List of usage examples for java.io File getName
public String getName()
From source file:edu.harvard.hul.ois.drs.pdfaconvert.PdfaConvert.java
public static void main(String[] args) throws IOException { if (logger == null) { System.out.println("About to initialize Log4j"); logger = LogManager.getLogger(); System.out.println("Finished initializing Log4j"); }//ww w .j av a2 s.c o m logger.debug("Entering main()"); // WIP: the following command line code was pulled from FITS Options options = new Options(); Option inputFileOption = new Option(PARAM_I, true, "input file"); options.addOption(inputFileOption); options.addOption(PARAM_V, false, "print version information"); options.addOption(PARAM_H, false, "help information"); options.addOption(PARAM_O, true, "output sub-directory"); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args, true); } catch (ParseException e) { System.err.println(e.getMessage()); System.exit(1); } // print version info if (cmd.hasOption(PARAM_V)) { if (StringUtils.isEmpty(applicationVersion)) { applicationVersion = "<not set>"; System.exit(1); } System.out.println("Version: " + applicationVersion); System.exit(0); } // print help info if (cmd.hasOption(PARAM_H)) { displayHelp(); System.exit(0); } // input parameter if (cmd.hasOption(PARAM_I)) { String input = cmd.getOptionValue(PARAM_I); boolean hasValue = cmd.hasOption(PARAM_I); logger.debug("Has option {} value: [{}]", PARAM_I, hasValue); String paramVal = cmd.getOptionValue(PARAM_I); logger.debug("value of option: [{}] ****", paramVal); File inputFile = new File(input); if (!inputFile.exists()) { logger.warn("{} does not exist or is not readable.", input); System.exit(1); } String subDir = cmd.getOptionValue(PARAM_O); PdfaConvert convert; if (!StringUtils.isEmpty(subDir)) { convert = new PdfaConvert(subDir); } else { convert = new PdfaConvert(); } if (inputFile.isDirectory()) { if (inputFile.listFiles() == null || inputFile.listFiles().length < 1) { logger.warn("Input directory is empty, nothing to process."); System.exit(1); } else { logger.debug("Have directory: [{}] with file count: {}", inputFile.getAbsolutePath(), inputFile.listFiles().length); DirectoryStream<Path> dirStream = null; dirStream = Files.newDirectoryStream(inputFile.toPath()); for (Path filePath : dirStream) { logger.debug("Have file name: {}", filePath.toString()); // Note: only handling files, not recursively going into sub-directories if (filePath.toFile().isFile()) { // Catch possible exception for each file so can handle other files in directory. try { convert.examine(filePath.toFile()); } catch (Exception e) { logger.error("Problem processing file: {} -- Error message: {}", filePath.getFileName(), e.getMessage()); } } else { logger.warn("Not a file so not processing: {}", filePath.toString()); // could be a directory but not recursing } } dirStream.close(); } } else { logger.debug("About to process file: {}", inputFile.getPath()); try { convert.examine(inputFile); } catch (Exception e) { logger.error("Problem processing file: {} -- Error message: {}", inputFile.getName(), e.getMessage()); logger.debug("Problem processing file: {} -- Error message: {}", inputFile.getName(), e.getMessage(), e); } } } else { System.err.println("Missing required option: " + PARAM_I); displayHelp(); System.exit(-1); } System.exit(0); }
From source file:pl.dpbz.poid.zadanie3.Main.java
public static void main(String args[]) throws UnsupportedAudioFileException, IOException { //Zassanie pliku File f = new File("ExampleSounds/artificial/easy/100Hz.wav"); Integer[] ints = WaveToSamplesConverter.convertWaveToIntSamples(f); double samplingFrequency = WaveToSamplesConverter.getSamplingFrequency(f); //Zwyky sound, ktry nie potrzebuje zespolonych elementw Sound s = new Sound(ints, samplingFrequency); //Obliczenie czstotliwoci przy pomocy fazwki PhaseSpaceMultiDimensional pS = new PhaseSpaceMultiDimensional(s); pS.setupPhaseSpace();/* w w w . ja va 2 s .co m*/ pS.computeFrequency(); System.out.println("Phase space " + pS.getFrequency()); //Zespolony dwik, ktry jest bardziej zoony ComplexSound cs = new ComplexSound(ints, samplingFrequency, 15); //To oblicza fouriera cs.setupElementsOfComplexSound(); //Tutaj obliczanie czstotliwoci przy pomocy fouriera CombFiltering cf = new CombFiltering(cs, samplingFrequency); cf.computeFrequency(); cf.drawComplexSound(); System.out.println("Comb Filtering " + cf.getFrequency()); //Przy sekwencjach nie ma majstrowania przy ustawieniach, uytkownik // zmiennie moe podawa tylko liczb prbek, reszt jak czstotliwo prbkowania // i audio format pobiera si z otwieranego pliku //Test sekwencji na fazie File file = new File("ExampleSounds/seq/DWK_violin.wav"); Integer[] seqInte = WaveToSamplesConverter.convertWaveToIntSamples(file); System.out.println("Samples overview " + seqInte.length); double seqSamplingFrequency = WaveToSamplesConverter.getSamplingFrequency(file); int samplesPerPart = 3000; SamplesToWaveConverter conv = new PhaseSpaceSampleConverter(seqSamplingFrequency, samplesPerPart, WaveToSamplesConverter.getAudioFormat(file)); conv.setupFrequenciesFromSamples(seqInte); System.out.println("Zapisuj"); conv.saveGeneratedSamples("XDPhase.wav"); //Test sekwencji na grzebieniu SamplesToWaveConverter conv2 = new CombFilteringSampleConverter(seqSamplingFrequency, samplesPerPart, WaveToSamplesConverter.getAudioFormat(file)); conv2.setupFrequenciesFromSamples(seqInte); System.out.println("Zapisuj"); conv2.saveGeneratedSamples("XDComb.wav"); //Rysowanie wykresu sygnau dwikowego final XYSeries dist = new XYSeries("P0"); int index = 0; for (Integer i : ints) { dist.add(index / samplingFrequency, i); index++; } final XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(dist); JFreeChart chart = ChartFactory.createXYLineChart(f.getName(), "index", "Distance", dataset, PlotOrientation.VERTICAL, true, true, false); XYPlot xyPlot = (XYPlot) chart.getPlot(); xyPlot.setDomainCrosshairVisible(true); xyPlot.setRangeCrosshairVisible(true); XYItemRenderer renderer = xyPlot.getRenderer(); renderer.setSeriesPaint(0, Color.blue); NumberAxis domain = (NumberAxis) xyPlot.getRangeAxis(); domain.setRange(-32768, 32768); ChartDrawer.drawChart(chart); System.out.println("FINISHED"); }
From source file:de.ipbhalle.metfusion.main.SubstructureSearch.java
public static void main(String[] args) { String token = "eeca1d0f-4c03-4d81-aa96-328cdccf171a"; //String token = "a1004d0f-9d37-47e0-acdd-35e58e34f603"; //test();/*from w w w . j av a 2 s. c o m*/ //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/136m0498_MSMS.mf"); //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/148m0859_MSMS.mf"); // File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/164m0445a_MSMS.mf"); //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/192m0757a_MSMS.mf"); //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/naringenin.mf"); //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/Known_BT_MSMS_ChemSp/1MeBT_MSMS.mf"); //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/150m0655a_MSMS.mf"); File file = new File( "C:/Users/Michael/Dropbox/Eawag_IPB_Shared_MassBank/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/192m0757b_MSMS.mf"); MetFusionBatchFileHandler mbf = new MetFusionBatchFileHandler(file); try { mbf.readFile(); } catch (IOException e) { //System.out.println(e.getMessage()); System.err.println( "Error reading from MetFusion settings file [" + file.getAbsolutePath() + "]. Aborting!"); System.exit(-1); } MetFusionBatchSettings settings = mbf.getBatchSettings(); List<String> absent = settings.getSubstrucAbsent(); List<String> present = settings.getSubstrucPresent(); for (String s : present) { System.out.println("present -> " + s); } for (String s : absent) { System.out.println("absent -> " + s); } String formula = settings.getMfFormula(); System.out.println("formula -> " + formula); boolean useFormulaAsQuery = true; boolean useSDF = false; String sdfFile = ""; if (useSDF) { sdfFile = "C:/Users/Michael/Dropbox/Eawag_IPB_Shared_MassBank/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/results_afterFormulaQuery/192m0757b_MSMS.sdf"; if (sdfFile.isEmpty()) { // TODO alternatively use SDF file from query file? System.err.println("SDF file needs to be specified! Exiting."); System.exit(-1); } } SubstructureSearch ss = new SubstructureSearch(present, absent, token, formula, mbf, useFormulaAsQuery, useSDF, sdfFile); ss.run(); List<ResultSubstructure> remaining = ss.getResultsRemaining(); List<Result> resultsForSDF = new ArrayList<Result>(); StringBuilder sb = new StringBuilder(); String sep = ","; for (ResultSubstructure rs : remaining) { sb.append(rs.getId()).append(sep); Result r = new Result(rs.getPort(), rs.getId(), rs.getName(), rs.getScore()); r.setMol(rs.getMol()); r.setSmiles(rs.getSmiles()); r.setInchi(rs.getInchi()); r.setInchikey(rs.getInchikey()); resultsForSDF.add(r); } String ids = sb.toString(); String fileSep = System.getProperty("file.separator"); if (!ids.isEmpty()) { ids = ids.substring(0, ids.length() - 1); System.out.println("ids -> " + ids); settings.setMfDatabaseIDs(ids); String filename = file.getName(); String prefix = filename.substring(0, filename.lastIndexOf(".")); filename = filename.replace(prefix, prefix + "_ids"); String dir = file.getParent(); System.out.println("dir -> " + dir); if (!dir.endsWith(fileSep)) dir += fileSep; File output = new File(file.getParent(), filename); mbf.writeFile(output, settings); SDFOutputHandler so = new SDFOutputHandler(dir + prefix + ".sdf"); boolean writeOK = so.writeOriginalResults(resultsForSDF, false); if (!writeOK) System.err.println("Error writing SDF [" + so.getFilename()); } }
From source file:imp.lstm.main.Driver.java
public static void main(String[] args) throws FileNotFoundException, IOException, ConfigurationException, InvalidParametersException { FileBasedConfigurationBuilder<PropertiesConfiguration> builder = new FileBasedConfigurationBuilder<>( PropertiesConfiguration.class).configure( new Parameters().properties().setFileName(args[0]).setThrowExceptionOnMissing(true) .setListDelimiterHandler(new DefaultListDelimiterHandler(';')) .setIncludesAllowed(false)); Configuration config = builder.getConfiguration(); String inputSongPath = config.getString("input_song"); String outputFolderPath = config.getString("output_folder"); String autoEncoderParamsPath = config.getString("auto_encoder_params"); String nameGeneratorParamsPath = config.getString("name_generator_params"); String queueFolderPath = config.getString("queue_folder"); String referenceQueuePath = config.getString("reference_queue", "nil"); String inputCorpusFolder = config.getString("input_corpus_folder"); boolean shouldWriteQueue = config.getBoolean("should_write_generated_queue"); boolean frankensteinTest = config.getBoolean("queue_tests_frankenstein"); boolean interpolateTest = config.getBoolean("queue_tests_interpolation"); boolean iterateOverCorpus = config.getBoolean("iterate_over_corpus", false); boolean shouldGenerateSongTitle = config.getBoolean("generate_song_title"); boolean shouldGenerateSong = config.getBoolean("generate_leadsheet"); LogTimer.initStartTime(); //start our logging timer to keep track of our execution time LogTimer.log("Creating name generator..."); //here is just silly code for generating name based on an LSTM lol $wag LSTM lstm = new LSTM(); FullyConnectedLayer fullLayer = new FullyConnectedLayer(Operations.None); Loadable titleNetLoader = new Loadable() { @Override/*from ww w . j a va 2s .c o m*/ public boolean load(INDArray array, String path) { String car = pathCar(path); String cdr = pathCdr(path); switch (car) { case "full": return fullLayer.load(array, cdr); case "lstm": return lstm.load(array, cdr); default: return false; } } }; LogTimer.log("Packing name generator from files..."); (new NetworkConnectomeLoader()).load(nameGeneratorParamsPath, titleNetLoader); String characterString = " !\"'[],-.01245679:?ABCDEFGHIJKLMNOPQRSTUVWYZabcdefghijklmnopqrstuvwxyz"; //Initialization LogTimer.log("Creating autoencoder..."); int inputSize = 34; int outputSize = EncodingParameters.noteEncoder.getNoteLength(); int featureVectorSize = 100; ProductCompressingAutoencoder autoencoder = new ProductCompressingAutoencoder(24, 48, 84 + 1, false); //create our network int numInterpolationDivisions = 5; //"pack" the network from weights and biases file directory LogTimer.log("Packing autoencoder from files"); (new NetworkConnectomeLoader()).load(autoEncoderParamsPath, autoencoder); File[] songFiles; if (iterateOverCorpus) { songFiles = new File(inputCorpusFolder).listFiles(); } else { songFiles = new File[] { new File(inputSongPath) }; } for (File inputFile : songFiles) { (new NetworkConnectomeLoader()).refresh(autoEncoderParamsPath, autoencoder, "initialstate"); String songTitle; if (shouldGenerateSong) { Random rand = new Random(); AVector charOut = Vector.createLength(characterString.length()); GroupedSoftMaxSampler sampler = new GroupedSoftMaxSampler( new Group[] { new Group(0, characterString.length(), true) }); songTitle = ""; for (int i = 0; i < 50; i++) { charOut = fullLayer.forward(lstm.step(charOut)); charOut = sampler.filter(charOut); int charIndex = 0; for (; charIndex < charOut.length(); charIndex++) { if (charOut.get(charIndex) == 1.0) { break; } } songTitle += characterString.substring(charIndex, charIndex + 1); } songTitle = songTitle.trim(); LogTimer.log("Generated song name: " + songTitle); } else { songTitle = "The Song We Never Name"; } LogTimer.log("Reading file..."); LeadSheetDataSequence inputSequence = LeadSheetIO.readLeadSheet(inputFile); //read our leadsheet to get a data vessel as retrieved in rbm-provisor LeadSheetDataSequence outputSequence = inputSequence.copy(); outputSequence.clearMelody(); if (interpolateTest) { LeadSheetDataSequence additionalOutput = outputSequence.copy(); for (int i = 0; i < numInterpolationDivisions; i++) { outputSequence.concat(additionalOutput.copy()); } } LeadSheetDataSequence decoderInputSequence = outputSequence.copy(); LogTimer.startLog("Encoding data..."); //TradingTimer.initStart(); //start our trading timer to keep track our our generation versus realtime play while (inputSequence.hasNext()) { //iterate through time steps in input data //TradingTimer.waitForNextTimedInput(); autoencoder.encodeStep(inputSequence.retrieve()); //feed the resultant input vector into the network if (advanceDecoding) { //if we are using advance decoding (we start decoding as soon as we can) if (autoencoder.canDecode()) { //if queue has enough data to decode from outputSequence.pushStep(null, null, autoencoder.decodeStep(decoderInputSequence.retrieve())); //take sampled data for a timestep from autoencoder //TradingTimer.logTimestep(); //log our time to TradingTimer so we can know how far ahead of realtime we are } } } LogTimer.endLog(); if (shouldWriteQueue) { String queueFilePath = queueFolderPath + java.io.File.separator + inputFile.getName().replace(".ls", ".q"); FragmentedNeuralQueue currQueue = autoencoder.getQueue(); currQueue.writeToFile(queueFilePath); LogTimer.log("Wrote queue " + inputFile.getName().replace(".ls", ".q") + " to file..."); } if (shouldGenerateSong) { if (interpolateTest) { FragmentedNeuralQueue refQueue = new FragmentedNeuralQueue(); refQueue.initFromFile(referenceQueuePath); FragmentedNeuralQueue currQueue = autoencoder.getQueue(); //currQueue.writeToFile(queueFilePath); autoencoder.setQueue(currQueue.copy()); while (autoencoder.hasDataStepsLeft()) { //we are done encoding all time steps, so just finish decoding!{ outputSequence.pushStep(null, null, autoencoder.decodeStep(decoderInputSequence.retrieve())); //take sampled data for a timestep from autoencoder //TradingTimer.logTimestep(); //log our time to TradingTimer so we can know how far ahead of realtime we are } for (int i = 1; i <= numInterpolationDivisions; i++) { System.out.println("Starting interpolation " + ((1.0 / numInterpolationDivisions) * (i))); (new NetworkConnectomeLoader()).refresh(autoEncoderParamsPath, autoencoder, "initialstate"); FragmentedNeuralQueue currCopy = currQueue.copy(); currCopy.basicInterpolate(refQueue, (1.0 / numInterpolationDivisions) * (i)); autoencoder.setQueue(currCopy); int timeStep = 0; while (autoencoder.hasDataStepsLeft()) { //we are done encoding all time steps, so just finish decoding!{ System.out.println("interpolation " + i + " step " + ++timeStep); outputSequence.pushStep(null, null, autoencoder.decodeStep(decoderInputSequence.retrieve())); //take sampled data for a timestep from autoencoder //TradingTimer.logTimestep(); //log our time to TradingTimer so we can know how far ahead of realtime we are } } } if (frankensteinTest) { LogTimer.startLog("Loading queues"); File queueFolder = new File(queueFolderPath); int numComponents = config.getInt("frankenstein_num_components", 5); int numCombinations = config.getInt("frankenstein_num_combinations", 6); double interpolationMagnitude = config.getDouble("frankenstein_magnitude", 2.0); if (queueFolder.isDirectory()) { File[] queueFiles = queueFolder.listFiles(new FilenameFilter() { @Override public boolean accept(File dir, String name) { return name.contains(".q"); } }); List<File> fileList = new ArrayList<>(); for (File file : queueFiles) { fileList.add(file); } Collections.shuffle(fileList); int numSelectedFiles = (numComponents > queueFiles.length) ? queueFiles.length : numComponents; for (int i = 0; i < queueFiles.length - numSelectedFiles; i++) { fileList.remove(fileList.size() - 1); } List<FragmentedNeuralQueue> queuePopulation = new ArrayList<>(fileList.size()); songTitle += " - a mix of "; for (File file : fileList) { FragmentedNeuralQueue newQueue = new FragmentedNeuralQueue(); newQueue.initFromFile(file.getPath()); queuePopulation.add(newQueue); songTitle += file.getName().replaceAll(".ls", "") + ", "; } LogTimer.endLog(); LeadSheetDataSequence additionalOutput = outputSequence.copy(); for (int i = 1; i < numCombinations; i++) { outputSequence.concat(additionalOutput.copy()); } decoderInputSequence = outputSequence.copy(); FragmentedNeuralQueue origQueue = autoencoder.getQueue(); for (int i = 0; i < numCombinations; i++) { LogTimer.startLog("Performing queue interpolation..."); AVector combinationStrengths = Vector.createLength(queuePopulation.size()); Random vectorRand = new Random(i); for (int j = 0; j < combinationStrengths.length(); j++) { combinationStrengths.set(j, vectorRand.nextDouble()); } combinationStrengths.divide(combinationStrengths.elementSum()); FragmentedNeuralQueue currQueue = origQueue.copy(); for (int k = 0; k < combinationStrengths.length(); k++) { currQueue.basicInterpolate(queuePopulation.get(k), combinationStrengths.get(k) * interpolationMagnitude); } LogTimer.endLog(); autoencoder.setQueue(currQueue); LogTimer.startLog("Refreshing autoencoder state..."); (new NetworkConnectomeLoader()).refresh(autoEncoderParamsPath, autoencoder, "initialstate"); LogTimer.endLog(); LogTimer.startLog("Decoding segment..."); while (autoencoder.hasDataStepsLeft()) { //we are done encoding all time steps, so just finish decoding!{ outputSequence.pushStep(null, null, autoencoder.decodeStep(decoderInputSequence.retrieve())); //take sampled data for a timestep from autoencoder //TradingTimer.logTimestep(); //log our time to TradingTimer so we can know how far ahead of realtime we are } LogTimer.endLog(); } } } while (autoencoder.hasDataStepsLeft()) { //we are done encoding all time steps, so just finish decoding!{ outputSequence.pushStep(null, null, autoencoder.decodeStep(decoderInputSequence.retrieve())); //take sampled data for a timestep from autoencoder //TradingTimer.logTimestep(); //log our time to TradingTimer so we can know how far ahead of realtime we are } LogTimer.log("Writing file..."); String outputFilename = outputFolderPath + java.io.File.separator + inputFile.getName().replace(".ls", "_Output"); //we'll write our generated file with the same name plus "_Output" LeadSheetIO.writeLeadSheet(outputSequence, outputFilename, songTitle); System.out.println(outputFilename); } else { autoencoder.setQueue(new FragmentedNeuralQueue()); } } LogTimer.log("Process finished"); //Done! }
From source file:ch.kostceco.tools.kostval.KOSTVal.java
/** Die Eingabe besteht aus 2 oder 3 Parameter: [0] Validierungstyp [1] Pfad zur Val-File [2] * option: Verbose/*from ww w . ja v a 2s .c o m*/ * * @param args * @throws IOException */ @SuppressWarnings("unused") 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); /* TODO: siehe Bemerkung im applicationContext-services.xml bezglich Injection in der * Superklasse aller Impl-Klassen ValidationModuleImpl validationModuleImpl = * (ValidationModuleImpl) context.getBean("validationmoduleimpl"); */ KOSTVal kostval = (KOSTVal) context.getBean("kostval"); File configFile = new File("configuration" + File.separator + "kostval.conf.xml"); // Ueberprfung des Parameters (Log-Verzeichnis) String pathToLogfile = kostval.getConfigurationService().getPathToLogfile(); File directoryOfLogfile = new File(pathToLogfile); if (!directoryOfLogfile.exists()) { directoryOfLogfile.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfLogfile.canWrite()) { System.out.println( kostval.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfLogfile)); System.exit(1); } if (!directoryOfLogfile.isDirectory()) { System.out.println(kostval.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); System.exit(1); } // Ist die Anzahl Parameter (mind. 2) korrekt? if (args.length < 2) { System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } File valDatei = new File(args[1]); File logDatei = null; logDatei = valDatei; // Informationen zum Arbeitsverzeichnis holen String pathToWorkDir = kostval.getConfigurationService().getPathToWorkDir(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ // Informationen holen, welche Formate validiert werden sollen String pdfaValidation = kostval.getConfigurationService().pdfaValidation(); String siardValidation = kostval.getConfigurationService().siardValidation(); String tiffValidation = kostval.getConfigurationService().tiffValidation(); String jp2Validation = kostval.getConfigurationService().jp2Validation(); // 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... String formatValOn = ""; // ermitteln welche Formate validiert werden knnen respektive eingeschaltet sind if (pdfaValidation.equals("yes")) { formatValOn = "PDF/A"; if (tiffValidation.equals("yes")) { formatValOn = formatValOn + ", TIFF"; } if (jp2Validation.equals("yes")) { formatValOn = formatValOn + ", JP2"; } if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (tiffValidation.equals("yes")) { formatValOn = "TIFF"; if (jp2Validation.equals("yes")) { formatValOn = formatValOn + ", JP2"; } if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (jp2Validation.equals("yes")) { formatValOn = "JP2"; if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (siardValidation.equals("yes")) { formatValOn = "SIARD"; } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_HEADER)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_END)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMATON, formatValOn)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_INFO)); System.out.println("KOST-Val"); System.out.println(""); if (args[0].equals("--format") && formatValOn.equals("")) { // Formatvalidierung aber alle Formate ausgeschlossen LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_NOFILEENDINGS))); System.out.println(kostval.getTextResourceService().getText(ERROR_NOFILEENDINGS)); System.exit(1); } File xslOrig = new File("resources" + File.separator + "kost-val.xsl"); File xslCopy = new File(directoryOfLogfile.getAbsolutePath() + File.separator + "kost-val.xsl"); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } 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(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir))); System.out.println( kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); System.exit(1); } } } // Im Pfad keine Sonderzeichen xml-Validierung SIP 1d und SIARD C strzen ab 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(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostval.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(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WRONG_JRE))); System.out.println(kostval.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } // bestehendes Workverzeichnis wieder anlegen if (!tmpDir.exists()) { tmpDir.mkdir(); } // Im workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir))); System.out.println(kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir)); System.exit(1); } /* Vorberitung fr eine allfllige Festhaltung bei unterschiedlichen PDFA-Validierungsresultaten * in einer PDF_Diagnosedatei sowie Zhler der SIP-Dateiformate */ String diaPath = kostval.getConfigurationService().getPathToDiagnose(); // Im diaverzeichnis besteht kein Schreibrecht File diaDir = new File(diaPath); if (!diaDir.exists()) { diaDir.mkdir(); } if (!diaDir.canWrite()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_DIADIRECTORY_NOTWRITABLE, diaDir))); System.out.println(kostval.getTextResourceService().getText(ERROR_DIADIRECTORY_NOTWRITABLE, diaDir)); System.exit(1); } File xmlDiaOrig = new File("resources" + File.separator + "KaD-Diagnosedaten.kost-val.xml"); File xmlDiaCopy = new File(diaPath + File.separator + "KaD-Diagnosedaten.kost-val.xml"); if (!xmlDiaCopy.exists()) { Util.copyFile(xmlDiaOrig, xmlDiaCopy); } File xslDiaOrig = new File("resources" + File.separator + "kost-val_KaDdia.xsl"); File xslDiaCopy = new File(diaPath + File.separator + "kost-val_KaDdia.xsl"); if (!xslDiaCopy.exists()) { Util.copyFile(xslDiaOrig, xslDiaCopy); } /* Ueberprfung des optionalen Parameters (2 -v --> im Verbose-mode werden die originalen Logs * nicht gelscht (PDFTron, Jhove & Co.) */ boolean verbose = false; if (args.length > 2) { if (!(args[2].equals("-v"))) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_PARAMETER_OPTIONAL_1))); System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_OPTIONAL_1)); System.exit(1); } else { verbose = true; } } /* Initialisierung TIFF-Modul B (JHove-Validierung) berprfen der Konfiguration: existiert die * jhove.conf am angebenen Ort? */ String jhoveConf = kostval.getConfigurationService().getPathToJhoveConfiguration(); File fJhoveConf = new File(jhoveConf); if (!fJhoveConf.exists() || !fJhoveConf.getName().equals("jhove.conf")) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_JHOVECONF_MISSING))); System.out.println(kostval.getTextResourceService().getText(ERROR_JHOVECONF_MISSING)); System.exit(1); } // Im Pfad keine Sonderzeichen xml-Validierung SIP 1d und SIARD C strzen ab name = valDatei.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(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // Ueberprfung des Parameters (Val-Datei): existiert die Datei? if (!valDatei.exists()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_VALFILE_FILENOTEXISTING))); System.out.println(kostval.getTextResourceService().getText(ERROR_VALFILE_FILENOTEXISTING)); System.exit(1); } if (args[0].equals("--format")) { LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT1)); Integer countNio = 0; Integer countSummaryNio = 0; Integer count = 0; Integer pdfaCountIo = 0; Integer pdfaCountNio = 0; Integer siardCountIo = 0; Integer siardCountNio = 0; Integer tiffCountIo = 0; Integer tiffCountNio = 0; Integer jp2CountIo = 0; Integer jp2CountNio = 0; // TODO: Formatvalidierung an einer Datei --> erledigt --> nur Marker if (!valDatei.isDirectory()) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } LOGGER.logError(kostval.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 = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (valFile) { // 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: Formatvalidierung ber ein Ordner --> erledigt --> nur Marker Map<String, File> fileMap = Util.getFileMap(valDatei, false); Set<String> fileMapKeys = fileMap.keySet(); for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory()) { valDatei = newFile; count = count + 1; // Ausgabe Dateizhler Ersichtlich das KOST-Val Dateien durchsucht System.out.print(count + " "); System.out.print("\r"); if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".jp2"))) && jp2Validation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { jp2CountIo = jp2CountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { jp2CountNio = jp2CountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".tiff") || valDatei.getAbsolutePath().toLowerCase().endsWith(".tif"))) && tiffValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { tiffCountIo = tiffCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { tiffCountNio = tiffCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".siard")) && siardValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { siardCountIo = siardCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { siardCountNio = siardCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".pdf") || valDatei.getAbsolutePath().toLowerCase().endsWith(".pdfa"))) && pdfaValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { pdfaCountIo = pdfaCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { pdfaCountNio = pdfaCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else { countNio = countNio + 1; } } } System.out.print(" "); System.out.print("\r"); if (countNio.equals(count)) { // keine Dateien Validiert LOGGER.logError( kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); System.out.println( kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.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 = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } countSummaryNio = pdfaCountNio + siardCountNio + tiffCountNio + jp2CountNio; if (countNio.equals(count)) { // keine Dateien Validiert bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else if (countSummaryNio == 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(); } } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); } else if (args[0].equals("--sip")) { LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT1)); // TODO: Sipvalidierung --> erledigt --> nur Marker boolean validFormat = false; File originalSipFile = valDatei; File unSipFile = valDatei; File outputFile3c = null; String fileName3c = null; File tmpDirZip = null; // zuerst eine Formatvalidierung ber den Content dies ist analog aufgebaut wie --format Integer countNio = 0; Integer countSummaryNio = 0; Integer countSummaryIo = 0; Integer count = 0; Integer pdfaCountIo = 0; Integer pdfaCountNio = 0; Integer siardCountIo = 0; Integer siardCountNio = 0; Integer tiffCountIo = 0; Integer tiffCountNio = 0; Integer jp2CountIo = 0; Integer jp2CountNio = 0; if (!valDatei.isDirectory()) { Boolean zip = false; // Eine ZIP Datei muss mit PK.. beginnen if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".zip") || valDatei.getAbsolutePath().toLowerCase().endsWith(".zip64"))) { FileReader fr = null; try { fr = new FileReader(valDatei); BufferedReader read = new BufferedReader(fr); // Hex 03 in Char umwandeln String str3 = "03"; int i3 = Integer.parseInt(str3, 16); char c3 = (char) i3; // Hex 04 in Char umwandeln String str4 = "04"; int i4 = Integer.parseInt(str4, 16); char c4 = (char) i4; // auslesen der ersten 4 Zeichen der Datei int length; int i; char[] buffer = new char[4]; length = read.read(buffer); for (i = 0; i != length; i++) ; // die beiden charArrays (soll und ist) mit einander vergleichen char[] charArray1 = buffer; char[] charArray2 = new char[] { 'P', 'K', c3, c4 }; if (Arrays.equals(charArray1, charArray2)) { // hchstwahrscheinlich ein ZIP da es mit 504B0304 respektive PK.. beginnt zip = true; } } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } } // wenn die Datei kein Directory ist, muss sie mit zip oder zip64 enden if ((!(valDatei.getAbsolutePath().toLowerCase().endsWith(".zip") || valDatei.getAbsolutePath().toLowerCase().endsWith(".zip64"))) || zip == false) { // Abbruch! D.h. Sip message beginnen, Meldung und Beenden ab hier bis System.exit( 1 ); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = originalSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, valDatei.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(valDatei.getAbsolutePath()); // die eigentliche Fehlermeldung LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_MODUL_Aa_SIP) + kostval.getTextResourceService().getText(ERROR_XML_AA_INCORRECTFILEENDING)); System.out.println(kostval.getTextResourceService().getText(ERROR_XML_AA_INCORRECTFILEENDING)); // Fehler im Validierten SIP --> invalide & Abbruch LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.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 = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else { // geziptes SIP --> in temp dir entzipen String toplevelDir = valDatei.getName(); int lastDotIdx = toplevelDir.lastIndexOf("."); toplevelDir = toplevelDir.substring(0, lastDotIdx); tmpDirZip = new File( tmpDir.getAbsolutePath() + File.separator + "ZIP" + File.separator + toplevelDir); try { Zip64Archiver.unzip(valDatei.getAbsolutePath(), tmpDirZip.getAbsolutePath()); } catch (Exception e) { try { Zip64Archiver.unzip64(valDatei, tmpDirZip); } catch (Exception e1) { // Abbruch! D.h. Sip message beginnen, Meldung und Beenden ab hier bis System.exit LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = originalSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, valDatei.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(valDatei.getAbsolutePath()); // die eigentliche Fehlermeldung LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_MODUL_Aa_SIP) + kostval.getTextResourceService().getText(ERROR_XML_AA_CANNOTEXTRACTZIP)); System.out.println( kostval.getTextResourceService().getText(ERROR_XML_AA_CANNOTEXTRACTZIP)); // Fehler im Validierten SIP --> invalide & Abbruch LOGGER.logError( kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError( kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.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 = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e2) { LOGGER.logError("<Error>" + kostval.getTextResourceService() .getText(ERROR_XML_UNKNOWN, e2.getMessage())); System.out.println("Exception: " + e2.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } } valDatei = tmpDirZip; File toplevelfolder = new File( valDatei.getAbsolutePath() + File.separator + valDatei.getName()); if (toplevelfolder.exists()) { valDatei = toplevelfolder; } unSipFile = valDatei; } } else { // SIP ist ein Ordner valDatei bleibt unverndert } // Vorgngige Formatvalidierung (Schritt 3c) Map<String, File> fileMap = Util.getFileMap(valDatei, false); Set<String> fileMapKeys = fileMap.keySet(); int pdf = 0; int tiff = 0; int siard = 0; int txt = 0; int csv = 0; int xml = 0; int xsd = 0; int wave = 0; int mp3 = 0; int jp2 = 0; int jpx = 0; int jpeg = 0; int png = 0; int dng = 0; int svg = 0; int mpeg2 = 0; int mp4 = 0; int xls = 0; int odt = 0; int ods = 0; int odp = 0; int other = 0; for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory() && newFile.getAbsolutePath().contains(File.separator + "content" + File.separator)) { valDatei = newFile; count = count + 1; // Ausgabe Dateizhler Ersichtlich das KOST-Val Dateien durchsucht System.out.print(count + " "); System.out.print("\r"); String extension = valDatei.getName(); int lastIndexOf = extension.lastIndexOf("."); if (lastIndexOf == -1) { // empty extension extension = "other"; } else { extension = extension.substring(lastIndexOf); } if (extension.equalsIgnoreCase(".pdf") || extension.equalsIgnoreCase(".pdfa")) { pdf = pdf + 1; } else if (extension.equalsIgnoreCase(".tiff") || extension.equalsIgnoreCase(".tif")) { tiff = tiff + 1; } else if (extension.equalsIgnoreCase(".siard")) { siard = siard + 1; } else if (extension.equalsIgnoreCase(".txt")) { txt = txt + 1; } else if (extension.equalsIgnoreCase(".csv")) { csv = csv + 1; } else if (extension.equalsIgnoreCase(".xml")) { xml = xml + 1; } else if (extension.equalsIgnoreCase(".xsd")) { xsd = xsd + 1; } else if (extension.equalsIgnoreCase(".wav")) { wave = wave + 1; } else if (extension.equalsIgnoreCase(".mp3")) { mp3 = mp3 + 1; } else if (extension.equalsIgnoreCase(".jp2")) { jp2 = jp2 + 1; } else if (extension.equalsIgnoreCase(".jpx") || extension.equalsIgnoreCase(".jpf")) { jpx = jpx + 1; } else if (extension.equalsIgnoreCase(".jpe") || extension.equalsIgnoreCase(".jpeg") || extension.equalsIgnoreCase(".jpg")) { jpeg = jpeg + 1; } else if (extension.equalsIgnoreCase(".png")) { png = png + 1; } else if (extension.equalsIgnoreCase(".dng")) { dng = dng + 1; } else if (extension.equalsIgnoreCase(".svg")) { svg = svg + 1; } else if (extension.equalsIgnoreCase(".mpeg") || extension.equalsIgnoreCase(".mpg")) { mpeg2 = mpeg2 + 1; } else if (extension.equalsIgnoreCase(".f4a") || extension.equalsIgnoreCase(".f4v") || extension.equalsIgnoreCase(".m4a") || extension.equalsIgnoreCase(".m4v") || extension.equalsIgnoreCase(".mp4")) { mp4 = mp4 + 1; } else if (extension.equalsIgnoreCase(".xls") || extension.equalsIgnoreCase(".xlw") || extension.equalsIgnoreCase(".xlsx")) { xls = xls + 1; } else if (extension.equalsIgnoreCase(".odt") || extension.equalsIgnoreCase(".ott")) { odt = odt + 1; } else if (extension.equalsIgnoreCase(".ods") || extension.equalsIgnoreCase(".ots")) { ods = ods + 1; } else if (extension.equalsIgnoreCase(".odp") || extension.equalsIgnoreCase(".otp")) { odp = odp + 1; } else { other = other + 1; } if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".jp2"))) && jp2Validation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { jp2CountIo = jp2CountIo + 1; } else { jp2CountNio = jp2CountNio + 1; } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".tiff") || valDatei.getAbsolutePath().toLowerCase().endsWith(".tif"))) && tiffValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { tiffCountIo = tiffCountIo + 1; } else { tiffCountNio = tiffCountNio + 1; } } else if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".siard")) && siardValidation.equals("yes")) { // Arbeitsverzeichnis zum Entpacken des Archivs erstellen String pathToWorkDirSiard = kostval.getConfigurationService().getPathToWorkDir(); File tmpDirSiard = new File(pathToWorkDirSiard + File.separator + "SIARD"); if (tmpDirSiard.exists()) { Util.deleteDir(tmpDirSiard); } if (!tmpDirSiard.exists()) { tmpDirSiard.mkdir(); } boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { siardCountIo = siardCountIo + 1; } else { siardCountNio = siardCountNio + 1; } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".pdf") || valDatei.getAbsolutePath().toLowerCase().endsWith(".pdfa"))) && pdfaValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { pdfaCountIo = pdfaCountIo + 1; } else { pdfaCountNio = pdfaCountNio + 1; } } else { countNio = countNio + 1; } } } countSummaryNio = pdfaCountNio + siardCountNio + tiffCountNio + jp2CountNio; countSummaryIo = pdfaCountIo + siardCountIo + tiffCountIo + jp2CountIo; int countSummaryIoP = 100 / count * countSummaryIo; int countSummaryNioP = 100 / count * countSummaryNio; int countNioP = 100 / count * countNio; String summary3c = kostval.getTextResourceService().getText(MESSAGE_XML_SUMMARY_3C, count, countSummaryIo, countSummaryNio, countNio, countSummaryIoP, countSummaryNioP, countNioP); if (countSummaryNio == 0) { // alle Validierten Dateien valide validFormat = true; fileName3c = "3c_Valide.txt"; } else { // Fehler in Validierten Dateien --> invalide validFormat = false; fileName3c = "3c_Invalide.txt"; } // outputFile3c = new File( directoryOfLogfile + fileName3c ); outputFile3c = new File(pathToWorkDir + File.separator + fileName3c); try { outputFile3c.createNewFile(); } catch (IOException e) { e.printStackTrace(); } if (countNio == count) { // keine Dateien Validiert LOGGER.logError(kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); System.out .println(kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); // Start Normale SIP-Validierung mit auswertung Format-Val. im 3c LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = unSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, originalSipFile.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(originalSipFile.getAbsolutePath()); Controllersip controller = (Controllersip) context.getBean("controllersip"); boolean okMandatory = false; okMandatory = controller.executeMandatory(valDatei, directoryOfLogfile); boolean ok = false; /* die Validierungen 1a - 1d sind obligatorisch, wenn sie bestanden wurden, knnen die * restlichen Validierungen, welche nicht zum Abbruch der Applikation fhren, ausgefhrt * werden. * * 1a wurde bereits getestet (vor der Formatvalidierung entsprechend fngt der Controller mit * 1b an */ if (okMandatory) { ok = controller.executeOptional(valDatei, directoryOfLogfile); } // Formatvalidierung validFormat ok = (ok && okMandatory && validFormat); if (ok) { // Validiertes SIP valide LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_VALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Valid"); System.out.println(""); } else { // Fehler im Validierten SIP --> invalide LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); } // ggf. Fehlermeldung 3c ergnzen Util.val3c(summary3c, logFile ); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.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.val3c(summary3c, 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 = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } StringBuffer command = new StringBuffer("rd " + tmpDir.getAbsolutePath() + " /s /q"); try { // KaD-Diagnose-Datei mit den neusten Anzahl Dateien pro KaD-Format Updaten DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); Document doc = dBuilder.parse(xmlDiaCopy); doc.getDocumentElement().normalize(); NodeList nList = doc.getElementsByTagName("KOSTVal_FFCounter"); for (int temp = 0; temp < nList.getLength(); temp++) { Node nNode = nList.item(temp); if (nNode.getNodeType() == Node.ELEMENT_NODE) { Element eElement = (Element) nNode; if (pdf > 0) { String pdfNodeString = eElement.getElementsByTagName("pdf").item(0).getTextContent(); int pdfNodeValue = Integer.parseInt(pdfNodeString); pdf = pdf + pdfNodeValue; Util.kadDia("<pdf>" + pdfNodeValue + "</pdf>", "<pdf>" + pdf + "</pdf>", xmlDiaCopy); } if (tiff > 0) { String tiffNodeString = eElement.getElementsByTagName("tiff").item(0).getTextContent(); int tiffNodeValue = Integer.parseInt(tiffNodeString); tiff = tiff + tiffNodeValue; Util.kadDia("<tiff>" + tiffNodeValue + "</tiff>", "<tiff>" + tiff + "</tiff>", xmlDiaCopy); } if (siard > 0) { String siardNodeString = eElement.getElementsByTagName("siard").item(0) .getTextContent(); int siardNodeValue = Integer.parseInt(siardNodeString); siard = siard + siardNodeValue; Util.kadDia("<siard>" + siardNodeValue + "</siard>", "<siard>" + siard + "</siard>", xmlDiaCopy); } if (txt > 0) { String txtNodeString = eElement.getElementsByTagName("txt").item(0).getTextContent(); int txtNodeValue = Integer.parseInt(txtNodeString); txt = txt + txtNodeValue; Util.kadDia("<txt>" + txtNodeValue + "</txt>", "<txt>" + txt + "</txt>", xmlDiaCopy); } if (csv > 0) { String csvNodeString = eElement.getElementsByTagName("csv").item(0).getTextContent(); int csvNodeValue = Integer.parseInt(csvNodeString); csv = csv + csvNodeValue; Util.kadDia("<csv>" + csvNodeValue + "</csv>", "<csv>" + csv + "</csv>", xmlDiaCopy); } if (xml > 0) { String xmlNodeString = eElement.getElementsByTagName("xml").item(0).getTextContent(); int xmlNodeValue = Integer.parseInt(xmlNodeString); xml = xml + xmlNodeValue; Util.kadDia("<xml>" + xmlNodeValue + "</xml>", "<xml>" + xml + "</xml>", xmlDiaCopy); } if (xsd > 0) { String xsdNodeString = eElement.getElementsByTagName("xsd").item(0).getTextContent(); int xsdNodeValue = Integer.parseInt(xsdNodeString); xsd = xsd + xsdNodeValue; Util.kadDia("<xsd>" + xsdNodeValue + "</xsd>", "<xsd>" + xsd + "</xsd>", xmlDiaCopy); } if (wave > 0) { String waveNodeString = eElement.getElementsByTagName("wave").item(0).getTextContent(); int waveNodeValue = Integer.parseInt(waveNodeString); wave = wave + waveNodeValue; Util.kadDia("<wave>" + waveNodeValue + "</wave>", "<wave>" + wave + "</wave>", xmlDiaCopy); } if (mp3 > 0) { String mp3NodeString = eElement.getElementsByTagName("mp3").item(0).getTextContent(); int mp3NodeValue = Integer.parseInt(mp3NodeString); mp3 = mp3 + mp3NodeValue; Util.kadDia("<mp3>" + mp3NodeValue + "</mp3>", "<mp3>" + mp3 + "</mp3>", xmlDiaCopy); } if (jp2 > 0) { String jp2NodeString = eElement.getElementsByTagName("jp2").item(0).getTextContent(); int jp2NodeValue = Integer.parseInt(jp2NodeString); jp2 = jp2 + jp2NodeValue; Util.kadDia("<jp2>" + jp2NodeValue + "</jp2>", "<jp2>" + jp2 + "</jp2>", xmlDiaCopy); } if (jpx > 0) { String jpxNodeString = eElement.getElementsByTagName("jpx").item(0).getTextContent(); int jpxNodeValue = Integer.parseInt(jpxNodeString); jpx = jpx + jpxNodeValue; Util.kadDia("<jpx>" + jpxNodeValue + "</jpx>", "<jpx>" + jpx + "</jpx>", xmlDiaCopy); } if (jpeg > 0) { String jpegNodeString = eElement.getElementsByTagName("jpeg").item(0).getTextContent(); int jpegNodeValue = Integer.parseInt(jpegNodeString); jpeg = jpeg + jpegNodeValue; Util.kadDia("<jpeg>" + jpegNodeValue + "</jpeg>", "<jpeg>" + jpeg + "</jpeg>", xmlDiaCopy); } if (png > 0) { String pngNodeString = eElement.getElementsByTagName("png").item(0).getTextContent(); int pngNodeValue = Integer.parseInt(pngNodeString); png = png + pngNodeValue; Util.kadDia("<png>" + pngNodeValue + "</png>", "<png>" + png + "</png>", xmlDiaCopy); } if (dng > 0) { String dngNodeString = eElement.getElementsByTagName("dng").item(0).getTextContent(); int dngNodeValue = Integer.parseInt(dngNodeString); dng = dng + dngNodeValue; Util.kadDia("<dng>" + dngNodeValue + "</dng>", "<dng>" + dng + "</dng>", xmlDiaCopy); } if (svg > 0) { String svgNodeString = eElement.getElementsByTagName("svg").item(0).getTextContent(); int svgNodeValue = Integer.parseInt(svgNodeString); svg = svg + svgNodeValue; Util.kadDia("<svg>" + svgNodeValue + "</svg>", "<svg>" + svg + "</svg>", xmlDiaCopy); } if (mpeg2 > 0) { String mpeg2NodeString = eElement.getElementsByTagName("mpeg2").item(0) .getTextContent(); int mpeg2NodeValue = Integer.parseInt(mpeg2NodeString); mpeg2 = mpeg2 + mpeg2NodeValue; Util.kadDia("<mpeg2>" + mpeg2NodeValue + "</mpeg2>", "<mpeg2>" + mpeg2 + "</mpeg2>", xmlDiaCopy); } if (mp4 > 0) { String mp4NodeString = eElement.getElementsByTagName("mp4").item(0).getTextContent(); int mp4NodeValue = Integer.parseInt(mp4NodeString); mp4 = mp4 + mp4NodeValue; Util.kadDia("<mp4>" + mp4NodeValue + "</mp4>", "<mp4>" + mp4 + "</mp4>", xmlDiaCopy); } if (xls > 0) { String xlsNodeString = eElement.getElementsByTagName("xls").item(0).getTextContent(); int xlsNodeValue = Integer.parseInt(xlsNodeString); xls = xls + xlsNodeValue; Util.kadDia("<xls>" + xlsNodeValue + "</xls>", "<xls>" + xls + "</xls>", xmlDiaCopy); } if (odt > 0) { String odtNodeString = eElement.getElementsByTagName("odt").item(0).getTextContent(); int odtNodeValue = Integer.parseInt(odtNodeString); odt = odt + odtNodeValue; Util.kadDia("<odt>" + odtNodeValue + "</odt>", "<odt>" + odt + "</odt>", xmlDiaCopy); } if (ods > 0) { String odsNodeString = eElement.getElementsByTagName("ods").item(0).getTextContent(); int odsNodeValue = Integer.parseInt(odsNodeString); ods = ods + odsNodeValue; Util.kadDia("<ods>" + odsNodeValue + "</ods>", "<ods>" + ods + "</ods>", xmlDiaCopy); } if (odp > 0) { String odpNodeString = eElement.getElementsByTagName("odp").item(0).getTextContent(); int odpNodeValue = Integer.parseInt(odpNodeString); odp = odp + odpNodeValue; Util.kadDia("<odp>" + odpNodeValue + "</odp>", "<odp>" + odp + "</odp>", xmlDiaCopy); } if (other > 0) { String otherNodeString = eElement.getElementsByTagName("other").item(0) .getTextContent(); int otherNodeValue = Integer.parseInt(otherNodeString); other = other + otherNodeValue; Util.kadDia("<other>" + otherNodeValue + "</other>", "<other>" + other + "</other>", xmlDiaCopy); } } } } catch (Exception e) { e.printStackTrace(); } if (ok) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (tmpDir.exists()) { Runtime rt = Runtime.getRuntime(); Process proc = rt.exec(command.toString()); } System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (tmpDir.exists()) { Runtime rt = Runtime.getRuntime(); Process proc = rt.exec(command.toString()); } System.exit(2); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); } else { /* Ueberprfung des Parameters (Val-Typ): format / sip args[0] ist nicht "--format" oder * "--sip" --> INVALIDE */ LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE))); System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } System.exit(1); } }
From source file:com.milaboratory.mitcr.cli.Main.java
public static void main(String[] args) { int o = 0;// w w w .j a va 2 s . c om BuildInformation buildInformation = BuildInformationProvider.get(); final boolean isProduction = "default".equals(buildInformation.scmBranch); // buildInformation.version != null && buildInformation.version.lastIndexOf("SNAPSHOT") < 0; orderingMap.put(PARAMETERS_SET_OPTION, o++); orderingMap.put(SPECIES_OPTION, o++); orderingMap.put(GENE_OPTION, o++); orderingMap.put(ERROR_CORECTION_LEVEL_OPTION, o++); orderingMap.put(QUALITY_THRESHOLD_OPTION, o++); orderingMap.put(AVERAGE_QUALITY_OPTION, o++); orderingMap.put(LQ_OPTION, o++); orderingMap.put(CLUSTERIZATION_OPTION, o++); orderingMap.put(INCLUDE_CYS_PHE_OPTION, o++); orderingMap.put(LIMIT_OPTION, o++); orderingMap.put(EXPORT_OPTION, o++); orderingMap.put(REPORT_OPTION, o++); orderingMap.put(REPORTING_LEVEL_OPTION, o++); orderingMap.put(PHRED33_OPTION, o++); orderingMap.put(PHRED64_OPTION, o++); orderingMap.put(THREADS_OPTION, o++); orderingMap.put(COMPRESSED_OPTION, o++); orderingMap.put(PRINT_HELP_OPTION, o++); orderingMap.put(PRINT_VERSION_OPTION, o++); orderingMap.put(PRINT_DEBUG_OPTION, o++); options.addOption(OptionBuilder.withArgName("preset name").hasArg() .withDescription("preset of pipeline parameters to use").create(PARAMETERS_SET_OPTION)); options.addOption(OptionBuilder.withArgName("species").hasArg() .withDescription("overrides species ['hs' for Homo sapiens, 'mm' for us Mus musculus] " + "(default for built-in presets is 'hs')") .create(SPECIES_OPTION)); options.addOption(OptionBuilder.withArgName("gene").hasArg() .withDescription("overrides gene: TRB or TRA (default value for built-in parameter sets is TRB)") .create(GENE_OPTION)); options.addOption(OptionBuilder.withArgName("0|1|2").hasArg() .withDescription( "overrides error correction level (0 = don't correct errors, 1 = correct sequenecing " + "errors only (see -" + QUALITY_THRESHOLD_OPTION + " and -" + LQ_OPTION + " options for details), " + "2 = also correct PCR errors (see -" + CLUSTERIZATION_OPTION + " option)") .create(ERROR_CORECTION_LEVEL_OPTION)); options.addOption(OptionBuilder.withArgName("value").hasArg().withDescription( "overrides quality threshold value for segment alignment and bad quality sequences " + "correction algorithms. 0 tells the program not to process quality information. (default is 25)") .create(QUALITY_THRESHOLD_OPTION)); if (!isProduction) options.addOption(OptionBuilder.hasArg(false) .withDescription("use this option to output average instead of " + "maximal, quality for CDR3 nucleotide sequences. (Experimental option, use with caution.)") .create(AVERAGE_QUALITY_OPTION)); options.addOption(OptionBuilder.withArgName("map | drop").hasArg() .withDescription("overrides low quality CDR3s processing strategy (drop = filter off, " + "map = map onto clonotypes created from the high quality CDR3s). This option makes no difference if " + "quality threshold (-" + QUALITY_THRESHOLD_OPTION + " option) is set to 0, or error correction " + "level (-" + ERROR_CORECTION_LEVEL_OPTION + ") is 0.") .create(LQ_OPTION)); options.addOption(OptionBuilder.withArgName("smd | ete").hasArg() .withDescription("overrides the PCR error correction algorithm: smd = \"save my diversity\", " + "ete = \"eliminate these errors\". Default value for built-in parameters is ete.") .create(CLUSTERIZATION_OPTION)); options.addOption(OptionBuilder.withArgName("0|1").hasArg() .withDescription("overrides weather include bounding Cys & Phe into CDR3 sequence") .create(INCLUDE_CYS_PHE_OPTION)); options.addOption( OptionBuilder.withArgName("# of reads").hasArg() .withDescription("limits the number of input sequencing reads, use this parameter to " + "normalize several datasets or to have a glance at the data") .create(LIMIT_OPTION)); options.addOption(OptionBuilder.withArgName("new name").hasArg() .withDescription("use this option to export presets to a local xml files").create(EXPORT_OPTION)); options.addOption(OptionBuilder.withArgName("file name").hasArg() .withDescription("use this option to write analysis report (summary) to file") .create(REPORT_OPTION)); options.addOption(OptionBuilder.withArgName("1|2|3").hasArg(true) .withDescription("output detalization level (1 = simple, 2 = medium, 3 = full, this format " + "could be deserialized using mitcr API). Affects only tab-delimited output. Default value is 3.") .create(REPORTING_LEVEL_OPTION)); options.addOption(OptionBuilder.hasArg(false).withDescription( "add this option if input file is in old illumina format with 64 byte offset for quality " + "string (MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)") .create(PHRED64_OPTION)); options.addOption(OptionBuilder.hasArg(false) .withDescription("add this option if input file is in Phred+33 format for quality values " + "(MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)") .create(PHRED33_OPTION)); options.addOption(OptionBuilder.withArgName("threads").hasArg() .withDescription( "specifies the number of CDR3 extraction threads (default = number of available CPU cores)") .create(THREADS_OPTION)); if (!isProduction) options.addOption(OptionBuilder.hasArg(false) .withDescription("use compressed data structures for storing individual " + "clone segments statistics (from which arises the clone segment information). This option reduces required " + "amount of memory, but introduces small stochastic errors into the algorithm which determines clone " + "segments. (Experimental option, use with caution.)") .create(COMPRESSED_OPTION)); options.addOption( OptionBuilder.hasArg(false).withDescription("print this message").create(PRINT_HELP_OPTION)); options.addOption(OptionBuilder.hasArg(false).withDescription("print version information") .create(PRINT_VERSION_OPTION)); options.addOption(OptionBuilder.hasArg(false) .withDescription("print additional information about analysis process").create(PRINT_DEBUG_OPTION)); PosixParser parser = new PosixParser(); try { long input_limit = -1; int threads = Runtime.getRuntime().availableProcessors(); int reporting_level = 3; int ec_level = 2; CommandLine cl = parser.parse(options, args, true); if (cl.hasOption(PRINT_HELP_OPTION)) { printHelp(); return; } boolean averageQuality = cl.hasOption(AVERAGE_QUALITY_OPTION), compressedAggregators = cl.hasOption(COMPRESSED_OPTION); if (cl.hasOption(PRINT_VERSION_OPTION)) { System.out.println("MiTCR by MiLaboratory, version: " + buildInformation.version); System.out.println("Branch: " + buildInformation.scmBranch); System.out.println("Built: " + buildInformation.buildDate + ", " + buildInformation.jdk + " JDK, " + "build machine: " + buildInformation.builtBy); System.out.println("SCM changeset: " + buildInformation.scmChangeset + " (" + buildInformation.scmDate.replace("\"", "") + ")"); return; } //Normal execution String paramName = cl.getOptionValue(PARAMETERS_SET_OPTION); if (paramName == null) { err.println("No parameters set is specified."); return; } Parameters params = ParametersIO.getParameters(paramName); if (params == null) { err.println("No parameters set found with name '" + paramName + "'."); return; } String value; if ((value = cl.getOptionValue(THREADS_OPTION)) != null) threads = Integer.decode(value); if ((value = cl.getOptionValue(REPORTING_LEVEL_OPTION)) != null) reporting_level = Integer.decode(value); if ((value = cl.getOptionValue(LIMIT_OPTION)) != null) input_limit = Long.decode(value); if ((value = cl.getOptionValue(GENE_OPTION)) != null) params.setGene(Gene.fromXML(value)); if ((value = cl.getOptionValue(SPECIES_OPTION)) != null) params.setSpecies(Species.getFromShortName(value)); if ((value = cl.getOptionValue(INCLUDE_CYS_PHE_OPTION)) != null) { if (value.equals("1")) params.getCDR3ExtractorParameters().setIncludeCysPhe(true); else if (value.equals("0")) params.getCDR3ExtractorParameters().setIncludeCysPhe(false); else { err.println("Illegal value for -" + INCLUDE_CYS_PHE_OPTION + " parameter."); return; } } if ((value = cl.getOptionValue(ERROR_CORECTION_LEVEL_OPTION)) != null) { int v = Integer.decode(value); ec_level = v; if (v == 0) { params.setCloneGeneratorParameters(new BasicCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.None); } else if (v == 1) { params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.None); } else if (v == 2) { params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.OneMismatch, .1f); } else throw new RuntimeException("This (" + v + ") error correction level is not supported."); } if ((value = cl.getOptionValue(QUALITY_THRESHOLD_OPTION)) != null) { int v = Integer.decode(value); if (v == 0) params.setQualityInterpretationStrategy(new DummyQualityInterpretationStrategy()); else params.setQualityInterpretationStrategy(new IlluminaQualityInterpretationStrategy((byte) v)); } if ((value = cl.getOptionValue(LQ_OPTION)) != null) if (ec_level > 0) switch (value) { case "map": params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters( ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .getSegmentInformationAggregationFactor(), 3, true)); break; case "drop": params.setCloneGeneratorParameters(new LQFilteringOffCloneGeneratorParameters( ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .getSegmentInformationAggregationFactor())); break; default: throw new RuntimeException("Wrong value for -" + LQ_OPTION + " option."); } if ((value = cl.getOptionValue(CLUSTERIZATION_OPTION)) != null) if (ec_level > 1) // == 2 switch (value) { case "smd": params.setClusterizationType(CloneClusterizationType.V2D1J2T3Explicit); break; case "ete": params.setClusterizationType(CloneClusterizationType.OneMismatch); break; default: throw new RuntimeException("Wrong value for -" + CLUSTERIZATION_OPTION + " option."); } ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .setAccumulatorType(AccumulatorType.get(compressedAggregators, averageQuality)); if ((value = cl.getOptionValue(EXPORT_OPTION)) != null) { //Exporting parameters ParametersIO.exportParameters(params, value); return; } String[] offArgs = cl.getArgs(); if (offArgs.length == 0) { err.println("Input file not specified."); return; } else if (offArgs.length == 1) { err.println("Output file not specified."); return; } else if (offArgs.length > 2) { err.println("Unrecognized argument."); return; } String inputFileName = offArgs[0]; String outputFileName = offArgs[1]; File input = new File(inputFileName); if (!input.exists()) { err.println("Input file not found."); return; } //TODO This also done inside SFastqReader constructor CompressionType compressionType = CompressionType.None; if (inputFileName.endsWith(".gz")) compressionType = CompressionType.GZIP; QualityFormat format = null; // If variable remains null file format will be detected automatically if (cl.hasOption(PHRED33_OPTION)) format = QualityFormat.Phred33; if (cl.hasOption(PHRED64_OPTION)) if (format == null) format = QualityFormat.Phred64; else { err.println( "Options: -" + PHRED33_OPTION + " and -" + PHRED64_OPTION + " are mutually exclusive"); return; } SFastqReader reads = format == null ? new SFastqReader(input, compressionType) : new SFastqReader(input, format, compressionType); OutputPort<SSequencingRead> inputToPipeline = reads; if (input_limit >= 0) inputToPipeline = new CountLimitingOutputPort<>(inputToPipeline, input_limit); SegmentLibrary library = DefaultSegmentLibrary.load(); AnalysisStatisticsAggregator statisticsAggregator = new AnalysisStatisticsAggregator(); FullPipeline pipeline = new FullPipeline(inputToPipeline, params, false, library); pipeline.setThreads(threads); pipeline.setAnalysisListener(statisticsAggregator); new Thread(new SmartProgressReporter(pipeline, err)).start(); // Printing status to the standard error stream pipeline.run(); if (cl.hasOption(PRINT_DEBUG_OPTION)) { err.println("Memory = " + (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())); err.println("Clusterization: " + pipeline.getQC().getReadsClusterized() + "% of reads, " + pipeline.getQC().getClonesClusterized() + " % clones"); } CloneSetClustered cloneSet = pipeline.getResult(); if ((value = cl.getOptionValue(REPORT_OPTION)) != null) { File file = new File(value); TablePrintStreamAdapter table; if (file.exists()) table = new TablePrintStreamAdapter(new FileOutputStream(file, true)); else { table = new TablePrintStreamAdapter(file); ReportExporter.printHeader(table); } //CloneSetQualityControl qc = new CloneSetQualityControl(library, params.getSpecies(), params.getGene(), cloneSet); ReportExporter.printRow(table, inputFileName, outputFileName, pipeline.getQC(), statisticsAggregator); table.close(); } if (outputFileName.endsWith(".cls")) ClsExporter.export(pipeline, outputFileName.replace(".cls", "") + " " + new Date().toString(), input.getName(), outputFileName); else { //Dry run if (outputFileName.startsWith("-")) return; ExportDetalizationLevel detalization = ExportDetalizationLevel.fromLevel(reporting_level); CompressionType compressionType1 = CompressionType.None; if (outputFileName.endsWith(".gz")) compressionType1 = CompressionType.GZIP; CloneSetIO.exportCloneSet(outputFileName, cloneSet, detalization, params, input.getAbsolutePath(), compressionType1); } } catch (ParseException | RuntimeException | IOException e) { err.println("Error occurred in the analysis pipeline."); err.println(); e.printStackTrace(); //printHelp(); } }
From source file:com.github.wshackle.java4cpp.J4CppMain.java
public static void main(String[] args) throws IOException, ClassNotFoundException { main_completed = false;/*www.j ava 2 s .c om*/ Options options = new Options(); options.addOption(Option.builder("?").desc("Print this message").longOpt("help").build()); options.addOption(Option.builder("n").hasArg().desc("C++ namespace for newly generated classes.") .longOpt("namespace").build()); options.addOption( Option.builder("c").hasArgs().desc("Single Java class to extract.").longOpt("classes").build()); options.addOption( Option.builder("p").hasArgs().desc("Java Package prefix to extract").longOpt("packages").build()); options.addOption(Option.builder("o").hasArg().desc("Output C++ source file.").longOpt("output").build()); options.addOption(Option.builder("j").hasArg().desc("Input jar file").longOpt("jar").build()); options.addOption(Option.builder("h").hasArg().desc("Output C++ header file.").longOpt("header").build()); options.addOption(Option.builder("l").hasArg() .desc("Maximum limit on classes to extract from jars.[default=200]").longOpt("limit").build()); options.addOption(Option.builder("v").desc("enable verbose output").longOpt("verbose").build()); options.addOption(Option.builder().hasArg().desc("Classes per output file.[default=10]") .longOpt(CLASSESPEROUTPUT).build()); options.addOption(Option.builder().hasArgs().desc( "Comma seperated list of nativeclass=javaclass native where nativeclass will be generated as an extension/implementation of the java class.") .longOpt("natives").build()); options.addOption(Option.builder().hasArg() .desc("library name for System.loadLibrary(...) for native extension classes") .longOpt("loadlibname").build()); String output = null; String header = null; String jar = null; Set<String> classnamesToFind = null; Set<String> packageprefixes = null; String loadlibname = null; Map<String, String> nativesNameMap = null; Map<String, Class> nativesClassMap = null; int limit = DEFAULT_LIMIT; int classes_per_file = 10; List<Class> classes = new ArrayList<>(); String limitstring = Integer.toString(limit); try { // parse the command line arguments System.out.println("args = " + Arrays.toString(args)); CommandLine line = new DefaultParser().parse(options, args); loadlibname = line.getOptionValue("loadlibname"); verbose = line.hasOption("verbose"); if (line.hasOption(CLASSESPEROUTPUT)) { String cpoStr = line.getOptionValue(CLASSESPEROUTPUT); try { int cpoI = Integer.valueOf(cpoStr); classes_per_file = cpoI; } catch (Exception e) { System.err.println("Option for " + CLASSESPEROUTPUT + "=\"" + cpoStr + "\""); printHelpAndExit(options, args); } } if (line.hasOption("natives")) { String natives[] = line.getOptionValues("natives"); if (verbose) { System.out.println("natives = " + Arrays.toString(natives)); } nativesNameMap = new HashMap<>(); nativesClassMap = new HashMap<>(); for (int i = 0; i < natives.length; i++) { int eq_index = natives[i].indexOf('='); String nativeClassName = natives[i].substring(0, eq_index).trim(); String javaClassName = natives[i].substring(eq_index + 1).trim(); Class javaClass = null; try { javaClass = Class.forName(javaClassName); } catch (ClassNotFoundException e) { //e.printStackTrace(); System.err.println("Class for " + javaClassName + " not found. (It may be found later in jar if specified.)"); } nativesNameMap.put(javaClassName, nativeClassName); if (javaClass != null) { nativesClassMap.put(nativeClassName, javaClass); if (!classes.contains(javaClass)) { classes.add(javaClass); } } } } // // validate that block-size has been set // if (line.hasOption("block-size")) { // // print the value of block-size // if(verbose) System.out.println(line.getOptionValue("block-size")); // } jar = line.getOptionValue("jar", jar); if (verbose) { System.out.println("jar = " + jar); } if (null != jar) { if (jar.startsWith("~/")) { jar = new File(new File(getHomeDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("./")) { jar = new File(new File(getCurrentDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("../")) { jar = new File(new File(getCurrentDir()).getParentFile(), jar.substring(3)).getCanonicalPath(); } } if (line.hasOption("classes")) { classnamesToFind = new HashSet<String>(); String classStrings[] = line.getOptionValues("classes"); if (verbose) { System.out.println("classStrings = " + Arrays.toString(classStrings)); } classnamesToFind.addAll(Arrays.asList(classStrings)); if (verbose) { System.out.println("classnamesToFind = " + classnamesToFind); } } // if (!line.hasOption("namespace")) { // if (classname != null && classname.length() > 0) { // namespace = classname.toLowerCase().replace(".", "_"); // } else if (jar != null && jar.length() > 0) { // int lastSep = jar.lastIndexOf(File.separator); // int start = Math.max(0, lastSep + 1); // int period = jar.indexOf('.', start + 1); // int end = Math.max(start + 1, period); // namespace = jar.substring(start, end).toLowerCase(); // namespace = namespace.replace(" ", "_"); // if (namespace.indexOf("-") > 0) { // namespace = namespace.substring(0, namespace.indexOf("-")); // } // } // } namespace = line.getOptionValue("namespace", namespace); if (verbose) { System.out.println("namespace = " + namespace); } if (null != namespace) { output = namespace + ".cpp"; } output = line.getOptionValue("output", output); if (verbose) { System.out.println("output = " + output); } if (null != output) { if (output.startsWith("~/")) { output = System.getProperty("user.home") + output.substring(1); } header = output.substring(0, output.lastIndexOf('.')) + ".h"; } else { output = "out.cpp"; } header = line.getOptionValue("header", header); if (verbose) { System.out.println("header = " + header); } if (null != header) { if (header.startsWith("~/")) { header = System.getProperty("user.home") + header.substring(1); } } else { header = "out.h"; } if (line.hasOption("packages")) { packageprefixes = new HashSet<String>(); packageprefixes.addAll(Arrays.asList(line.getOptionValues("packages"))); } if (line.hasOption("limit")) { limitstring = line.getOptionValue("limit", Integer.toString(DEFAULT_LIMIT)); limit = Integer.valueOf(limitstring); } if (line.hasOption("help")) { printHelpAndExit(options, args); } } catch (ParseException exp) { if (verbose) { System.out.println("Unexpected exception:" + exp.getMessage()); } printHelpAndExit(options, args); } Set<Class> excludedClasses = new HashSet<>(); Set<String> foundClassNames = new HashSet<>(); excludedClasses.add(Object.class); excludedClasses.add(String.class); excludedClasses.add(void.class); excludedClasses.add(Void.class); excludedClasses.add(Class.class); excludedClasses.add(Enum.class); Set<String> packagesSet = new TreeSet<>(); List<URL> urlsList = new ArrayList<>(); String cp = System.getProperty("java.class.path"); if (verbose) { System.out.println("System.getProperty(\"java.class.path\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } cp = System.getenv("CLASSPATH"); if (verbose) { System.out.println("System.getenv(\"CLASSPATH\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } if (verbose) { System.out.println("urlsList = " + urlsList); } if (null != jar && jar.length() > 0) { Path jarPath = FileSystems.getDefault().getPath(jar); ZipInputStream zip = new ZipInputStream(Files.newInputStream(jarPath, StandardOpenOption.READ)); URL jarUrl = new URL("jar:file:" + jarPath.toFile().getCanonicalPath() + "!/"); urlsList.add(jarUrl); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); for (ZipEntry entry = zip.getNextEntry(); entry != null; entry = zip.getNextEntry()) { // This ZipEntry represents a class. Now, what class does it represent? String entryName = entry.getName(); if (verbose) { System.out.println("entryName = " + entryName); } if (!entry.isDirectory() && entryName.endsWith(".class")) { if (entryName.indexOf('$') >= 0) { continue; } String classFileName = entry.getName().replace('/', '.'); String className = classFileName.substring(0, classFileName.length() - ".class".length()); if (classnamesToFind != null && classnamesToFind.size() > 0 && !classnamesToFind.contains(className)) { if (verbose) { System.out.println("skipping className=" + className + " because it does not found in=" + classnamesToFind); } continue; } try { Class clss = cl.loadClass(className); if (null != nativesClassMap && null != nativesNameMap && nativesNameMap.containsKey(className)) { nativesClassMap.put(nativesNameMap.get(className), clss); if (!classes.contains(clss)) { classes.add(clss); } } if (packageprefixes != null && packageprefixes.size() > 0) { if (null == clss.getPackage()) { continue; } final String pkgName = clss.getPackage().getName(); boolean matchFound = false; for (String prefix : packageprefixes) { if (pkgName.startsWith(prefix)) { matchFound = true; break; } } if (!matchFound) { continue; } } Package p = clss.getPackage(); if (null != p) { packagesSet.add(clss.getPackage().getName()); } if (!classes.contains(clss) && isAddableClass(clss, excludedClasses)) { if (null != classnamesToFind && classnamesToFind.contains(className) && !foundClassNames.contains(className)) { foundClassNames.add(className); if (verbose) { System.out.println("foundClassNames = " + foundClassNames); } } // if(verbose) System.out.println("clss = " + clss); classes.add(clss); // Class superClass = clss.getSuperclass(); // while (null != superClass // && !classes.contains(superClass) // && isAddableClass(superClass, excludedClasses)) { // classes.add(superClass); // superClass = superClass.getSuperclass(); // } } } catch (ClassNotFoundException | NoClassDefFoundError ex) { System.err.println( "Caught " + ex.getClass().getName() + ":" + ex.getMessage() + " for className=" + className + ", entryName=" + entryName + ", jarPath=" + jarPath); } } } } if (null != classnamesToFind) { if (verbose) { System.out.println("Checking classnames arguments"); } for (String classname : classnamesToFind) { if (verbose) { System.out.println("classname = " + classname); } if (foundClassNames.contains(classname)) { if (verbose) { System.out.println("foundClassNames.contains(" + classname + ")"); } continue; } try { if (classes.contains(Class.forName(classname))) { if (verbose) { System.out.println("Classes list already contains: " + classname); } continue; } } catch (Exception e) { } if (null != classname && classname.length() > 0) { urlsList.add(new URL("file://" + System.getProperty("user.dir") + "/")); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); Class c = null; try { c = cl.loadClass(classname); } catch (ClassNotFoundException e) { System.err.println("Class " + classname + " not found "); } if (verbose) { System.out.println("c = " + c); } if (null == c) { try { c = ClassLoader.getSystemClassLoader().loadClass(classname); } catch (ClassNotFoundException e) { if (verbose) { System.out.println("System ClassLoader failed to find " + classname); } } } if (null != c) { classes.add(c); } else { System.err.println("Class " + classname + " not found"); } } } if (verbose) { System.out.println("Finished checking classnames arguments"); } } if (classes == null || classes.size() < 1) { if (null == nativesClassMap || nativesClassMap.keySet().size() < 1) { System.err.println("No Classes specified or found."); System.exit(1); } } if (verbose) { System.out.println("Classes found = " + classes.size()); } if (classes.size() > limit) { System.err.println("limit=" + limit); System.err.println( "Too many classes please use -c or -p options to limit classes or -l to increase limit."); if (verbose) { System.out.println("packagesSet = " + packagesSet); } System.exit(1); } List<Class> newClasses = new ArrayList<Class>(); for (Class clss : classes) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } try { Field fa[] = clss.getDeclaredFields(); for (Field f : fa) { if (Modifier.isPublic(f.getModifiers())) { Class fClass = f.getType(); if (!classes.contains(fClass) && !newClasses.contains(fClass) && isAddableClass(fClass, excludedClasses)) { newClasses.add(fClass); } } } } catch (NoClassDefFoundError e) { e.printStackTrace(); } for (Method m : clss.getDeclaredMethods()) { if (m.isSynthetic()) { continue; } if (!Modifier.isPublic(m.getModifiers()) || Modifier.isAbstract(m.getModifiers())) { continue; } Class retType = m.getReturnType(); if (verbose) { System.out.println("Checking dependancies for Method = " + m); } if (!classes.contains(retType) && !newClasses.contains(retType) && isAddableClass(retType, excludedClasses)) { newClasses.add(retType); superClass = retType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } for (Class paramType : m.getParameterTypes()) { if (!classes.contains(paramType) && !newClasses.contains(paramType) && isAddableClass(paramType, excludedClasses)) { newClasses.add(paramType); superClass = paramType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } } if (null != nativesClassMap) { for (Class clss : nativesClassMap.values()) { if (null != clss) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } if (verbose) { System.out.println("Dependency classes needed = " + newClasses.size()); } classes.addAll(newClasses); List<Class> newOrderClasses = new ArrayList<>(); for (Class clss : classes) { if (newOrderClasses.contains(clss)) { continue; } Class superClass = clss.getSuperclass(); Stack<Class> stack = new Stack<>(); while (null != superClass && !newOrderClasses.contains(superClass) && !superClass.equals(java.lang.Object.class)) { stack.push(superClass); superClass = superClass.getSuperclass(); } while (!stack.empty()) { newOrderClasses.add(stack.pop()); } newOrderClasses.add(clss); } classes = newOrderClasses; if (verbose) { System.out.println("Total number of classes = " + classes.size()); System.out.println("classes = " + classes); } String forward_header = header.substring(0, header.lastIndexOf('.')) + "_fwd.h"; Map<String, String> map = new HashMap<>(); map.put(JAR, jar != null ? jar : ""); map.put("%CLASSPATH_PREFIX%", getCurrentDir() + ((jar != null) ? (File.pathSeparator + ((new File(jar).getCanonicalPath()).replace("\\", "\\\\"))) : "")); map.put("%FORWARD_HEADER%", forward_header); map.put("%HEADER%", header); map.put("%PATH_SEPERATOR%", File.pathSeparator); String tabs = ""; String headerDefine = forward_header.substring(Math.max(0, forward_header.indexOf(File.separator))) .replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassName + ".java"))) { if (javaClass.isInterface()) { pw.println("public class " + nativeClassName + " implements " + javaClass.getCanonicalName() + ", AutoCloseable{"); } else { pw.println("public class " + nativeClassName + " extends " + javaClass.getCanonicalName() + " implements AutoCloseable{"); } if (null != loadlibname && loadlibname.length() > 0) { pw.println(TAB_STRING + "static {"); pw.println(TAB_STRING + TAB_STRING + "System.loadLibrary(\"" + loadlibname + "\");"); pw.println(TAB_STRING + "}"); pw.println(); } pw.println(TAB_STRING + "public " + nativeClassName + "() {"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "private long nativeAddress=0;"); pw.println(TAB_STRING + "private boolean nativeDeleteOnClose=false;"); pw.println(); pw.println(TAB_STRING + "protected " + nativeClassName + "(final long nativeAddress) {"); pw.println(TAB_STRING + TAB_STRING + "this.nativeAddress = nativeAddress;"); pw.println(TAB_STRING + "}"); pw.println(TAB_STRING + "private native void nativeDelete();"); pw.println(); pw.println(TAB_STRING + "@Override"); pw.println(TAB_STRING + "public synchronized void close() {"); // pw.println(TAB_STRING + TAB_STRING + "if(nativeAddress != 0 && nativeDeleteOnClose) {"); pw.println(TAB_STRING + TAB_STRING + "nativeDelete();"); // pw.println(TAB_STRING + TAB_STRING + "}"); // pw.println(TAB_STRING + TAB_STRING + "nativeAddress=0;"); // pw.println(TAB_STRING + TAB_STRING + "nativeDeleteOnClose=false;"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "protected void finalizer() {"); pw.println(TAB_STRING + TAB_STRING + "close();"); pw.println(TAB_STRING + "}"); pw.println(); Method ma[] = javaClass.getDeclaredMethods(); for (Method m : ma) { int modifiers = m.getModifiers(); if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !m.isDefault() && !m.isSynthetic()) { pw.println(); pw.println(TAB_STRING + "@Override"); String params = ""; for (int i = 0; i < m.getParameterTypes().length; i++) { params += m.getParameterTypes()[i].getCanonicalName() + " param" + i; if (i < m.getParameterTypes().length - 1) { params += ","; } } pw.println(TAB_STRING + "native public " + m.getReturnType().getCanonicalName() + " " + m.getName() + "(" + params + ");"); // + IntStream.range(0, m.getParameterTypes().length) // .mapToObj(i -> m.getParameterTypes()[i].getCanonicalName() + " param" + i) // .collect(Collectors.joining(",")) + ");"); } } pw.println("}"); } } } try (PrintWriter pw = new PrintWriter(new FileWriter(forward_header))) { tabs = ""; processTemplate(pw, map, "header_fwd_template_start.h", tabs); Class lastClass = null; for (int class_index = 0; class_index < classes.size(); class_index++) { Class clss = classes.get(class_index); String clssOnlyName = getCppClassName(clss); tabs = openClassNamespace(clss, pw, tabs, lastClass); tabs += TAB_STRING; pw.println(tabs + "class " + clssOnlyName + ";"); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classes.size() - 1)) ? classes.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } processTemplate(pw, map, "header_fwd_template_end.h", tabs); } headerDefine = header.substring(Math.max(0, header.indexOf(File.separator))).replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (classes_per_file < 1) { classes_per_file = classes.size(); } final int num_class_segments = (classes.size() > 1) ? ((classes.size() + classes_per_file - 1) / classes_per_file) : 1; String fmt = "%d"; if (num_class_segments > 10) { fmt = "%02d"; } if (num_class_segments > 100) { fmt = "%03d"; } String header_file_base = header; if (header_file_base.endsWith(".h")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 2); } else if (header_file_base.endsWith(".hh")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 3); } else if (header_file_base.endsWith(".hpp")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 4); } try (PrintWriter pw = new PrintWriter(new FileWriter(header))) { tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; pw.println("#include \"" + header_segment_file + "\""); } if (null != nativesClassMap) { tabs = TAB_STRING; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); pw.println(); pw.println(tabs + "class " + nativeClassName + "Context;"); pw.println(); map.put(CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; pw.println(tabs + nativeClassName + "Context *context;"); pw.println(tabs + nativeClassName + "();"); pw.println(tabs + "~" + nativeClassName + "();"); Method methods[] = javaClass.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { pw.println(tabs + getNativeMethodCppDeclaration(method, javaClass)); } } pw.println(tabs + "void initContext(" + nativeClassName + "Context *ctx,bool isref);"); pw.println(tabs + "void deleteContext();"); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + nativeClassName); } } tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; try (PrintWriter pw = new PrintWriter(new FileWriter(header_segment_file))) { tabs = ""; //processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); pw.println("// Never include this file (" + header_segment_file + ") directly. include " + header + " instead."); pw.println(); Class lastClass = null; final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); tabs += TAB_STRING; processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (Modifier.isAbstract(clss.getModifiers()) || clss.isInterface()) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "() {};"); pw.println(tabs + "public:"); } else { if (constructors.length > 0) { pw.println(tabs + "protected:"); } pw.println(tabs + clssOnlyName + "();"); if (constructors.length > 0) { pw.println(tabs + "public:"); } } } for (Constructor c : constructors) { if (c.getParameterTypes().length == 0 && Modifier.isProtected(c.getModifiers())) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "();"); pw.println(tabs + "public:"); } if (checkConstructor(c, clss, classes)) { continue; } if (c.getParameterTypes().length == 1 && clss.isAssignableFrom(c.getParameterTypes()[0])) { continue; } if (!Modifier.isPublic(c.getModifiers())) { continue; } if (c.getParameterTypes().length == 1) { if (c.getParameterTypes()[0].getName().equals(clss.getName())) { // if(verbose) System.out.println("skipping constructor."); continue; } } if (!checkParameters(c.getParameterTypes(), classes)) { continue; } pw.println( tabs + clssOnlyName + getCppParamDeclarations(c.getParameterTypes(), clss) + ";"); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + ";"); } } pw.println(tabs + "~" + clssOnlyName + "();"); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldGetterDeclaration(field, clss)); } if (addSetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldSetterDeclaration(field, clss)); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (!checkMethod(method, classes)) { continue; } if ((method.getModifiers() & Modifier.PUBLIC) == Modifier.PUBLIC) { pw.println(tabs + getCppDeclaration(method, clss)); } if (isArrayStringMethod(method)) { pw.println(tabs + getCppModifiers(method.getModifiers()) + getCppType(method.getReturnType(), clss) + " " + fixMethodName(method) + "(int argc,const char **argv);"); } if (isMethodToMakeEasy(method)) { pw.println(tabs + getEasyCallCppDeclaration(method, clss)); } } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + clssOnlyName); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); pw.println(); lastClass = clss; } //processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String output_segment_file = output; if (output_segment_file.endsWith(".cpp")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 4); } else if (output_segment_file.endsWith(".cc")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 3); } output_segment_file += "" + String.format(fmt, segment_index) + ".cpp"; try (PrintWriter pw = new PrintWriter(new FileWriter(output_segment_file))) { tabs = ""; if (segment_index < 1) { processTemplate(pw, map, "cpp_template_start_first.cpp", tabs); } else { processTemplate(pw, map, CPP_TEMPLATE_STARTCPP, tabs); } final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); Class lastClass = null; for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(FULL_CLASS_NAME, clssName); String fcjs = classToJNISignature(clss); fcjs = fcjs.substring(1, fcjs.length() - 1); map.put(FULL_CLASS_JNI_SIGNATURE, fcjs); if (verbose) { System.out.println("fcjs = " + fcjs); } map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); map.put("%INITIALIZE_CONTEXT%", ""); map.put("%INITIALIZE_CONTEXT_REF%", ""); processTemplate(pw, map, CPP_START_CLASSCPP, tabs); Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (!Modifier.isAbstract(clss.getModifiers()) && !clss.isInterface()) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + "() : " + classToCppBase(clss) + "((jobject)NULL,false) {"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, CPP_NEWCPP, tabs); pw.println(tabs + "}"); pw.println(); } } for (Constructor c : constructors) { if (checkConstructor(c, clss, classes)) { continue; } Class[] paramClasses = c.getParameterTypes(); pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getCppParamDeclarations(paramClasses, clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); tabs = tabs + TAB_STRING; map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")V"); map.put(CONSTRUCTOR_ARGS, (paramClasses.length > 0 ? "," : "") + getCppParamNames(paramClasses)); processTemplate(pw, map, CPP_NEWCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); pw.println(tabs + "}"); pw.println(); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); processTemplate(pw, map, "cpp_start_easy_constructor.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } processTemplate(pw, map, "cpp_new_easy_internals.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_constructor.cpp", tabs); pw.println(tabs + "}"); } } pw.println(); pw.println(tabs + "// Destructor for " + clssName); pw.println(tabs + clssOnlyName + "::~" + clssOnlyName + "() {"); pw.println(tabs + "\t// Place-holder for later extensibility."); pw.println(tabs + "}"); pw.println(); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field getter for " + field.getName()); pw.println(getCppFieldGetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = field.getType(); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put(METHOD_ARGS, ""); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_getfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_getfield.cpp", tabs); } pw.println(tabs + "}"); } if (addSetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field setter for " + field.getName()); pw.println(getCppFieldSetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = void.class; map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); Class[] paramClasses = new Class[] { field.getType() }; String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(field.getType())); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_setfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_setfield.cpp", tabs); } pw.println(tabs + "}"); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (checkMethod(method, classes)) { pw.println(); pw.println(getCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); map.put(METHOD_NAME, method.getName()); if (fixMethodName(method).contains("equals2")) { if (verbose) { System.out.println("debug me"); } } map.put("%JAVA_METHOD_NAME%", method.getName()); Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); Class returnClass = method.getReturnType(); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")" + classToJNISignature(returnClass)); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); tabs += TAB_STRING; if (!Modifier.isStatic(method.getModifiers())) { processTemplate(pw, map, CPP_METHODCPP, tabs); } else { processTemplate(pw, map, CPP_STATIC_METHODCPP, tabs); } tabs = tabs.substring(0, tabs.length() - TAB_STRING.length()); pw.println(tabs + "}"); if (isArrayStringMethod(method)) { map.put(METHOD_RETURN_STORE, isVoid(returnClass) ? "" : getCppType(returnClass, clss) + " returnVal="); map.put(METHOD_RETURN_GET, isVoid(returnClass) ? "return ;" : "return returnVal;"); processTemplate(pw, map, CPP_EASY_STRING_ARRAY_METHODCPP, tabs); } else if (isMethodToMakeEasy(method)) { pw.println(); pw.println(tabs + "// Easy call alternative for " + method.getName()); pw.println(getEasyCallCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); tabs += TAB_STRING; map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclareOut(returnClass, clss)); processTemplate(pw, map, "cpp_start_easy_method.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } String methodArgsIn = getCppParamNamesIn(paramClasses); String retStoreOut = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnOutVarType(returnClass, clss) + ") "; pw.println(tabs + retStoreOut + fixMethodName(method) + "(" + methodArgsIn + ");"); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_method.cpp", tabs); if (!isVoid(returnClass)) { pw.println(tabs + "return retVal;"); } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } } } processTemplate(pw, map, CPP_END_CLASSCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } if (segment_index < 1) { if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put("%INITIALIZE_CONTEXT%", "context=NULL; initContext(NULL,false);"); map.put("%INITIALIZE_CONTEXT_REF%", "context=NULL; initContext(objref.context,true);"); tabs += TAB_STRING; processTemplate(pw, map, CPP_START_CLASSCPP, tabs); pw.println(); pw.println(tabs + nativeClassName + "::" + nativeClassName + "() : " + getModifiedClassName(javaClass).replace(".", "::") + "((jobject)NULL,false) {"); tabs += TAB_STRING; pw.println(tabs + "context=NULL;"); pw.println(tabs + "initContext(NULL,false);"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, "cpp_new_native.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); pw.println(tabs + "// Destructor for " + nativeClassName); pw.println(tabs + nativeClassName + "::~" + nativeClassName + "() {"); pw.println(tabs + TAB_STRING + "if(NULL != context) {"); pw.println(tabs + TAB_STRING + TAB_STRING + "deleteContext();"); pw.println(tabs + TAB_STRING + "}"); pw.println(tabs + TAB_STRING + "context=NULL;"); pw.println(tabs + "}"); pw.println(); // pw.println(tabs + "public:"); // pw.println(tabs + nativeClassName + "();"); // pw.println(tabs + "~" + nativeClassName + "();"); tabs = tabs.substring(TAB_STRING.length()); // Method methods[] = javaClass.getDeclaredMethods(); // for (int j = 0; j < methods.length; j++) { // Method method = methods[j]; // int modifiers = method.getModifiers(); // if (!Modifier.isPublic(modifiers)) { // continue; // } // pw.println(tabs + getCppDeclaration(method, javaClass)); // } // pw.println(tabs + "}; // end class " + nativeClassName); processTemplate(pw, map, CPP_END_CLASSCPP, tabs); } } processTemplate(pw, map, "cpp_template_end_first.cpp", tabs); tabs = ""; if (null != nativesClassMap) { pw.println("using namespace " + namespace + ";"); pw.println("#ifdef __cplusplus"); pw.println("extern \"C\" {"); pw.println("#endif"); int max_method_count = 0; tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put(METHOD_ONFAIL, "return;"); Method methods[] = javaClass.getDeclaredMethods(); if (max_method_count < methods.length) { max_method_count = methods.length; } for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); pw.println(); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String argsToAdd = method.getParameterTypes().length > 0 ? "," + paramDecls.substring(1, paramDecls.length() - 1) : ""; pw.println("JNIEXPORT " + getCppType(returnClass, javaClass) + " JNICALL Java_" + nativeClassName + "_" + method.getName() + "(JNIEnv *env, jobject jthis" + argsToAdd + ") {"); tabs = TAB_STRING; processTemplate(pw, map, "cpp_native_wrap.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println("}"); pw.println(); } } pw.println("JNIEXPORT void JNICALL Java_" + nativeClassName + "_nativeDelete(JNIEnv *env, jobject jthis) {"); tabs += TAB_STRING; map.put(METHOD_ONFAIL, getOnFailString(void.class, javaClass)); processTemplate(pw, map, "cpp_native_delete.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } pw.println("#ifdef __cplusplus"); pw.println("} // end extern \"C\""); pw.println("#endif"); map.put("%MAX_METHOD_COUNT%", Integer.toString(max_method_count + 1)); processTemplate(pw, map, "cpp_start_register_native.cpp", tabs); for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, "cpp_start_register_native_class.cpp", tabs); tabs += TAB_STRING; Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, method.getName()); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(method.getParameterTypes()) + ")" + classToJNISignature(method.getReturnType())); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); method_number++; } } map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, "nativeDelete"); map.put(JNI_SIGNATURE, "()V"); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); map.put("%NUM_NATIVE_METHODS%", Integer.toString(method_number)); processTemplate(pw, map, "cpp_end_register_native_class.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); } processTemplate(pw, map, "cpp_end_register_native.cpp", tabs); } else { pw.println("// No Native classes : registerNativMethods not needed."); pw.println("static void registerNativeMethods(JNIEnv *env) {}"); } } else { processTemplate(pw, map, CPP_TEMPLATE_ENDCPP, tabs); } } if (null != nativesClassMap) { tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { String nativeClassName = e.getKey(); File nativeClassHeaderFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".h"); map.put("%NATIVE_CLASS_HEADER%", nativeClassHeaderFile.getName()); map.put(CLASS_NAME, nativeClassName); if (nativeClassHeaderFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassHeaderFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassHeaderFile))) { processTemplate(pw, map, "header_native_imp.h", tabs); } } File nativeClassCppFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".cpp"); if (nativeClassCppFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassCppFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassCppFile))) { processTemplate(pw, map, "cpp_native_imp_start.cpp", tabs); Class javaClass = e.getValue(); Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); // String methodArgs = getCppParamNames(paramClasses); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String methodArgs = method.getParameterTypes().length > 0 ? paramDecls.substring(1, paramDecls.length() - 1) : ""; map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_TYPE%", getCppType(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); processTemplate(pw, map, "cpp_native_imp_stub.cpp", tabs); } } processTemplate(pw, map, "cpp_native_imp_end.cpp", tabs); } } } } } main_completed = true; }
From source file:edu.msu.cme.rdp.abundstats.cli.AbundMain.java
public static void main(String[] args) throws IOException { File inputFile; File resultDir = new File("."); RPlotter plotter = null;/*from w ww .j a v a2 s .co m*/ boolean isClusterFile = true; List<AbundStatsCalculator> statCalcs = new ArrayList(); double clustCutoffFrom = Double.MIN_VALUE, clustCutoffTo = Double.MAX_VALUE; String usage = "Main [options] <cluster file>"; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("result-dir")) { resultDir = new File(line.getOptionValue("result-dir")); if (!resultDir.exists() && !resultDir.mkdirs()) { throw new Exception( "Result directory " + resultDir + " does not exist and could not be created"); } } if (line.hasOption("R-location")) { plotter = new RPlotter(); plotter.setCommandTemplate(rplotterTemplate); plotter.setRPath(line.getOptionValue("R-location")); plotter.setOutFileExt(".png"); if (!new File(plotter.getRPath()).canExecute()) { throw new Exception(plotter.getRPath() + " does not exist or is not exectuable"); } } if (line.hasOption("lower-cutoff")) { clustCutoffFrom = Double.valueOf(line.getOptionValue("lower-cutoff")); } if (line.hasOption("upper-cutoff")) { clustCutoffTo = Double.valueOf(line.getOptionValue("upper-cutoff")); } if (line.hasOption("jaccard")) { statCalcs.add(new Jaccard(true)); } if (line.hasOption("sorensen")) { statCalcs.add(new Sorensen(true)); } if (line.hasOption("otu-table")) { isClusterFile = false; } if (statCalcs.isEmpty()) { throw new Exception("Must specify at least one stat to compute (jaccard, sorensen)"); } args = line.getArgs(); if (args.length != 1) { throw new Exception("Unexpected number of command line arguments"); } inputFile = new File(args[0]); } catch (Exception e) { new HelpFormatter().printHelp(usage, options); System.err.println("Error: " + e.getMessage()); return; } if (isClusterFile) { RDPClustParser parser; parser = new RDPClustParser(inputFile); try { if (parser.getClusterSamples().size() == 1) { throw new IOException("Cluster file must have more than one sample"); } List<Cutoff> cutoffs = parser.getCutoffs(clustCutoffFrom, clustCutoffTo); if (cutoffs.isEmpty()) { throw new IOException( "No cutoffs in cluster file in range [" + clustCutoffFrom + "-" + clustCutoffTo + "]"); } for (Cutoff cutoff : cutoffs) { List<Sample> samples = new ArrayList(); for (ClusterSample clustSample : parser.getClusterSamples()) { Sample s = new Sample(clustSample.getName()); for (Cluster clust : cutoff.getClusters().get(clustSample.getName())) { s.addSpecies(clust.getNumberOfSeqs()); } samples.add(s); } processSamples(samples, statCalcs, resultDir, cutoff.getCutoff() + "_", plotter); } } finally { parser.close(); } } else { List<Sample> samples = new ArrayList(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); String line = reader.readLine(); if (line == null || line.split("\\s+").length < 2) { throw new IOException("Must be 2 or more samples for abundance statistic calculations!"); } int numSamples = line.split("\\s+").length; boolean header = true; try { Integer.valueOf(line.split("\\s+")[0]); header = false; } catch (Exception e) { } if (header) { for (String s : line.split("\\s+")) { samples.add(new Sample(s)); } } else { int sample = 0; for (String s : line.split("\\s+")) { samples.add(new Sample("" + sample)); samples.get(sample).addSpecies(Integer.valueOf(s)); sample++; } } int lineno = 2; while ((line = reader.readLine()) != null) { if (line.trim().equals("")) { continue; } int sample = 0; if (line.split("\\s+").length != numSamples) { System.err.println( "Line number " + lineno + " didn't have the expected number of samples (contained " + line.split("\\s+").length + ", expected " + numSamples + ")"); } for (String s : line.split("\\s+")) { samples.get(sample).addSpecies(Integer.valueOf(s)); sample++; } lineno++; } processSamples(samples, statCalcs, resultDir, inputFile.getName(), plotter); } }
From source file:com.thesmartweb.swebrank.Main.java
/** * @param args the command line arguments *///from w w w . j a v a2 s . c o m public static void main(String[] args) { Path input_path = Paths.get("//mnt//var//DBs//inputsL10//nba//");//input directory String output_parent_directory = "//mnt//var//DBs//outputsConfL10//nba//";//output directory String config_path = "//mnt//var//DBs//config//";//input directory //---Disable apache log manually---- //System.setProperty("org.apache.commons.logging.Log","org.apache.commons.logging.impl.NoOpLog"); System.setProperty("org.apache.commons.logging.Log", "org.apache.commons.logging.impl.Log4JLogger"); //--------------Domain that is searched---------- String domain = ""; //------------------search engine related options---------------------- List<String> queries = null; int results_number = 0;//the number of results that are returned from each search engine List<Boolean> enginechoice = null; //list element #0. True/False Bing //list element #1. True/False Google //list element #2. True/False Yahoo! //list element #3. True/False Merged //-----------Moz options--------------------- List<Boolean> mozMetrics = null; //The list is going to contain the moz related input in the following order //list element #1. True/False, True we use Moz API, false not //list element #2. True if we use Domain Authority //list element #3. True if we use External MozRank //list element #4. True if we use MozRank //list element #5. True if we use MozTrust //list element #6. True if we use Subdomain MozRank //list element #7. True if we use Page Authority //only one is used (the first to be set to true) boolean moz_threshold_option = false;//set to true we use the threshold Double moz_threshold = 0.0;//if we want to have a threshold in moz int top_count_moz = 0;//if we want to get the moz top-something results //---------------Semantic Analysis method---------------- List<Boolean> ContentSemantics = null; int SensebotConcepts = 0;//define the amount of concepts that sensebot is going to recognize List<Double> SWebRankSettings = null; //------(string)directory is going to be used later----- String output_child_directory; //-------we get all the paths of the txt (input) files from the input directory------- DataManipulation getfiles = new DataManipulation();//class responsible for the extraction of paths Collection<File> inputs_files;//array to include the paths of the txt files inputs_files = getfiles.getinputfiles(input_path.toString(), "txt");//method to retrieve all the path of the input documents //------------read the txt files------------ for (File input : inputs_files) { ReadInput ri = new ReadInput();//function to read the input boolean check_reading_input = ri.perform(input); if (check_reading_input) { domain = ri.domain; //---------- queries = ri.queries; results_number = ri.results_number; enginechoice = ri.enginechoice; //------------ mozMetrics = ri.mozMetrics; moz_threshold_option = ri.moz_threshold_option; moz_threshold = ri.moz_threshold.doubleValue(); //--------------- ContentSemantics = ri.ContentSemantics; SWebRankSettings = ri.SWebRankSettings; } int top_visible = 0;//option to set the amount of results you can get in the merged search engine //------if we choose to use a Moz metric or Visibility score for our ranking, we need to set the results_number for the search engines to its max which is 50 //-----we set the top results number for moz or Visibility rank---- if (mozMetrics.get(0) || enginechoice.get(3)) { if (mozMetrics.get(0)) { top_count_moz = results_number; } //if moz is true, top_count_moz gets the value of result number if (enginechoice.get(3)) { top_visible = results_number; } //if merged engine is true, top_visible gets the value of result number results_number = 50;//this is the max amount of results that you can get from the search engine APIs } //-----if we want to use Moz we should check first if it works if (mozMetrics.get(0)) { Moz Moz = new Moz(); //---if it works, moz remains true, otherwise it is set to false mozMetrics.add(0, Moz.check(config_path)); //if it is false and we have chosen to use Visibility score with Moz, we reset back to the standard settings (ranking and not merged) //therefore, we reset the number of results from 50 to the top_count_moz which contained the original number of results if (!mozMetrics.get(0)) { if (!enginechoice.get(3)) { results_number = top_count_moz; } } } //----------we set the wordLists that we are going to use--------------------- List<String> finalList = new ArrayList<String>();//finalList is going to contain all the content in the end Total_analysis ta = new Total_analysis();//we call total analysis int iteration_counter = 0;//the iteration_counter is used in order to count the number of iterations of the algorithm and to be checked with perf_limit //this list of arraylists is going to contain all the wordLists that are produced for every term of the String[] query, //in order to calculate the NGD scores between every term of the wordList and the term that was used as query in order to produce the spesific wordList List<ArrayList<String>> array_wordLists = new ArrayList<>(); List<String> wordList_previous = new ArrayList<>(); List<String> wordList_new = new ArrayList<>(); double convergence = 0;//we create the convergence percentage and initialize it String conv_percentages = "";//string that contains all the convergence percentages DataManipulation wordsmanipulation = new DataManipulation();//method to manipulate various word data (String, list<String>, etc) do { //if we run the algorithm for the 1st time we already have the query so we skip the loop below that produces the new array of query if (iteration_counter != 0) { wordList_previous = wordList_new; //we add the previous wordList to the finalList finalList = wordsmanipulation.AddAList(wordList_previous, finalList); List<String> query_new_list_total = new ArrayList<>(); int iteration_previous = iteration_counter - 1; Combinations_Engine cn = new Combinations_Engine();//call the class to combine the terms produced for (String query : queries) { List<String> ids = new ArrayList<>(); if (enginechoice.get(0)) { String id = domain + "/" + query + "/bing" + "/" + iteration_previous; ids.add(id); } if (enginechoice.get(1)) { String id = domain + "/" + query + "/google" + "/" + iteration_previous; ids.add(id); } if (enginechoice.get(2)) { String id = domain + "/" + query + "/yahoo" + "/" + iteration_previous; ids.add(id); } ElasticGetWordList ESget = new ElasticGetWordList();//we call this class to get the wordlist from the Elastic Search List<String> maxWords = ESget.getMaxWords(ids, SWebRankSettings.get(9).intValue(), config_path);//we are going to get a max amount of words int query_index = queries.indexOf(query); int size_query_new = SWebRankSettings.get(10).intValue();//the amount of new queries we are willing to create //we create the new queries for every query of the previous round by combining the words produced from this query List<String> query_new_list = cn.perform(maxWords, SWebRankSettings.get(7), queries, SWebRankSettings.get(6), query_index, size_query_new, config_path); //we add the list of new queries to the total list that containas all the new queries query_new_list_total.addAll(query_new_list); System.out.println("query pointer=" + query_index + ""); } //---------------------the following cleans a list from null and duplicates query_new_list_total = wordsmanipulation.clearListString(query_new_list_total); //--------------we create the new directory that our files are going to be saved String txt_directory = FilenameUtils.getBaseName(input.getName()); output_child_directory = output_parent_directory + txt_directory + "_level_" + iteration_counter + "//"; //----------------append the wordlist to a file------------------ wordsmanipulation.AppendWordList(query_new_list_total, output_child_directory + "queries_" + iteration_counter + ".txt"); if (query_new_list_total.size() < 1) { break; } //if we don't create new queries we end the while loop //total analysis' function is going to do all the work and return back what we need ta = new Total_analysis(); ta.perform(wordList_previous, iteration_counter, output_child_directory, domain, enginechoice, query_new_list_total, results_number, top_visible, mozMetrics, moz_threshold_option, moz_threshold.doubleValue(), top_count_moz, ContentSemantics, SensebotConcepts, SWebRankSettings, config_path); //we get the array of wordlists array_wordLists = ta.getarray_wordLists(); //get the wordlist that includes all the new queries wordList_new = ta.getwordList_total(); //---------------------the following cleans a list from null and duplicates------------- wordList_new = wordsmanipulation.clearListString(wordList_new); //----------------append the wordlist to a file-------------------- wordsmanipulation.AppendWordList(wordList_new, output_child_directory + "wordList.txt"); //the concergence percentage of this iteration convergence = ta.getConvergence();//we are going to use convergence score to check the convergence //a string that contains all the convergence percentage for each round separated by \n character conv_percentages = conv_percentages + "\n" + convergence; //a file that is going to include the convergence percentages wordsmanipulation.AppendString(conv_percentages, output_child_directory + "convergence_percentage.txt"); //we add the new wordList to the finalList finalList = wordsmanipulation.AddAList(wordList_new, finalList); //we set the query array to be equal to the query new total that we have created queries = query_new_list_total; //we increment the iteration_counter in order to count the iterations of the algorithm and to use the perf_limit iteration_counter++; } else {//the following source code is performed on the 1st run of the loop //------------we extract the parent path of the file String txt_directory = FilenameUtils.getBaseName(input.getName()); //----------we create a string that is going to be used for the corresponding directory of outputs output_child_directory = output_parent_directory + txt_directory + "_level_" + iteration_counter + "//"; //we call total analysis function performOld ta.perform(wordList_new, iteration_counter, output_child_directory, domain, enginechoice, queries, results_number, top_visible, mozMetrics, moz_threshold_option, moz_threshold.doubleValue(), top_count_moz, ContentSemantics, SensebotConcepts, SWebRankSettings, config_path); //we get the array of wordlists array_wordLists = ta.getarray_wordLists(); //get the wordlist that includes all the new queries wordList_new = ta.getwordList_total(); //---------------------the following cleans a list from null and duplicates wordList_new = wordsmanipulation.clearListString(wordList_new); //----------------append the wordlist to a file wordsmanipulation.AppendWordList(wordList_new, output_child_directory + "wordList.txt"); //----------------------------------------- iteration_counter++;//increase the iteration_counter that counts the iterations of the algorithm } } while (convergence < SWebRankSettings.get(5).doubleValue() && iteration_counter < SWebRankSettings.get(8).intValue());//while the convergence percentage is below the limit and the iteration_counter below the performance limit if (iteration_counter == 1) { finalList = wordsmanipulation.AddAList(wordList_new, finalList); } //--------------------content List---------------- if (!finalList.isEmpty()) { //---------------------the following cleans the final list from null and duplicates finalList = wordsmanipulation.clearListString(finalList); //write the keywords to a file boolean flag_file = false;//boolean flag to declare successful write to file flag_file = wordsmanipulation.AppendWordList(finalList, output_parent_directory + "total_content.txt"); if (!flag_file) { System.out.print("can not create the content file for: " + output_parent_directory + "total_content.txt"); } } //we are going to save the total content with its convergence on the ElasticSearch cluster in a separated index //Node node = nodeBuilder().client(true).clusterName("lshrankldacluster").node(); //Client client = node.client(); //get the elastic search indexes in a list List<String> elasticIndexes = ri.GetKeyFile(config_path, "elasticSearchIndexes"); Settings settings = ImmutableSettings.settingsBuilder().put("cluster.name", "lshrankldacluster") .build(); Client client = new TransportClient(settings) .addTransportAddress(new InetSocketTransportAddress("localhost", 9300)); JSONObject objEngineLevel = new JSONObject(); objEngineLevel.put("TotalContent", finalList);//we save the total content objEngineLevel.put("Convergences", conv_percentages);//we save the convergence percentages IndexRequest indexReq = new IndexRequest(elasticIndexes.get(0), "content", domain);//we save also the domain indexReq.source(objEngineLevel); IndexResponse indexRes = client.index(indexReq).actionGet(); //node.close(); client.close(); //----------------------convergence percentages writing to file--------------- //use the conv_percentages string if (conv_percentages.length() != 0) { boolean flag_file = false;//boolean flag to declare successful write to file flag_file = wordsmanipulation.AppendString(conv_percentages, output_parent_directory + "convergence_percentages.txt"); if (!flag_file) { System.out.print("can not create the convergence file for: " + output_parent_directory + "convergence_percentages.txt"); } } } }
From source file:ch.kostceco.tools.siardexcerpt.SIARDexcerpt.java
/** Die Eingabe besteht aus mind 3 Parameter: [0] Pfad zur SIARD-Datei oder Verzeichnis [1] * configfile [2] Modul//from w w w. java 2 s . c o m * * bersicht der Module: --init --search --extract sowie --finish * * bei --search kommen danach noch die Suchtexte und bei --extract die Schlssel * * @param args * @throws IOException */ public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); /** SIARDexcerpt: Aufbau des Tools * * 1) init: Config Kopieren und ggf SIARD-Datei ins Workverzeichnis entpacken * * 2) search: gemss config die Tabelle mit Suchtext befragen und Ausgabe des Resultates * * 3) extract: mit den Keys anhand der config einen Records herausziehen und anzeigen * * 4) finish: Config-Kopie sowie Workverzeichnis lschen */ /* TODO: siehe Bemerkung im applicationContext-services.xml bezglich Injection in der * Superklasse aller Impl-Klassen ValidationModuleImpl validationModuleImpl = * (ValidationModuleImpl) context.getBean("validationmoduleimpl"); */ SIARDexcerpt siardexcerpt = (SIARDexcerpt) context.getBean("siardexcerpt"); // Ist die Anzahl Parameter (mind 3) korrekt? if (args.length < 3) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } String module = new String(args[2]); File siardDatei = new File(args[0]); File configFile = new File(args[1]); /* arg 1 gibt den Pfad zur configdatei an. Da dieser in ConfigurationServiceImpl hartcodiert * ist, wird diese nach "configuration/SIARDexcerpt.conf.xml" kopiert. */ File configFileHard = new File("configuration" + File.separator + "SIARDexcerpt.conf.xml"); // excerpt ist der Standardwert wird aber anhand der config dann gesetzt File directoryOfOutput = new File("excerpt"); // temp_SIARDexcerpt ist der Standardwert wird aber anhand der config dann gesetzt File tmpDir = new File("temp_SIARDexcerpt"); boolean okA = false; boolean okB = false; boolean okC = false; // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } if (module.equalsIgnoreCase("--init")) { /** 1) init: Config Kopieren und ggf SIARD-Datei ins Workverzeichnis entpacken * * a) config muss existieren und SIARDexcerpt.conf.xml noch nicht * * b) Excerptverzeichnis mit schreibrechte und ggf anlegen * * c) Workverzeichnis muss leer sein und mit schreibrechte * * d) SIARD-Datei entpacken * * e) Struktur-Check SIARD-Verzeichnis * * TODO: Erledigt */ System.out.println("SIARDexcerpt: init"); /** a) config muss existieren und SIARDexcerpt.conf.xml noch nicht */ if (!configFile.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_CONFIGFILE_FILENOTEXISTING, configFile.getAbsolutePath())); System.exit(1); } if (configFileHard.exists()) { System.out .println(siardexcerpt.getTextResourceService().getText(ERROR_CONFIGFILEHARD_FILEEXISTING)); System.exit(1); } Util.copyFile(configFile, configFileHard); /** b) Excerptverzeichnis mit schreibrechte und ggf anlegen */ String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfOutput.canWrite()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfOutput)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } if (!directoryOfOutput.isDirectory()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } /** c) Workverzeichnis muss leer sein und mit schreibrechte */ String pathToWorkDir = siardexcerpt.getConfigurationService().getPathToWorkDir(); 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) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } } } if (!tmpDir.exists()) { tmpDir.mkdir(); } // Im Workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, pathToWorkDir)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } /** d) SIARD-Datei entpacken */ if (!siardDatei.exists()) { // SIARD-Datei existiert nicht System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_SIARDFILE_FILENOTEXISTING, siardDatei.getAbsolutePath())); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } if (!siardDatei.isDirectory()) { /* SIARD-Datei ist eine Datei * * Die Datei muss ins Workverzeichnis extrahiert werden. Dies erfolgt im Modul A. * * danach der Pfad zu SIARD-Datei dorthin zeigen lassen */ Controllerexcerpt controllerexcerpt = (Controllerexcerpt) context.getBean("controllerexcerpt"); File siardDateiNew = new File(pathToWorkDir + File.separator + siardDatei.getName()); okA = controllerexcerpt.executeA(siardDatei, siardDateiNew, ""); if (!okA) { // SIARD Datei konte nicht entpackt werden System.out.println(MESSAGE_XML_MODUL_A); System.out.println(ERROR_XML_A_CANNOTEXTRACTZIP); // Lschen des Arbeitsverzeichnisses und configFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } // Fehler Extraktion --> invalide System.exit(2); } else { @SuppressWarnings("unused") File siardDateiOld = siardDatei; siardDatei = siardDateiNew; } } else { /* SIARD-Datei entpackt oder Datei war bereits ein Verzeichnis. * * Gerade bei grsseren SIARD-Dateien ist es sinnvoll an einer Stelle das ausgepackte SIARD * zu haben, damit diese nicht immer noch extrahiert werden muss */ } /** e) Struktur-Check SIARD-Verzeichnis */ File content = new File(siardDatei.getAbsolutePath() + File.separator + "content"); File header = new File(siardDatei.getAbsolutePath() + File.separator + "header"); File xsd = new File( siardDatei.getAbsolutePath() + File.separator + "header" + File.separator + "metadata.xsd"); File metadata = new File( siardDatei.getAbsolutePath() + File.separator + "header" + File.separator + "metadata.xml"); if (!content.exists() || !header.exists() || !xsd.exists() || !metadata.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_XML_B_STRUCTURE)); // Lschen des Arbeitsverzeichnisses und configFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } // Fehler Extraktion --> invalide System.exit(2); } else { // Struktur sieht plausibel aus, extraktion kann starten } } // End init if (module.equalsIgnoreCase("--search")) { /** 2) search: gemss config die Tabelle mit Suchtext befragen und Ausgabe des Resultates * * a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext * * b) Suchtext einlesen * * c) search.xml vorbereiten (Header) und xsl in Output kopieren * * d) grep ausfhren * * e) Suchergebnis speichern und anzeigen (via GUI) * * TODO: Noch offen */ System.out.println("SIARDexcerpt: search"); String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } /** a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext */ if (args.length < 4) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } if (!siardDatei.isDirectory()) { File siardDateiNew = new File(tmpDir.getAbsolutePath() + File.separator + siardDatei.getName()); if (!siardDateiNew.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_NOINIT)); System.exit(1); } else { siardDatei = siardDateiNew; } } /** b) Suchtext einlesen */ String searchString = new String(args[3]); /** c) search.xml vorbereiten (Header) und xsl in Output kopieren */ // Zeitstempel der Datenextraktion java.util.Date nowStartS = new java.util.Date(); java.text.SimpleDateFormat sdfStartS = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStartS = sdfStartS.format(nowStartS); /* Der SearchString kann zeichen enthalten, welche nicht im Dateinamen vorkommen drfen. * Entsprechend werden diese normalisiert */ String searchStringFilename = searchString.replaceAll("/", "_"); searchStringFilename = searchStringFilename.replaceAll(">", "_"); searchStringFilename = searchStringFilename.replaceAll("<", "_"); searchStringFilename = searchStringFilename.replace(".*", "_"); searchStringFilename = searchStringFilename.replaceAll("___", "_"); searchStringFilename = searchStringFilename.replaceAll("__", "_"); String outDateiNameS = siardDatei.getName() + "_" + searchStringFilename + "_SIARDsearch.xml"; outDateiNameS = outDateiNameS.replaceAll("__", "_"); // Informationen zum Archiv holen String archiveS = siardexcerpt.getConfigurationService().getArchive(); // Konfiguration des Outputs, ein File Logger wird zustzlich erstellt LogConfigurator logConfiguratorS = (LogConfigurator) context.getBean("logconfigurator"); String outFileNameS = logConfiguratorS.configure(directoryOfOutput.getAbsolutePath(), outDateiNameS); File outFileSearch = new File(outFileNameS); // Ab hier kann ins Output geschrieben werden... // Informationen zum XSL holen String pathToXSLS = siardexcerpt.getConfigurationService().getPathToXSLsearch(); File xslOrigS = new File(pathToXSLS); File xslCopyS = new File(directoryOfOutput.getAbsolutePath() + File.separator + xslOrigS.getName()); if (!xslCopyS.exists()) { Util.copyFile(xslOrigS, xslCopyS); } LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_HEADER, xslCopyS.getName())); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStartS)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_ARCHIVE, archiveS)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_INFO)); /** d) search: dies ist in einem eigenen Modul realisiert */ Controllerexcerpt controllerexcerptS = (Controllerexcerpt) context.getBean("controllerexcerpt"); okB = controllerexcerptS.executeB(siardDatei, outFileSearch, searchString); /** e) Ausgabe und exitcode */ if (!okB) { // Suche konnte nicht erfolgen LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_MODUL_B)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(ERROR_XML_B_CANNOTSEARCHRECORD)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); System.out.println(MESSAGE_XML_MODUL_B); System.out.println(ERROR_XML_B_CANNOTSEARCHRECORD); System.out.println(""); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Fehler Extraktion --> invalide System.exit(2); } else { // Suche konnte durchgefhrt werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Record konnte extrahiert werden System.exit(0); } } // End search if (module.equalsIgnoreCase("--excerpt")) { /** 3) extract: mit den Keys anhand der config einen Records herausziehen und anzeigen * * a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext * * b) extract.xml vorbereiten (Header) und xsl in Output kopieren * * c) extraktion: dies ist in einem eigenen Modul realisiert * * d) Ausgabe und exitcode * * TODO: Erledigt */ System.out.println("SIARDexcerpt: extract"); String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } /** a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext */ if (args.length < 4) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } if (!siardDatei.isDirectory()) { File siardDateiNew = new File(tmpDir.getAbsolutePath() + File.separator + siardDatei.getName()); if (!siardDateiNew.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_NOINIT)); System.exit(1); } else { siardDatei = siardDateiNew; } } /** b) extract.xml vorbereiten (Header) und xsl in Output kopieren */ // Zeitstempel der Datenextraktion 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); String excerptString = new String(args[3]); String outDateiName = siardDatei.getName() + "_" + excerptString + "_SIARDexcerpt.xml"; // Informationen zum Archiv holen String archive = siardexcerpt.getConfigurationService().getArchive(); // Konfiguration des Outputs, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String outFileName = logConfigurator.configure(directoryOfOutput.getAbsolutePath(), outDateiName); File outFile = new File(outFileName); // Ab hier kann ins Output geschrieben werden... // Informationen zum XSL holen String pathToXSL = siardexcerpt.getConfigurationService().getPathToXSL(); File xslOrig = new File(pathToXSL); File xslCopy = new File(directoryOfOutput.getAbsolutePath() + File.separator + xslOrig.getName()); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_HEADER, xslCopy.getName())); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_ARCHIVE, archive)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_INFO)); /** c) extraktion: dies ist in einem eigenen Modul realisiert */ Controllerexcerpt controllerexcerpt = (Controllerexcerpt) context.getBean("controllerexcerpt"); okC = controllerexcerpt.executeC(siardDatei, outFile, excerptString); /** d) Ausgabe und exitcode */ if (!okC) { // Record konnte nicht extrahiert werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_MODUL_C)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(ERROR_XML_C_CANNOTEXTRACTRECORD)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); System.out.println(MESSAGE_XML_MODUL_C); System.out.println(ERROR_XML_C_CANNOTEXTRACTRECORD); System.out.println(""); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Fehler Extraktion --> invalide System.exit(2); } else { // Record konnte extrahiert werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Record konnte extrahiert werden System.exit(0); } } // End extract if (module.equalsIgnoreCase("--finish")) { /** 4) finish: Config-Kopie sowie Workverzeichnis lschen * * TODO: Erledigt */ System.out.println("SIARDexcerpt: finish"); // Lschen des Arbeitsverzeichnisses und confiFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } } // End finish }