List of usage examples for java.io File isFile
public boolean isFile()
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//*from ww w . j a v a 2 s. c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:CommandLineInterpreter.java
/** * Main method, command line input will get parsed here. * * @param args//from www . ja v a 2 s.c o m */ public static void main(String[] args) { // // test-arguments: // args = new String[] { "1.9", "-gui" }; boolean success = false; if (args.length == 1) { String arg = args[0].trim().replaceAll("[-]+", ""); if (arg.equals("help") || arg.equals("h")) printHelp(null); } if (args.length == 0) { printHelp("ONE ARGUMENT NEEDED"); } else { try { boolean guiAlert = false; Float minVersion = null; File resourcesFile = null; // ------------------------------------------------ // // -- // ------------------------------------------------ // final String minJavaVersionArgument = args[0]; if (!minJavaVersionArgument.trim().isEmpty()) { try { minVersion = Float.parseFloat(minJavaVersionArgument); } catch (Exception e) { // do nothing } } if (minVersion == null || minVersion > 2 || minVersion < 1.6) { printHelp("VERSION STRING IS NOT VALID"); } // ------------------------------------------------ // // -- // ------------------------------------------------ // for (int i = 1; i < (args.length <= 3 ? args.length : 3); i++) { final String argument = args[i].trim(); if (argument.equals("-gui")) { guiAlert = true; } else { String resourcesFilePath = argument; if (!resourcesFilePath.isEmpty()) { resourcesFile = new File(resourcesFilePath); if (!resourcesFile.exists() || !resourcesFile.isFile() || !resourcesFile.canRead()) { printHelp("RESOURCES FILE IS NOT VALID\n[" + resourcesFile.getAbsolutePath() + "]"); } } } } // ------------------------------------------------ // // -- // ------------------------------------------------ // success = checkJREVersion(minVersion, guiAlert); if (success && resourcesFile != null) { success = checkResources(resourcesFile, guiAlert); } } catch (Exception e) { success = false; e.printStackTrace(); } } if (!success) { // set error exit code System.exit(1); } }
From source file:herddb.server.ServerMain.java
public static void main(String... args) { try {//from w w w.j a va 2 s. c o m LOG.log(Level.INFO, "Starting HerdDB version {0}", herddb.utils.Version.getVERSION()); Properties configuration = new Properties(); boolean configFileFromParameter = false; for (int i = 0; i < args.length; i++) { String arg = args[i]; if (!arg.startsWith("-")) { File configFile = new File(args[i]).getAbsoluteFile(); LOG.log(Level.INFO, "Reading configuration from {0}", configFile); try (InputStreamReader reader = new InputStreamReader(new FileInputStream(configFile), StandardCharsets.UTF_8)) { configuration.load(reader); } configFileFromParameter = true; } else if (arg.equals("--use-env")) { System.getenv().forEach((key, value) -> { System.out.println("Considering env as system property " + key + " -> " + value); System.setProperty(key, value); }); } else if (arg.startsWith("-D")) { int equals = arg.indexOf('='); if (equals > 0) { String key = arg.substring(2, equals); String value = arg.substring(equals + 1); System.setProperty(key, value); } } } if (!configFileFromParameter) { File configFile = new File("conf/server.properties").getAbsoluteFile(); LOG.log(Level.INFO, "Reading configuration from {0}", configFile); if (configFile.isFile()) { try (InputStreamReader reader = new InputStreamReader(new FileInputStream(configFile), StandardCharsets.UTF_8)) { configuration.load(reader); } } } System.getProperties().forEach((k, v) -> { String key = k + ""; if (!key.startsWith("java") && !key.startsWith("user")) { configuration.put(k, v); } }); LogManager.getLogManager().readConfiguration(); Runtime.getRuntime().addShutdownHook(new Thread("ctrlc-hook") { @Override public void run() { System.out.println("Ctrl-C trapped. Shutting down"); ServerMain _brokerMain = runningInstance; if (_brokerMain != null) { _brokerMain.close(); } } }); runningInstance = new ServerMain(configuration); runningInstance.start(); runningInstance.join(); } catch (Throwable t) { t.printStackTrace(); System.exit(1); } }
From source file:it.univpm.deit.semedia.musicuri.utils.experimental.LambdaCalculator.java
public static void main(String[] args) throws Exception { //***************************************************************************** //************************* F I L E I N P U T *************************** //***************************************************************************** if ((args.length == 1) && (new File(args[0]).exists())) { // get the file's canonical path File givenHandle = new File(args[0]); String queryAudioCanonicalPath = givenHandle.getCanonicalPath(); System.out.println("Input: " + queryAudioCanonicalPath); //PerformanceStatistic tempStat; SummaryStatistics lambdaSummary = SummaryStatistics.newInstance(); if (givenHandle.isDirectory()) { File[] list = givenHandle.listFiles(); if (list.length == 0) { System.out.println("Directory is empty"); return; } else { ArrayList allStats = new ArrayList(); File currentFile; for (int i = 0; i < list.length; i++) { currentFile = list[i]; try { if (Toolset.isSupportedAudioFile(currentFile)) { System.out.println("\nCalculating optimal lambda : " + currentFile.getName()); lambdaSummary.addValue(getBestLambda(new MusicURIQuery(currentFile))); }//from ww w . j av a 2s .c o m } catch (Exception e) { e.printStackTrace(); } } // System.out.println("\n\nStatistics for Test Case: " + queryAudioCanonicalPath); // mergeStatistics(allStats); } } if (givenHandle.isFile()) { if (Toolset.isSupportedAudioFile(givenHandle)) { // tempStat = getBestLambda (new MusicURIQuery(givenHandle)); // if (tempStat!=null) // { // //tempStat.printStatistics(); // ArrayList allStats = new ArrayList(); // allStats.add(tempStat); // mergeStatistics(allStats); // } // else // System.out.println("Error in identification "); } } } //end if else { System.err.println("LambdaCalculator"); System.err.println("Usage: java tester.LambdaCalculator {directory}"); } }
From source file:edu.ucsd.crbs.cws.App.java
License:asdf
public static void main(String[] args) { Job.REFS_ENABLED = false;/* w w w.j a va2s . co m*/ Workflow.REFS_ENABLED = false; try { OptionParser parser = new OptionParser() { { accepts(UPLOAD_WF_ARG, "Add/Update Workflow").withRequiredArg().ofType(File.class) .describedAs("Kepler .kar file"); //accepts(LOAD_TEST,"creates lots of workflows and jobs"); accepts(SYNC_WITH_CLUSTER_ARG, "Submits & Synchronizes Workflow Jobs on local cluster with CRBS Workflow Webservice. Requires --" + PROJECT_ARG + " --" + PORTALNAME_ARG + " --" + PORTAL_URL_ARG + " --" + HELP_EMAIL_ARG).withRequiredArg().ofType(String.class).describedAs("URL"); accepts(GEN_OLD_KEPLER_XML_ARG, "Generates version 1.x kepler xml for given workflow") .withRequiredArg().ofType(String.class).describedAs("wfid or .kar file"); accepts(UPLOAD_FILE_ARG, "Registers and uploads Workspace file to REST service") .withRequiredArg().ofType(File.class); accepts(REGISTER_FILE_ARG, "Registers Workspace file to REST service (DOES NOT UPLOAD FILE TO REST SERVICE)") .withRequiredArg().ofType(File.class); accepts(GET_WORKSPACE_FILE_INFO_ARG, "Outputs JSON of specified workspace file(s)") .withRequiredArg().ofType(String.class).describedAs("workspace file id"); accepts(GET_WORKFLOW_ARG, "Outputs JSON of specified Workflow").withRequiredArg() .ofType(Long.class).describedAs("Workflow Id"); accepts(DOWNLOAD_FILE_ARG, "Downloads Workspace file").withRequiredArg().ofType(String.class) .describedAs("workspace file id"); accepts(UPDATE_PATH_ARG, "Updates Workspace file path").withRequiredArg().ofType(String.class) .describedAs("workspace file id"); accepts(PATH_ARG, "Sets WorkspaceFile file path. Used in coordination with --" + UPDATE_PATH_ARG) .withRequiredArg().ofType(String.class).describedAs("file path"); accepts(URL_ARG, "URL to use with --" + UPLOAD_WF_ARG + ", --" + UPLOAD_FILE_ARG + ", --" + GET_WORKSPACE_FILE_INFO_ARG + " flags").withRequiredArg().ofType(String.class) .describedAs("URL"); accepts(EXAMPLE_JSON_ARG, "Outputs example JSON of Job, User, Workflow, and WorkspaceFile objects"); accepts(WF_EXEC_DIR_ARG, "Workflow Execution Directory").withRequiredArg().ofType(File.class) .describedAs("Directory"); accepts(WF_DIR_ARG, "Workflows Directory").withRequiredArg().ofType(File.class) .describedAs("Directory"); accepts(KEPLER_SCRIPT_ARG, "Kepler").withRequiredArg().ofType(File.class).describedAs("Script"); accepts(QUEUE_ARG, "SGE Queue").withRequiredArg().ofType(String.class).describedAs("Queue"); accepts(CAST_ARG, "Panfishcast binary").withRequiredArg().ofType(File.class) .describedAs("panfishcast"); accepts(STAT_ARG, "Panfishstat binary").withRequiredArg().ofType(File.class) .describedAs("panfishstat"); accepts(LOGIN_ARG, "User Login").withRequiredArg().ofType(String.class).describedAs("username"); accepts(TOKEN_ARG, "User Token").withRequiredArg().ofType(String.class).describedAs("token"); accepts(RUN_AS_ARG, "User to run as (for power accounts that can run as other users)") .withRequiredArg().ofType(String.class).describedAs("runas"); accepts(OWNER_ARG, "Sets owner when creating Workspace file and Workflow").withRequiredArg() .ofType(String.class).describedAs("username"); accepts(JOB_ID_ARG, "Sets source job id for Workspace file when used with --" + UPLOAD_FILE_ARG + " and --" + REGISTER_FILE_ARG).withRequiredArg().ofType(Long.class) .describedAs("Job Id"); accepts(MD5_ARG, "Sets md5 for Workspace file when used with --" + UPLOAD_FILE_ARG + " and --" + REGISTER_FILE_ARG).withRequiredArg().ofType(String.class) .describedAs("MD5 message digest"); accepts(SIZE_ARG, "Sets size in bytes for Workspace file when used with --" + UPLOAD_FILE_ARG + " and --" + REGISTER_FILE_ARG).withRequiredArg().ofType(Long.class) .describedAs("Size of file/dir in bytes"); accepts(RESAVE_WORKSPACEFILE_ARG, "Resaves Workspace file").withRequiredArg().ofType(Long.class) .describedAs("WorkspaceFile Id or -1 to resave all"); accepts(RESAVE_JOB_ARG, "Resaves Job").withRequiredArg().ofType(Long.class) .describedAs("Job Id or -1 to resave all"); accepts(RESAVE_WORKFLOW_ARG, "Resaves Workflow").withRequiredArg().ofType(Long.class) .describedAs("Workflow Id or -1 to resave all"); accepts(PREVIEW_WORKFLOW_ARG, "Preview Workflow on Web, requires --" + URL_ARG + " currently it should be: http://imafish.dynamic.ucsd.edu/cws/makepreview") .withRequiredArg().ofType(File.class).describedAs("Kepler .kar file"); accepts(DESCRIPTION_ARG, "Description for WorkspaceFile").withRequiredArg() .ofType(String.class); accepts(TYPE_ARG, "Type of WorkspaceFile").withRequiredArg().ofType(String.class); accepts(NAME_ARG, "Sets name for Workspace file when used with --" + UPLOAD_FILE_ARG + " and --" + REGISTER_FILE_ARG).withRequiredArg().ofType(String.class) .describedAs("WorkspaceFile name"); accepts(REGISTER_JAR_ARG, "Path to Jar to register WorkspaceFiles").withRequiredArg() .ofType(File.class).describedAs("Path to this jar"); accepts(GET_JOB_ARG, "Gets job from service in JSON format, requires --" + URL_ARG) .withRequiredArg().ofType(Long.class).describedAs("Job Id"); accepts(GET_WORKSPACE_FILE_ARG, "Gets WorkspaceFile from service in JSON format, requires --" + URL_ARG) .withRequiredArg().ofType(Long.class) .describedAs("WorkspaceFile Id or -1 for all"); accepts(PROJECT_ARG, "Project name ie CRBS. Used with --" + SYNC_WITH_CLUSTER_ARG) .withRequiredArg().ofType(String.class); accepts(PORTALNAME_ARG, "Portal name ie SLASH portal Used with --" + SYNC_WITH_CLUSTER_ARG) .withRequiredArg().ofType(String.class); accepts(PORTAL_URL_ARG, "Portal url ie http://slashsegmentation.com Used with --" + SYNC_WITH_CLUSTER_ARG) .withRequiredArg().ofType(String.class); accepts(HELP_EMAIL_ARG, "Help and reply to email address Used with --" + SYNC_WITH_CLUSTER_ARG) .withRequiredArg().ofType(String.class); accepts(BCC_EMAIL_ARG, "Blind Carbon copy email address Used with --" + SYNC_WITH_CLUSTER_ARG) .withRequiredArg().ofType(String.class); accepts(WORKSPACE_FILE_FAILED_ARG, "Denotes whether workspacefile failed (true) or not (false). Used with --" + UPDATE_PATH_ARG).withRequiredArg().ofType(Boolean.class) .describedAs("false = success and true = failed"); accepts(ERROR_EMAIL_ARG, "Email to receive notifications if errors are encountered. Used with --" + SYNC_WITH_CLUSTER_ARG).withRequiredArg().ofType(String.class); accepts(HELP_ARG).forHelp(); } }; OptionSet optionSet = null; try { optionSet = parser.parse(args); } catch (OptionException oe) { System.err.println("\nThere was an error parsing arguments: " + oe.getMessage() + "\n\n"); parser.printHelpOn(System.err); System.exit(1); } if (optionSet.has(HELP_ARG) || (!optionSet.has(SYNC_WITH_CLUSTER_ARG) && !optionSet.has(UPLOAD_WF_ARG)) && !optionSet.has(EXAMPLE_JSON_ARG) && !optionSet.has(UPLOAD_FILE_ARG) && !optionSet.has(GET_WORKSPACE_FILE_INFO_ARG) && !optionSet.has(UPDATE_PATH_ARG) && !optionSet.has(REGISTER_FILE_ARG) && !optionSet.has(RESAVE_WORKSPACEFILE_ARG) && !optionSet.has(RESAVE_JOB_ARG) && !optionSet.has(RESAVE_WORKFLOW_ARG) && !optionSet.has(PREVIEW_WORKFLOW_ARG) && !optionSet.has(GEN_OLD_KEPLER_XML_ARG) && !optionSet.has(GET_JOB_ARG) && !optionSet.has(GET_WORKSPACE_FILE_ARG) && !optionSet.has(GET_WORKFLOW_ARG)) { System.out.println(PROGRAM_HELP + "\n"); parser.printHelpOn(System.out); System.exit(0); } if (optionSet.has(EXAMPLE_JSON_ARG)) { renderExampleWorkflowsAndTasksAsJson(); System.exit(0); } if (optionSet.has(GET_JOB_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + GET_JOB_ARG + " flag"); getJobAsJson(optionSet); System.exit(0); } if (optionSet.has(GET_WORKSPACE_FILE_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + GET_WORKSPACE_FILE_ARG + " flag"); getWorkspaceFileAsJson(optionSet); System.exit(0); } if (optionSet.has(GET_WORKFLOW_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + GET_WORKFLOW_ARG + " flag"); getWorkflowAsJson(optionSet); System.exit(0); } MultivaluedMapFactory multivaluedMapFactory = new MultivaluedMapFactoryImpl(); if (optionSet.has(GEN_OLD_KEPLER_XML_ARG)) { String workflowFileOrId = (String) optionSet.valueOf(GEN_OLD_KEPLER_XML_ARG); File workflowFile = new File(workflowFileOrId); Workflow w = null; //if value is a file attempt to load it as a workflow file if (workflowFile.exists() && workflowFile.isFile()) { w = getWorkflowFromFile(workflowFile); if (w == null) { throw new Exception("Unable to extract workflow from file: " + workflowFile); } } else { //assume the value is a workflow id and get it from the service //but fail if url is missing failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + GEN_OLD_KEPLER_XML_ARG + " flag"); User u = getUserFromOptionSet(optionSet); WorkflowRestDAOImpl workflowDAO = new WorkflowRestDAOImpl(); workflowDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); workflowDAO.setUser(u); w = workflowDAO.getWorkflowById(workflowFileOrId, u); if (w == null) { throw new Exception("Unable to extract workflow from id: " + workflowFileOrId); } } VersionOneWorkflowXmlWriter xmlWriter = new VersionOneWorkflowXmlWriter(); StringWriter sw = new StringWriter(); xmlWriter.write(sw, w); System.out.println(sw.toString()); System.exit(0); } if (optionSet.has(PREVIEW_WORKFLOW_ARG)) { failIfOptionSetMissingURL(optionSet, "--" + PREVIEW_WORKFLOW_ARG + " flag"); File workflowFile = (File) optionSet.valueOf(PREVIEW_WORKFLOW_ARG); Workflow w = getWorkflowFromFile(workflowFile); if (w == null) { throw new Exception("Unable to extract workflow from file"); } uploadPreviewWorkflowFile((String) optionSet.valueOf(URL_ARG), w); System.exit(0); } if (optionSet.has(REGISTER_FILE_ARG)) { addNewWorkspaceFile(optionSet, false, REGISTER_FILE_ARG); System.exit(0); } if (optionSet.has(RESAVE_WORKSPACEFILE_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + RESAVE_WORKSPACEFILE_ARG + " flag"); WorkspaceFileRestDAOImpl workspaceFileDAO = new WorkspaceFileRestDAOImpl(); User u = getUserFromOptionSet(optionSet); workspaceFileDAO.setUser(u); workspaceFileDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); Long workspaceId = (Long) optionSet.valueOf(RESAVE_WORKSPACEFILE_ARG); if (workspaceId == -1) { System.out.println("Resaving all workspace files"); List<WorkspaceFile> wsfList = workspaceFileDAO.getWorkspaceFiles(null, null, null, null, null); if (wsfList != null) { System.out.println("Found " + wsfList.size() + " workspace files to resave"); for (WorkspaceFile wsf : wsfList) { System.out.println("WorkspaceFile Id: " + wsf.getId()); workspaceFileDAO.resave(wsf.getId()); } } } else { workspaceFileDAO.resave(workspaceId); } System.exit(0); } if (optionSet.has(RESAVE_JOB_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + RESAVE_JOB_ARG + " flag"); JobRestDAOImpl jobDAO = new JobRestDAOImpl(); User u = getUserFromOptionSet(optionSet); jobDAO.setUser(u); jobDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); Long jobId = (Long) optionSet.valueOf(RESAVE_JOB_ARG); if (jobId == -1) { System.out.println("Resaving all jobs"); List<Job> jobList = jobDAO.getJobs(null, null, null, true, true, Boolean.TRUE); if (jobList != null) { System.out.println("Found " + jobList.size() + " jobs to resave"); for (Job j : jobList) { System.out.println("job id: " + j.getId()); jobDAO.resave(j.getId()); } } } else { jobDAO.resave(jobId); } System.exit(0); } if (optionSet.has(RESAVE_WORKFLOW_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + RESAVE_WORKFLOW_ARG + " flag"); WorkflowRestDAOImpl workflowDAO = new WorkflowRestDAOImpl(); User u = getUserFromOptionSet(optionSet); workflowDAO.setUser(u); workflowDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); Long workflowId = (Long) optionSet.valueOf(RESAVE_WORKFLOW_ARG); if (workflowId == -1) { System.out.println("Resaving all workflows"); List<Workflow> workflowList = workflowDAO.getAllWorkflows(true, Boolean.TRUE); if (workflowList != null) { System.out.println("Found " + workflowList.size() + " workflow(s) to resave"); for (Workflow w : workflowList) { System.out.println("workflow id: " + w.getId()); workflowDAO.resave(w.getId()); } } } else { workflowDAO.resave(workflowId); } System.exit(0); } if (optionSet.has(UPDATE_PATH_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + UPDATE_PATH_ARG + " flag"); User u = getUserFromOptionSet(optionSet); String workspaceId = (String) optionSet.valueOf(UPDATE_PATH_ARG); String path = null; if (optionSet.has(PATH_ARG)) { path = (String) optionSet.valueOf(PATH_ARG); } String size = null; if (optionSet.has(SIZE_ARG)) { size = ((Long) optionSet.valueOf(SIZE_ARG)).toString(); } if (optionSet.has(MD5_ARG)) { //wsp.setMd5((String)optionSet.valueOf(MD5_ARG)); } Boolean isFailed = null; if (optionSet.has(WORKSPACE_FILE_FAILED_ARG)) { isFailed = (Boolean) optionSet.valueOf(WORKSPACE_FILE_FAILED_ARG); } WorkspaceFileRestDAOImpl workspaceFileDAO = new WorkspaceFileRestDAOImpl(); workspaceFileDAO.setUser(u); workspaceFileDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); workspaceFileDAO.updatePathSizeAndFailStatus(Long.parseLong(workspaceId), path, size, isFailed); System.exit(0); } if (optionSet.has(SYNC_WITH_CLUSTER_ARG)) { // @TODO NEED TO MAKE JOPT DO THIS REQUIRED FLAG CHECKING STUFF if (!optionSet.has(WF_EXEC_DIR_ARG)) { System.err.println( "-" + WF_EXEC_DIR_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(2); } if (!optionSet.has(WF_DIR_ARG)) { System.err.println("-" + WF_DIR_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(3); } if (!optionSet.has(KEPLER_SCRIPT_ARG)) { System.err.println( "-" + KEPLER_SCRIPT_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(4); } if (!optionSet.has(CAST_ARG)) { System.err.println("-" + CAST_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(5); } if (!optionSet.has(STAT_ARG)) { System.err.println("-" + STAT_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(6); } if (!optionSet.has(QUEUE_ARG)) { System.err.println("-" + QUEUE_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(7); } if (!optionSet.has(REGISTER_JAR_ARG)) { System.err.println( "-" + REGISTER_JAR_ARG + " is required with -" + SYNC_WITH_CLUSTER_ARG + " flag"); System.exit(8); } failIfOptionSetMissingLoginOrToken(optionSet, "--" + SYNC_WITH_CLUSTER_ARG + " flag"); File castFile = (File) optionSet.valueOf(CAST_ARG); String castPath = castFile.getAbsolutePath(); File statFile = (File) optionSet.valueOf(STAT_ARG); String statPath = statFile.getAbsolutePath(); String queue = (String) optionSet.valueOf(QUEUE_ARG); File wfExecDir = (File) optionSet.valueOf(WF_EXEC_DIR_ARG); File wfDir = (File) optionSet.valueOf(WF_DIR_ARG); File keplerScript = (File) optionSet.valueOf(KEPLER_SCRIPT_ARG); String registerJar = null; if (optionSet.has(REGISTER_JAR_ARG)) { File registerJarFile = (File) optionSet.valueOf(REGISTER_JAR_ARG); registerJar = registerJarFile.getAbsolutePath(); } JobEmailNotificationData emailNotifyData = getJobEmailNotificationData(optionSet); User u = getUserFromOptionSet(optionSet); ObjectifyService.ofy(); String url = (String) optionSet.valueOf(SYNC_WITH_CLUSTER_ARG); JobRestDAOImpl jobDAO = new JobRestDAOImpl(); jobDAO.setRestURL(url); jobDAO.setUser(u); System.out.println("Running sync with cluster"); WorkspaceFileRestDAOImpl workspaceFileDAO = new WorkspaceFileRestDAOImpl(); workspaceFileDAO.setRestURL(url); workspaceFileDAO.setUser(u); JobPath jobPath = new JobPathImpl(wfExecDir.getAbsolutePath()); WorkspaceFilePathSetterImpl pathSetter = new WorkspaceFilePathSetterImpl(workspaceFileDAO); // Submit jobs to scheduler JobSubmissionManager submitter = new JobSubmissionManager(jobDAO, workspaceFileDAO, pathSetter, jobPath, wfDir.getAbsolutePath(), keplerScript.getAbsolutePath(), castPath, queue, u, url, registerJar, emailNotifyData); submitter.submitJobs(); // Update job status for all jobs in system MapOfJobStatusFactoryImpl jobStatusFactory = new MapOfJobStatusFactoryImpl(statPath); WorkflowFailedParser workflowFailedParser = new WorkflowFailedParserImpl(); JobStatusUpdater updater = new JobStatusUpdater(jobDAO, jobStatusFactory, workflowFailedParser, jobPath); updater.updateJobs(); System.exit(0); } if (optionSet.has(App.GET_WORKSPACE_FILE_INFO_ARG)) { failIfOptionSetMissingURLOrLoginOrToken(optionSet, "--" + GET_WORKSPACE_FILE_INFO_ARG + " flag"); WorkspaceFileRestDAOImpl workspaceFileDAO = new WorkspaceFileRestDAOImpl(); workspaceFileDAO.setRestURL((String) optionSet.valueOf(URL_ARG)); List<WorkspaceFile> wsFiles = workspaceFileDAO .getWorkspaceFilesById((String) optionSet.valueOf(GET_WORKSPACE_FILE_INFO_ARG), null); if (wsFiles != null) { ObjectMapper om = new ObjectMapper(); ObjectWriter ow = om.writerWithDefaultPrettyPrinter(); System.out.print("["); boolean first = true; for (WorkspaceFile wsf : wsFiles) { if (first == false) { System.out.println(","); } else { first = false; } System.out.print(ow.writeValueAsString(wsf)); } System.out.println("]"); } else { System.err.println("[]"); } System.exit(0); } if (optionSet.has(UPLOAD_FILE_ARG)) { addNewWorkspaceFile(optionSet, true, UPLOAD_FILE_ARG); System.exit(0); } if (optionSet.has(UPLOAD_WF_ARG)) { Long parentWfId = null; String postURL = null; if (optionSet.has(URL_ARG)) { postURL = (String) optionSet.valueOf(URL_ARG); failIfOptionSetMissingLoginOrToken(optionSet, "--" + UPLOAD_WF_ARG + " and --" + URL_ARG + " flag"); } File workflowFile = (File) optionSet.valueOf(UPLOAD_WF_ARG); Workflow w = getWorkflowFromFile(workflowFile); if (w != null) { if (optionSet.has(OWNER_ARG)) { w.setOwner((String) optionSet.valueOf(OWNER_ARG)); } ObjectMapper om = new ObjectMapper(); if (parentWfId != null) { w.setId(parentWfId); } if (postURL == null) { System.out.println("\n--- JSON Representation of Workflow ---"); ObjectWriter ow = om.writerWithDefaultPrettyPrinter(); System.out.println(ow.writeValueAsString(w)); System.out.flush(); System.out.println("---------------------------------------"); } else { postURL = new StringBuilder().append(postURL).append(Constants.SLASH) .append(Constants.REST_PATH).append(Constants.SLASH) .append(Constants.WORKFLOWS_PATH).toString(); ClientConfig cc = new DefaultClientConfig(); cc.getClasses().add(StringProvider.class); cc.getClasses().add(MultiPartWriter.class); Client client = Client.create(cc); client.setFollowRedirects(true); WebResource resource = client.resource(postURL); String workflowAsJson = om.writeValueAsString(w); User u = getUserFromOptionSet(optionSet); client.addFilter(new HTTPBasicAuthFilter(u.getLogin(), u.getToken())); MultivaluedMap queryParams = multivaluedMapFactory.getMultivaluedMap(u); String response = resource.queryParams(queryParams).type(MediaType.APPLICATION_JSON_TYPE) .entity(workflowAsJson).post(String.class); Workflow workflowRes = om.readValue(response, Workflow.class); ObjectWriter ow = om.writerWithDefaultPrettyPrinter(); if (workflowRes.getWorkflowFileUploadURL() == null) { throw new Exception( "No upload url found for workflow!!!" + ow.writeValueAsString(workflowRes)); } uploadWorkflowFile(workflowRes, workflowFile); } } } } catch (Exception ex) { ex.printStackTrace(); System.err.println("Caught Exception: " + ex.getMessage()); System.exit(2); } System.exit(0); }
From source file:net.sourceforge.msscodefactory.cfasterisk.v2_4.CFAsteriskSwingHttpCLI.CFAsteriskSwingHttpCLI.java
public static void main(String args[]) { final String S_ProcName = "CFAsteriskSwingHttpCLI.main() "; initConsoleLog();// w w w.ja v a 2s . com boolean fastExit = false; String homeDirName = System.getProperty("HOME"); if (homeDirName == null) { homeDirName = System.getProperty("user.home"); if (homeDirName == null) { log.message(S_ProcName + "ERROR: Home directory not set"); return; } } File homeDir = new File(homeDirName); if (!homeDir.exists()) { log.message(S_ProcName + "ERROR: Home directory \"" + homeDirName + "\" does not exist"); return; } if (!homeDir.isDirectory()) { log.message(S_ProcName + "ERROR: Home directory \"" + homeDirName + "\" is not a directory"); return; } CFAsteriskClientConfigurationFile cFAsteriskClientConfig = new CFAsteriskClientConfigurationFile(); String cFAsteriskClientConfigFileName = homeDir.getPath() + File.separator + ".cfasteriskclientrc"; cFAsteriskClientConfig.setFileName(cFAsteriskClientConfigFileName); File cFAsteriskClientConfigFile = new File(cFAsteriskClientConfigFileName); if (!cFAsteriskClientConfigFile.exists()) { String cFAsteriskKeyStoreFileName = homeDir.getPath() + File.separator + ".msscfjceks"; cFAsteriskClientConfig.setKeyStore(cFAsteriskKeyStoreFileName); InetAddress localHost; try { localHost = InetAddress.getLocalHost(); } catch (UnknownHostException e) { localHost = null; } if (localHost == null) { log.message(S_ProcName + "ERROR: LocalHost is null"); return; } String hostName = localHost.getHostName(); if ((hostName == null) || (hostName.length() <= 0)) { log.message("ERROR: LocalHost.HostName is null or empty"); return; } String userName = System.getProperty("user.name"); if ((userName == null) || (userName.length() <= 0)) { log.message("ERROR: user.name is null or empty"); return; } String deviceName = hostName.replaceAll("[^\\w]", "_").toLowerCase() + "-" + userName.replaceAll("[^\\w]", "_").toLowerCase(); cFAsteriskClientConfig.setDeviceName(deviceName); cFAsteriskClientConfig.save(); log.message(S_ProcName + "INFO: Created CFAsterisk client configuration file " + cFAsteriskClientConfigFileName); fastExit = true; } if (!cFAsteriskClientConfigFile.isFile()) { log.message(S_ProcName + "ERROR: Proposed client configuration file " + cFAsteriskClientConfigFileName + " is not a file."); fastExit = true; } if (!cFAsteriskClientConfigFile.canRead()) { log.message(S_ProcName + "ERROR: Permission denied attempting to read client configuration file " + cFAsteriskClientConfigFileName); fastExit = true; } cFAsteriskClientConfig.load(); if (fastExit) { return; } // Configure logging Properties sysProps = System.getProperties(); sysProps.setProperty("log4j.rootCategory", "WARN"); sysProps.setProperty("org.apache.commons.logging.Log", "org.apache.commons.logging.impl.Log4JLogger"); Logger httpLogger = Logger.getLogger("org.apache.http"); httpLogger.setLevel(Level.WARN); // The Invoker and it's implementation CFAsteriskXMsgClientHttpSchema invoker = new CFAsteriskXMsgClientHttpSchema(); // And now for the client side cache implementation that invokes it ICFAsteriskSchemaObj clientSchemaObj = new CFAsteriskSchemaObj() { public void logout() { CFAsteriskXMsgClientHttpSchema invoker = (CFAsteriskXMsgClientHttpSchema) getBackingStore(); try { invoker.logout(getAuthorization()); } catch (RuntimeException e) { } setAuthorization(null); } }; clientSchemaObj.setBackingStore(invoker); // And stitch the response handler to reference our client instance invoker.setResponseHandlerSchemaObj(clientSchemaObj); // And now we can stitch together the CLI to the SAX loader code CFAsteriskSwingHttpCLI cli = new CFAsteriskSwingHttpCLI(); cli.setXMsgClientHttpSchema(invoker); cli.setSchema(clientSchemaObj); ICFAsteriskSwingSchema swing = cli.getSwingSchema(); swing.setClientConfigurationFile(cFAsteriskClientConfig); swing.setSchema(clientSchemaObj); swing.setClusterName("system"); swing.setTenantName("system"); swing.setSecUserName("system"); JFrame jframe = cli.getDesktop(); jframe.setVisible(true); jframe.toFront(); }
From source file:gov.nasa.ensemble.dictionary.nddl.ParseInterpreter.java
public static void main(String[] args) throws Exception { try {// w ww .j a v a2s . c om CommandLineArguments cmd = new CommandLineArguments(args); // Create a resource set to hold the resources. // ResourceSet resourceSet = new ResourceSetImpl(); // Register the package to ensure it is available during loading. // resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap() .put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMIResourceFactoryImpl()); resourceSet.getPackageRegistry().put(DictionaryPackage.eNS_URI, DictionaryPackage.eINSTANCE); // Construct the URI for the instance file. // The argument is treated as a file path only if it denotes an // existing file. // Otherwise, it's directly treated as a URL. // File file = new File(cmd.getValue(Option.ACTIVITY_DICTIONARY_FILE)); URI uri = file.isFile() ? URI.createFileURI(file.getAbsolutePath()) : URI.createURI(cmd.getValue(Option.ACTIVITY_DICTIONARY_FILE)); try { // Demand load resource for this file. // Resource resource = resourceSet.getResource(uri, true); EActivityDictionary eActivityDictionary = (EActivityDictionary) resource.getContents().get(0); ParseInterpreter parseInterpreter = new ParseInterpreter(eActivityDictionary, cmd.getValue(Option.CPU_STATE), cmd.getValue(Option.CPU_VALUE), cmd.getIntValue(Option.BOOT), cmd.getIntValue(Option.SHUTDOWN), cmd.getIntValue(Option.GAP)); parseInterpreter.interpretAD(false); String path = cmd.getValue(Option.OUTPUT_DIRECTORY_PATH); path = path + uri.trimFileExtension().lastSegment(); FileOutputStream objStream = new FileOutputStream(path + "-objects.nddl"); FileOutputStream modelStream = new FileOutputStream(path + "-model.nddl"); FileOutputStream initStateStream = new FileOutputStream(path + "-initial-state.nddl"); objStream.flush(); modelStream.flush(); initStateStream.flush(); parseInterpreter.writeObjects(objStream); objStream.close(); parseInterpreter.writeCompats(modelStream, path + "-objects.nddl"); modelStream.close(); parseInterpreter.writeInitialState(initStateStream, path + "-model.nddl"); } catch (RuntimeException exception) { System.out.println("Problem loading " + uri); exception.printStackTrace(); } } catch (Exception e) { System.out.println(getManPageText()); } }
From source file:com.edduarte.protbox.Protbox.java
public static void main(String... args) { // activate debug / verbose mode if (args.length != 0) { List<String> argsList = Arrays.asList(args); if (argsList.contains("-v")) { Constants.verbose = true;/*from w ww. j av a2s . c o m*/ } } // use System's look and feel try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { // If the System's look and feel is not obtainable, continue execution with JRE look and feel } // check this is a single instance try { new ServerSocket(1882); } catch (IOException ex) { JOptionPane.showMessageDialog(null, "Another instance of Protbox is already running.\n" + "Please close the other instance first.", "Protbox already running", JOptionPane.ERROR_MESSAGE); System.exit(1); } // check if System Tray is supported by this operative system if (!SystemTray.isSupported()) { JOptionPane.showMessageDialog(null, "Your operative system does not support system tray functionality.\n" + "Please try running Protbox on another operative system.", "System tray not supported", JOptionPane.ERROR_MESSAGE); System.exit(1); } // add PKCS11 providers FileFilter fileFilter = new AndFileFilter(new WildcardFileFilter(Lists.newArrayList("*.config")), HiddenFileFilter.VISIBLE); File[] providersConfigFiles = new File(Constants.PROVIDERS_DIR).listFiles(fileFilter); if (providersConfigFiles != null) { for (File f : providersConfigFiles) { try { List<String> lines = FileUtils.readLines(f); String aliasLine = lines.stream().filter(line -> line.contains("alias")).findFirst().get(); lines.remove(aliasLine); String alias = aliasLine.split("=")[1].trim(); StringBuilder sb = new StringBuilder(); for (String s : lines) { sb.append(s); sb.append("\n"); } Provider p = new SunPKCS11(new ReaderInputStream(new StringReader(sb.toString()))); Security.addProvider(p); pkcs11Providers.put(p.getName(), alias); } catch (IOException | ProviderException ex) { if (ex.getMessage().equals("Initialization failed")) { ex.printStackTrace(); String s = "The following error occurred:\n" + ex.getCause().getMessage() + "\n\nIn addition, make sure you have " + "an available smart card reader connected before opening the application."; JTextArea textArea = new JTextArea(s); textArea.setColumns(60); textArea.setLineWrap(true); textArea.setWrapStyleWord(true); textArea.setSize(textArea.getPreferredSize().width, 1); JOptionPane.showMessageDialog(null, textArea, "Error loading PKCS11 provider", JOptionPane.ERROR_MESSAGE); System.exit(1); } else { ex.printStackTrace(); JOptionPane.showMessageDialog(null, "Error while setting up PKCS11 provider from configuration file " + f.getName() + ".\n" + ex.getMessage(), "Error loading PKCS11 provider", JOptionPane.ERROR_MESSAGE); } } } } // adds a shutdown hook to save instantiated directories into files when the application is being closed Runtime.getRuntime().addShutdownHook(new Thread(Protbox::exit)); // get system tray and run tray applet tray = SystemTray.getSystemTray(); SwingUtilities.invokeLater(() -> { if (Constants.verbose) { logger.info("Starting application"); } //Start a new TrayApplet object trayApplet = TrayApplet.getInstance(); }); // prompts the user to choose which provider to use ProviderListWindow.showWindow(Protbox.pkcs11Providers.keySet(), providerName -> { // loads eID token eIDTokenLoadingWindow.showPrompt(providerName, (returnedUser, returnedCertificateData) -> { user = returnedUser; certificateData = returnedCertificateData; // gets a password to use on the saved registry files (for loading and saving) final AtomicReference<Consumer<SecretKey>> consumerHolder = new AtomicReference<>(null); consumerHolder.set(password -> { registriesPasswordKey = password; try { // if there are serialized files, load them if they can be decoded by this user's private key final List<SavedRegistry> serializedDirectories = new ArrayList<>(); if (Constants.verbose) { logger.info("Reading serialized registry files..."); } File[] registryFileList = new File(Constants.REGISTRIES_DIR).listFiles(); if (registryFileList != null) { for (File f : registryFileList) { if (f.isFile()) { byte[] data = FileUtils.readFileToByteArray(f); try { Cipher cipher = Cipher.getInstance("AES"); cipher.init(Cipher.DECRYPT_MODE, registriesPasswordKey); byte[] registryDecryptedData = cipher.doFinal(data); serializedDirectories.add(new SavedRegistry(f, registryDecryptedData)); } catch (GeneralSecurityException ex) { if (Constants.verbose) { logger.info("Inserted Password does not correspond to " + f.getName()); } } } } } // if there were no serialized directories, show NewDirectory window to configure the first folder if (serializedDirectories.isEmpty() || registryFileList == null) { if (Constants.verbose) { logger.info("No registry files were found: running app as first time!"); } NewRegistryWindow.start(true); } else { // there were serialized directories loadRegistry(serializedDirectories); trayApplet.repaint(); showTrayApplet(); } } catch (AWTException | IOException | GeneralSecurityException | ReflectiveOperationException | ProtboxException ex) { JOptionPane.showMessageDialog(null, "The inserted password was invalid! Please try another one!", "Invalid password!", JOptionPane.ERROR_MESSAGE); insertPassword(consumerHolder.get()); } }); insertPassword(consumerHolder.get()); }); }); }
From source file:it.univpm.deit.semedia.musicuri.core.MusicURISearch.java
/** * Identifies the MusicURIReference that most closely matches the given audio file * @param args the audio file to identify *///from w ww. j a v a2 s . co m public static void main(String[] args) throws Exception { MusicURISearch engine = new MusicURISearch((Toolset.getCWD() + "db\\"), "MusicURIReferences.db"); // MusicURIDatabase db = new MusicURIDatabase ("C:/Eclipse/workspace/MusicURI/db/", "MusicURIReferences.db"); // MusicURISearch engine = new MusicURISearch (db); //MusicURISearch engine = new MusicURISearch ("D:/10References/", "MusicURIReferences.db"); //***************************************************************************** //************************* F I L E I N P U T *************************** //***************************************************************************** if ((args.length == 1) && (new File(args[0]).exists())) { // get the file's canonical path File givenHandle = new File(args[0]); boolean finalResortIsCombinedDistance = true; String queryAudioCanonicalPath = givenHandle.getCanonicalPath(); System.out.println("Input: " + queryAudioCanonicalPath); PerformanceStatistic tempStat; if (givenHandle.isDirectory()) { File[] list = givenHandle.listFiles(); if (list.length == 0) { System.out.println("Directory is empty"); return; } else { ArrayList allStats = new ArrayList(); File currentFile; int truePositives = 0; int falsePositives = 0; int trueNegatives = 0; int falseNegatives = 0; if (finalResortIsCombinedDistance) System.out.println(" Final resort is combined distance"); else System.out.println(" Final resort is audio signature distance"); for (int i = 0; i < list.length; i++) { currentFile = list[i]; try { if (Toolset.isSupportedAudioFile(currentFile)) { System.out.println("\nIdentifying : " + currentFile.getName()); tempStat = engine.getIdentificationPerformance(new MusicURIQuery(givenHandle), true, true, 0.09f, finalResortIsCombinedDistance); //identify (new MusicURIQuery(currentFile), true, true, 0.09f, finalResortIsCombinedDistance, 1); if (tempStat != null) allStats.add(tempStat); if (tempStat.isTruePositive()) truePositives++; if (tempStat.isFalsePositive()) falsePositives++; if (tempStat.isTrueNegative()) trueNegatives++; if (tempStat.isFalseNegative()) falseNegatives++; System.out.println( "\nTrue Positives : " + truePositives + "/" + allStats.size()); System.out .println("False Positives : " + falsePositives + "/" + allStats.size()); System.out .println("True Negatives : " + trueNegatives + "/" + allStats.size()); System.out .println("False Negatives : " + falseNegatives + "/" + allStats.size()); } } catch (Exception e) { e.printStackTrace(); } } System.out.println("\n\nStatistics for Test Case: " + queryAudioCanonicalPath); engine.mergeStatistics(allStats); } } //end if givenHandle is Directory if (givenHandle.isFile()) { if (Toolset.isSupportedAudioFile(givenHandle)) { //tempStat = engine.getIdentificationPerformance (new MusicURIQuery(givenHandle), true, true, 0.09f, finalResortIsCombinedDistance); tempStat = engine.getIdentificationPerformance(new MusicURIQuery(givenHandle), false, false, 0.09f, false); //identify (new MusicURIQuery(givenHandle), true, true, 0.09f, finalResortIsCombinedDistance, 1); if (tempStat != null) { System.out.println("\nIdentification completed"); //tempStat.printStatistics(); ArrayList allStats = new ArrayList(); allStats.add(tempStat); engine.mergeStatistics(allStats); } else System.out.println("Error in identification "); } } } //end if else { System.err.println("MusicURISearch"); System.err.println("Usage: java it.univpm.deit.semedia.musicuri.core.MusicURISearch {unknown.mp3}"); } }
From source file:Main.java
public static File[] getXMLFiles(File folder) { List<File> aList = new ArrayList<File>(); File[] files = folder.listFiles(); for (File pf : files) { if (pf.isFile() && getFileExtensionName(pf).indexOf("xml") != -1) { aList.add(pf);/*from w w w . ja v a2s. com*/ } } return aList.toArray(new File[aList.size()]); }