List of usage examples for java.util Map get
V get(Object key);
From source file:de.tudarmstadt.ukp.experiments.dip.wp1.documents.Step1PrepareContainers.java
public static void main(String[] args) throws IOException { // queries with narratives in CSV File queries = new File(args[0]); File relevantInformationExamplesFile = new File(args[1]); Map<Integer, Map<Integer, List<String>>> relevantInformationMap = parseRelevantInformationFile( relevantInformationExamplesFile); // output dir File outputDir = new File(args[2]); if (!outputDir.exists()) { outputDir.mkdirs();/*from w w w . j a v a2s . c o m*/ } // iterate over queries CSVParser csvParser = CSVParser.parse(queries, Charset.forName("utf-8"), CSVFormat.DEFAULT); for (CSVRecord record : csvParser) { // create new container, fill, and store QueryResultContainer container = new QueryResultContainer(); container.qID = record.get(0); container.query = record.get(1); // Fill some dummy text first container.relevantInformationExamples.addAll(Collections.singletonList("ERROR. Information missing.")); container.irrelevantInformationExamples .addAll(Collections.singletonList("ERROR. Information missing.")); // and now fill it with existing information if available Integer queryID = Integer.valueOf(container.qID); if (relevantInformationMap.containsKey(queryID)) { if (relevantInformationMap.get(queryID).containsKey(0)) { container.irrelevantInformationExamples = new ArrayList<>( relevantInformationMap.get(queryID).get(0)); } if (relevantInformationMap.get(queryID).containsKey(1)) { container.relevantInformationExamples = new ArrayList<>( relevantInformationMap.get(queryID).get(1)); } } File outputFile = new File(outputDir, container.qID + ".xml"); FileUtils.writeStringToFile(outputFile, container.toXML()); System.out.println("Finished " + outputFile); } }
From source file:com.act.lcms.db.analysis.StandardIonAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/*w w w. ja v a2 s . c o m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); StandardIonAnalysis analysis = new StandardIonAnalysis(); HashMap<Integer, Plate> plateCache = new HashMap<>(); String plateBarcode = cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE); String inputChemicals = cl.getOptionValue(OPTION_STANDARD_CHEMICAL); String medium = cl.getOptionValue(OPTION_MEDIUM); // If standard chemical is specified, do standard LCMS ion selection analysis if (inputChemicals != null && !inputChemicals.equals("")) { String[] chemicals; if (!inputChemicals.contains(",")) { chemicals = new String[1]; chemicals[0] = inputChemicals; } else { chemicals = inputChemicals.split(","); } String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + CSV_FORMAT; String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); String[] headerStrings = { "Molecule", "Plate Bar Code", "LCMS Detection Results" }; CSVPrinter printer = new CSVPrinter(new FileWriter(outAnalysis), CSVFormat.DEFAULT.withHeader(headerStrings)); for (String inputChemical : chemicals) { List<StandardWell> standardWells; Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); if (plateBarcode != null && medium != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlateAndMedium(db, inputChemical, queryPlate.getId(), medium); } else if (plateBarcode != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, inputChemical, queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, inputChemical); } if (standardWells.size() == 0) { throw new RuntimeException("Found no LCMS wells for " + inputChemical); } // Sort in descending order of media where MeOH and Water related media are promoted to the top and // anything derived from yeast media are demoted. Collections.sort(standardWells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { if (StandardWell.doesMediaContainYeastExtract(o1.getMedia()) && !StandardWell.doesMediaContainYeastExtract(o2.getMedia())) { return 1; } else { return 0; } } }); Map<StandardWell, StandardIonResult> wellToIonRanking = StandardIonAnalysis .getBestMetlinIonsForChemical(inputChemical, lcmsDir, db, standardWells, plottingDirectory); if (wellToIonRanking.size() != standardWells.size() && !cl.hasOption(OPTION_OVERRIDE_NO_SCAN_FILE_FOUND)) { throw new Exception("Could not find a scan file associated with one of the standard wells"); } for (StandardWell well : wellToIonRanking.keySet()) { LinkedHashMap<String, XZ> snrResults = wellToIonRanking.get(well).getAnalysisResults(); String snrRankingResults = ""; int numResultsToShow = 0; Plate plateForWellToAnalyze = Plate.getPlateById(db, well.getPlateId()); for (Map.Entry<String, XZ> ionToSnrAndTime : snrResults.entrySet()) { if (numResultsToShow > 3) { break; } String ion = ionToSnrAndTime.getKey(); XZ snrAndTime = ionToSnrAndTime.getValue(); snrRankingResults += String.format(ion + " (%.2f SNR at %.2fs); ", snrAndTime.getIntensity(), snrAndTime.getTime()); numResultsToShow++; } String[] resultSet = { inputChemical, plateForWellToAnalyze.getBarcode() + " " + well.getCoordinatesString() + " " + well.getMedia() + " " + well.getConcentration(), snrRankingResults }; printer.printRecord(resultSet); } } try { printer.flush(); printer.close(); } catch (IOException e) { System.err.println("Error while flushing/closing csv writer."); e.printStackTrace(); } } else { // Get the set of chemicals that includes the construct and all it's intermediates Pair<ConstructEntry, List<ChemicalAssociatedWithPathway>> constructAndPathwayChems = analysis .getChemicalsForConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT)); System.out.format("Construct: %s\n", constructAndPathwayChems.getLeft().getCompositionId()); for (ChemicalAssociatedWithPathway pathwayChem : constructAndPathwayChems.getRight()) { System.out.format(" Pathway chem %s\n", pathwayChem.getChemical()); // Get all the standard wells for the pathway chemicals. These wells contain only the // the chemical added with controlled solutions (ie no organism or other chemicals in the // solution) List<StandardWell> standardWells; if (plateBarcode != null) { Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, pathwayChem.getChemical(), queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, pathwayChem.getChemical()); } for (StandardWell wellToAnalyze : standardWells) { List<StandardWell> negativeControls = analysis.getViableNegativeControlsForStandardWell(db, wellToAnalyze); Map<StandardWell, List<ScanFile>> allViableScanFiles = analysis .getViableScanFilesForStandardWells(db, wellToAnalyze, negativeControls); List<String> primaryStandardScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(wellToAnalyze)) { primaryStandardScanFileNames.add(scanFile.getFilename()); } Plate plate = plateCache.get(wellToAnalyze.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, wellToAnalyze.getPlateId()); plateCache.put(plate.getId(), plate); } System.out.format(" Standard well: %s @ %s, '%s'%s%s\n", plate.getBarcode(), wellToAnalyze.getCoordinatesString(), wellToAnalyze.getChemical(), wellToAnalyze.getMedia() == null ? "" : String.format(" in %s", wellToAnalyze.getMedia()), wellToAnalyze.getConcentration() == null ? "" : String.format(" @ %s", wellToAnalyze.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(primaryStandardScanFileNames, ", ")); for (StandardWell negCtrlWell : negativeControls) { plate = plateCache.get(negCtrlWell.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, negCtrlWell.getPlateId()); plateCache.put(plate.getId(), plate); } List<String> negativeControlScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(negCtrlWell)) { negativeControlScanFileNames.add(scanFile.getFilename()); } System.out.format(" Viable negative: %s @ %s, '%s'%s%s\n", plate.getBarcode(), negCtrlWell.getCoordinatesString(), negCtrlWell.getChemical(), negCtrlWell.getMedia() == null ? "" : String.format(" in %s", negCtrlWell.getMedia()), negCtrlWell.getConcentration() == null ? "" : String.format(" @ %s", negCtrlWell.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(negativeControlScanFileNames, ", ")); // TODO: do something useful with the standard wells and their scan files, and then stop all the printing. } } } } } }
From source file:net.ontopia.topicmaps.cmdlineutils.rdbms.RDBMSIndexTool.java
public static void main(String[] argv) throws Exception { // Initialize logging CmdlineUtils.initializeLogging();/* ww w . java2s . c om*/ // Register logging options CmdlineOptions options = new CmdlineOptions("RDBMSIndexTool", argv); CmdlineUtils.registerLoggingOptions(options); // Parse command line options try { options.parse(); } catch (CmdlineOptions.OptionsException e) { System.err.println("Error: " + e.getMessage()); System.exit(1); } // Get command line arguments String[] args = options.getArguments(); if (args.length != 1) { usage(); System.exit(3); } // load database schema project ClassLoader cloader = RDBMSIndexTool.class.getClassLoader(); InputStream istream = cloader.getResourceAsStream("net/ontopia/topicmaps/impl/rdbms/config/schema.xml"); Project dbp = DatabaseProjectReader.loadProject(istream); // open database connection String propfile = args[0]; ConnectionFactoryIF cf = new DefaultConnectionFactory(PropertyUtils.loadProperties(new File(propfile)), true); Connection conn = cf.requestConnection(); try { DatabaseMetaData dbm = conn.getMetaData(); boolean downcase = dbm.storesLowerCaseIdentifiers(); Map extra_indexes = new TreeMap(); Map missing_indexes = new TreeMap(); Iterator tables = dbp.getTables().iterator(); while (tables.hasNext()) { Table table = (Table) tables.next(); String table_name = (downcase ? table.getName().toLowerCase() : table.getName()); //! System.out.println("T :" + table_name); // get primary keys from database Map pkeys = getPrimaryKeys(table_name, dbm); // get indexes from database Map indexes = getIndexes(table_name, dbm); Map dindexes = new HashMap(); if (table.getPrimaryKeys() != null) { String pkey = table_name + '(' + StringUtils.join(table.getPrimaryKeys(), ',') + ')'; if (!pkeys.containsKey(pkey)) System.out.println("PKM: " + pkey); } Iterator iter = table.getIndexes().iterator(); while (iter.hasNext()) { Index index = (Index) iter.next(); String i = table_name + '(' + StringUtils.join(index.getColumns(), ',') + ')'; String index_name = (downcase ? index.getName().toLowerCase() : index.getName()); dindexes.put(i, index_name); } Set extra = new HashSet(indexes.keySet()); extra.removeAll(dindexes.keySet()); extra.removeAll(pkeys.keySet()); if (!extra.isEmpty()) { Iterator i = extra.iterator(); while (i.hasNext()) { Object k = i.next(); extra_indexes.put(k, indexes.get(k)); } } Set missing = new HashSet(dindexes.keySet()); missing.addAll(pkeys.keySet()); missing.removeAll(indexes.keySet()); if (!missing.isEmpty()) { Iterator i = missing.iterator(); while (i.hasNext()) { Object k = i.next(); missing_indexes.put(k, dindexes.get(k)); } } } if (!extra_indexes.isEmpty()) System.out.println("/* --- Extra indexes ----------------------------------------- */"); Iterator eiter = extra_indexes.keySet().iterator(); while (eiter.hasNext()) { Object k = eiter.next(); System.out.println("drop index " + extra_indexes.get(k) + "; /* " + k + " */"); } if (!missing_indexes.isEmpty()) System.out.println("/* --- Missing indexes---------------------------------------- */"); Iterator miter = missing_indexes.keySet().iterator(); while (miter.hasNext()) { Object k = miter.next(); System.out.println("create index " + missing_indexes.get(k) + " on " + k + ";"); } } finally { conn.rollback(); conn.close(); } }
From source file:ch.kostceco.tools.kostsimy.KOSTSimy.java
/** Die Eingabe besteht aus 2 Parameter: [0] Original-Ordner [1] Replica-Ordner * //w ww .jav a 2s.c om * @param args * @throws IOException */ public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); // Zeitstempel Start java.util.Date nowStart = new java.util.Date(); java.text.SimpleDateFormat sdfStart = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStart = sdfStart.format(nowStart); KOSTSimy kostsimy = (KOSTSimy) context.getBean("kostsimy"); File configFile = new File("configuration" + File.separator + "kostsimy.conf.xml"); // Ueberprfung des Parameters (Log-Verzeichnis) String pathToLogfile = kostsimy.getConfigurationService().getPathToLogfile(); File directoryOfLogfile = new File(pathToLogfile); if (!directoryOfLogfile.exists()) { directoryOfLogfile.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfLogfile.canWrite()) { System.out.println( kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfLogfile)); System.exit(1); } if (!directoryOfLogfile.isDirectory()) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); System.exit(1); } // Ist die Anzahl Parameter (2) korrekt? if (args.length > 3) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } File origDir = new File(args[0]); File repDir = new File(args[1]); File logDatei = null; logDatei = origDir; // Informationen zum Arbeitsverzeichnis holen String pathToWorkDir = kostsimy.getConfigurationService().getPathToWorkDir(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ // Konfiguration des Loggings, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String logFileName = logConfigurator.configure(directoryOfLogfile.getAbsolutePath(), logDatei.getName()); File logFile = new File(logFileName); // Ab hier kann ins log geschrieben werden... LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_END)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_INFO)); System.out.println("KOST-Simy"); System.out.println(""); if (!origDir.exists()) { // Das Original-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath())); System.exit(1); } if (!repDir.exists()) { // Das Replica-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath())); System.exit(1); } File xslOrig = new File("resources" + File.separator + "kost-simy.xsl"); File xslCopy = new File(directoryOfLogfile.getAbsolutePath() + File.separator + "kost-simy.xsl"); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } // Informationen zur prozentualen Stichprobe holen String randomTest = kostsimy.getConfigurationService().getRandomTest(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ int iRandomTest = 100; try { iRandomTest = Integer.parseInt(randomTest); } catch (Exception ex) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } if (iRandomTest > 100 || iRandomTest < 1) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } File tmpDir = new File(pathToWorkDir); /* bestehendes Workverzeichnis Abbruch wenn nicht leer, da am Schluss das Workverzeichnis * gelscht wird und entsprechend bestehende Dateien gelscht werden knnen */ if (tmpDir.exists()) { if (tmpDir.isDirectory()) { // Get list of file in the directory. When its length is not zero the folder is not empty. String[] files = tmpDir.list(); if (files.length > 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); System.exit(1); } } } // Im Pfad keine Sonderzeichen Programme knnen evtl abstrzen String patternStr = "[^!#\\$%\\(\\)\\+,\\-_\\.=@\\[\\]\\{\\}\\~:\\\\a-zA-Z0-9 ]"; Pattern pattern = Pattern.compile(patternStr); String name = tmpDir.getAbsolutePath(); String[] pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } // bestehendes Workverzeichnis wieder anlegen if (!tmpDir.exists()) { tmpDir.mkdir(); File origDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "orig"); File repDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "rep"); origDirTmp.mkdir(); repDirTmp.mkdir(); } // Im workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir)); System.exit(1); } // Im Pfad keine Sonderzeichen --> Absturzgefahr name = origDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } name = repDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE1)); float count = 0; int countNio = 0; int countIo = 0; float countVal = 0; int countNotVal = 0; float percentage = (float) 0.0; if (!origDir.isDirectory()) { // TODO: Bildervergleich zweier Dateien --> erledigt --> nur Marker if (repDir.isDirectory()) { // Das Replica-ist ein Verzeichnis, aber Original eine Datei LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath())); System.exit(1); } boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repDir, tmpDir); float statIo = 0; int statNio = 0; float statUn = 0; if (compFile) { statIo = 100; } else { statNio = 100; } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (compFile) { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Validierte Datei valide System.exit(0); } else { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierte Datei --> invalide System.exit(2); } } else { // TODO: Bildervergleich zweier Verzeichnisse --> in Arbeit --> nur Marker if (!repDir.isDirectory()) { // Das Replica-ist eine Datei, aber Original ein Ordner LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath())); System.exit(1); } Map<String, File> fileMap = Util.getFileMap(origDir, false); Set<String> fileMapKeys = fileMap.keySet(); boolean other = false; for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory()) { origDir = newFile; count = count + 1; if ((origDir.getAbsolutePath().toLowerCase().endsWith(".pdf") || origDir.getAbsolutePath().toLowerCase().endsWith(".pdfa") || origDir.getAbsolutePath().toLowerCase().endsWith(".tif") || origDir.getAbsolutePath().toLowerCase().endsWith(".tiff") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpeg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpe") || origDir.getAbsolutePath().toLowerCase().endsWith(".jp2") || origDir.getAbsolutePath().toLowerCase().endsWith(".gif") || origDir.getAbsolutePath().toLowerCase().endsWith(".png") || origDir.getAbsolutePath().toLowerCase().endsWith(".bmp"))) { percentage = 100 / count * countVal; if (percentage < iRandomTest) { // if ( 100 / count * (countVal + 1) <= iRandomTest ) { countVal = countVal + 1; String origWithOutExt = FilenameUtils.removeExtension(origDir.getName()); File repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdf"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdfa"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tiff"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpeg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpe"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jp2"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".gif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".png"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".bmp"); if (!repFile.exists()) { other = true; LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService() .getText(ERROR_NOREP, origDir.getName())); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } } } } } } } } } if (!other) { boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repFile, tmpDir); if (compFile) { // Vergleich bestanden countIo = countIo + 1; } else { // Vergleich nicht bestanden countNio = countNio + 1; } } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy.getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDING, origDir)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); System.out.println(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); } float statIo = 100 / (float) count * (float) countIo; float statNio = 100 / (float) count * (float) countNio; float statUn = 100 - statIo - statNio; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else if (countNio == 0) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // alle Validierten Dateien valide System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierten Dateien --> invalide System.exit(2); } if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } } }
From source file:com.thed.zapi.cloud.sample.FetchExecuteUpdate.java
public static void main(String[] args) throws JSONException, URISyntaxException, ParseException, IOException { final String issueSearchUri = API_SEARCH_ISSUES.replace("{SERVER}", jiraBaseURL); /**// w w w. j a va2s .c o m * Get Test Issues by JQL * */ //Json object for JQL search JSONObject jqlJsonObj = new JSONObject(); jqlJsonObj.put("jql", "project = SUP"); // Replace the value with Valid JQL jqlJsonObj.put("startAt", 0); jqlJsonObj.put("maxResults", 21); // maxResults to be returned by search jqlJsonObj.put("fieldsByKeys", false); String[] IssueIds = getIssuesByJQL(issueSearchUri, userName, password, jqlJsonObj); // System.out.println(ArrayUtils.toString(IssueIds)); /** * Add tests to Cycle * */ final String addTestsUri = API_ADD_TESTS.replace("{SERVER}", zephyrBaseUrl) + cycleId; /** Create JSON object by providing input values */ String[] IssueIds = new String[25]; JSONObject addTestsObj = new JSONObject(); addTestsObj.put("issues", IssueIds); addTestsObj.put("method", "1"); addTestsObj.put("projectId", projectId); addTestsObj.put("versionId", versionId); StringEntity addTestsJSON = null; try { addTestsJSON = new StringEntity(addTestsObj.toString()); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); } addTestsToCycle(addTestsUri, client, accessKey, addTestsJSON); /** * Get Execution Id's by CycleId and Add them to Ad Hoc cycle of * UnScheduled Version * */ Map<String, String> executionIds = new HashMap<String, String>(); final String getExecutionsUri = API_GET_EXECUTIONS.replace("{SERVER}", zephyrBaseUrl) + cycleId + "?projectId=" + projectId + "&versionId=" + versionId; executionIds = getExecutionsByCycleId(getExecutionsUri, client, accessKey); /** * Bulk Update Executions with Status by Execution Id * */ JSONObject statusObj = new JSONObject(); statusObj.put("id", "1"); JSONObject executeTestsObj = new JSONObject(); executeTestsObj.put("status", statusObj); executeTestsObj.put("cycleId", cycleId); executeTestsObj.put("projectId", projectId); executeTestsObj.put("versionId", versionId); executeTestsObj.put("comment", "Executed by ZAPI Cloud"); for (String key : executionIds.keySet()) { final String updateExecutionUri = API_UPDATE_EXECUTION.replace("{SERVER}", zephyrBaseUrl) + key; // System.out.println(updateExecutionUri); // System.out.println(executionIds.get(key)); executeTestsObj.put("issueId", executionIds.get(key)); // System.out.println(executeTestsObj.toString()); StringEntity executeTestsJSON = null; try { executeTestsJSON = new StringEntity(executeTestsObj.toString()); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); } updateExecutions(updateExecutionUri, client, accessKey, executeTestsJSON); } }
From source file:joshelser.as2015.query.Query.java
public static void main(String[] args) throws Exception { JCommander commander = new JCommander(); final Opts options = new Opts(); commander.addObject(options);//from w w w. j av a2 s .c o m commander.setProgramName("Query"); try { commander.parse(args); } catch (ParameterException ex) { commander.usage(); System.err.println(ex.getMessage()); System.exit(1); } ClientConfiguration conf = ClientConfiguration.loadDefault(); if (null != options.clientConfFile) { conf = new ClientConfiguration(new PropertiesConfiguration(options.clientConfFile)); } conf.withInstance(options.instanceName).withZkHosts(options.zookeepers); ZooKeeperInstance inst = new ZooKeeperInstance(conf); Connector conn = inst.getConnector(options.user, new PasswordToken(options.password)); BatchScanner bs = conn.createBatchScanner(options.table, Authorizations.EMPTY, 16); try { bs.setRanges(Collections.singleton(new Range())); final Text categoryText = new Text("category"); bs.fetchColumn(categoryText, new Text("name")); bs.fetchColumn(new Text("review"), new Text("score")); bs.fetchColumn(new Text("review"), new Text("userId")); bs.addScanIterator(new IteratorSetting(50, "wri", WholeRowIterator.class)); final Text colf = new Text(); Map<String, List<Integer>> scoresByUser = new HashMap<>(); for (Entry<Key, Value> entry : bs) { SortedMap<Key, Value> row = WholeRowIterator.decodeRow(entry.getKey(), entry.getValue()); Iterator<Entry<Key, Value>> iter = row.entrySet().iterator(); if (!iter.hasNext()) { // row was empty continue; } Entry<Key, Value> categoryEntry = iter.next(); categoryEntry.getKey().getColumnFamily(colf); if (!colf.equals(categoryText)) { throw new IllegalArgumentException("Unknown!"); } if (!categoryEntry.getValue().toString().equals("books")) { // not a book review continue; } if (!iter.hasNext()) { continue; } Entry<Key, Value> reviewScore = iter.next(); if (!iter.hasNext()) { continue; } Entry<Key, Value> reviewUserId = iter.next(); String userId = reviewUserId.getValue().toString(); if (userId.equals("unknown")) { // filter unknow user id continue; } List<Integer> scores = scoresByUser.get(userId); if (null == scores) { scores = new ArrayList<>(); scoresByUser.put(userId, scores); } scores.add(Float.valueOf(reviewScore.getValue().toString()).intValue()); } for (Entry<String, List<Integer>> entry : scoresByUser.entrySet()) { int sum = 0; for (Integer val : entry.getValue()) { sum += val; } System.out.println(entry.getKey() + " => " + new Float(sum) / entry.getValue().size()); } } finally { bs.close(); } }
From source file:com.me.jvmi.Main.java
public static void main(String[] args) throws IOException { final Path localProductImagesPath = Paths.get("/Volumes/jvmpubfs/WEB/images/products/"); final Path uploadCSVFile = Paths.get("/Users/jbabic/Documents/products/upload.csv"); final Config config = new Config(Paths.get("../config.properties")); LuminateOnlineClient luminateClient2 = new LuminateOnlineClient("https://secure2.convio.net/jvmi/admin/", 3);//from w w w . j a va 2 s . co m luminateClient2.login(config.luminateUser(), config.luminatePassword()); Set<String> completed = new HashSet<>( IOUtils.readLines(Files.newBufferedReader(Paths.get("completed.txt")))); try (InputStream is = Files.newInputStream(Paths.get("donforms.csv")); PrintWriter pw = new PrintWriter(new FileOutputStream(new File("completed.txt"), true))) { for (String line : IOUtils.readLines(is)) { if (completed.contains(line)) { System.out.println("completed: " + line); continue; } try { luminateClient2.editDonationForm(line, "-1"); pw.println(line); System.out.println("done: " + line); pw.flush(); } catch (Exception e) { System.out.println("skipping: " + line); e.printStackTrace(); } } } // luminateClient2.editDonationForm("8840", "-1"); // Collection<String> ids = luminateClient2.donFormSearch("", true); // // CSVFormat csvFileFormat = CSVFormat.DEFAULT.withRecordSeparator("\n"); // try (FileWriter fileWriter = new FileWriter(new File("donforms.csv")); // CSVPrinter csvFilePrinter = new CSVPrinter(fileWriter, csvFileFormat);) { // // for (String id : ids) { // csvFilePrinter.printRecord(id); // } // } // if (true) { return; } Collection<InputRecord> records = parseInput(uploadCSVFile); LuminateFTPClient ftp = new LuminateFTPClient("customerftp.convio.net"); ftp.login(config.ftpUser(), config.ftpPassword()); ProductImages images = new ProductImages(localProductImagesPath, ftp); validateImages(records, images); Map<String, DPCSClient> dpcsClients = new HashMap<>(); dpcsClients.put("us", new DPCSClient("https://donor.dpconsulting.com/NewDDI/Logon.asp?client=jvm")); dpcsClients.put("ca", new DPCSClient("https://donor.dpconsulting.com/NewDDI/Logon.asp?client=jvcn")); dpcsClients.put("uk", new DPCSClient("https://donor.dpconsulting.com/NewDDI/Logon.asp?client=jvuk")); for (DPCSClient client : dpcsClients.values()) { client.login(config.dpcsUser(), config.dpcsPassword()); } Map<String, LuminateOnlineClient> luminateClients = new HashMap<>(); luminateClients.put("us", new LuminateOnlineClient("https://secure2.convio.net/jvmi/admin/", 10)); luminateClients.put("ca", new LuminateOnlineClient("https://secure3.convio.net/jvmica/admin/", 10)); luminateClients.put("uk", new LuminateOnlineClient("https://secure3.convio.net/jvmiuk/admin/", 10)); Map<String, EcommerceProductFactory> ecommFactories = new HashMap<>(); ecommFactories.put("us", new EcommerceProductFactory(dpcsClients.get("us"), images, Categories.us)); ecommFactories.put("ca", new EcommerceProductFactory(dpcsClients.get("ca"), images, Categories.ca)); ecommFactories.put("uk", new EcommerceProductFactory(dpcsClients.get("uk"), images, Categories.uk)); List<String> countries = Arrays.asList("us", "ca", "uk"); boolean error = false; for (InputRecord record : records) { for (String country : countries) { if (record.ignore(country)) { System.out.println("IGNORE: " + country + " " + record); continue; } try { EcommerceProductFactory ecommFactory = ecommFactories.get(country); LuminateOnlineClient luminateClient = luminateClients.get(country); luminateClient.login(config.luminateUser(), config.luminatePassword()); ECommerceProduct product = ecommFactory.createECommerceProduct(record); luminateClient.createOrUpdateProduct(product); } catch (Exception e) { System.out.println("ERROR: " + country + " " + record); //System.out.println(e.getMessage()); error = true; e.printStackTrace(); } } } if (!error) { for (String country : countries) { LuminateOnlineClient luminateClient = luminateClients.get(country); DPCSClient dpcsClient = dpcsClients.get(country); luminateClient.close(); dpcsClient.close(); } } }
From source file:de.tudarmstadt.ukp.experiments.dip.wp1.documents.Step6HITPreparator.java
public static void main(String[] args) throws Exception { // input dir - list of xml query containers // step5-linguistic-annotation/ System.err.println("Starting step 6 HIT Preparation"); File inputDir = new File(args[0]); // output dir File outputDir = new File(args[1]); if (outputDir.exists()) { outputDir.delete();//from w w w . j av a2s . c o m } outputDir.mkdir(); List<String> queries = new ArrayList<>(); // iterate over query containers int countClueWeb = 0; int countSentence = 0; for (File f : FileUtils.listFiles(inputDir, new String[] { "xml" }, false)) { QueryResultContainer queryResultContainer = QueryResultContainer .fromXML(FileUtils.readFileToString(f, "utf-8")); if (queries.contains(f.getName()) || queries.size() == 0) { // groups contain only non-empty documents Map<Integer, List<QueryResultContainer.SingleRankedResult>> groups = new HashMap<>(); // split to groups according to number of sentences for (QueryResultContainer.SingleRankedResult rankedResult : queryResultContainer.rankedResults) { if (rankedResult.originalXmi != null) { byte[] bytes = new BASE64Decoder() .decodeBuffer(new ByteArrayInputStream(rankedResult.originalXmi.getBytes())); JCas jCas = JCasFactory.createJCas(); XmiCasDeserializer.deserialize(new ByteArrayInputStream(bytes), jCas.getCas()); Collection<Sentence> sentences = JCasUtil.select(jCas, Sentence.class); int groupId = sentences.size() / 40; if (rankedResult.originalXmi == null) { System.err.println("Empty document: " + rankedResult.clueWebID); } else { if (!groups.containsKey(groupId)) { groups.put(groupId, new ArrayList<>()); } } //handle it groups.get(groupId).add(rankedResult); countClueWeb++; } } for (Map.Entry<Integer, List<QueryResultContainer.SingleRankedResult>> entry : groups.entrySet()) { Integer groupId = entry.getKey(); List<QueryResultContainer.SingleRankedResult> rankedResults = entry.getValue(); // make sure the results are sorted // DEBUG // for (QueryResultContainer.SingleRankedResult r : rankedResults) { // System.out.print(r.rank + "\t"); // } Collections.sort(rankedResults, (o1, o2) -> o1.rank.compareTo(o2.rank)); // iterate over results for one query and group for (int i = 0; i < rankedResults.size() && i < TOP_RESULTS_PER_GROUP; i++) { QueryResultContainer.SingleRankedResult rankedResult = rankedResults.get(i); QueryResultContainer.SingleRankedResult r = rankedResults.get(i); int rank = r.rank; MustacheFactory mf = new DefaultMustacheFactory(); Mustache mustache = mf.compile("template/template.html"); String queryId = queryResultContainer.qID; String query = queryResultContainer.query; // make the first letter uppercase query = query.substring(0, 1).toUpperCase() + query.substring(1); List<String> relevantInformationExamples = queryResultContainer.relevantInformationExamples; List<String> irrelevantInformationExamples = queryResultContainer.irrelevantInformationExamples; byte[] bytes = new BASE64Decoder() .decodeBuffer(new ByteArrayInputStream(rankedResult.originalXmi.getBytes())); JCas jCas = JCasFactory.createJCas(); XmiCasDeserializer.deserialize(new ByteArrayInputStream(bytes), jCas.getCas()); List<generators.Sentence> sentences = new ArrayList<>(); List<Integer> paragraphs = new ArrayList<>(); paragraphs.add(0); for (WebParagraph webParagraph : JCasUtil.select(jCas, WebParagraph.class)) { for (Sentence s : JCasUtil.selectCovered(Sentence.class, webParagraph)) { String sentenceBegin = String.valueOf(s.getBegin()); generators.Sentence sentence = new generators.Sentence(s.getCoveredText(), sentenceBegin); sentences.add(sentence); countSentence++; } int SentenceID = paragraphs.get(paragraphs.size() - 1); if (sentences.size() > 120) while (SentenceID < sentences.size()) { if (!paragraphs.contains(SentenceID)) paragraphs.add(SentenceID); SentenceID = SentenceID + 120; } paragraphs.add(sentences.size()); } System.err.println("Output dir: " + outputDir); int startID = 0; int endID; for (int j = 0; j < paragraphs.size(); j++) { endID = paragraphs.get(j); int sentLength = endID - startID; if (sentLength > 120 || j == paragraphs.size() - 1) { if (sentLength > 120) { endID = paragraphs.get(j - 1); j--; } sentLength = endID - startID; if (sentLength <= 40) groupId = 40; else if (sentLength <= 80 && sentLength > 40) groupId = 80; else if (sentLength > 80) groupId = 120; File folder = new File(outputDir + "/" + groupId); if (!folder.exists()) { System.err.println("creating directory: " + outputDir + "/" + groupId); boolean result = false; try { folder.mkdir(); result = true; } catch (SecurityException se) { //handle it } if (result) { System.out.println("DIR created"); } } String newHtmlFile = folder.getAbsolutePath() + "/" + f.getName() + "_" + rankedResult.clueWebID + "_" + sentLength + ".html"; System.err.println("Printing a file: " + newHtmlFile); File newHTML = new File(newHtmlFile); int t = 0; while (newHTML.exists()) { newHTML = new File(folder.getAbsolutePath() + "/" + f.getName() + "_" + rankedResult.clueWebID + "_" + sentLength + "." + t + ".html"); t++; } mustache.execute(new PrintWriter(new FileWriter(newHTML)), new generators(query, relevantInformationExamples, irrelevantInformationExamples, sentences.subList(startID, endID), queryId, rank)) .flush(); startID = endID; } } } } } } System.out.println("Printed " + countClueWeb + " documents with " + countSentence + " sentences"); }
From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step5GoldLabelEstimator.java
@SuppressWarnings("unchecked") public static void main(String[] args) throws Exception { String inputDir = args[0];/* ww w . j a v a2 s . co m*/ File outputDir = new File(args[1]); if (!outputDir.exists()) { outputDir.mkdirs(); } // we will process only a subset first List<AnnotatedArgumentPair> allArgumentPairs = new ArrayList<>(); Collection<File> files = IOHelper.listXmlFiles(new File(inputDir)); for (File file : files) { allArgumentPairs.addAll((List<AnnotatedArgumentPair>) XStreamTools.getXStream().fromXML(file)); } // collect turkers and csv List<String> turkerIDs = extractAndSortTurkerIDs(allArgumentPairs); String preparedCSV = prepareCSV(allArgumentPairs, turkerIDs); // save CSV and run MACE Path tmpDir = Files.createTempDirectory("mace"); File maceInputFile = new File(tmpDir.toFile(), "input.csv"); FileUtils.writeStringToFile(maceInputFile, preparedCSV, "utf-8"); File outputPredictions = new File(tmpDir.toFile(), "predictions.txt"); File outputCompetence = new File(tmpDir.toFile(), "competence.txt"); // run MACE MACE.main(new String[] { "--iterations", "500", "--threshold", String.valueOf(MACE_THRESHOLD), "--restarts", "50", "--outputPredictions", outputPredictions.getAbsolutePath(), "--outputCompetence", outputCompetence.getAbsolutePath(), maceInputFile.getAbsolutePath() }); // read back the predictions and competence List<String> predictions = FileUtils.readLines(outputPredictions, "utf-8"); // check the output if (predictions.size() != allArgumentPairs.size()) { throw new IllegalStateException("Wrong size of the predicted file; expected " + allArgumentPairs.size() + " lines but was " + predictions.size()); } String competenceRaw = FileUtils.readFileToString(outputCompetence, "utf-8"); String[] competence = competenceRaw.split("\t"); if (competence.length != turkerIDs.size()) { throw new IllegalStateException( "Expected " + turkerIDs.size() + " competence number, got " + competence.length); } // rank turkers by competence Map<String, Double> turkerIDCompetenceMap = new TreeMap<>(); for (int i = 0; i < turkerIDs.size(); i++) { turkerIDCompetenceMap.put(turkerIDs.get(i), Double.valueOf(competence[i])); } // sort by value descending Map<String, Double> sortedCompetences = IOHelper.sortByValue(turkerIDCompetenceMap, false); System.out.println("Sorted turker competences: " + sortedCompetences); // assign the gold label and competence for (int i = 0; i < allArgumentPairs.size(); i++) { AnnotatedArgumentPair annotatedArgumentPair = allArgumentPairs.get(i); String goldLabel = predictions.get(i).trim(); // might be empty if (!goldLabel.isEmpty()) { // so far the gold label has format aXXX_aYYY_a1, aXXX_aYYY_a2, or aXXX_aYYY_equal // strip now only the gold label annotatedArgumentPair.setGoldLabel(goldLabel); } // update turker competence for (AnnotatedArgumentPair.MTurkAssignment assignment : annotatedArgumentPair.mTurkAssignments) { String turkID = assignment.getTurkID(); int turkRank = getTurkerRank(turkID, sortedCompetences); assignment.setTurkRank(turkRank); double turkCompetence = turkerIDCompetenceMap.get(turkID); assignment.setTurkCompetence(turkCompetence); } } // now sort the data back according to their original file name Map<String, List<AnnotatedArgumentPair>> fileNameAnnotatedPairsMap = new HashMap<>(); for (AnnotatedArgumentPair argumentPair : allArgumentPairs) { String fileName = IOHelper.createFileName(argumentPair.getDebateMetaData(), argumentPair.getArg1().getStance()); if (!fileNameAnnotatedPairsMap.containsKey(fileName)) { fileNameAnnotatedPairsMap.put(fileName, new ArrayList<AnnotatedArgumentPair>()); } fileNameAnnotatedPairsMap.get(fileName).add(argumentPair); } // and save them to the output file for (Map.Entry<String, List<AnnotatedArgumentPair>> entry : fileNameAnnotatedPairsMap.entrySet()) { String fileName = entry.getKey(); List<AnnotatedArgumentPair> argumentPairs = entry.getValue(); File outputFile = new File(outputDir, fileName); // and save all sampled pairs into a XML file XStreamTools.toXML(argumentPairs, outputFile); System.out.println("Saved " + argumentPairs.size() + " pairs to " + outputFile); } }
From source file:org.test.LookupSVNUsers.java
/** * @param args/*from www . j a v a 2 s. c om*/ * @throws IOException */ public static void main(String[] args) throws IOException { if (args.length != 2) { log.error("USAGE: <svn users file(input)> <git authors file (output)>"); System.exit(-1); } Set<String> unmatchedNameSet = new LinkedHashSet<String>(); Map<String, GitUser> gitUserMap = new LinkedHashMap<String, GitUser>(); String svnAuthorsFile = args[0]; List<String> lines = FileUtils.readLines(new File(svnAuthorsFile)); for (String line : lines) { // intentionally handle both upper and lower case varients of the same name. String svnUserName = line.trim(); if (svnUserName.contains("(")) continue; // skip over this line as we can't use it on the url if (gitUserMap.keySet().contains(svnUserName)) continue; // skip this duplicate. log.info("starting on user = " + svnUserName); String gitName = extractFullName(svnUserName); if (gitName == null) { gitName = extractFullName(svnUserName.toLowerCase()); } if (gitName == null) { unmatchedNameSet.add(svnUserName); } else { gitUserMap.put(svnUserName, new GitUser(svnUserName, gitName)); log.info("mapped user (" + svnUserName + ") to: " + gitName); } } List<String> mergedList = new ArrayList<String>(); mergedList.add("# GENERATED "); List<String> userNameList = new ArrayList<String>(); userNameList.addAll(gitUserMap.keySet()); Collections.sort(userNameList); for (String userName : userNameList) { GitUser gUser = gitUserMap.get(userName); mergedList.add(gUser.getSvnAuthor() + " = " + gUser.getGitUser() + " <" + gUser.getSvnAuthor() + "@users.sourceforge.net>"); } for (String username : unmatchedNameSet) { log.warn("failed to match SVN User = " + username); // add in the unmatched entries as is. mergedList.add(username + " = " + username + " <" + username + "@users.sourceforge.net>"); } FileUtils.writeLines(new File(args[1]), "UTF-8", mergedList); }