580 lines
20 KiB
Java
Executable File
580 lines
20 KiB
Java
Executable File
package org.gcube.dataanalysis.dataminer.poolmanager.util;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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***REMOVED***
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Calendar;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.LinkedList;
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***REMOVED***
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***REMOVED***
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import java.util.TimeZone;
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import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
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import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException;
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import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException;
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***REMOVED***
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***REMOVED***
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import org.tmatesoft.svn.core.SVNCommitInfo;
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import org.tmatesoft.svn.core.SVNErrorMessage;
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***REMOVED***
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import org.tmatesoft.svn.core.SVNNodeKind;
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import org.tmatesoft.svn.core.internal.wc.SVNFileUtil;
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import org.tmatesoft.svn.core.internal.wc.admin.SVNChecksumInputStream;
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import org.tmatesoft.svn.core.io.ISVNEditor;
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import org.tmatesoft.svn.core.io.SVNRepository;
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import org.tmatesoft.svn.core.io.diff.SVNDeltaGenerator;
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/**
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* Created by ggiammat on 5/9/17.
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*/
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public abstract class SVNUpdater ***REMOVED***
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private SVNRepository svnRepository;
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private Configuration configuration;
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private Logger logger;
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public SVNUpdater(Configuration configuration) throws SVNException ***REMOVED***
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this.configuration = configuration;
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this.svnRepository = SVNRepositoryManager.getInstance(configuration).getSvnRepository();
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this.logger = LoggerFactory.getLogger(SVNUpdater.class);
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***REMOVED***
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***REMOVED*** public void updateRPRotoDeps(Algorithm algorithm) ***REMOVED***
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***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoOSDepsList(), algorithm.getOSDependencies());
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***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getCranDependencies());
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***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoGitHubDepsList(), algorithm.getGitHubDependencies());
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***REMOVED******REMOVED***
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public String getDependencyFile(String language/*, String env*/)
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***REMOVED***
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return getDependencyFile(this.configuration,language);
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***REMOVED***
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private String getDependencyFile (Configuration configuration, String language)
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***REMOVED***
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this.logger.debug("Getting dependency file for language "+language);
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switch (language)
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***REMOVED***
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case "R":
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return configuration.getSVNCRANDepsList();
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case "R-blackbox":
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return configuration.getSVNRBDepsList();
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case "Java":
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return configuration.getSVNJavaDepsList();
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case "Knime-Workflow":
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return configuration.getSVNKWDepsList();
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case "Knime-Workflow4.1":
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return configuration.getSVNKW4_1DepsList();
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case "Linux-compiled":
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return configuration.getSVNLinuxCompiledDepsList();
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case "Octave":
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return configuration.getSVNOctaveDepsList();
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case "Python":
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return configuration.getSVNPythonDepsList();
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case "Python3.6":
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return configuration.getSVNPython3_6DepsList();
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case "Pre-Installed":
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return configuration.getSVNPreInstalledDepsList();
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case "Windows-compiled":
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return configuration.getSVNWCDepsList();
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default:
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***REMOVED***
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***REMOVED***
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***REMOVED***
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public boolean updateSVNAlgorithmList(Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/)
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***REMOVED***
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return this.updateSVNAlgorithmList(this.configuration.getSVNAlgorithmsList(), algorithm, targetVRE, category, algorithm_type, user);
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***REMOVED***
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public void updateAlgorithmFiles(File a) throws SVNException, SVNCommitException***REMOVED***
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***REMOVED***this.updateAlgorithmList(this.configuration.getSVNMainAlgoRepo(), a);
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this.updateAlgorithmList(this.configuration.getRepository(), a);
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***REMOVED***
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private void updateAlgorithmList(String svnMainAlgoRepo, File algorithmsFile) throws SVNException, SVNCommitException
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***REMOVED***
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this.logger.debug("Adding .jar file: " + algorithmsFile + " to repository " + svnMainAlgoRepo);
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try
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***REMOVED***
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if (fileExists(svnMainAlgoRepo+File.separator+algorithmsFile.getName(), -1))
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***REMOVED***
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this.updateFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo, algorithmsFile.getName());
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***REMOVED***
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else this.putFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo,algorithmsFile.getName());
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***REMOVED***
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catch (FileNotFoundException e)
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***REMOVED***
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this.logger.error("Temporary algorithm file not found: this exception should not happen",e);
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***REMOVED***
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finally
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***REMOVED***
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this.svnRepository.closeSession();
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***REMOVED***
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***REMOVED***
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public void putFile(FileInputStream fileInputSreeam, String destinationFolder, String fileName) throws SVNException, SVNCommitException
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***REMOVED***
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this.logger.debug("Putting new file on the SVN repository");
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final ISVNEditor commitEditor = svnRepository.getCommitEditor("Add algorithm to list", null);
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commitEditor.openRoot(-1);
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commitEditor.openDir(destinationFolder, -1);
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String filePath = destinationFolder + "/" + fileName;
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commitEditor.addFile(filePath, null, -1);
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commitEditor.applyTextDelta(filePath, null);
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SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
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String checksum = deltaGenerator.sendDelta(filePath, fileInputSreeam, commitEditor, true);
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commitEditor.closeFile(filePath, checksum);
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commitEditor.closeDir();
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commitEditor.closeDir();
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SVNCommitInfo info = commitEditor.closeEdit();
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SVNErrorMessage errorMessage = info.getErrorMessage();
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if (errorMessage != null)
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***REMOVED***
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this.logger.error("Operation failed: "+errorMessage.getFullMessage());
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throw new SVNCommitException(errorMessage,fileName);
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***REMOVED***
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this.logger.debug("Operation completed");
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***REMOVED***
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public void updateFile(FileInputStream fileInputStream, String destinationFolder, String fileName) throws SVNException, SVNCommitException ***REMOVED***
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this.logger.debug("Updating existing file on the SVN repository");
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final ISVNEditor commitEditor = svnRepository.getCommitEditor("Updating algorithm", null);
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commitEditor.openRoot(-1);
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commitEditor.openDir(destinationFolder, -1);
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String filePath = destinationFolder + "/" + fileName;
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***REMOVED*** if (fileExists(filePath, -1)) ***REMOVED*** ***REMOVED*** updating existing file
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commitEditor.openFile(filePath, -1);
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***REMOVED******REMOVED*** else ***REMOVED*** ***REMOVED*** creating new file
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***REMOVED***commitEditor.addFile(filePath, null, -1);
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***REMOVED******REMOVED***
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commitEditor.applyTextDelta(filePath, null);
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SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
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String checksum = deltaGenerator.sendDelta(filePath, fileInputStream, commitEditor, true);
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commitEditor.closeFile(filePath, checksum);
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commitEditor.closeDir();
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commitEditor.closeDir();
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SVNCommitInfo info = commitEditor.closeEdit();
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SVNErrorMessage errorMessage = info.getErrorMessage();
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if (errorMessage != null)
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***REMOVED***
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this.logger.error("Operation failed: "+errorMessage.getFullMessage());
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throw new SVNCommitException(errorMessage,fileName+" to be updated");
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***REMOVED***
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this.logger.debug("Operation completed");
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***REMOVED***
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public boolean fileExists(String path, long revision) throws SVNException ***REMOVED***
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SVNNodeKind kind = svnRepository.checkPath(path, revision);
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if (kind == SVNNodeKind.FILE) ***REMOVED***
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return true;
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***REMOVED***
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return false;
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***REMOVED***
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***REMOVED*** public static ByteArrayInputStream reteriveByteArrayInputStream(File file) throws IOException
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***REMOVED*** ***REMOVED***
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***REMOVED***
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***REMOVED*** return new ByteArrayInputStream(FileUtils.readFileToByteArray(file));
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***REMOVED******REMOVED***
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private boolean updateSVNAlgorithmList(String file, Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/)
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***REMOVED***
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boolean response = false;
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try ***REMOVED***
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this.logger.debug("Updating algorithm list: " + file);
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final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
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List<String> newContent = new LinkedList<>(Arrays.asList(lines));
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***REMOVED*** check if the algorithm is already in the list (match the class name) and delete the content
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for (String l : lines) ***REMOVED***
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if (l.contains(algorithm.getClazz())) ***REMOVED***
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newContent.remove(l);
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***REMOVED***System.out.println("Not updating algorithm list beacuse already present");
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***REMOVED***return;
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***REMOVED***
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***REMOVED***
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***REMOVED*** the algorithm is not in the list or must be overwritten cause some modification. Add it
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newContent.add(this.generateAlgorithmEntry(algorithm, targetVRE, category,algorithm_type/*, env*/));
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***REMOVED*** Collections.sort(newContent);
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final SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
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byte[] originalContents = byteArrayOutputStream.toByteArray();
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final ISVNEditor commitEditor = svnRepository.getCommitEditor("update algorithm list", null);
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commitEditor.openRoot(-1);
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commitEditor.openFile(file, -1);
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ByteArrayOutputStream baos = new ByteArrayOutputStream();
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for (String line : newContent) ***REMOVED***
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baos.write(line.getBytes());
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baos.write("\n".getBytes());
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***REMOVED***
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byte[] bytes = baos.toByteArray();
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commitEditor.applyTextDelta(file, md5(originalContents));
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final String checksum = deltaGenerator.sendDelta(file, new ByteArrayInputStream(originalContents), 0,
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new ByteArrayInputStream(bytes), commitEditor, true);
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commitEditor.closeFile(file, checksum);
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SVNCommitInfo info = commitEditor.closeEdit();
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SVNErrorMessage errorMessage = info.getErrorMessage();
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if (errorMessage != null)
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***REMOVED***
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this.logger.error("Operation failed: "+errorMessage.getFullMessage());
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response = false;
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***REMOVED***
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else response = true;
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***REMOVED***
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catch (Exception ex)
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***REMOVED***
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this.logger.error("Unable to commit algorithm list",ex);
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response = false;
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***REMOVED***
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finally
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***REMOVED***
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svnRepository.closeSession();
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***REMOVED***
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return response;
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***REMOVED***
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public String generateAlgorithmEntry(Algorithm algorithm, String targetVRE, String category, String algorithm_type/*,String env*/) throws ParseException ***REMOVED***
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***REMOVED***Timestamp timestamp = new Timestamp(System.currentTimeMillis());
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***REMOVED***long unixTime = System.currentTimeMillis() / 1000L;
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StringBuffer sb = new StringBuffer("| ");
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sb.append(algorithm.getName() + " | ");
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sb.append(algorithm.getFullname() + " | ");
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sb.append(category + " | ");
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sb.append("DataMinerPoolManager | ");
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sb.append("<notextile>./addAlgorithm.sh " + algorithm.getName() + " " + algorithm.getCategory() + " "
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+ algorithm.getClazz() + " " + targetVRE + " " + algorithm_type + " N "
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+ algorithm.getPackageURL() + " \"" + algorithm.getDescription() + "\" </notextile> | ");
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sb.append("none | ");
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sb.append(this.getTimeZone() + " | ");
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this.logger.info("Algo details: "+sb.toString());
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return sb.toString();
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***REMOVED***
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public Collection<String> getUndefinedDependencies(String file, Collection<Dependency> deps) throws GenericException
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***REMOVED***
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try
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***REMOVED***
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***REMOVED*** SendMail sm = new SendMail();
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***REMOVED*** NotificationHelper nh = new NotificationHelper();
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List<String> undefined = new LinkedList<String>();
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***REMOVED***to fix in next release: if the file is not present for that language in the service.properties then skip and return null list of string
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***REMOVED***just to uncomment the following lines
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if(file.isEmpty())***REMOVED***
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return undefined;
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***REMOVED***
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this.logger.debug("Checking dependencies list: " + file);
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List<String> validDependencies = new LinkedList<String>();
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for (String singlefile: CheckMethod.getFiles(file))***REMOVED***
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final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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svnRepository.getFile(singlefile, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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for(String l: byteArrayOutputStream.toString().split("\\r?\\n"))***REMOVED***
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validDependencies.add(l.trim());
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***REMOVED******REMOVED***
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this.logger.debug("Valid dependencies are: "+validDependencies);
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for(Dependency d: deps)***REMOVED***
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String depName = d.getName();
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if(!validDependencies.contains(depName))***REMOVED***
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undefined.add(depName);
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***REMOVED***
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***REMOVED***
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return undefined;
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***REMOVED***
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***REMOVED***
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***REMOVED*** for (String a : lines) ***REMOVED***
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***REMOVED*** for (String b : ldep) ***REMOVED***
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***REMOVED*** if (b.equals(a)) ***REMOVED***
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***REMOVED*** System.out.println("The following dependency is correctly written: " + b);
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***REMOVED*** ***REMOVED*** else
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***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED***
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***REMOVED*** boolean check = false;
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***REMOVED*** try ***REMOVED***
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***REMOVED*** System.out.println("Checking dependencies list: " + file);
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***REMOVED*** final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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***REMOVED*** svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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***REMOVED*** String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
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***REMOVED***
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***REMOVED*** ***REMOVED*** if(deps.isEmpty())***REMOVED***
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***REMOVED*** ***REMOVED*** sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody());
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***REMOVED*** ***REMOVED*** Exception e = new Exception("No dependency specified for this
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***REMOVED*** ***REMOVED*** algorithm");
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***REMOVED*** ***REMOVED*** throw e;
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***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED*** ***REMOVED***
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***REMOVED***
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***REMOVED*** ***REMOVED*** else if (!deps.isEmpty()) ***REMOVED***
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***REMOVED*** List<String> ldep = new LinkedList<>();
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***REMOVED*** for (Dependency d : deps) ***REMOVED***
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***REMOVED*** ldep.add(d.getName());
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***REMOVED*** ***REMOVED***
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***REMOVED*** for (String a : lines) ***REMOVED***
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***REMOVED*** for (String b : ldep) ***REMOVED***
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***REMOVED*** if (b.equals(a)) ***REMOVED***
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***REMOVED*** System.out.println("The following dependency is correctly written: " + b);
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***REMOVED*** check = true;
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***REMOVED*** ***REMOVED*** else
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***REMOVED*** check = false;
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***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED*** catch (Exception a) ***REMOVED***
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***REMOVED*** a.getMessage();
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***REMOVED*** ***REMOVED***
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***REMOVED***
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***REMOVED*** return check;
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***REMOVED*** catch (SVNException e)
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***REMOVED***
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throw new GenericException(e);
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***REMOVED***
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***REMOVED***
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public boolean checkIfAvaialable(String file, Collection<Dependency> deps) throws SVNException ***REMOVED***
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***REMOVED***SendMail sm = new SendMail();
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***REMOVED***NotificationHelper nh = new NotificationHelper();
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boolean check = false;
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try ***REMOVED***
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this.logger.info("Checking dependencies list: " + file);
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final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
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***REMOVED*** if(deps.isEmpty())***REMOVED***
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***REMOVED*** sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody());
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***REMOVED*** Exception e = new Exception("No dependency specified for this
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***REMOVED*** algorithm");
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***REMOVED*** throw e;
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***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED*** else if (!deps.isEmpty()) ***REMOVED***
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List<String> ldep = new LinkedList<>();
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for (Dependency d : deps) ***REMOVED***
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ldep.add(d.getName());
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***REMOVED***
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for (String a : lines) ***REMOVED***
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for (String b : ldep) ***REMOVED***
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if (b.equals(a)) ***REMOVED***
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System.out.println("The following dependency is correctly written: " + b);
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check = true;
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***REMOVED*** else
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check = false;
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***REMOVED***
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***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED*** catch (Exception a)
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***REMOVED***
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this.logger.error(a.getMessage(),a);
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***REMOVED***
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return check;
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***REMOVED***
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public void updateSVN(String file, Collection<Dependency> deps) ***REMOVED***
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try ***REMOVED***
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this.logger.info("Updating dependencies list: " + file);
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final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
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List<String> ldep = new LinkedList<>();
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for (Dependency d : deps) ***REMOVED***
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ldep.add(d.getName());
|
|
***REMOVED***
|
|
List<String> aa = this.checkMatch(lines, ldep);
|
|
Collections.sort(aa);
|
|
|
|
final SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
|
|
|
|
byte[] originalContents = byteArrayOutputStream.toByteArray();
|
|
|
|
final ISVNEditor commitEditor = svnRepository.getCommitEditor("update dependencies", null);
|
|
commitEditor.openRoot(-1);
|
|
commitEditor.openFile(file, -1);
|
|
|
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
|
|
|
for (String line : aa) ***REMOVED***
|
|
baos.write(line.getBytes());
|
|
baos.write("\n".getBytes());
|
|
|
|
***REMOVED***
|
|
byte[] bytes = baos.toByteArray();
|
|
|
|
commitEditor.applyTextDelta(file, md5(originalContents));
|
|
|
|
final String checksum = deltaGenerator.sendDelta(file, new ByteArrayInputStream(originalContents), 0,
|
|
new ByteArrayInputStream(bytes), commitEditor, true);
|
|
|
|
|
|
commitEditor.closeFile(file, checksum);
|
|
commitEditor.closeEdit();
|
|
|
|
***REMOVED*** catch (Exception ex) ***REMOVED***
|
|
ex.printStackTrace();
|
|
***REMOVED***
|
|
|
|
finally ***REMOVED***
|
|
svnRepository.closeSession();
|
|
***REMOVED***
|
|
***REMOVED***
|
|
|
|
public static String md5(byte[] contents) ***REMOVED***
|
|
final byte[] tmp = new byte[1024];
|
|
final SVNChecksumInputStream checksumStream = new SVNChecksumInputStream(new ByteArrayInputStream(contents),
|
|
"md5");
|
|
try ***REMOVED***
|
|
while (checksumStream.read(tmp) > 0) ***REMOVED***
|
|
***REMOVED***
|
|
***REMOVED***
|
|
return checksumStream.getDigest();
|
|
***REMOVED*** catch (IOException e) ***REMOVED***
|
|
***REMOVED*** never happens
|
|
e.printStackTrace();
|
|
***REMOVED***
|
|
***REMOVED*** finally ***REMOVED***
|
|
SVNFileUtil.closeFile(checksumStream);
|
|
***REMOVED***
|
|
***REMOVED***
|
|
public List<String> checkMatch(String[] lines, List<String> ls) ***REMOVED***
|
|
Set<String> ss = new HashSet<String>(ls);
|
|
ss.addAll(Arrays.asList(lines));
|
|
return new ArrayList<>(ss);
|
|
***REMOVED***
|
|
|
|
|
|
public String getTimeZone() throws ParseException***REMOVED***
|
|
Calendar cal = Calendar.getInstance();
|
|
cal.getTime();
|
|
DateFormat formatter = new SimpleDateFormat("EEE MMM dd HH:mm:ss zzz yyyy");
|
|
Date fromDate = formatter.parse(cal.getTime().toString());
|
|
TimeZone central = TimeZone.getTimeZone("UTC");
|
|
formatter.setTimeZone(central);
|
|
this.logger.info(formatter.format(fromDate));
|
|
return formatter.format(fromDate);
|
|
***REMOVED***
|
|
|
|
public static void main(String[] args) throws SVNException, ParseException ***REMOVED***
|
|
|
|
|
|
|
|
***REMOVED*** SVNUpdater c = new SVNUpdater();
|
|
|
|
***REMOVED***File a = new File("/home/ngalante/Desktop/testCiro");
|
|
***REMOVED***File b = new File ("/home/ngalante/Desktop/testB");
|
|
***REMOVED***long unixTime = System.currentTimeMillis() / 1000L;
|
|
***REMOVED***System.out.println(unixTime);
|
|
***REMOVED***c.updateAlgorithmFiles(a);
|
|
***REMOVED***c.updateAlgorithmFiles(b);
|
|
***REMOVED***Timestamp timestamp = new Timestamp(System.currentTimeMillis());
|
|
|
|
Calendar cal = Calendar.getInstance();
|
|
cal.getTime();
|
|
DateFormat formatter = new SimpleDateFormat("EEE MMM dd HH:mm:ss zzz yyyy");
|
|
Date fromDate = formatter.parse(cal.getTime().toString());
|
|
TimeZone central = TimeZone.getTimeZone("UTC");
|
|
formatter.setTimeZone(central);
|
|
System.out.println(formatter.format(fromDate));
|
|
|
|
|
|
|
|
***REMOVED***
|
|
|
|
|
|
|
|
|
|
***REMOVED***
|