (read > 0) {\n data.append(buffer, 0, read);\n }\n \n } while (read >= 0);\n \n return data.toString(); \n } \n #location 15 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n static String load(File in, String charsetName) throws IOException { \n InputStream inStream = new FileInputStream(in);\n String data = readInputStream(inStream, charsetName);\n inStream.close();\n return data;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Node nextSibling() {\n if (parentNode == null)\n return null; // root\n \n List siblings = parentNode.childNodes;\n Integer index = indexInList(this, siblings);\n Validate.notNull(index);\n if (siblings.size() > index+1)\n return siblings.get(index+1);\n else\n return null;\n } \n #location 8 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Node nextSibling() {\n if (parentNode == null)\n return null; // root\n \n List siblings = parentNode.childNodes;\n Integer index = siblingIndex();\n Validate.notNull(index);\n if (siblings.size() > index+1)\n return siblings.get(index+1);\n else\n return null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Document normalise() {\n if (select(\"html\").isEmpty())\n appendElement(\"html\");\n if (head() == null)\n select(\"html\").first().prependElement(\"head\");\n if (body() == null)\n select(\"html\").first().appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(select(\"html\").first());\n normalise(this); \n\n return this;\n } \n #location 11 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Document normalise() {\n Element htmlEl = findFirstElementByTagName(\"html\", this);\n if (htmlEl == null)\n htmlEl = appendElement(\"html\");\n if (head() == null)\n htmlEl.prependElement(\"head\");\n if (body() == null)\n htmlEl.appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(htmlEl);\n normalise(this); \n\n return this;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void insert(Token.Character characterToken) {\n Node node;\n // characters in script and style go in as datanodes, not text nodes\n final String tagName = currentElement().tagName();\n final String data = characterToken.getData();\n\n if (characterToken.isCData())\n node = new CDataNode(data);\n else if (tagName.equals(\"script\") || tagName.equals(\"style\"))\n node = new DataNode(data);\n else\n node = new TextNode(data);\n currentElement().appendChild(node); // doesn't use insertNode, because we don't foster these; and will always have a stack.\n } \n #location 13 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n ParseSettings defaultSettings() {\n return ParseSettings.htmlDefault;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public boolean matchesWhitespace() {\n return !isEmpty() && Character.isWhitespace(peek());\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public boolean matchesWhitespace() {\n return !isEmpty() && Character.isWhitespace(queue.charAt(pos));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n\tpublic void testAppendTo() {\n\t\tString parentHtml = \"
    \";\n\t\tString childHtml = \"
    \";\n\n\t\tElement parentElement = Jsoup.parse(parentHtml).getElementsByClass(\"a\").first();\n\t\tElement childElement = Jsoup.parse(childHtml).getElementsByClass(\"b\").first();\n\n\t\tchildElement.attr(\"class\", \"test-class\").appendTo(parentElement).attr(\"id\", \"testId\");\n\t\tassertEquals(\"test-class\", childElement.attr(\"class\"));\n\t\tassertEquals(\"testId\", childElement.attr(\"id\"));\n\t\tassertThat(parentElement.attr(\"id\"), not(equalTo(\"testId\")));\n\t\tassertThat(parentElement.attr(\"class\"), not(equalTo(\"test-class\")));\n\t\tassertSame(childElement, parentElement.children().first());\n\t\tassertSame(parentElement, childElement.parent());\n\t} \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n\tpublic void testAppendTo() {\n\t\tString parentHtml = \"
    \";\n\t\tString childHtml = \"

    Two

    \";\n\n\t\tDocument parentDoc = Jsoup.parse(parentHtml);\n\t\tElement parent = parentDoc.body();\n Document childDoc = Jsoup.parse(childHtml);\n\n Element div = childDoc.select(\"div\").first();\n Element p = childDoc.select(\"p\").first();\n Element appendTo1 = div.appendTo(parent);\n assertEquals(div, appendTo1);\n\n Element appendTo2 = p.appendTo(div);\n assertEquals(p, appendTo2);\n\n assertEquals(\"
    \\n
    \\n

    Two

    \\n
    \", parentDoc.body().html());\n assertEquals(\"\", childDoc.body().html()); // got moved out\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n Element pop() {\n // todo - dev, remove validation check\n if (stack.peekLast().nodeName().equals(\"td\") && !state.name().equals(\"InCell\"))\n Validate.isFalse(true, \"pop td not in cell\");\n if (stack.peekLast().nodeName().equals(\"html\"))\n Validate.isFalse(true, \"popping html!\");\n return stack.pollLast();\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n HtmlTreeBuilder() {}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Document normalise() {\n if (select(\"html\").isEmpty())\n appendElement(\"html\");\n if (head() == null)\n select(\"html\").first().prependElement(\"head\");\n if (body() == null)\n select(\"html\").first().appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(select(\"html\").first());\n normalise(this); \n\n return this;\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Document normalise() {\n Element htmlEl = findFirstElementByTagName(\"html\", this);\n if (htmlEl == null)\n htmlEl = appendElement(\"html\");\n if (head() == null)\n htmlEl.prependElement(\"head\");\n if (body() == null)\n htmlEl.appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(htmlEl);\n normalise(this); \n\n return this;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void outerHtmlHead(StringBuilder accum, int depth) {\n if (isBlock() || (parent() != null && parent().tag().canContainBlock() && siblingIndex() == 0))\n indent(accum, depth);\n accum\n .append(\"<\")\n .append(tagName())\n .append(attributes.html());\n\n if (childNodes.isEmpty() && tag.isEmpty())\n accum.append(\" />\");\n else\n accum.append(\">\");\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n boolean preserveWhitespace() {\n return tag.preserveWhitespace() || parent() != null && parent().preserveWhitespace();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n\n int i = 0;\n BufferedReader input = new BufferedReader(new InputStreamReader(stream, ASCII));\n CharacterReader reader = new CharacterReader(input);\n\n while (!reader.isEmpty()) {\n // NotNestedLessLess=10913,824;1887\n\n final String name = reader.consumeTo('=');\n reader.advance();\n final int cp1 = Integer.parseInt(reader.consumeToAny(codeDelims), codepointRadix);\n final char codeDelim = reader.current();\n reader.advance();\n final int cp2;\n if (codeDelim == ',') {\n cp2 = Integer.parseInt(reader.consumeTo(';'), codepointRadix);\n reader.advance();\n } else {\n cp2 = empty;\n }\n String indexS = reader.consumeTo('\\n');\n // default git checkout on windows will add a \\r there, so remove\n if (indexS.charAt(indexS.length() - 1) == '\\r') {\n indexS = indexS.substring(0, indexS.length() - 1);\n }\n final int index = Integer.parseInt(indexS, codepointRadix);\n reader.advance();\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n }\n Validate.isTrue(i == size, \"Unexpected count of entities loaded for \" + file);\n } \n #location 48 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n\n int i = 0;\n BufferedReader input = null;\n try {\n input = new BufferedReader(new InputStreamReader(stream, ASCII));\n CharacterReader reader = new CharacterReader(input);\n\n while (!reader.isEmpty()) {\n // NotNestedLessLess=10913,824;1887\n\n final String name = reader.consumeTo('=');\n reader.advance();\n final int cp1 = Integer.parseInt(reader.consumeToAny(codeDelims), codepointRadix);\n final char codeDelim = reader.current();\n reader.advance();\n final int cp2;\n if (codeDelim == ',') {\n cp2 = Integer.parseInt(reader.consumeTo(';'), codepointRadix);\n reader.advance();\n } else {\n cp2 = empty;\n }\n String indexS = reader.consumeTo('\\n');\n // default git checkout on windows will add a \\r there, so remove\n if (indexS.charAt(indexS.length() - 1) == '\\r') {\n indexS = indexS.substring(0, indexS.length() - 1);\n }\n final int index = Integer.parseInt(indexS, codepointRadix);\n reader.advance();\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n }\n } finally {\n try {\n if (input != null) {\n input.close();\n }\n } catch (IOException e1) {\n //ignore exception\n }\n }\n Validate.isTrue(i == size, \"Unexpected count of entities loaded for \" + file);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void outerHtml(StringBuilder accum) {\n new NodeTraversor(new OuterHtmlVisitor(accum, ownerDocument().outputSettings())).traverse(this);\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected void outerHtml(StringBuilder accum) {\n new NodeTraversor(new OuterHtmlVisitor(accum, getOutputSettings())).traverse(this);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public boolean matchesWord() {\n return !isEmpty() && Character.isLetterOrDigit(peek());\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public boolean matchesWord() {\n return !isEmpty() && Character.isLetterOrDigit(queue.charAt(pos));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testNextElementSiblings() {\n Document doc = Jsoup.parse(\"
  • a
    • \" +\n \"
  • b
    • \" +\n \"
  • c
    • \");\n Element element = doc.getElementById(\"a\");\n List elementSiblings = element.nextElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(2, elementSiblings.size());\n\n Element element1 = doc.getElementById(\"c\");\n List elementSiblings1 = element1.nextElementSiblings();\n assertNull(elementSiblings1);\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testNextElementSiblings() {\n Document doc = Jsoup.parse(\"
      \" +\n \"
    • a
      • \" +\n \"
    • b
      • \" +\n \"
    • c
      • \" +\n \"
    \" +\n \"
    \" +\n \"
  • d
    • \" +\n \"
    \");\n\n Element element = doc.getElementById(\"a\");\n List elementSiblings = element.nextElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(2, elementSiblings.size());\n assertEquals(\"b\", elementSiblings.get(0).id());\n assertEquals(\"c\", elementSiblings.get(1).id());\n\n Element element1 = doc.getElementById(\"b\");\n List elementSiblings1 = element1.nextElementSiblings();\n assertNotNull(elementSiblings1);\n assertEquals(1, elementSiblings1.size());\n assertEquals(\"c\", elementSiblings1.get(0).id());\n\n Element element2 = doc.getElementById(\"c\");\n List elementSiblings2 = element2.nextElementSiblings();\n assertEquals(0, elementSiblings2.size());\n\n Element ul = doc.getElementById(\"ul\");\n List elementSiblings3 = ul.nextElementSiblings();\n assertNotNull(elementSiblings3);\n assertEquals(1, elementSiblings3.size());\n assertEquals(\"div\", elementSiblings3.get(0).id());\n\n Element div = doc.getElementById(\"div\");\n List elementSiblings4 = div.nextElementSiblings();\n try {\n Element elementSibling = elementSiblings4.get(0);\n fail(\"This element should has no next siblings\");\n } catch (IndexOutOfBoundsException e) {\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public Document normalise() {\n if (select(\"html\").isEmpty())\n appendElement(\"html\");\n if (head() == null)\n select(\"html\").first().prependElement(\"head\");\n if (body() == null)\n select(\"html\").first().appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(select(\"html\").first());\n normalise(this); \n\n return this;\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public Document normalise() {\n Element htmlEl = findFirstElementByTagName(\"html\", this);\n if (htmlEl == null)\n htmlEl = appendElement(\"html\");\n if (head() == null)\n htmlEl.prependElement(\"head\");\n if (body() == null)\n htmlEl.appendElement(\"body\");\n\n // pull text nodes out of root, html, and head els, and push into body. non-text nodes are already taken care\n // of. do in inverse order to maintain text order.\n normalise(head());\n normalise(htmlEl);\n normalise(this); \n\n return this;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void removeChild(Node out) {\n Validate.isTrue(out.parentNode == this);\n int index = indexInList(out, childNodes);\n childNodes.remove(index);\n out.parentNode = null;\n } \n #location 3 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected void removeChild(Node out) {\n Validate.isTrue(out.parentNode == this);\n int index = out.siblingIndex();\n childNodes.remove(index);\n reindexChildren();\n out.parentNode = null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testNextElementSiblings() {\n Document doc = Jsoup.parse(\"
  • a
    • \" +\n \"
  • b
    • \" +\n \"
  • c
    • \");\n Element element = doc.getElementById(\"a\");\n List elementSiblings = element.nextElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(2, elementSiblings.size());\n\n Element element1 = doc.getElementById(\"c\");\n List elementSiblings1 = element1.nextElementSiblings();\n assertNull(elementSiblings1);\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testNextElementSiblings() {\n Document doc = Jsoup.parse(\"
      \" +\n \"
    • a
      • \" +\n \"
    • b
      • \" +\n \"
    • c
      • \" +\n \"
    \" +\n \"
    \" +\n \"
  • d
    • \" +\n \"
    \");\n\n Element element = doc.getElementById(\"a\");\n List elementSiblings = element.nextElementSiblings();\n assertNotNull(elementSiblings);\n assertEquals(2, elementSiblings.size());\n assertEquals(\"b\", elementSiblings.get(0).id());\n assertEquals(\"c\", elementSiblings.get(1).id());\n\n Element element1 = doc.getElementById(\"b\");\n List elementSiblings1 = element1.nextElementSiblings();\n assertNotNull(elementSiblings1);\n assertEquals(1, elementSiblings1.size());\n assertEquals(\"c\", elementSiblings1.get(0).id());\n\n Element element2 = doc.getElementById(\"c\");\n List elementSiblings2 = element2.nextElementSiblings();\n assertEquals(0, elementSiblings2.size());\n\n Element ul = doc.getElementById(\"ul\");\n List elementSiblings3 = ul.nextElementSiblings();\n assertNotNull(elementSiblings3);\n assertEquals(1, elementSiblings3.size());\n assertEquals(\"div\", elementSiblings3.get(0).id());\n\n Element div = doc.getElementById(\"div\");\n List elementSiblings4 = div.nextElementSiblings();\n try {\n Element elementSibling = elementSiblings4.get(0);\n fail(\"This element should has no next siblings\");\n } catch (IndexOutOfBoundsException e) {\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n\n int i = 0;\n BufferedReader input = new BufferedReader(new InputStreamReader(stream, ASCII));\n CharacterReader reader = new CharacterReader(input);\n\n while (!reader.isEmpty()) {\n // NotNestedLessLess=10913,824;1887\n\n final String name = reader.consumeTo('=');\n reader.advance();\n final int cp1 = Integer.parseInt(reader.consumeToAny(codeDelims), codepointRadix);\n final char codeDelim = reader.current();\n reader.advance();\n final int cp2;\n if (codeDelim == ',') {\n cp2 = Integer.parseInt(reader.consumeTo(';'), codepointRadix);\n reader.advance();\n } else {\n cp2 = empty;\n }\n String indexS = reader.consumeTo('\\n');\n // default git checkout on windows will add a \\r there, so remove\n if (indexS.charAt(indexS.length() - 1) == '\\r') {\n indexS = indexS.substring(0, indexS.length() - 1);\n }\n final int index = Integer.parseInt(indexS, codepointRadix);\n reader.advance();\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n }\n Validate.isTrue(i == size, \"Unexpected count of entities loaded for \" + file);\n } \n #location 13 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n\n int i = 0;\n BufferedReader input = null;\n try {\n input = new BufferedReader(new InputStreamReader(stream, ASCII));\n CharacterReader reader = new CharacterReader(input);\n\n while (!reader.isEmpty()) {\n // NotNestedLessLess=10913,824;1887\n\n final String name = reader.consumeTo('=');\n reader.advance();\n final int cp1 = Integer.parseInt(reader.consumeToAny(codeDelims), codepointRadix);\n final char codeDelim = reader.current();\n reader.advance();\n final int cp2;\n if (codeDelim == ',') {\n cp2 = Integer.parseInt(reader.consumeTo(';'), codepointRadix);\n reader.advance();\n } else {\n cp2 = empty;\n }\n String indexS = reader.consumeTo('\\n');\n // default git checkout on windows will add a \\r there, so remove\n if (indexS.charAt(indexS.length() - 1) == '\\r') {\n indexS = indexS.substring(0, indexS.length() - 1);\n }\n final int index = Integer.parseInt(indexS, codepointRadix);\n reader.advance();\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n }\n } finally {\n try {\n if (input != null) {\n input.close();\n }\n } catch (IOException e1) {\n //ignore exception\n }\n }\n Validate.isTrue(i == size, \"Unexpected count of entities loaded for \" + file);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void insert(Token.Character characterToken) {\n final Node node;\n final Element el = currentElement();\n final String tagName = el.normalName();\n final String data = characterToken.getData();\n\n if (characterToken.isCData())\n node = new CDataNode(data);\n else if (tagName.equals(\"script\") || tagName.equals(\"style\"))\n node = new DataNode(data);\n else\n node = new TextNode(data);\n el.appendChild(node); // doesn't use insertNode, because we don't foster these; and will always have a stack.\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n ParseSettings defaultSettings() {\n return ParseSettings.htmlDefault;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void outerHtml(StringBuilder accum) {\n String html = StringEscapeUtils.escapeHtml(getWholeText());\n if (parent() instanceof Element && !((Element) parent()).preserveWhitespace()) {\n html = normaliseWhitespace(html);\n }\n\n if (siblingIndex() == 0 && parentNode instanceof Element && ((Element) parentNode).tag().canContainBlock() && !isBlank())\n indent(accum);\n accum.append(html);\n } \n #location 7 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n void outerHtmlHead(StringBuilder accum, int depth) {\n String html = StringEscapeUtils.escapeHtml(getWholeText());\n if (parent() instanceof Element && !((Element) parent()).preserveWhitespace()) {\n html = normaliseWhitespace(html);\n }\n\n if (siblingIndex() == 0 && parentNode instanceof Element && ((Element) parentNode).tag().canContainBlock() && !isBlank())\n indent(accum, depth);\n accum.append(html);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static Document load(File in, String charsetName, String baseUri) throws IOException {\n InputStream inStream = new FileInputStream(in);\n ByteBuffer byteData = readToByteBuffer(inStream);\n Document doc = parseByteData(byteData, charsetName, baseUri);\n inStream.close();\n return doc;\n } \n #location 6 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static Document load(File in, String charsetName, String baseUri) throws IOException {\n InputStream inStream = null;\n try {\n inStream = new FileInputStream(in);\n ByteBuffer byteData = readToByteBuffer(inStream);\n return parseByteData(byteData, charsetName, baseUri);\n } finally {\n if (inStream != null)\n inStream.close();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String consumeCssIdentifier() {\n StringBuilder accum = new StringBuilder();\n Character c = peek();\n while (!isEmpty() && (Character.isLetterOrDigit(c) || c.equals('-') || c.equals('_'))) {\n accum.append(consume());\n c = peek();\n }\n return accum.toString();\n } \n #location 4 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public String consumeCssIdentifier() {\n int start = pos;\n while (!isEmpty() && (matchesWord() || matchesAny('-', '_')))\n pos++;\n\n return queue.substring(start, pos);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void replaceChild(Node out, Node in) {\n Validate.isTrue(out.parentNode == this);\n Validate.notNull(in);\n if (in.parentNode != null)\n in.parentNode.removeChild(in);\n \n Integer index = indexInList(out, childNodes);\n childNodes.set(index, in);\n in.parentNode = this;\n out.parentNode = null;\n } \n #location 8 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected void replaceChild(Node out, Node in) {\n Validate.isTrue(out.parentNode == this);\n Validate.notNull(in);\n if (in.parentNode != null)\n in.parentNode.removeChild(in);\n \n Integer index = out.siblingIndex();\n childNodes.set(index, in);\n in.parentNode = this;\n in.setSiblingIndex(index);\n out.parentNode = null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n protected void addChildren(int index, Node... children) {\n Validate.noNullElements(children);\n final List nodes = ensureChildNodes();\n\n for (Node child : children) {\n reparentChild(child);\n }\n nodes.addAll(index, Arrays.asList(children));\n reindexChildren(index);\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n protected void addChildren(int index, Node... children) {\n Validate.notNull(children);\n if (children.length == 0) {\n return;\n }\n final List nodes = ensureChildNodes();\n\n // fast path - if used as a wrap (index=0, children = child[0].parent.children - do inplace\n final Node firstParent = children[0].parent();\n if (firstParent != null && firstParent.childNodeSize() == children.length) {\n boolean sameList = true;\n final List firstParentNodes = firstParent.childNodes();\n // identity check contents to see if same\n int i = children.length;\n while (i-- > 0) {\n if (children[i] != firstParentNodes.get(i)) {\n sameList = false;\n break;\n }\n }\n firstParent.empty();\n nodes.addAll(index, Arrays.asList(children));\n i = children.length;\n while (i-- > 0) {\n children[i].parentNode = this;\n }\n reindexChildren(index);\n return;\n }\n\n Validate.noNullElements(children);\n for (Node child : children) {\n reparentChild(child);\n }\n nodes.addAll(index, Arrays.asList(children));\n reindexChildren(index);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static String unescape(String string) {\n if (!string.contains(\"&\"))\n return string;\n\n Matcher m = unescapePattern.matcher(string); // &(#(x|X)?([0-9a-fA-F]+)|[a-zA-Z]+);?\n StringBuffer accum = new StringBuffer(string.length()); // pity matcher can't use stringbuilder, avoid syncs\n\n while (m.find()) {\n int charval = -1;\n String num = m.group(3);\n if (num != null) {\n try {\n int base = m.group(2) != null ? 16 : 10; // 2 is hex indicator\n charval = Integer.valueOf(num, base);\n } catch (NumberFormatException e) {\n } // skip\n } else {\n String name = m.group(1).toLowerCase();\n if (full.containsKey(name))\n charval = full.get(name);\n }\n\n if (charval != -1 || charval > 0xFFFF) { // out of range\n String c = Character.toString((char) charval);\n m.appendReplacement(accum, c);\n } else {\n m.appendReplacement(accum, m.group(0)); // replace with original string\n }\n }\n m.appendTail(accum);\n return accum.toString();\n } \n #location 18 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n static String unescape(String string) {\n if (!string.contains(\"&\"))\n return string;\n\n Matcher m = unescapePattern.matcher(string); // &(#(x|X)?([0-9a-fA-F]+)|[a-zA-Z]+);?\n StringBuffer accum = new StringBuffer(string.length()); // pity matcher can't use stringbuilder, avoid syncs\n\n while (m.find()) {\n int charval = -1;\n String num = m.group(3);\n if (num != null) {\n try {\n int base = m.group(2) != null ? 16 : 10; // 2 is hex indicator\n charval = Integer.valueOf(num, base);\n } catch (NumberFormatException e) {\n } // skip\n } else {\n String name = m.group(1);\n if (full.containsKey(name))\n charval = full.get(name);\n }\n\n if (charval != -1 || charval > 0xFFFF) { // out of range\n String c = Character.toString((char) charval);\n m.appendReplacement(accum, c);\n } else {\n m.appendReplacement(accum, m.group(0)); // replace with original string\n }\n }\n m.appendTail(accum);\n return accum.toString();\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n BufferedReader reader = new BufferedReader(new InputStreamReader(stream));\n String entry;\n int i = 0;\n try {\n while ((entry = reader.readLine()) != null) {\n // NotNestedLessLess=10913,824;1887\n final Matcher match = entityPattern.matcher(entry);\n if (match.find()) {\n final String name = match.group(1);\n final int cp1 = Integer.parseInt(match.group(2), codepointRadix);\n final int cp2 = match.group(3) != null ? Integer.parseInt(match.group(3), codepointRadix) : empty;\n final int index = Integer.parseInt(match.group(4), codepointRadix);\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n }\n\n }\n reader.close();\n } catch (IOException err) {\n throw new IllegalStateException(\"Error reading resource \" + file);\n }\n } \n #location 36 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static void load(EscapeMode e, String file, int size) {\n e.nameKeys = new String[size];\n e.codeVals = new int[size];\n e.codeKeys = new int[size];\n e.nameVals = new String[size];\n\n InputStream stream = Entities.class.getResourceAsStream(file);\n if (stream == null)\n throw new IllegalStateException(\"Could not read resource \" + file + \". Make sure you copy resources for \" + Entities.class.getCanonicalName());\n\n int i = 0;\n try {\n ByteBuffer bytes = DataUtil.readToByteBuffer(stream, 0);\n String contents = Charset.forName(\"ascii\").decode(bytes).toString();\n CharacterReader reader = new CharacterReader(contents);\n\n while (!reader.isEmpty()) {\n // NotNestedLessLess=10913,824;1887\n\n final String name = reader.consumeTo('=');\n reader.advance();\n final int cp1 = Integer.parseInt(reader.consumeToAny(codeDelims), codepointRadix);\n final char codeDelim = reader.current();\n reader.advance();\n final int cp2;\n if (codeDelim == ',') {\n cp2 = Integer.parseInt(reader.consumeTo(';'), codepointRadix);\n reader.advance();\n } else {\n cp2 = empty;\n }\n final int index = Integer.parseInt(reader.consumeTo('\\n'), codepointRadix);\n reader.advance();\n\n e.nameKeys[i] = name;\n e.codeVals[i] = cp1;\n e.codeKeys[index] = cp1;\n e.nameVals[index] = name;\n\n if (cp2 != empty) {\n multipoints.put(name, new String(new int[]{cp1, cp2}, 0, 2));\n }\n i++;\n\n\n }\n } catch (IOException err) {\n throw new IllegalStateException(\"Error reading resource \" + file);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private void parseStartTag() {\n tq.consume(\"<\");\n Attributes attributes = new Attributes();\n\n String tagName = tq.consumeWord();\n while (!tq.matches(\"<\") && !tq.matches(\"/>\") && !tq.matches(\">\") && !tq.isEmpty()) {\n Attribute attribute = parseAttribute();\n if (attribute != null)\n attributes.put(attribute);\n }\n\n Tag tag = Tag.valueOf(tagName);\n StartTag startTag = new StartTag(tag, attributes);\n Element child = new Element(startTag);\n\n boolean emptyTag;\n if (tq.matchChomp(\"/>\")) { // empty tag, don't add to stack\n emptyTag = true;\n } else {\n tq.matchChomp(\">\"); // safe because checked above (or ran out of data)\n emptyTag = false;\n }\n\n // pc data only tags (textarea, script): chomp to end tag, add content as text node\n if (tag.isData()) {\n String data = tq.chompTo(\"\");\n TextNode textNode = TextNode.createFromEncoded(data);\n child.addChild(textNode);\n\n if (tag.equals(titleTag))\n doc.setTitle(child.text());\n }\n\n // switch between html, head, body, to preserve doc structure\n if (tag.equals(htmlTag)) {\n doc.getAttributes().mergeAttributes(attributes);\n } else if (tag.equals(headTag)) {\n doc.getHead().getAttributes().mergeAttributes(attributes);\n // head is on stack from start, no action required\n } else if (last().getTag().equals(headTag) && !headTag.canContain(tag)) {\n // switch to body\n stack.removeLast();\n stack.addLast(doc.getBody());\n last().addChild(child);\n if (!emptyTag)\n stack.addLast(child);\n } else if (tag.equals(bodyTag) && last().getTag().equals(htmlTag)) {\n doc.getBody().getAttributes().mergeAttributes(attributes);\n stack.removeLast();\n stack.addLast(doc.getBody());\n } else {\n Element parent = popStackToSuitableContainer(tag);\n parent.addChild(child);\n if (!emptyTag && !tag.isData()) // TODO: only check for data here because last() == head is wrong; should be ancestor is head\n stack.addLast(child);\n }\n } \n #location 54 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private void parseStartTag() {\n tq.consume(\"<\");\n Attributes attributes = new Attributes();\n\n String tagName = tq.consumeWord();\n while (!tq.matchesAny(\"<\", \"/>\", \">\") && !tq.isEmpty()) {\n Attribute attribute = parseAttribute();\n if (attribute != null)\n attributes.put(attribute);\n }\n\n Tag tag = Tag.valueOf(tagName);\n StartTag startTag = new StartTag(tag, attributes);\n Element child = new Element(startTag);\n\n boolean emptyTag;\n if (tq.matchChomp(\"/>\")) { // empty tag, don't add to stack\n emptyTag = true;\n } else {\n tq.matchChomp(\">\"); // safe because checked above (or ran out of data)\n emptyTag = false;\n }\n\n // pc data only tags (textarea, script): chomp to end tag, add content as text node\n if (tag.isData()) {\n String data = tq.chompTo(\"\");\n TextNode textNode = TextNode.createFromEncoded(data); // TODO: maybe have this be another data type? So doesn't come back in text()?\n child.addChild(textNode);\n\n if (tag.equals(titleTag))\n doc.setTitle(child.text());\n }\n\n // switch between html, head, body, to preserve doc structure\n if (tag.equals(htmlTag)) {\n doc.getAttributes().mergeAttributes(attributes);\n } else if (tag.equals(headTag)) {\n doc.getHead().getAttributes().mergeAttributes(attributes);\n // head is on stack from start, no action required\n } else if (last().getTag().equals(headTag) && !headTag.canContain(tag)) {\n // switch to body\n stack.removeLast();\n stack.addLast(doc.getBody());\n last().addChild(child);\n if (!emptyTag)\n stack.addLast(child);\n } else if (tag.equals(bodyTag) && last().getTag().equals(htmlTag)) {\n doc.getBody().getAttributes().mergeAttributes(attributes);\n stack.removeLast();\n stack.addLast(doc.getBody());\n } else {\n Element parent = popStackToSuitableContainer(tag);\n parent.addChild(child);\n if (!emptyTag && !tag.isData()) // TODO: only check for data here because last() == head is wrong; should be ancestor is head\n stack.addLast(child);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static String ihVal(String key, Document doc) {\n return doc.select(\"th:contains(\" + key + \") + td\").first().text();\n } \n #location 2 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n private static String ihVal(String key, Document doc) {\n final Element first = doc.select(\"th:contains(\" + key + \") + td\").first();\n return first != null ? first.text() : null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n void outerHtmlHead(Appendable accum, int depth, Document.OutputSettings out) throws IOException {\n if (out.prettyPrint() && ((siblingIndex() == 0 && parentNode instanceof Element && ((Element) parentNode).tag().formatAsBlock() && !isBlank()) || (out.outline() && siblingNodes().size()>0 && !isBlank()) ))\n indent(accum, depth, out);\n\n boolean normaliseWhite = out.prettyPrint() && !Element.preserveWhitespace(parent());\n Entities.escape(accum, coreValue(), out, false, normaliseWhite, false);\n } \n #location 5 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n void outerHtmlHead(Appendable accum, int depth, Document.OutputSettings out) throws IOException {\n final boolean prettyPrint = out.prettyPrint();\n if (prettyPrint && ((siblingIndex() == 0 && parentNode instanceof Element && ((Element) parentNode).tag().formatAsBlock() && !isBlank()) || (out.outline() && siblingNodes().size()>0 && !isBlank()) ))\n indent(accum, depth, out);\n\n final boolean normaliseWhite = prettyPrint && !Element.preserveWhitespace(parentNode);\n final boolean stripWhite = prettyPrint && parentNode instanceof Document;\n Entities.escape(accum, coreValue(), out, false, normaliseWhite, stripWhite);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testNamespace() throws Exception\n {\n final String namespace = \"TestNamespace\";\n \n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).retryPolicy(new RetryOneTime(1)).namespace(namespace).build();\n client.start();\n try\n {\n String actualPath = client.create().forPath(\"/test\", new byte[0]);\n Assert.assertEquals(actualPath, \"/test\");\n Assert.assertNotNull(client.getZookeeperClient().getZooKeeper().exists(\"/\" + namespace + \"/test\", false));\n Assert.assertNull(client.getZookeeperClient().getZooKeeper().exists(\"/test\", false));\n\n actualPath = client.nonNamespaceView().create().forPath(\"/non\", new byte[0]);\n Assert.assertEquals(actualPath, \"/non\");\n Assert.assertNotNull(client.getZookeeperClient().getZooKeeper().exists(\"/non\", false));\n\n client.create().forPath(\"/test/child\", \"hey\".getBytes());\n byte[] bytes = client.getData().forPath(\"/test/child\");\n Assert.assertEquals(bytes, \"hey\".getBytes());\n\n bytes = client.nonNamespaceView().getData().forPath(\"/\" + namespace + \"/test/child\");\n Assert.assertEquals(bytes, \"hey\".getBytes());\n }\n finally\n {\n client.close();\n }\n } \n #location 26 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testNamespace() throws Exception\n {\n final String namespace = \"TestNamespace\";\n \n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).retryPolicy(new RetryOneTime(1)).namespace(namespace).build();\n client.start();\n try\n {\n String actualPath = client.create().forPath(\"/test\");\n Assert.assertEquals(actualPath, \"/test\");\n Assert.assertNotNull(client.getZookeeperClient().getZooKeeper().exists(\"/\" + namespace + \"/test\", false));\n Assert.assertNull(client.getZookeeperClient().getZooKeeper().exists(\"/test\", false));\n\n actualPath = client.nonNamespaceView().create().forPath(\"/non\");\n Assert.assertEquals(actualPath, \"/non\");\n Assert.assertNotNull(client.getZookeeperClient().getZooKeeper().exists(\"/non\", false));\n\n client.create().forPath(\"/test/child\", \"hey\".getBytes());\n byte[] bytes = client.getData().forPath(\"/test/child\");\n Assert.assertEquals(bytes, \"hey\".getBytes());\n\n bytes = client.nonNamespaceView().getData().forPath(\"/\" + namespace + \"/test/child\");\n Assert.assertEquals(bytes, \"hey\".getBytes());\n }\n finally\n {\n client.close();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testNamespaceInBackground() throws Exception\n {\n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).namespace(\"aisa\").retryPolicy(new RetryOneTime(1)).build();\n client.start();\n try\n {\n final SynchronousQueue queue = new SynchronousQueue();\n CuratorListener listener = new CuratorListener()\n {\n @Override\n public void eventReceived(CuratorFramework client, CuratorEvent event) throws Exception\n {\n if ( event.getType() == CuratorEventType.EXISTS )\n {\n queue.put(event.getPath());\n }\n }\n };\n\n client.getCuratorListenable().addListener(listener);\n client.create().forPath(\"/base\", new byte[0]);\n client.checkExists().inBackground().forPath(\"/base\");\n\n String path = queue.poll(10, TimeUnit.SECONDS);\n Assert.assertEquals(path, \"/base\");\n\n client.getCuratorListenable().removeListener(listener);\n\n BackgroundCallback callback = new BackgroundCallback()\n {\n @Override\n public void processResult(CuratorFramework client, CuratorEvent event) throws Exception\n {\n queue.put(event.getPath());\n }\n };\n client.getChildren().inBackground(callback).forPath(\"/base\");\n path = queue.poll(10, TimeUnit.SECONDS);\n Assert.assertEquals(path, \"/base\");\n }\n finally\n {\n client.close();\n }\n } \n #location 18 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testNamespaceInBackground() throws Exception\n {\n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).namespace(\"aisa\").retryPolicy(new RetryOneTime(1)).build();\n client.start();\n try\n {\n final SynchronousQueue queue = new SynchronousQueue();\n CuratorListener listener = new CuratorListener()\n {\n @Override\n public void eventReceived(CuratorFramework client, CuratorEvent event) throws Exception\n {\n if ( event.getType() == CuratorEventType.EXISTS )\n {\n queue.put(event.getPath());\n }\n }\n };\n\n client.getCuratorListenable().addListener(listener);\n client.create().forPath(\"/base\");\n client.checkExists().inBackground().forPath(\"/base\");\n\n String path = queue.poll(10, TimeUnit.SECONDS);\n Assert.assertEquals(path, \"/base\");\n\n client.getCuratorListenable().removeListener(listener);\n\n BackgroundCallback callback = new BackgroundCallback()\n {\n @Override\n public void processResult(CuratorFramework client, CuratorEvent event) throws Exception\n {\n queue.put(event.getPath());\n }\n };\n client.getChildren().inBackground(callback).forPath(\"/base\");\n path = queue.poll(10, TimeUnit.SECONDS);\n Assert.assertEquals(path, \"/base\");\n }\n finally\n {\n client.close();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testNamespaceWithWatcher() throws Exception\n {\n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).namespace(\"aisa\").retryPolicy(new RetryOneTime(1)).build();\n client.start();\n try\n {\n final SynchronousQueue queue = new SynchronousQueue();\n Watcher watcher = new Watcher()\n {\n @Override\n public void process(WatchedEvent event)\n {\n try\n {\n queue.put(event.getPath());\n }\n catch ( InterruptedException e )\n {\n throw new Error(e);\n }\n }\n };\n client.create().forPath(\"/base\", new byte[0]);\n client.getChildren().usingWatcher(watcher).forPath(\"/base\");\n client.create().forPath(\"/base/child\", new byte[0]);\n\n String path = queue.take();\n Assert.assertEquals(path, \"/base\");\n }\n finally\n {\n client.close();\n }\n } \n #location 18 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testNamespaceWithWatcher() throws Exception\n {\n CuratorFrameworkFactory.Builder builder = CuratorFrameworkFactory.builder();\n CuratorFramework client = builder.connectString(server.getConnectString()).namespace(\"aisa\").retryPolicy(new RetryOneTime(1)).build();\n client.start();\n try\n {\n final SynchronousQueue queue = new SynchronousQueue();\n Watcher watcher = new Watcher()\n {\n @Override\n public void process(WatchedEvent event)\n {\n try\n {\n queue.put(event.getPath());\n }\n catch ( InterruptedException e )\n {\n throw new Error(e);\n }\n }\n };\n client.create().forPath(\"/base\");\n client.getChildren().usingWatcher(watcher).forPath(\"/base\");\n client.create().forPath(\"/base/child\");\n\n String path = queue.take();\n Assert.assertEquals(path, \"/base\");\n }\n finally\n {\n client.close();\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void transactionObject(final String trytes) {\n\n if (StringUtils.isEmpty(trytes)) {\n log.warn(\"Warning: empty trytes in input for transactionObject\");\n return;\n }\n\n // validity check\n for (int i = 2279; i < 2295; i++) {\n if (trytes.charAt(i) != '9') {\n log.warn(\"Trytes {} does not seem a valid tryte\", trytes);\n return;\n }\n }\n\n int[] transactionTrits = Converter.trits(trytes);\n int[] hash = new int[243];\n\n ICurl curl = SpongeFactory.create(SpongeFactory.Mode.CURL);\n // generate the correct transaction hash\n curl.reset();\n curl.absorb(transactionTrits, 0, transactionTrits.length);\n curl.squeeze(hash, 0, hash.length);\n\n this.setHash(Converter.trytes(hash));\n this.setSignatureFragments(trytes.substring(0, 2187));\n this.setAddress(trytes.substring(2187, 2268));\n this.setValue(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6804, 6837)));\n this.setTag(trytes.substring(2295, 2322));\n this.setTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6966, 6993)));\n this.setCurrentIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6993, 7020)));\n this.setLastIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7020, 7047)));\n this.setBundle(trytes.substring(2349, 2430));\n this.setTrunkTransaction(trytes.substring(2430, 2511));\n this.setBranchTransaction(trytes.substring(2511, 2592));\n this.setNonce(trytes.substring(2592, 2673));\n } \n #location 21 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void transactionObject(final String trytes) {\n\n if (StringUtils.isEmpty(trytes)) {\n log.warn(\"Warning: empty trytes in input for transactionObject\");\n return;\n }\n\n // validity check\n for (int i = 2279; i < 2295; i++) {\n if (trytes.charAt(i) != '9') {\n log.warn(\"Trytes {} does not seem a valid tryte\", trytes);\n return;\n }\n }\n\n int[] transactionTrits = Converter.trits(trytes);\n int[] hash = new int[243];\n\n ICurl curl = SpongeFactory.create(SpongeFactory.Mode.CURLP81);\n // generate the correct transaction hash\n curl.reset();\n curl.absorb(transactionTrits, 0, transactionTrits.length);\n curl.squeeze(hash, 0, hash.length);\n\n this.setHash(Converter.trytes(hash));\n this.setSignatureFragments(trytes.substring(0, 2187));\n this.setAddress(trytes.substring(2187, 2268));\n this.setValue(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6804, 6837)));\n this.setObsoleteTag(trytes.substring(2295, 2322));\n this.setTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6966, 6993)));\n this.setCurrentIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6993, 7020)));\n this.setLastIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7020, 7047)));\n this.setBundle(trytes.substring(2349, 2430));\n this.setTrunkTransaction(trytes.substring(2430, 2511));\n this.setBranchTransaction(trytes.substring(2511, 2592));\n this.setTag(trytes.substring(2592, 2619));\n this.setAttachmentTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7857, 7884)) / 1000);\n this.setAttachmentTimestampLowerBound(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7884, 7911)));\n this.setAttachmentTimestampUpperBound(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7911, 7938)));\n this.setNonce(trytes.substring(2646, 2673));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public GetTransferResponse getTransfers(String seed, Integer start, Integer end, Boolean inclusionStates) throws ArgumentException, InvalidBundleException, InvalidSignatureException {\n start = start != null ? 0 : start;\n end = end == null ? null : end;\n inclusionStates = inclusionStates != null ? inclusionStates : null;\n\n if (start > end || end > (start + 500)) {\n throw new ArgumentException();\n }\n\n GetNewAddressResponse gnr = getNewAddress(seed, start, false, end == null ? end - start : end, true);\n if (gnr != null && gnr.getAddresses() != null) {\n Bundle[] bundles = bundlesFromAddresses(gnr.getAddresses().toArray(new String[gnr.getAddresses().size()]), inclusionStates);\n return GetTransferResponse.create(bundles);\n }\n return null;\n } \n #location 6 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public GetTransferResponse getTransfers(String seed, Integer start, Integer end, Boolean inclusionStates) throws ArgumentException, InvalidBundleException, InvalidSignatureException {\n // validate & if needed pad seed\n if ( (seed = InputValidator.validateSeed(seed)) == null) {\n throw new IllegalStateException(\"Invalid Seed\");\n }\n\n start = start != null ? 0 : start;\n end = end == null ? null : end;\n inclusionStates = inclusionStates != null ? inclusionStates : null;\n\n if (start > end || end > (start + 500)) {\n throw new ArgumentException();\n }\n StopWatch sw = new StopWatch();\n sw.start();\n System.out.println(\"GetTransfer started\");\n GetNewAddressResponse gnr = getNewAddress(seed, start, false, end == null ? end - start : end, true);\n if (gnr != null && gnr.getAddresses() != null) {\n System.out.println(\"GetTransfers after getNewAddresses \" + sw.getTime() + \" ms\");\n Bundle[] bundles = bundlesFromAddresses(gnr.getAddresses().toArray(new String[gnr.getAddresses().size()]), inclusionStates);\n System.out.println(\"GetTransfers after bundlesFromAddresses \" + sw.getTime() + \" ms\");\n sw.stop();\n\n return GetTransferResponse.create(bundles);\n }\n sw.stop();\n return null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void transactionObject(final String trytes) {\n\n if (StringUtils.isEmpty(trytes)) {\n log.warn(\"Warning: empty trytes in input for transactionObject\");\n return;\n }\n\n // validity check\n for (int i = 2279; i < 2295; i++) {\n if (trytes.charAt(i) != '9') {\n log.warn(\"Trytes {} does not seem a valid tryte\", trytes);\n return;\n }\n }\n\n int[] transactionTrits = Converter.trits(trytes);\n int[] hash = new int[243];\n\n ICurl curl = SpongeFactory.create(SpongeFactory.Mode.CURL);\n // generate the correct transaction hash\n curl.reset();\n curl.absorb(transactionTrits, 0, transactionTrits.length);\n curl.squeeze(hash, 0, hash.length);\n\n this.setHash(Converter.trytes(hash));\n this.setSignatureFragments(trytes.substring(0, 2187));\n this.setAddress(trytes.substring(2187, 2268));\n this.setValue(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6804, 6837)));\n this.setTag(trytes.substring(2295, 2322));\n this.setTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6966, 6993)));\n this.setCurrentIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6993, 7020)));\n this.setLastIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7020, 7047)));\n this.setBundle(trytes.substring(2349, 2430));\n this.setTrunkTransaction(trytes.substring(2430, 2511));\n this.setBranchTransaction(trytes.substring(2511, 2592));\n this.setNonce(trytes.substring(2592, 2673));\n } \n #location 21 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public void transactionObject(final String trytes) {\n\n if (StringUtils.isEmpty(trytes)) {\n log.warn(\"Warning: empty trytes in input for transactionObject\");\n return;\n }\n\n // validity check\n for (int i = 2279; i < 2295; i++) {\n if (trytes.charAt(i) != '9') {\n log.warn(\"Trytes {} does not seem a valid tryte\", trytes);\n return;\n }\n }\n\n int[] transactionTrits = Converter.trits(trytes);\n int[] hash = new int[243];\n\n ICurl curl = SpongeFactory.create(SpongeFactory.Mode.CURLP81);\n // generate the correct transaction hash\n curl.reset();\n curl.absorb(transactionTrits, 0, transactionTrits.length);\n curl.squeeze(hash, 0, hash.length);\n\n this.setHash(Converter.trytes(hash));\n this.setSignatureFragments(trytes.substring(0, 2187));\n this.setAddress(trytes.substring(2187, 2268));\n this.setValue(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6804, 6837)));\n this.setObsoleteTag(trytes.substring(2295, 2322));\n this.setTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6966, 6993)));\n this.setCurrentIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 6993, 7020)));\n this.setLastIndex(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7020, 7047)));\n this.setBundle(trytes.substring(2349, 2430));\n this.setTrunkTransaction(trytes.substring(2430, 2511));\n this.setBranchTransaction(trytes.substring(2511, 2592));\n this.setTag(trytes.substring(2592, 2619));\n this.setAttachmentTimestamp(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7857, 7884)) / 1000);\n this.setAttachmentTimestampLowerBound(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7884, 7911)));\n this.setAttachmentTimestampUpperBound(Converter.longValue(Arrays.copyOfRange(transactionTrits, 7911, 7938)));\n this.setNonce(trytes.substring(2646, 2673));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public GetTransferResponse getTransfers(String seed, Integer start, Integer end, Boolean inclusionStates) throws ArgumentException, InvalidBundleException, InvalidSignatureException {\n start = start != null ? 0 : start;\n end = end == null ? null : end;\n inclusionStates = inclusionStates != null ? inclusionStates : null;\n\n if (start > end || end > (start + 500)) {\n throw new ArgumentException();\n }\n\n GetNewAddressResponse gnr = getNewAddress(seed, start, false, end == null ? end - start : end, true);\n if (gnr != null && gnr.getAddresses() != null) {\n Bundle[] bundles = bundlesFromAddresses(gnr.getAddresses().toArray(new String[gnr.getAddresses().size()]), inclusionStates);\n return GetTransferResponse.create(bundles);\n }\n return null;\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n public GetTransferResponse getTransfers(String seed, Integer start, Integer end, Boolean inclusionStates) throws ArgumentException, InvalidBundleException, InvalidSignatureException {\n // validate & if needed pad seed\n if ( (seed = InputValidator.validateSeed(seed)) == null) {\n throw new IllegalStateException(\"Invalid Seed\");\n }\n\n start = start != null ? 0 : start;\n end = end == null ? null : end;\n inclusionStates = inclusionStates != null ? inclusionStates : null;\n\n if (start > end || end > (start + 500)) {\n throw new ArgumentException();\n }\n StopWatch sw = new StopWatch();\n sw.start();\n System.out.println(\"GetTransfer started\");\n GetNewAddressResponse gnr = getNewAddress(seed, start, false, end == null ? end - start : end, true);\n if (gnr != null && gnr.getAddresses() != null) {\n System.out.println(\"GetTransfers after getNewAddresses \" + sw.getTime() + \" ms\");\n Bundle[] bundles = bundlesFromAddresses(gnr.getAddresses().toArray(new String[gnr.getAddresses().size()]), inclusionStates);\n System.out.println(\"GetTransfers after bundlesFromAddresses \" + sw.getTime() + \" ms\");\n sw.stop();\n\n return GetTransferResponse.create(bundles);\n }\n sw.stop();\n return null;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private synchronized boolean send(byte[] bytes) {\n // buffering\n if (pendings.position() + bytes.length > pendings.capacity()) {\n LOG.severe(\"Cannot send logs to \" + server.toString());\n return false;\n }\n pendings.put(bytes);\n\n try {\n // suppress reconnection burst\n if (!reconnector.enableReconnection(System.currentTimeMillis())) {\n return true;\n }\n\n // check whether connection is established or not\n reconnect();\n\n // write data\n out.write(getBuffer());\n out.flush();\n\n clearBuffer();\n } catch (IOException e) {\n // close socket\n close();\n }\n return true;\n } \n #location 25 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private synchronized boolean send(byte[] bytes) {\n // buffering\n if (pendings.position() + bytes.length > pendings.capacity()) {\n LOG.severe(\"Cannot send logs to \" + server.toString());\n return false;\n }\n pendings.put(bytes);\n\n try {\n // suppress reconnection burst\n if (!reconnector.enableReconnection(System.currentTimeMillis())) {\n return true;\n }\n\n // send pending data\n flush();\n } catch (IOException e) {\n // close socket\n close();\n }\n return true;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n } \n #location 9 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n\n props.remove(Config.FLUENT_SENDER_CLASS);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void run() throws IOException {\n\tSocket socket = serverSock.accept();\n\tBufferedInputStream in = new BufferedInputStream(socket.getInputStream());\n\t// TODO\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void run() {\n\ttry {\n\t final Socket socket = serverSocket.accept();\n\t Thread th = new Thread() {\n\t\tpublic void run() {\n\t\t try {\n\t\t\tprocess.process(msgpack, socket);\n\t\t } catch (IOException e) { // ignore\n\t\t }\n\t\t}\n\t };\n\t th.start();\n\t} catch (IOException e) {\n\t e.printStackTrace();\n\t}\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n } \n #location 8 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n\n props.remove(Config.FLUENT_SENDER_CLASS);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private synchronized boolean send(byte[] bytes) {\n // buffering\n if (pendings.position() + bytes.length > pendings.capacity()) {\n LOG.severe(\"Cannot send logs to \" + server.toString());\n return false;\n }\n pendings.put(bytes);\n\n try {\n // suppress reconnection burst\n if (!reconnector.enableReconnection(System.currentTimeMillis())) {\n return true;\n }\n\n // send pending data\n flush();\n } catch (IOException e) {\n // close socket\n close();\n }\n return true;\n } \n #location 19 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private synchronized boolean send(byte[] bytes) {\n // buffering\n if (pendings.position() + bytes.length > pendings.capacity()) {\n LOG.severe(\"Cannot send logs to \" + server.toString());\n return false;\n }\n pendings.put(bytes);\n\n // suppress reconnection burst\n if (!reconnector.enableReconnection(System.currentTimeMillis())) {\n return true;\n }\n\n // send pending data\n flush();\n\n return true;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n } \n #location 10 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n @Test\n public void testClose() throws Exception {\n // use NullSender\n Properties props = System.getProperties();\n props.setProperty(Config.FLUENT_SENDER_CLASS, NullSender.class.getName());\n\n // create logger objects\n FluentLogger.getLogger(\"tag1\");\n FluentLogger.getLogger(\"tag2\");\n FluentLogger.getLogger(\"tag3\");\n\n Map loggers;\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(3, loggers.size());\n }\n\n // close and delete\n FluentLogger.close();\n {\n loggers = FluentLogger.getLoggers();\n assertEquals(0, loggers.size());\n }\n\n props.remove(Config.FLUENT_SENDER_CLASS);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void run() {\n while (!finished.get()) {\n try {\n final Socket socket = serverSocket.accept();\n Runnable r = new Runnable() {\n public void run() {\n try {\n MessagePack msgpack = new MessagePack();\n msgpack.register(Event.class, MockEventTemplate.INSTANCE);\n process.process(msgpack, socket);\n } catch (IOException e) {\n // ignore\n }\n }\n };\n new Thread(r).start();\n } catch (IOException e) {\n // ignore\n }\n }\n } \n #location 16 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void run() {\n while (!finished.get()) {\n try {\n final Socket socket = serverSocket.accept();\n socket.setSoLinger(true, 0);\n clientSockets.add(socket);\n Runnable r = new Runnable() {\n public void run() {\n try {\n MessagePack msgpack = new MessagePack();\n msgpack.register(Event.class, MockEventTemplate.INSTANCE);\n process.process(msgpack, socket);\n } catch (IOException e) {\n // ignore\n }\n }\n };\n new Thread(r).start();\n } catch (IOException e) {\n // ignore\n }\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void run() throws IOException {\n\tSocket socket = serverSock.accept();\n\tBufferedInputStream in = new BufferedInputStream(socket.getInputStream());\n\t// TODO\n } \n #location 3 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void run() {\n\ttry {\n\t final Socket socket = serverSocket.accept();\n\t Thread th = new Thread() {\n\t\tpublic void run() {\n\t\t try {\n\t\t\tprocess.process(msgpack, socket);\n\t\t } catch (IOException e) { // ignore\n\t\t }\n\t\t}\n\t };\n\t th.start();\n\t} catch (IOException e) {\n\t e.printStackTrace();\n\t}\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testRenderMultipleObjects() { \n \n TestObject testObject = new TestObject();\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(testObject);\n \n \n assertEquals(testObject, result.getRenderable());\n\n // step 2: add a second object (string is just a dummy)\n // => we expect to get a map from the result now...\n String string = new String(\"test\");\n \n result.render(string);\n \n assertTrue(result.getRenderable() instanceof Map);\n Map resultMap = (Map) result.getRenderable();\n assertEquals(string, resultMap.get(\"string\"));\n assertEquals(testObject, resultMap.get(\"testObject\"));\n \n // step 3: add same object => we expect an illegal argument exception as the map\n // cannot handle that case:\n TestObject anotherObject = new TestObject();\n boolean gotException = false;\n try {\n result.render(anotherObject);\n } catch (IllegalArgumentException e) {\n gotException = true;\n }\n \n assertTrue(gotException);\n \n \n // step 4: add an entry\n Entry entry = new AbstractMap.SimpleImmutableEntry(\"anotherObject\", anotherObject);\n result.render(entry);\n resultMap = (Map) result.getRenderable();\n assertEquals(3, resultMap.size());\n assertEquals(anotherObject, resultMap.get(\"anotherObject\"));\n \n \n // step 5: add another map and check that conversion works:\n Map mapToRender = Maps.newHashMap();\n \n String anotherString = new String(\"anotherString\");\n TestObject anotherTestObject = new TestObject();\n mapToRender.put(\"anotherString\", anotherString);\n mapToRender.put(\"anotherTestObject\", anotherTestObject);\n result.render(mapToRender);\n \n \n resultMap = (Map) result.getRenderable();\n assertEquals(5, resultMap.size());\n assertEquals(anotherString, resultMap.get(\"anotherString\"));\n assertEquals(anotherTestObject, resultMap.get(\"anotherTestObject\"));\n \n \n \n } \n #location 21 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testRenderMultipleObjects() { \n \n TestObject testObject = new TestObject();\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(testObject);\n \n \n assertEquals(testObject, result.getRenderable());\n\n // step 2: add a second object (string is just a dummy)\n // => we expect to get a map from the result now...\n String string = new String(\"test\");\n \n result.render(string);\n \n assertTrue(result.getRenderable() instanceof Map);\n Map resultMap = (Map) result.getRenderable();\n assertEquals(string, resultMap.get(\"string\"));\n assertEquals(testObject, resultMap.get(\"testObject\"));\n \n // step 3: add same object => we expect an illegal argument exception as the map\n // cannot handle that case:\n TestObject anotherObject = new TestObject();\n boolean gotException = false;\n try {\n result.render(anotherObject);\n } catch (IllegalArgumentException e) {\n gotException = true;\n }\n \n assertTrue(gotException);\n \n \n // step 4: add an entry\n Entry entry = new AbstractMap.SimpleImmutableEntry(\"anotherObject\", anotherObject);\n result.render(entry);\n resultMap = (Map) result.getRenderable();\n assertEquals(3, resultMap.size());\n assertEquals(anotherObject, resultMap.get(\"anotherObject\"));\n \n \n // step 5: add another map and check that conversion works:\n Map mapToRender = Maps.newHashMap();\n \n String anotherString = new String(\"anotherString\");\n TestObject anotherTestObject = new TestObject();\n mapToRender.put(\"anotherString\", anotherString);\n mapToRender.put(\"anotherTestObject\", anotherTestObject);\n result.render(mapToRender);\n \n \n resultMap = (Map) result.getRenderable();\n assertEquals(2, resultMap.size());\n assertEquals(anotherString, resultMap.get(\"anotherString\"));\n assertEquals(anotherTestObject, resultMap.get(\"anotherTestObject\"));\n \n \n \n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testRenderingOfStringObjectPairsWorks() { \n String object1 = new String(\"stringy1\");\n String object2 = new String(\"stringy2\");\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(\"object1\", object1);\n result.render(\"object2\", object2);\n Map resultMap = (Map) result.getRenderable(); \n \n assertEquals(object1, resultMap.get(\"object1\"));\n assertEquals(object2, resultMap.get(\"object2\"));\n \n \n ///////////////////////////////////////////////////////////////////////\n // check that empty render throws exception\n ///////////////////////////////////////////////////////////////////////\n boolean gotException = false;\n try {\n \n // will throw exception\n result.render();\n \n } catch (IllegalArgumentException e) {\n gotException = true;\n }\n \n assertTrue(gotException);\n \n ///////////////////////////////////////////////////////////////////////\n // check that too many arguments in render(...) throws exception\n ///////////////////////////////////////////////////////////////////////\n gotException = false;\n try {\n \n // will throw exception\n result.render(object1, object2, new String(\"three\"));\n \n } catch (IllegalArgumentException e) {\n gotException = true;\n }\n \n assertTrue(gotException);\n \n \n ///////////////////////////////////////////////////////////////////////\n // check that \"correct\" two string render throws exception\n // when first parameter is not a string\n ///////////////////////////////////////////////////////////////////////\n gotException = false;\n try {\n \n // will throw exception\n result.render(new TestObject(), object2);\n \n } catch (IllegalArgumentException e) {\n gotException = true;\n }\n \n assertTrue(gotException);\n \n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testRenderingOfStringObjectPairsWorks() { \n String object1 = new String(\"stringy1\");\n String object2 = new String(\"stringy2\");\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(\"object1\", object1);\n result.render(\"object2\", object2);\n Map resultMap = (Map) result.getRenderable(); \n \n assertEquals(object1, resultMap.get(\"object1\"));\n assertEquals(object2, resultMap.get(\"object2\")); \n \n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static String makeJsonRequest(String url) {\n\n\t\tStringBuffer sb = new StringBuffer();\n\t\ttry {\n\n\t\t\tDefaultHttpClient httpClient = new DefaultHttpClient();\n\t\t\tHttpGet getRequest = new HttpGet(url);\n\t\t\tgetRequest.addHeader(\"accept\", \"application/json\");\n\n\t\t\tHttpResponse response;\n\n\t\t\tresponse = httpClient.execute(getRequest);\n\n\t\t\tif (response.getStatusLine().getStatusCode() != 200) {\n\t\t\t\tthrow new RuntimeException(\"Failed : HTTP error code : \"\n\t\t\t\t + response.getStatusLine().getStatusCode());\n\t\t\t}\n\n\t\t\tBufferedReader br = new BufferedReader(new InputStreamReader(\n\t\t\t (response.getEntity().getContent())));\n\n\t\t\tString output;\n\t\t\twhile ((output = br.readLine()) != null) {\n\t\t\t\tsb.append(output);\n\t\t\t}\n\n\t\t\thttpClient.getConnectionManager().shutdown();\n\t\t} catch (ClientProtocolException e) {\n\t\t\t// TODO Auto-generated catch block\n\t\t\te.printStackTrace();\n\t\t} catch (IOException e) {\n\t\t\t// TODO Auto-generated catch block\n\t\t\te.printStackTrace();\n\t\t}\n\n\t\treturn sb.toString();\n\n\t} \n #location 28 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public static String makeJsonRequest(String url) {\n\t\t\n\t\tMap headers = Maps.newHashMap();\n\t\theaders.put(\"accept\", \"application/json\");\n\t\t\n\t\treturn makeRequest(url, headers);\n\n\t}" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void parse() {\n Map params;\n RouteParameter param;\n \n // no named parameters is null\n params = RouteParameter.parse(\"/user\");\n assertThat(params, is(nullValue()));\n \n params = RouteParameter.parse(\"/user/{id}/{email: [0-9]+}\");\n \n param = params.get(\"id\");\n assertThat(param.getName(), is(\"id\"));\n assertThat(param.getToken(), is(\"{id}\"));\n assertThat(param.getRegex(), is(nullValue()));\n \n param = params.get(\"email\");\n assertThat(param.getName(), is(\"email\"));\n assertThat(param.getToken(), is(\"{email: [0-9]+}\"));\n assertThat(param.getRegex(), is(\"[0-9]+\"));\n } \n #location 12 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void parse() {\n Map params;\n RouteParameter param;\n \n // no named parameters is null\n params = RouteParameter.parse(\"/user\");\n assertThat(params, aMapWithSize(0));\n \n params = RouteParameter.parse(\"/user/{id}/{email: [0-9]+}\");\n \n param = params.get(\"id\");\n assertThat(param.getName(), is(\"id\"));\n assertThat(param.getToken(), is(\"{id}\"));\n assertThat(param.getRegex(), is(nullValue()));\n \n param = params.get(\"email\");\n assertThat(param.getName(), is(\"email\"));\n assertThat(param.getToken(), is(\"{email: [0-9]+}\"));\n assertThat(param.getRegex(), is(\"[0-9]+\"));\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testRenderEntryAndMakeSureMapIsCreated() { \n String stringy = new String(\"stringy\");\n \n Entry entry \n = new SimpleImmutableEntry(\"stringy\", stringy);\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(entry);\n Map resultMap = (Map) result.getRenderable(); \n \n assertEquals(stringy, resultMap.get(\"stringy\"));\n \n } \n #location 13 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testRenderEntryAndMakeSureMapIsCreated() { \n String stringy = new String(\"stringy\");\n \n // step 1: add one object.\n Result result = new Result(200);\n result.render(\"stringy\", stringy);\n Map resultMap = (Map) result.getRenderable(); \n \n assertEquals(stringy, resultMap.get(\"stringy\"));\n \n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n static private SourceSnippet readFromInputStream(InputStream is,\n URI source,\n int lineFrom,\n int lineTo) throws IOException {\n if (lineTo <= 0) {\n throw new IllegalArgumentException(\"lineTo was <= 0\");\n }\n \n // just zero this out\n if (lineFrom < 0) {\n lineFrom = 0;\n }\n \n if (lineTo < lineFrom) {\n throw new IllegalArgumentException(\"lineTo was < lineFrom\");\n }\n \n BufferedReader in = new BufferedReader(\n new InputStreamReader(is));\n \n List lines = new ArrayList<>();\n \n int i = 0;\n String line;\n while ((line = in.readLine()) != null) {\n i++; // lines index are 1-based\n if (i >= lineFrom) {\n if (i <= lineTo) {\n lines.add(line);\n } else {\n break;\n }\n }\n }\n \n if (lines.isEmpty()) {\n return null;\n }\n \n // since file may not contain enough lines for requested lineTo -- \n // we caclulate the actual range here by number read \"from\" line.\n return new SourceSnippet(source, lines, lineFrom, lineFrom + lines.size());\n } \n #location 42 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n static private SourceSnippet readFromInputStream(InputStream is,\n URI source,\n int lineFrom,\n int lineTo) throws IOException {\n // did the user provide a strange range (e.g. negative values)?\n // this sometimes may happen when a range is provided like an error\n // on line 3 and you want 5 before and 5 after\n if (lineFrom < 1 && lineTo > 0) {\n // calculate intended range\n int intendedRange = lineTo - lineFrom;\n lineFrom = 1;\n lineTo = lineFrom + intendedRange;\n }\n else if (lineFrom < 0 && lineTo < 0) {\n if (lineFrom < lineTo) {\n int intendedRange = -1 * (lineFrom - lineTo);\n lineFrom = 1;\n lineTo = lineFrom + intendedRange;\n }\n else {\n // giving up\n return null;\n }\n }\n \n BufferedReader in = new BufferedReader(\n new InputStreamReader(is));\n \n List lines = new ArrayList<>();\n \n int i = 0;\n String line;\n while ((line = in.readLine()) != null) {\n i++; // lines index are 1-based\n if (i >= lineFrom) {\n if (i <= lineTo) {\n lines.add(line);\n } else {\n break;\n }\n }\n }\n \n if (lines.isEmpty()) {\n return null;\n }\n \n // since file may not contain enough lines for requested lineTo -- \n // we caclulate the actual range here by number read \"from\" line\n // since we are inclusive and not zero based we adjust the \"from\" by 1\n return new SourceSnippet(source, lines, lineFrom, lineFrom + lines.size() - 1);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String makeRequest(String url, Map headers) {\n\n StringBuffer sb = new StringBuffer();\n try {\n\n HttpGet getRequest = new HttpGet(url);\n\n if (headers != null) {\n // add all headers\n for (Entry header : headers.entrySet()) {\n getRequest.addHeader(header.getKey(), header.getValue());\n }\n }\n\n HttpResponse response;\n\n response = httpClient.execute(getRequest);\n\n BufferedReader br = new BufferedReader(new InputStreamReader(\n response.getEntity().getContent(), \"UTF-8\"));\n\n String output;\n while ((output = br.readLine()) != null) {\n sb.append(output);\n }\n\n getRequest.releaseConnection();\n\n } catch (Exception e) {\n throw new RuntimeException(e);\n }\n\n return sb.toString();\n\n } \n #location 29 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public String makeRequest(String url, Map headers) {\n\n StringBuffer sb = new StringBuffer();\n BufferedReader br = null;\n try {\n\n HttpGet getRequest = new HttpGet(url);\n\n if (headers != null) {\n // add all headers\n for (Entry header : headers.entrySet()) {\n getRequest.addHeader(header.getKey(), header.getValue());\n }\n }\n\n HttpResponse response;\n\n response = httpClient.execute(getRequest);\n\n br = new BufferedReader(new InputStreamReader(response.getEntity().getContent(), \"UTF-8\"));\n\n String output;\n while ((output = br.readLine()) != null) {\n sb.append(output);\n }\n\n getRequest.releaseConnection();\n\n } catch (Exception e) {\n throw new RuntimeException(e);\n } finally {\n if (br != null) {\n try {\n br.close();\n } catch (IOException e) {\n LOG.error(\"Failed to close resource\", e);\n }\n }\n }\n\n return sb.toString();\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public void handleTemplateException(TemplateException te,\n Environment env,\n Writer out) {\n\n if (ninjaProperties.isProd()) {\n \n PrintWriter pw = (out instanceof PrintWriter) ? (PrintWriter) out\n : new PrintWriter(out);\n pw.println(\n \"\"\n + \"\"\n + \"\"\n + \"\"\n + \"
    \"\n + \"\"\n + \"\"\n + \"
    \");\n pw.println(\"Ooops. A really strange error occurred. Please contact admin if error persists.\");\n pw.println(\"
    \");\n pw.flush();\n pw.close();\n \n logger.log(Level.SEVERE, \"Templating error. This should not happen in production\", te);\n \n \n\n } else {\n \n // print out full stacktrace if we are in test or dev mode\n\n PrintWriter pw = (out instanceof PrintWriter) ? (PrintWriter) out\n : new PrintWriter(out);\n pw.println(\"\"\n + \"\"\n + \"\"\n + \"\"\n + \"\"\n + \"    \"\n + \"\"\n + \"\"\n + \"
    \"\n + \"FreeMarker template error!\"\n + \"
    \");\n            te.printStackTrace(pw);\n            pw.println(\"
    \");\n pw.flush();\n pw.close();\n \n logger.log(Level.SEVERE, \"Templating error.\", te);\n }\n\n } \n #location 62 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public void handleTemplateException(TemplateException te,\n Environment env,\n Writer out) throws TemplateException {\n\n if (!ninjaProperties.isProd()) {\n // print out full stacktrace if we are in test or dev mode\n\n PrintWriter pw = (out instanceof PrintWriter) ? (PrintWriter) out\n : new PrintWriter(out);\n pw.println(\"\"\n + \"\"\n + \"\"\n + \"\"\n + \"\"\n + \"    \"\n + \"\"\n + \"\"\n + \"
    \"\n + \"FreeMarker template error!\"\n + \"
    \");\n            te.printStackTrace(pw);\n            pw.println(\"
    \");\n pw.flush();\n pw.close();\n logger.error(\"Templating error.\", te);\n }\n // Let the exception bubble up to the central handlers\n // so the application can return the correct error page\n // or perform some other application specific action.\n throw te;\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public Object invoke(MethodInvocation invocation) throws Throwable {\n \n final UnitOfWork unitOfWork;\n \n // Only start a new unit of work if the entitymanager is empty\n // otherwise someone else has started the unit of work already\n // and we do nothing\n // Please compare to com.google.inject.persist.jpa.JpaLocalTxnInterceptor\n // we just mimick that interceptor\n //\n // IMPORTANT:\n // Nesting of begin() end() of unitOfWork is NOT allowed. Contrary to\n // the documentation of Google Guice as of March 2014.\n // Related Ninja issue: https://github.com/ninjaframework/ninja/issues/157\n if (entityManagerProvider.get() == null) {\n \n unitOfWork = unitOfWorkProvider.get();\n unitOfWork.begin();\n didWeStartWork.set(Boolean.TRUE);\n\n } else {\n // If unit of work already started we don't do anything here...\n // another UnitOfWorkInterceptor point point will take care...\n // This happens if you are nesting your calls.\n return invocation.proceed();\n }\n\n try {\n\n return invocation.proceed();\n\n } finally {\n\n if (null != didWeStartWork.get()) {\n \n didWeStartWork.remove();\n unitOfWork.end();\n \n }\n\n }\n\n } \n #location 19 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public Object invoke(MethodInvocation invocation) throws Throwable {\n \n if (null == didWeStartWork.get()) {\n \n unitOfWork.begin();\n didWeStartWork.set(Boolean.TRUE);\n \n } else {\n // If unit of work already started we don't do anything here...\n // another UnitOfWorkInterceptor point point will take care...\n // This happens if you are nesting your calls.\n return invocation.proceed();\n }\n\n try {\n\n return invocation.proceed();\n\n } finally {\n\n if (null != didWeStartWork.get()) {\n \n didWeStartWork.remove();\n unitOfWork.end();\n \n }\n\n }\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public String makePostRequestWithFormParameters(String url,\n Map headers,\n Map formParameters) {\n\n StringBuffer sb = new StringBuffer();\n\n try {\n\n HttpPost postRequest = new HttpPost(url);\n\n if (headers != null) {\n // add all headers\n for (Entry header : headers.entrySet()) {\n postRequest.addHeader(header.getKey(), header.getValue());\n }\n }\n\n // add form parameters:\n List formparams = new ArrayList();\n if (formParameters != null) {\n\n for (Entry parameter : formParameters\n .entrySet()) {\n\n formparams.add(new BasicNameValuePair(parameter.getKey(),\n parameter.getValue()));\n }\n\n }\n\n // encode form parameters and add\n UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams);\n postRequest.setEntity(entity);\n\n HttpResponse response;\n\n response = httpClient.execute(postRequest);\n\n BufferedReader br = new BufferedReader(new InputStreamReader(\n response.getEntity().getContent(), \"UTF-8\"));\n\n String output;\n while ((output = br.readLine()) != null) {\n sb.append(output);\n }\n\n postRequest.releaseConnection();\n\n } catch (Exception e) {\n throw new RuntimeException(e);\n }\n\n return sb.toString();\n\n } \n #location 49 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n public String makePostRequestWithFormParameters(String url,\n Map headers,\n Map formParameters) {\n\n StringBuffer sb = new StringBuffer();\n BufferedReader br = null;\n try {\n\n HttpPost postRequest = new HttpPost(url);\n\n if (headers != null) {\n // add all headers\n for (Entry header : headers.entrySet()) {\n postRequest.addHeader(header.getKey(), header.getValue());\n }\n }\n\n // add form parameters:\n List formparams = new ArrayList();\n if (formParameters != null) {\n\n for (Entry parameter : formParameters\n .entrySet()) {\n\n formparams.add(new BasicNameValuePair(parameter.getKey(),\n parameter.getValue()));\n }\n\n }\n\n // encode form parameters and add\n UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams);\n postRequest.setEntity(entity);\n\n HttpResponse response;\n\n response = httpClient.execute(postRequest);\n\n br = new BufferedReader(new InputStreamReader(response.getEntity().getContent(), \"UTF-8\"));\n\n String output;\n while ((output = br.readLine()) != null) {\n sb.append(output);\n }\n\n postRequest.releaseConnection();\n\n } catch (Exception e) {\n throw new RuntimeException(e);\n } finally {\n if (br != null) {\n try {\n br.close();\n } catch (IOException e) {\n LOG.error(\"Failed to close resource\", e);\n }\n }\n }\n\n return sb.toString();\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testAllConstants() {\n\n \n Configuration configuration =\n SwissKnife.loadConfigurationFromClasspathInUtf8(\"conf/all_constants.conf\", this\n .getClass());\n\n assertEquals(\"LANGUAGES\", configuration.getString(NinjaConstant.applicationLanguages));\n \n assertEquals(\"PREFIX\", configuration.getString(NinjaConstant.applicationCookiePrefix));\n\n assertEquals(\"NAME\", configuration.getString(NinjaConstant.applicationName));\n \n assertEquals(\"SECRET\", configuration.getString(NinjaConstant.applicationSecret));\n \n assertEquals(\"SERVER_NAME\", configuration.getString(NinjaConstant.serverName));\n\n assertEquals(9999, configuration.getInt(NinjaConstant.sessionExpireTimeInSeconds));\n\n assertEquals(false, configuration.getBoolean(NinjaConstant.sessionSendOnlyIfChanged));\n\n assertEquals(false, configuration.getBoolean(NinjaConstant.sessionTransferredOverHttpsOnly));\n\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testAllConstants() {\n\n \n Configuration configuration =\n SwissKnife.loadConfigurationInUtf8(\"conf/all_constants.conf\");\n\n assertEquals(\"LANGUAGES\", configuration.getString(NinjaConstant.applicationLanguages));\n \n assertEquals(\"PREFIX\", configuration.getString(NinjaConstant.applicationCookiePrefix));\n\n assertEquals(\"NAME\", configuration.getString(NinjaConstant.applicationName));\n \n assertEquals(\"SECRET\", configuration.getString(NinjaConstant.applicationSecret));\n \n assertEquals(\"SERVER_NAME\", configuration.getString(NinjaConstant.serverName));\n\n assertEquals(9999, configuration.getInt(NinjaConstant.sessionExpireTimeInSeconds));\n\n assertEquals(false, configuration.getBoolean(NinjaConstant.sessionSendOnlyIfChanged));\n\n assertEquals(false, configuration.getBoolean(NinjaConstant.sessionTransferredOverHttpsOnly));\n\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public boolean runSteps(FlowSpec scenario, FlowStepStatusNotifier flowStepStatusNotifier) {\n\n ScenarioExecutionState scenarioExecutionState = new ScenarioExecutionState();\n\n for(Step thisStep : scenario.getSteps()){\n // Another way to get the String\n // String requestJson = objectMapper.valueToTree(thisStep.getRequest()).toString();\n\n final String requestJsonAsString = thisStep.getRequest().toString();\n LOGGER.info(String.format(\"\\n###RAW: Journey:%s, Step:%s\", scenario.getFlowName(), thisStep.getName()));\n\n StepExecutionState stepExecutionState = new StepExecutionState();\n stepExecutionState.addStep(thisStep.getName());\n\n String resolvedRequestJson = jsonTestProcesor.resolveRequestJson(\n requestJsonAsString,\n scenarioExecutionState.getResolvedScenarioState()\n );\n stepExecutionState.addRequest(resolvedRequestJson);\n\n String executionResult;\n try{\n String serviceName = thisStep.getUrl();\n String operationName = thisStep.getOperation();\n\n // REST call execution\n Boolean isRESTCall = false;\n if( serviceName != null && serviceName.contains(\"/\")) {\n isRESTCall = true;\n }\n if(isRESTCall) {\n serviceName = getFullyQualifiedRestUrl(serviceName);\n executionResult = serviceExecutor.executeRESTService(serviceName, operationName, resolvedRequestJson);\n }\n else {\n executionResult = serviceExecutor.executeJavaService(serviceName, operationName, resolvedRequestJson);\n }\n\n stepExecutionState.addResponse(executionResult);\n scenarioExecutionState.addStepState(stepExecutionState.getResolvedStep());\n\n // Handle assertion section\n String resolvedAssertionJson = jsonTestProcesor.resolveRequestJson(\n thisStep.getAssertions().toString(),\n scenarioExecutionState.getResolvedScenarioState()\n );\n\n LOGGER.info(\"\\n---------> Assertion: <----------\\n\"\n + prettyPrintJson(resolvedAssertionJson));\n\n // TODO: Collect the assertion result into this list, say field by field\n List asserters = jsonTestProcesor.createAssertersFrom(resolvedAssertionJson);\n List failureResults = new ArrayList<>(); //<-- write code\n\n // TODO: During this step: if assertion failed\n if (!failureResults.isEmpty()) {\n return flowStepStatusNotifier.notifyFlowStepAssertionFailed(scenario.getFlowName(), thisStep.getName(), failureResults);\n }\n\n // TODO: Otherwise test passed\n //return flowStepStatusNotifier.notifyFlowStepExecutionPassed(scenario.getFlowName(), thisStep.getName());\n\n } catch(Exception ex){\n // During this step: if any exception occurred\n return flowStepStatusNotifier.notifyFlowStepExecutionException(\n scenario.getFlowName(),\n thisStep.getName(),\n new RuntimeException(\"Smart Step execution failed. Details:\" + ex)\n );\n }\n }\n\n /*\n * There were no steps to execute and the framework will display the test status as Green than Red.\n * Red symbolises failure, but nothing has failed here.\n */\n return true;\n } \n #location 33 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public boolean runSteps(FlowSpec scenario, FlowStepStatusNotifier flowStepStatusNotifier) {\n\n LOGGER.info(\"\\n-------------------------- Scenario:{} -------------------------\\n\", scenario.getFlowName());\n\n ScenarioExecutionState scenarioExecutionState = new ScenarioExecutionState();\n\n for(Step thisStep : scenario.getSteps()){\n // Another way to get the String\n // String requestJson = objectMapper.valueToTree(thisStep.getRequest()).toString();\n\n final String requestJsonAsString = thisStep.getRequest().toString();\n\n StepExecutionState stepExecutionState = new StepExecutionState();\n stepExecutionState.addStep(thisStep.getName());\n\n String resolvedRequestJson = jsonTestProcesor.resolveStringJson(\n requestJsonAsString,\n scenarioExecutionState.getResolvedScenarioState()\n );\n stepExecutionState.addRequest(resolvedRequestJson);\n\n String executionResult;\n final String logPrefixRelationshipId = createRelationshipId();\n try{\n String serviceName = thisStep.getUrl();\n String operationName = thisStep.getOperation();\n\n // Resolve the URL patterns if any\n serviceName = jsonTestProcesor.resolveStringJson(\n serviceName,\n scenarioExecutionState.getResolvedScenarioState()\n );\n\n //\n logCorelationshipPrinter.aRequestBuilder()\n .relationshipId(logPrefixRelationshipId)\n .requestTimeStamp(LocalDateTime.now())\n .step(thisStep.getName())\n .url(serviceName)\n .method(operationName)\n .request(SmartUtils.prettyPrintJson(resolvedRequestJson));\n //\n\n // REST call execution\n Boolean isRESTCall = false;\n if( serviceName != null && serviceName.contains(\"/\")) {\n isRESTCall = true;\n }\n if(isRESTCall) {\n serviceName = getFullyQualifiedRestUrl(serviceName);\n executionResult = serviceExecutor.executeRESTService(serviceName, operationName, resolvedRequestJson);\n }\n else {\n executionResult = serviceExecutor.executeJavaService(serviceName, operationName, resolvedRequestJson);\n }\n\n //\n logCorelationshipPrinter.aResponseBuilder()\n .relationshipId(logPrefixRelationshipId)\n .responseTimeStamp(LocalDateTime.now())\n .response(executionResult);\n //\n\n stepExecutionState.addResponse(executionResult);\n scenarioExecutionState.addStepState(stepExecutionState.getResolvedStep());\n\n // Handle assertion section\n String resolvedAssertionJson = jsonTestProcesor.resolveStringJson(\n thisStep.getAssertions().toString(),\n scenarioExecutionState.getResolvedScenarioState()\n );\n\n LOGGER.info(\"\\n---------> Assertion: <----------\\n{}\", prettyPrintJson(resolvedAssertionJson));\n\n List asserters = jsonTestProcesor.createAssertersFrom(resolvedAssertionJson);\n List failureResults = jsonTestProcesor.assertAllAndReturnFailed(asserters, executionResult); //<-- write code\n\n // TODO: During this step: if assertion failed\n if (!failureResults.isEmpty()) {\n return flowStepStatusNotifier.notifyFlowStepAssertionFailed(scenario.getFlowName(), thisStep.getName(), failureResults);\n }\n\n // TODO: Otherwise test passed\n flowStepStatusNotifier.notifyFlowStepExecutionPassed(scenario.getFlowName(), thisStep.getName());\n\n } catch(Exception ex){\n logCorelationshipPrinter.aResponseBuilder()\n .relationshipId(logPrefixRelationshipId)\n .responseTimeStamp(LocalDateTime.now())\n .response(ex.getMessage());\n\n // During this step: if any exception occurred\n return flowStepStatusNotifier.notifyFlowStepExecutionException(\n scenario.getFlowName(),\n thisStep.getName(),\n new RuntimeException(\"Smart Step execution failed. Details:\" + ex)\n );\n }\n finally {\n logCorelationshipPrinter.print();\n }\n }\n\n /*\n * There were no steps to execute and the framework will display the test status as Green than Red.\n * Red symbolises failure, but nothing has failed here.\n */\n return true;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Test\n public void testRawRecordingSpeed() throws Exception {\n Histogram histogram = new Histogram(highestTrackableValue, numberOfSignificantValueDigits);\n // Warm up:\n long startTime = System.nanoTime();\n recordLoop(histogram, warmupLoopLength);\n long endTime = System.nanoTime();\n long deltaUsec = (endTime - startTime) / 1000L;\n long rate = 1000000 * warmupLoopLength / deltaUsec;\n System.out.println(\"Warmup:\\n\" + warmupLoopLength + \" value recordings completed in \" +\n deltaUsec + \" usec, rate = \" + rate + \" value recording calls per sec.\");\n histogram.reset();\n // Wait a bit to make sure compiler had a cache to do it's stuff:\n try {\n Thread.sleep(1000);\n } catch (InterruptedException e) {\n }\n startTime = System.nanoTime();\n recordLoop(histogram, timingLoopCount);\n endTime = System.nanoTime();\n deltaUsec = (endTime - startTime) / 1000L;\n rate = 1000000 * timingLoopCount / deltaUsec;\n System.out.println(\"Timing:\");\n System.out.println(timingLoopCount + \" value recordings completed in \" +\n deltaUsec + \" usec, rate = \" + rate + \" value recording calls per sec.\");\n rate = 1000000 * histogram.getHistogramData().getTotalCount() / deltaUsec;\n System.out.println(histogram.getHistogramData().getTotalCount() + \" raw recorded entries completed in \" +\n deltaUsec + \" usec, rate = \" + rate + \" recorded values per sec.\");\n } \n #location 26 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Test\n public void testRawRecordingSpeed() throws Exception {\n testRawRecordingSpeedAtExpectedInterval(1000000000);\n testRawRecordingSpeedAtExpectedInterval(10000);\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n private static synchronized List loadJson() throws IOException {\n InputStream inStream = MenuJsonUtils.class.getResourceAsStream(config);\n BufferedReader reader = new BufferedReader(new InputStreamReader(inStream, Charset.forName(\"UTF-8\")));\n\n StringBuilder json = new StringBuilder();\n String tmp;\n while ((tmp = reader.readLine()) != null) {\n json.append(tmp);\n }\n\n List menus = JSONArray.parseArray(json.toString(), Menu.class);\n return menus;\n } \n #location 12 \n #vulnerability type RESOURCE_LEAK", "output": "#fixed code\n private static synchronized List loadJson() throws IOException {\n InputStream inStream = MenuJsonUtils.class.getResourceAsStream(config);\n BufferedReader reader = new BufferedReader(new InputStreamReader(inStream, Charset.forName(\"UTF-8\")));\n\n StringBuilder json = new StringBuilder();\n String tmp;\n try {\n while ((tmp = reader.readLine()) != null) {\n json.append(tmp);\n }\n } catch (IOException e) {\n throw e;\n } finally {\n reader.close();\n inStream.close();\n }\n\n List menus = JSONArray.parseArray(json.toString(), Menu.class);\n return menus;\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n @Override\n public void postHandle(HttpServletRequest request, HttpServletResponse response, HandlerMethod handler, ModelAndView modelAndView) throws Exception {\n PostVO ret = (PostVO) modelAndView.getModelMap().get(\"view\");\n Object editing = modelAndView.getModel().get(\"editing\");\n if (null == editing && ret != null) {\n PostVO post = new PostVO();\n BeanUtils.copyProperties(ret, post);\n if (check(ret.getId(), ret.getAuthor().getId())) {\n post.setContent(replace(post.getContent()));\n } else {\n String c = post.getContent().replaceAll(\"<hide>\", \"\");\n c = c.replaceAll(\"</hide>\", \"\");\n post.setContent(c);\n }\n modelAndView.getModelMap().put(\"view\", post);\n }\n } \n #location 9 \n #vulnerability type NULL_DEREFERENCE", "output": "#fixed code\n @Override\n public void postHandle(HttpServletRequest request, HttpServletResponse response, HandlerMethod handler, ModelAndView modelAndView) throws Exception {\n PostVO ret = (PostVO) modelAndView.getModelMap().get(\"view\");\n Object editing = modelAndView.getModel().get(\"editing\");\n if (null == editing && ret != null) {\n PostVO post = new PostVO();\n BeanUtils.copyProperties(ret, post);\n if (check(ret.getId(), ret.getAuthor().getId())) {\n String c = post.getContent().replaceAll(\"\\\\[hide\\\\]([\\\\s\\\\S]*)\\\\[\\\\/hide\\\\]\", SHOW);\n post.setContent(c);\n } else {\n String c = post.getContent().replaceAll(\"\\\\[hide\\\\]([\\\\s\\\\S]*)\\\\[\\\\/hide\\\\]\", \"$1\");\n post.setContent(c);\n }\n modelAndView.getModelMap().put(\"view\", post);\n }\n }" }, { "instruction": "Below is the vulnerable code, please generate the patch based on the following information.", "input": "#vulnerable code \n public static void main(String[] args) throws Exception {\n \n // STEP-1: read input parameters and validate them\n if (args.length < 2) {\n System.err.println(\"Usage: SecondarySortUsingGroupByKey \");\n System.exit(1);\n }\n String inputPath = args[0];\n System.out.println(\"inputPath=\" + inputPath);\n String outputPath = args[1];\n System.out.println(\"outputPath=\" + outputPath);\n\n // STEP-2: Connect to the Sark master by creating JavaSparkContext object\n final JavaSparkContext ctx = SparkUtil.createJavaSparkContext();\n\n // STEP-3: Use ctx to create JavaRDD\n // input record format: <,>