List of usage examples for java.util ArrayList add
public boolean add(E e)
From source file:com.genentech.chemistry.tool.align.SDFAlign.java
public static void main(String... args) { Options options = new Options(); Option opt = new Option("in", true, "input sd file"); opt.setRequired(true);/* w w w . j a va 2 s . c o m*/ options.addOption(opt); opt = new Option("out", true, "output file"); opt.setRequired(true); options.addOption(opt); opt = new Option("method", true, "fss|sss|MCS|clique (default mcs)."); options.addOption(opt); opt = new Option("ref", true, "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported"); options.addOption(opt); opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image."); options.addOption(opt); opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output."); options.addOption(opt); opt = new Option("atomMatch", true, "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n" + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n" + "Queryfeatures are considered only if default is used."); options.addOption(opt); opt = new Option("bondMatch", true, "Sequence of none|default specifing how bonds are matched cf. oe document."); options.addOption(opt); opt = new Option("keepCoreHydrogens", false, "If not specified the hydrigen atoms are removed from the core."); options.addOption(opt); opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd."); options.addOption(opt); opt = new Option("doNotOptimize", false, "If specified the RMSD is computed without moving optimizing the overlay."); options.addOption(opt); opt = new Option("quiet", false, "Reduced warining messages"); options.addOption(opt); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { exitWithHelp(e.getMessage(), options); } if (cmd.getArgs().length > 0) exitWithHelp("To many arguments", options); // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms int atomExpr = OEExprOpts.DefaultAtoms; int bondExpr = OEExprOpts.DefaultBonds; String atomMatch = cmd.getOptionValue("atomMatch"); if (atomMatch == null) atomMatch = ""; atomMatch = '|' + atomMatch.toLowerCase() + '|'; String bondMatch = cmd.getOptionValue("bondMatch"); if (bondMatch == null) bondMatch = ""; bondMatch = '|' + bondMatch.toLowerCase() + '|'; String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String refFile = cmd.getOptionValue("ref"); String method = cmd.getOptionValue("method"); String rmsdTag = cmd.getOptionValue("rmsdTag"); String oMol = cmd.getOptionValue("outputMol"); boolean doMirror = cmd.hasOption("mirror"); boolean doOptimize = !cmd.hasOption("doNotOptimize"); boolean quiet = cmd.hasOption("quiet"); OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase()); if (atomMatch.startsWith("|none")) atomExpr = 0; if (atomMatch.contains("|hcount|")) atomExpr |= OEExprOpts.HCount; if (atomMatch.contains("|noAromatic|")) atomExpr &= (~OEExprOpts.Aromaticity); if (bondMatch.startsWith("|none")) bondExpr = 0; ArrayList<OEMol> refmols = new ArrayList<OEMol>(); if (refFile != null) { oemolistream reffs = new oemolistream(refFile); if (!is3DFormat(reffs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); reffs.SetFormat(OEFormat.MDL); int aromodel = OEIFlavor.Generic.OEAroModelOpenEye; int qflavor = reffs.GetFlavor(reffs.GetFormat()); reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel)); OEMol rmol = new OEMol(); while (oechem.OEReadMDLQueryFile(reffs, rmol)) { if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); rmol = new OEMol(); } rmol.delete(); if (refmols.size() == 0) throw new Error("reference file had no entries"); reffs.close(); } oemolistream fitfs = new oemolistream(inFile); if (!is3DFormat(fitfs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); oemolostream ofs = new oemolostream(outFile); if (!is3DFormat(ofs.GetFormat())) oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates"); AlignInterface aligner = null; OEGraphMol fitmol = new OEGraphMol(); if (oechem.OEReadMolecule(fitfs, fitmol)) { if (refmols.size() == 0) { OEMol rmol = new OEMol(fitmol); if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); } if ("sss".equalsIgnoreCase(method)) { aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("clique".equalsIgnoreCase(method)) { aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("fss".equalsIgnoreCase(method)) { if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch")) exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options); aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror); } else { aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } do { aligner.align(fitmol); oechem.OEWriteMolecule(ofs, fitmol); } while (oechem.OEReadMolecule(fitfs, fitmol)); } fitmol.delete(); if (aligner != null) aligner.close(); for (OEMolBase mol : refmols) mol.delete(); fitfs.close(); ofs.close(); }
From source file:eqtlmappingpipeline.util.ModuleEqtlNeutrophilReplication.java
/** * @param args the command line arguments *///from www .j a v a 2 s . co m public static void main(String[] args) throws IOException, LdCalculatorException { System.out.println(HEADER); System.out.println(); System.out.flush(); //flush to make sure header is before errors try { Thread.sleep(25); //Allows flush to complete } catch (InterruptedException ex) { } CommandLineParser parser = new PosixParser(); final CommandLine commandLine; try { commandLine = parser.parse(OPTIONS, args, true); } catch (ParseException ex) { System.err.println("Invalid command line arguments: " + ex.getMessage()); System.err.println(); new HelpFormatter().printHelp(" ", OPTIONS); System.exit(1); return; } final String[] genotypesBasePaths = commandLine.getOptionValues("g"); final RandomAccessGenotypeDataReaderFormats genotypeDataType; final String replicationQtlFilePath = commandLine.getOptionValue("e"); final String interactionQtlFilePath = commandLine.getOptionValue("i"); final String outputFilePath = commandLine.getOptionValue("o"); final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld")); final int window = Integer.parseInt(commandLine.getOptionValue("w")); System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths)); System.out.println("Interaction file: " + interactionQtlFilePath); System.out.println("Replication file: " + replicationQtlFilePath); System.out.println("Output: " + outputFilePath); System.out.println("LD: " + ldCutoff); System.out.println("Window: " + window); try { if (commandLine.hasOption("G")) { genotypeDataType = RandomAccessGenotypeDataReaderFormats .valueOf(commandLine.getOptionValue("G").toUpperCase()); } else { if (genotypesBasePaths[0].endsWith(".vcf")) { System.err.println( "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file."); System.exit(1); return; } try { genotypeDataType = RandomAccessGenotypeDataReaderFormats .matchFormatToPath(genotypesBasePaths[0]); } catch (GenotypeDataException e) { System.err .println("Unable to determine input 1 type based on specified path. Please specify -G"); System.exit(1); return; } } } catch (IllegalArgumentException e) { System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G") + "\" is not a valid input data format"); System.exit(1); return; } final RandomAccessGenotypeData genotypeData; try { genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null, 0.8); } catch (TabixFileNotFoundException e) { LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n" + "Please see README on how to create a tabix file"); System.exit(1); return; } catch (IOException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } catch (IncompatibleMultiPartGenotypeDataException e) { LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e); System.exit(1); return; } catch (GenotypeDataException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } ChrPosTreeMap<ArrayList<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>(); CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t'); replicationQtlReader.readNext();//skip header String[] replicationLine; while ((replicationLine = replicationQtlReader.readNext()) != null) { try { GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL])); if (variant == null) { continue; } ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]), replicationLine[REPLICATION_GENE_COL], Double.parseDouble(replicationLine[REPLICATION_BETA_COL]), variant.getAlternativeAlleles().get(0).getAlleleAsString()); ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(), replicationQtl.getPos()); if (posReplicationQtls == null) { posReplicationQtls = new ArrayList<>(); replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls); } posReplicationQtls.add(replicationQtl); } catch (Exception e) { System.out.println(Arrays.toString(replicationLine)); throw e; } } int interactionSnpNotInGenotypeData = 0; int noReplicationQtlsInWindow = 0; int noReplicationQtlsInLd = 0; int multipleReplicationQtlsInLd = 0; int replicationTopSnpNotInGenotypeData = 0; final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0'); final String[] outputLine = new String[14]; int c = 0; outputLine[c++] = "Chr"; outputLine[c++] = "Pos"; outputLine[c++] = "SNP"; outputLine[c++] = "Gene"; outputLine[c++] = "Module"; outputLine[c++] = "DiscoveryZ"; outputLine[c++] = "ReplicationZ"; outputLine[c++] = "DiscoveryZCorrected"; outputLine[c++] = "ReplicationZCorrected"; outputLine[c++] = "DiscoveryAlleleAssessed"; outputLine[c++] = "ReplicationAlleleAssessed"; outputLine[c++] = "bestLd"; outputLine[c++] = "bestLd_dist"; outputLine[c++] = "nextLd"; outputWriter.writeNext(outputLine); HashSet<String> notFound = new HashSet<>(); CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t'); interactionQtlReader.readNext();//skip header String[] interactionQtlLine; while ((interactionQtlLine = interactionQtlReader.readNext()) != null) { String snp = interactionQtlLine[1]; String chr = interactionQtlLine[2]; int pos = Integer.parseInt(interactionQtlLine[3]); String gene = interactionQtlLine[4]; String alleleAssessed = interactionQtlLine[9]; String module = interactionQtlLine[12]; double discoveryZ = Double.parseDouble(interactionQtlLine[10]); GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos); if (interactionQtlVariant == null) { System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos); ++interactionSnpNotInGenotypeData; continue; } ReplicationQtl bestMatch = null; double bestMatchR2 = Double.NaN; Ld bestMatchLd = null; double nextBestR2 = Double.NaN; ArrayList<ReplicationQtl> sameSnpQtls = replicationQtls.get(chr, pos); if (sameSnpQtls != null) { for (ReplicationQtl sameSnpQtl : sameSnpQtls) { if (sameSnpQtl.getGene().equals(gene)) { bestMatch = sameSnpQtl; bestMatchR2 = 1; } } } NavigableMap<Integer, ArrayList<ReplicationQtl>> potentionalReplicationQtls = replicationQtls .getChrRange(chr, pos - window, true, pos + window, true); for (ArrayList<ReplicationQtl> potentialReplicationQtls : potentionalReplicationQtls.values()) { for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) { if (!potentialReplicationQtl.getGene().equals(gene)) { continue; } GeneticVariant potentialReplicationQtlVariant = genotypeData .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos()); if (potentialReplicationQtlVariant == null) { notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos()); ++replicationTopSnpNotInGenotypeData; continue; } Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant); double r2 = ld.getR2(); if (r2 > 1) { r2 = 1; } if (bestMatch == null) { bestMatch = potentialReplicationQtl; bestMatchR2 = r2; bestMatchLd = ld; } else if (r2 > bestMatchR2) { bestMatch = potentialReplicationQtl; nextBestR2 = bestMatchR2; bestMatchR2 = r2; bestMatchLd = ld; } } } double replicationZ = Double.NaN; double replicationZCorrected = Double.NaN; double discoveryZCorrected = Double.NaN; String replicationAlleleAssessed = null; if (bestMatch != null) { replicationZ = bestMatch.getBeta(); replicationAlleleAssessed = bestMatch.getAssessedAllele(); if (pos != bestMatch.getPos()) { String commonHap = null; double commonHapFreq = -1; for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) { double f = hapFreq.getValue(); if (f > commonHapFreq) { commonHapFreq = f; commonHap = hapFreq.getKey(); } } String[] commonHapAlleles = StringUtils.split(commonHap, '/'); discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1; replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } else { discoveryZCorrected = discoveryZ; replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } } c = 0; outputLine[c++] = chr; outputLine[c++] = String.valueOf(pos); outputLine[c++] = snp; outputLine[c++] = gene; outputLine[c++] = module; outputLine[c++] = String.valueOf(discoveryZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected); outputLine[c++] = alleleAssessed; outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAssessedAllele()); outputLine[c++] = String.valueOf(bestMatchR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos())); outputLine[c++] = String.valueOf(nextBestR2); outputWriter.writeNext(outputLine); } outputWriter.close(); for (String e : notFound) { System.err.println("Not found: " + e); } System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData); System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow); System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd); System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd); System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData); }
From source file:fr.iphc.grid.jobmanager.JobManager.java
/** * @param args/*from w w w . j ava 2s. c o m*/ */ public static void main(String[] args) throws Exception { JobManager command = new JobManager(); CommandLine line = command.parse(args); ArrayList<File> JdlList = new ArrayList<File>(); Global.getOutputexecutor = Executors.newFixedThreadPool(10); Initialize init = new Initialize(); String SetupFile = "setup_vigrid.xml"; if (line.hasOption(OPT_SETUP)) { SetupFile = line.getOptionValue(OPT_SETUP); } if ((new File(SetupFile).isFile())) { init.GlobalSetup(SetupFile); } // Init Job if (line.hasOption(OPT_JOB)) { File file = new File(line.getOptionValue(OPT_JOB)); if ((file.isFile())) { JdlList.add(file); } else { System.err.println("The file " + file + " doesn't exist"); System.exit(-1); } } else { File file = new File(line.getOptionValue(OPT_FILEJOB)); if ((file.isFile())) { JdlList = init.InitJdl(file); } else { System.err.println("The file " + file + " doesn't exist"); System.exit(-1); } } if (line.hasOption(OPT_WAIT)) { Global.TIMEOUTWAIT = Integer.parseInt(line.getOptionValue(OPT_WAIT)); } if (line.hasOption(OPT_RUN)) { Global.TIMEOUTRUN = Integer.parseInt(line.getOptionValue(OPT_RUN)); } if (line.hasOption(OPT_END)) { Global.TIMEOUTEND = Integer.parseInt(line.getOptionValue(OPT_END)); } if (line.hasOption(OPT_LOGDISPLAY)) { Global.SEUILDISPLAYLOG = Float.parseFloat(line.getOptionValue(OPT_LOGDISPLAY)); } init.InitJob(JdlList); // Init Url Ce if (line.hasOption(OPT_QUEUE)) { Global.file = new File(line.getOptionValue(OPT_QUEUE)); } if (line.hasOption(OPT_BAD)) { Global.BadCe = new File(line.getOptionValue(OPT_BAD)); } if (line.hasOption(OPT_OPTIMIZETIMEOUTRUN)) { Global.OPTTIMEOUTRUN = false; } if (line.hasOption(OPT_CWD)) { File theDir = new File(line.getOptionValue(OPT_CWD)); if (!theDir.exists()) { if (!theDir.mkdirs()) { System.err.println("Working directory create failed: " + line.getOptionValue(OPT_CWD)); System.exit(-1); } } Global.Cwd = line.getOptionValue(OPT_CWD); } else { Global.Cwd = System.getProperty("user.dir"); } if (!(new File(Global.Cwd)).canWrite()) { System.err.println(" Write permission denied : " + Global.Cwd); System.exit(-1); } System.out.println("Current working directory : " + Global.Cwd); Date start = new Date(); init.PrintGlobalSetup(); init.InitUrl(Global.file); init.InitSosCe(); init.rmLoadFailed(Global.Cwd + "/loadFailed.txt"); System.out.println("CE: " + Global.ListUrl.size() + " Nb JOB: " + Global.ListJob.size() + " " + new Date()); if (Global.ListJob.size() < 6) { // pour obtenir rapport de 0.8 Global.OPTTIMEOUTRUN = false; } // check if we can connect to the grid try { SessionFactory.createSession(true); } catch (NoSuccessException e) { System.err.println("Could not connect to the grid at all (" + e.getMessage() + ")"); System.err.println("Aborting"); System.exit(0); } // Launch Tread Job JobThread st = new JobThread(Global.ListJob, Global.ListUrl); st.start(); LoggingThread logst = new LoggingThread(Global.ListJob, Global.ListUrl, Global.SEUILDISPLAYLOG); logst.start(); // create Thread Hook intercept kill +CNTL+C Thread hook = new Thread() { public void run() { try { for (Jdl job : Global.ListJob) { if (job.getJobId() != null) { JobThread.jobCancel(job.getJobId()); } } } catch (Exception e) { System.err.println("Thread Hook:\n" + e.getMessage()); } // give it a change to display final job state try { sleep(5000); } catch (InterruptedException e) { e.printStackTrace(); } } }; Runtime.getRuntime().addShutdownHook(hook); // Integer timer = 180 * 60 * 1000; Date now = new Date(); // Boolean Fin = false; while ((!Global.END) && ((now.getTime() - start.getTime()) < Global.TIMEOUTEND * 60 * 1000)) { // TOEND // en // minutes now = new Date(); // int mb = 1024*1024; // Getting the runtime reference from system // Runtime runtime = Runtime.getRuntime(); // System.out.println("##### Heap utilization statistics [MB] // #####"); // Print used memory // System.out.println("Used Memory:" // + (runtime.totalMemory() - runtime.freeMemory()) / mb); // Print free memory // System.out.println("Free Memory:" // + runtime.freeMemory() / mb); // Print total available memory // System.out.println("Total Memory:" + runtime.totalMemory() / mb); // Print Maximum available memory // System.out.println("Max Memory:" + runtime.maxMemory() / mb); // // System.out.println("NB: "+nb_end); // if ((float)(runtime.totalMemory() - // runtime.freeMemory())/(float)runtime.maxMemory() > (float)0.3){ // System.out.println ("GC: "+(float)(runtime.totalMemory() - // runtime.freeMemory())/runtime.maxMemory()); // System.gc(); // }; sleep(15 * 1000); // in ms // System.gc(); // Fin=true; // for (Jdl job : Global.ListJob) { // if (job.getJob() != null) { // System.out.println("JOB: "+job.getId()+"\t"+job.getStatus()); // if (job.getStatus().compareTo("END")==0){ // ((JobImpl) job.getJob()).postStagingAndCleanup(); // System.out.println("END JOB: "+job.getId()); // job.setStatus("END"); // } // if (job.getStatus().compareTo("END")!=0){ // Fin=false; // } // System.out.println("JOB: "+job.getId()+"\t"+job.getStatus() + // "\t"+job.getFail()+"\t"+job.getNodeCe()); // } // } // while ((Global.END==0) && ((new // Date().getTime()-start.getTime())<timer)){ } // Boolean end_load=false; // while (!end_load){ // end_load=true; // for(Jdl job:Global.ListJob){ // if (job.getStatus().equals("LOAD")){ // end_load=false; // } // } // } System.out.println("END JOB: " + now); st.halt(); logst.halt(); Iterator<Url> k = Global.ListUrl.iterator(); while (k.hasNext()) { Url url = k.next(); System.out.println("URL: " + url.getUrl()); } Iterator<Jdl> m = Global.ListJob.iterator(); while (m.hasNext()) { Jdl job = m.next(); System.out.println( "JOB: " + job.getId() + "\t" + job.getFail() + "\t" + job.getStatus() + "\t" + job.getNodeCe()); } System.out.println(start + " " + new Date()); System.exit(0); }
From source file:de.prozesskraft.pkraft.Manager.java
public static void main(String[] args) throws org.apache.commons.cli.ParseException, CloneNotSupportedException { // try/*from w w w . ja v a 2s.c om*/ // { // if (args.length != 1) // { // System.out.println("Please specify Inputfile and Outputfile (prozessinstanz.lri)"); // } // // } // catch (ArrayIndexOutOfBoundsException e) // { // System.out.println("***ArrayIndexOutOfBoundsException: Please specify procesdefinition.lrd and processinstance.lri\n" + e.toString()); // } /*---------------------------- get options from ini-file ----------------------------*/ File inifile = new java.io.File( WhereAmI.getInstallDirectoryAbsolutePath(Manager.class) + "/" + "../etc/pkraft-manager.ini"); if (inifile.exists()) { try { ini = new Ini(inifile); } catch (InvalidFileFormatException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (IOException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } else { System.err.println("ini file does not exist: " + inifile.getAbsolutePath()); System.exit(1); exit = true; } /*---------------------------- create boolean options ----------------------------*/ Option help = new Option("help", "print this message"); Option v = new Option("v", "prints version and build-date"); /*---------------------------- create argument options ----------------------------*/ Option instance = OptionBuilder.withArgName("instance").hasArg() .withDescription("[mandatory] process instance file") // .isRequired() .create("instance"); Option stop = OptionBuilder.withArgName("stop") // .hasArg() .withDescription("[optional] stops a running manager for given instance") // .isRequired() .create("stop"); Option kill = OptionBuilder.withArgName("kill") // .hasArg() .withDescription("[optional] kills all applications that have been started by steps") // .isRequired() .create("kill"); /*---------------------------- create options object ----------------------------*/ Options options = new Options(); options.addOption(help); options.addOption(v); options.addOption(instance); options.addOption(stop); options.addOption(kill); /*---------------------------- create the parser ----------------------------*/ CommandLineParser parser = new GnuParser(); try { // parse the command line arguments line = parser.parse(options, args); } // catch ( ParseException exp ) catch (Exception exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage()); exiter(); } /*---------------------------- usage/help ----------------------------*/ if (line.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("manager", options); exit = true; System.exit(0); } else if (line.hasOption("v")) { System.out.println("author: info@prozesskraft.de"); System.out.println("version: [% version %]"); System.out.println("date: [% date %]"); exit = true; System.exit(0); } else if (!(line.hasOption("instance"))) { exiter(); } /*---------------------------- die lizenz ueberpruefen und ggf abbrechen ----------------------------*/ // check for valid license ArrayList<String> allPortAtHost = new ArrayList<String>(); allPortAtHost.add(ini.get("license-server", "license-server-1")); allPortAtHost.add(ini.get("license-server", "license-server-2")); allPortAtHost.add(ini.get("license-server", "license-server-3")); MyLicense lic = new MyLicense(allPortAtHost, "1", "user-edition", "0.1"); // lizenz-logging ausgeben for (String actLine : (ArrayList<String>) lic.getLog()) { System.err.println(actLine); } // abbruch, wenn lizenz nicht valide if (!lic.isValid()) { exit = true; System.exit(1); } /*---------------------------- business logic ----------------------------*/ Process actualProcess = null; try { Process p1 = new Process(); // die dauer des loops festlegen. Dies soll kein standardwert sein, da sonst bei vielen subprozessen die Prozessorlast stark oszilliert // zwischen 12 und 17 sekunden // Random rand = new Random(System.currentTimeMillis()); // int loop_period_seconds = rand.nextInt((17 - 12) + 1) + 12; // System.err.println("loop period is randomly set to: "+loop_period_seconds); fileBinary = new java.io.File(line.getOptionValue("instance")); String pathBinary = ""; if (fileBinary.exists()) { pathBinary = fileBinary.getAbsolutePath(); System.err.println("file does exist: " + pathBinary); } else { System.err.println("file does not exist: " + fileBinary.getAbsolutePath()); exiter(); } if (line.hasOption("stop") || line.hasOption("kill")) { p1.setInfilebinary(pathBinary); Process p2 = p1.readBinary(); p2.log("debug", "setting new manager-Id (0) to signal actual manager (" + p2.getManagerid() + ") that he is no longer in charge "); System.err.println("info: stopping instance"); System.err.println("debug: setting new manager-Id (0) to signal actual manager (" + p2.getManagerid() + ") that he is no longer in charge "); p2.setManagerid(0); p2.run = false; p2.setOutfilebinary(pathBinary); p2.writeBinary(); if (line.hasOption("kill")) { System.err.println("info: killing all steps of instance"); String returnStringOfKills = p2.kill(); System.err.println("info: killing returns: " + returnStringOfKills); } boolean pradar = (!(p2.isWrapper())); // pradar checkout if (pradar) { pradarAttend(p2.getRootdir() + "/process.pmb"); // pradarCheckout(p2.getId(), p2.getName(), "0"); } exit = true; System.exit(0); } startZyklischerThread(0); // prozessinstanz einlesen p1.setInfilebinary(pathBinary); managerid = p1.genManagerid(); Process p2; p2 = p1.readBinary(); // beim aufruf des programms wird erstmal die instanz occupiert p2.setManagerid(managerid); System.err.println("debug: manager " + managerid + ": occupying instance."); p2.log("info", "manager " + managerid + ": occupying instance."); p2.log("debug", "manager " + managerid + ": setting new manager-id to signal other running managers that they are not longer needed."); p2.log("debug", "manager " + managerid + ": setting binary file for input to: " + pathBinary); // System.out.println("setting binary file for input to: "+line.getOptionValue("instance")); p2.log("debug", "manager " + managerid + ": reading binary file: " + pathBinary); p2.setInfilebinary(pathBinary); p2.setOutfilebinary(pathBinary); p2.log("debug", "manager " + managerid + ": setting binary file for output: " + pathBinary); // instanz auf platte schreiben (um anderen managern zu signalisieren, dass sie nicht mehr gebraucht werden // System.out.println("setting manager-id to: "+managerid); p2.log("debug", "manager " + managerid + ": writing process to binary file to occupy instance."); // wenn es kein wrapper-prozess ist, dann soll die komunikation mit pradar vom manager uebernommen werden boolean pradar = (!(p2.isWrapper())); System.err.println("debug: setting instance to run"); p2.run = true; // pradar checkin if (pradar && p2.run && p2.touchInMillis == 0) { pradarAttend(p2.getRootdir() + "/process.pmb"); // p2.log("debug", "pradar-checkin id="+p2.getId()+", process="+p2.getName()+", processversion="+p2.getVersion()+", id2="+p2.getId2()+", parentid="+p2.getParentid()+", resource="+p2.getRootdir()+"/process.pmb"); // pradarCheckin(p2.getId(), p2.getName(), p2.getVersion(), p2.getId2(), p2.getParentid(), getPid(), p2.getRootdir()+"/process.pmb"); } System.err.println("debug: writing binary"); p2.writeBinary(); // process weiter schubsen pushProcessAsFarAsPossible(pathBinary, false); // try // { // // der thread soll so lange schlafen, wie die periode lang ist. die schlafdauer wird mit der anzahl multipliziert, wie oft das loadAverage zu hoch war (max 5) // int faktorForPeriod = Math.min(10, p2.counterLoadAverageTooHigh + 1); // // int secondsToSleep = loop_period_seconds * faktorForPeriod; // System.err.println("debug: sleeping for " + secondsToSleep + " seconds"); // // int millisecondsToSleep = secondsToSleep*1000; // System.err.println("debug: sleeping for " + millisecondsToSleep + " milliseconds"); // // Thread.sleep(millisecondsToSleep); // } // catch (InterruptedException e) // { // // TODO Auto-generated catch block // e.printStackTrace(); // // // ausgabe in das debugLogFile // exiterException(actualProcess.getOutfilebinary(), e); // } } catch (Exception e) { if (actualProcess != null) { actualProcess.log("fatal", e.getMessage() + "\n" + Arrays.toString(e.getStackTrace())); updateFile(actualProcess); e.printStackTrace(); // ausgabe in das debugLogFile exiterException(actualProcess.getOutfilebinary(), e); } exit = true; System.exit(10); } }
From source file:edu.harvard.i2b2.adminTool.dataModel.PDORequestMessageModel.java
public static void main(String[] args) throws Exception { PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String conceptPath = new String( "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"); ArrayList<String> paths = new ArrayList<String>(); paths.add(conceptPath); conceptPath = new String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); paths.add(conceptPath);// www . j ava2 s . co m ArrayList<String> ppaths = new ArrayList<String>(); conceptPath = new String("\\Providers\\BWH"); ppaths.add(conceptPath); pdoFactory.requestXmlMessage(null, "1545", new Integer(0), new Integer(10), false); }
From source file:fr.inria.edelweiss.kgdqp.core.FedInferrencingCLI.java
public static void main(String args[]) throws ParseException, EngineException, InterruptedException { List<String> endpoints = new ArrayList<String>(); String queryPath = null;/*from w w w . java 2 s. c o m*/ boolean rulesSelection = false; File rulesDir = null; File ontDir = null; Options options = new Options(); Option helpOpt = new Option("h", "help", false, "print this message"); Option queryOpt = new Option("q", "query", true, "specify the sparql query file"); Option endpointOpt = new Option("e", "endpoint", true, "a federated sparql endpoint URL"); Option versionOpt = new Option("v", "version", false, "print the version information and exit"); Option rulesOpt = new Option("r", "rulesDir", true, "directory containing the inference rules"); Option ontOpt = new Option("o", "ontologiesDir", true, "directory containing the ontologies for rules selection"); // Option selOpt = new Option("s", "rulesSelection", false, "if set to true, only the applicable rules are run"); options.addOption(queryOpt); options.addOption(endpointOpt); options.addOption(helpOpt); options.addOption(versionOpt); options.addOption(rulesOpt); options.addOption(ontOpt); // options.addOption(selOpt); String header = "Corese/KGRAM distributed rule engine command line interface"; String footer = "\nPlease report any issue to alban.gaignard@cnrs.fr, olivier.corby@inria.fr"; CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("kgdqp", header, options, footer, true); System.exit(0); } if (!cmd.hasOption("e")) { logger.info("You must specify at least the URL of one sparql endpoint !"); System.exit(0); } else { endpoints = new ArrayList<String>(Arrays.asList(cmd.getOptionValues("e"))); } if (cmd.hasOption("o")) { rulesSelection = true; String ontDirPath = cmd.getOptionValue("o"); ontDir = new File(ontDirPath); if (!ontDir.isDirectory()) { logger.warn(ontDirPath + " is not a valid directory path."); System.exit(0); } } if (!cmd.hasOption("r")) { logger.info("You must specify a path for inference rules directory !"); System.exit(0); } else if (rulesSelection) { } if (cmd.hasOption("v")) { logger.info("version 3.0.4-SNAPSHOT"); System.exit(0); } String rulesDirPath = cmd.getOptionValue("r"); rulesDir = new File(rulesDirPath); if (!rulesDir.isDirectory()) { logger.warn(rulesDirPath + " is not a valid directory path."); System.exit(0); } ///////////////// Graph graph = Graph.create(); QueryProcessDQP execDQP = QueryProcessDQP.create(graph); for (String url : endpoints) { try { execDQP.addRemote(new URL(url), WSImplem.REST); } catch (MalformedURLException ex) { logger.error(url + " is not a well-formed URL"); System.exit(1); } } // Local rules graph initialization Graph rulesG = Graph.create(); Load ld = Load.create(rulesG); if (rulesSelection) { // Ontology loading if (ontDir.isDirectory()) { for (File o : ontDir.listFiles()) { logger.info("Loading " + o.getAbsolutePath()); ld.load(o.getAbsolutePath()); } } } // Rules loading if (rulesDir.isDirectory()) { for (File r : rulesDir.listFiles()) { logger.info("Loading " + r.getAbsolutePath()); ld.load(r.getAbsolutePath()); } } // Rule engine initialization RuleEngine ruleEngine = RuleEngine.create(graph); ruleEngine.set(execDQP); StopWatch sw = new StopWatch(); logger.info("Federated graph size : " + graph.size()); logger.info("Rules graph size : " + rulesG.size()); // Rule selection logger.info("Rules selection"); QueryProcess localKgram = QueryProcess.create(rulesG); ArrayList<String> applicableRules = new ArrayList<String>(); sw.start(); String rulesSelQuery = ""; if (rulesSelection) { rulesSelQuery = pertinentRulesQuery; } else { rulesSelQuery = allRulesQuery; } Mappings maps = localKgram.query(rulesSelQuery); logger.info("Rules selected in " + sw.getTime() + " ms"); logger.info("Applicable rules : " + maps.size()); // Selected rule loading for (Mapping map : maps) { IDatatype dt = (IDatatype) map.getValue("?res"); String rule = dt.getLabel(); //loading rule in the rule engine // logger.info("Adding rule : " + rule); applicableRules.add(rule); ruleEngine.addRule(rule); } // Rules application on distributed sparql endpoints logger.info("Rules application (" + applicableRules.size() + " rules)"); ExecutorService threadPool = Executors.newCachedThreadPool(); RuleEngineThread ruleThread = new RuleEngineThread(ruleEngine); sw.reset(); sw.start(); // ruleEngine.process(); threadPool.execute(ruleThread); threadPool.shutdown(); //monitoring loop while (!threadPool.isTerminated()) { System.out.println("******************************"); System.out.println(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); System.out.println("Rule engine running for " + sw.getTime() + " ms"); System.out.println("Federated graph size : " + graph.size()); Thread.sleep(10000); } logger.info("Federated graph size : " + graph.size()); logger.info(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); ///////////// Query file processing // StringBuffer fileData = new StringBuffer(1000); // BufferedReader reader = null; // try { // reader = new BufferedReader(new FileReader(queryPath)); // } catch (FileNotFoundException ex) { // logger.error("Query file "+queryPath+" not found !"); // System.exit(1); // } // char[] buf = new char[1024]; // int numRead = 0; // try { // while ((numRead = reader.read(buf)) != -1) { // String readData = String.valueOf(buf, 0, numRead); // fileData.append(readData); // buf = new char[1024]; // } // reader.close(); // } catch (IOException ex) { // logger.error("Error while reading query file "+queryPath); // System.exit(1); // } // // String sparqlQuery = fileData.toString(); // // Query q = exec.compile(sparqlQuery,null); // System.out.println(q); // // StopWatch sw = new StopWatch(); // sw.start(); // Mappings map = exec.query(sparqlQuery); // int dqpSize = map.size(); // System.out.println("--------"); // long time = sw.getTime(); // System.out.println(time + " " + dqpSize); }
From source file:eqtlmappingpipeline.util.ModuleEqtWestraReplication.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 IOException, LdCalculatorException { System.out.println(HEADER); System.out.println(); System.out.flush(); //flush to make sure header is before errors try { Thread.sleep(25); //Allows flush to complete } catch (InterruptedException ex) { } CommandLineParser parser = new PosixParser(); final CommandLine commandLine; try { commandLine = parser.parse(OPTIONS, args, true); } catch (ParseException ex) { System.err.println("Invalid command line arguments: " + ex.getMessage()); System.err.println(); new HelpFormatter().printHelp(" ", OPTIONS); System.exit(1); return; } final String[] genotypesBasePaths = commandLine.getOptionValues("g"); final RandomAccessGenotypeDataReaderFormats genotypeDataType; final String replicationQtlFilePath = commandLine.getOptionValue("e"); final String interactionQtlFilePath = commandLine.getOptionValue("i"); final String outputFilePath = commandLine.getOptionValue("o"); final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld")); final int window = Integer.parseInt(commandLine.getOptionValue("w")); System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths)); System.out.println("Interaction file: " + interactionQtlFilePath); System.out.println("Replication file: " + replicationQtlFilePath); System.out.println("Output: " + outputFilePath); System.out.println("LD: " + ldCutoff); System.out.println("Window: " + window); try { if (commandLine.hasOption("G")) { genotypeDataType = RandomAccessGenotypeDataReaderFormats .valueOf(commandLine.getOptionValue("G").toUpperCase()); } else { if (genotypesBasePaths[0].endsWith(".vcf")) { System.err.println( "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file."); System.exit(1); return; } try { genotypeDataType = RandomAccessGenotypeDataReaderFormats .matchFormatToPath(genotypesBasePaths[0]); } catch (GenotypeDataException e) { System.err .println("Unable to determine input 1 type based on specified path. Please specify -G"); System.exit(1); return; } } } catch (IllegalArgumentException e) { System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G") + "\" is not a valid input data format"); System.exit(1); return; } final RandomAccessGenotypeData genotypeData; try { genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null, 0.8); } catch (TabixFileNotFoundException e) { LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n" + "Please see README on how to create a tabix file"); System.exit(1); return; } catch (IOException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } catch (IncompatibleMultiPartGenotypeDataException e) { LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e); System.exit(1); return; } catch (GenotypeDataException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } ChrPosTreeMap<ArrayList<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>(); CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t'); String[] replicationHeader = replicationQtlReader.readNext(); String[] replicationLine; while ((replicationLine = replicationQtlReader.readNext()) != null) { try { GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL])); if (variant == null) { continue; } Alleles variantAlleles = variant.getVariantAlleles(); String[] replicationAllelesString = StringUtils.split(replicationLine[REPLICATION_ALLELES_COL], '/'); Alleles replicationAlleles = Alleles.createBasedOnString(replicationAllelesString[0], replicationAllelesString[1]); Allele assessedAlleleReplication = Allele.create(replicationLine[REPLICATION_ALLELE_ASSESSED_COL]); boolean isAmbigous = replicationAlleles.isAtOrGcSnp(); if (!variantAlleles.equals(replicationAlleles)) { if (variantAlleles.equals(replicationAlleles.getComplement())) { assessedAlleleReplication = assessedAlleleReplication.getComplement(); } else { continue; } } ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]), replicationLine[REPLICATION_GENE_COL], Double.parseDouble(replicationLine[REPLICATION_BETA_COL]), assessedAlleleReplication.getAlleleAsString(), replicationLine, isAmbigous); ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(), replicationQtl.getPos()); if (posReplicationQtls == null) { posReplicationQtls = new ArrayList<>(); replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls); } posReplicationQtls.add(replicationQtl); } catch (Exception e) { System.out.println(Arrays.toString(replicationLine)); throw e; } } int interactionSnpNotInGenotypeData = 0; int noReplicationQtlsInWindow = 0; int noReplicationQtlsInLd = 0; int multipleReplicationQtlsInLd = 0; int replicationTopSnpNotInGenotypeData = 0; final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0'); final String[] outputLine = new String[15 + EXTRA_COL_FROM_REPLICATION.length]; int c = 0; outputLine[c++] = "Chr"; outputLine[c++] = "Pos"; outputLine[c++] = "SNP"; outputLine[c++] = "Gene"; outputLine[c++] = "Module"; outputLine[c++] = "DiscoveryZ"; outputLine[c++] = "ReplicationZ"; outputLine[c++] = "DiscoveryZCorrected"; outputLine[c++] = "ReplicationZCorrected"; outputLine[c++] = "DiscoveryAlleleAssessed"; outputLine[c++] = "ReplicationAlleleAssessed"; outputLine[c++] = "bestLd"; outputLine[c++] = "bestLd_dist"; outputLine[c++] = "nextLd"; outputLine[c++] = "replicationAmbigous"; for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = replicationHeader[EXTRA_COL_FROM_REPLICATION[i]]; } outputWriter.writeNext(outputLine); HashSet<String> notFound = new HashSet<>(); CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t'); interactionQtlReader.readNext();//skip header String[] interactionQtlLine; while ((interactionQtlLine = interactionQtlReader.readNext()) != null) { String snp = interactionQtlLine[1]; String chr = interactionQtlLine[2]; int pos = Integer.parseInt(interactionQtlLine[3]); String gene = interactionQtlLine[4]; String alleleAssessed = interactionQtlLine[9]; String module = interactionQtlLine[12]; double discoveryZ = Double.parseDouble(interactionQtlLine[10]); GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos); if (interactionQtlVariant == null) { System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos); ++interactionSnpNotInGenotypeData; continue; } ReplicationQtl bestMatch = null; double bestMatchR2 = Double.NaN; Ld bestMatchLd = null; double nextBestR2 = Double.NaN; ArrayList<ReplicationQtl> sameSnpQtls = replicationQtls.get(chr, pos); if (sameSnpQtls != null) { for (ReplicationQtl sameSnpQtl : sameSnpQtls) { if (sameSnpQtl.getGene().equals(gene)) { bestMatch = sameSnpQtl; bestMatchR2 = 1; } } } NavigableMap<Integer, ArrayList<ReplicationQtl>> potentionalReplicationQtls = replicationQtls .getChrRange(chr, pos - window, true, pos + window, true); for (ArrayList<ReplicationQtl> potentialReplicationQtls : potentionalReplicationQtls.values()) { for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) { if (!potentialReplicationQtl.getGene().equals(gene)) { continue; } GeneticVariant potentialReplicationQtlVariant = genotypeData .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos()); if (potentialReplicationQtlVariant == null) { notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos()); ++replicationTopSnpNotInGenotypeData; continue; } Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant); double r2 = ld.getR2(); if (r2 > 1) { r2 = 1; } if (bestMatch == null) { bestMatch = potentialReplicationQtl; bestMatchR2 = r2; bestMatchLd = ld; } else if (r2 > bestMatchR2) { bestMatch = potentialReplicationQtl; nextBestR2 = bestMatchR2; bestMatchR2 = r2; bestMatchLd = ld; } } } double replicationZ = Double.NaN; double replicationZCorrected = Double.NaN; double discoveryZCorrected = Double.NaN; String replicationAlleleAssessed = null; if (bestMatch != null) { replicationZ = bestMatch.getBeta(); replicationAlleleAssessed = bestMatch.getAssessedAllele(); if (pos != bestMatch.getPos()) { String commonHap = null; double commonHapFreq = -1; for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) { double f = hapFreq.getValue(); if (f > commonHapFreq) { commonHapFreq = f; commonHap = hapFreq.getKey(); } } String[] commonHapAlleles = StringUtils.split(commonHap, '/'); discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1; replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } else { discoveryZCorrected = discoveryZ; replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; //replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) || alleleAssessed.equals(String.valueOf(Utils.getComplementNucleotide(replicationAlleleAssessed.charAt(0)))) ? replicationZ : replicationZ * -1; } } c = 0; outputLine[c++] = chr; outputLine[c++] = String.valueOf(pos); outputLine[c++] = snp; outputLine[c++] = gene; outputLine[c++] = module; outputLine[c++] = String.valueOf(discoveryZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected); outputLine[c++] = alleleAssessed; outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAssessedAllele()); outputLine[c++] = String.valueOf(bestMatchR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos())); outputLine[c++] = String.valueOf(nextBestR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.isIsAmbigous()); if (bestMatch == null) { for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = "NA"; } } else { for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = bestMatch.getLine()[EXTRA_COL_FROM_REPLICATION[i]]; } } outputWriter.writeNext(outputLine); } outputWriter.close(); for (String e : notFound) { System.err.println("Not found: " + e); } System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData); System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow); System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd); System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd); System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData); }
From source file:guardar.en.base.de.datos.MainServidor.java
public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException { Mongo mongo = new Mongo("localhost", 27017); // nombre de la base de datos DB database = mongo.getDB("paginas"); // coleccion de la db DBCollection collection = database.getCollection("indice"); DBCollection collection_textos = database.getCollection("tabla"); ArrayList<String> lista_textos = new ArrayList(); try {/*from w w w.j a v a2 s. com*/ ServerSocket servidor = new ServerSocket(4545); // Crear un servidor en pausa hasta que un cliente llegue. while (true) { String aux = new String(); lista_textos.clear(); Socket clienteNuevo = servidor.accept();// Si llega se acepta. // Queda en pausa otra vez hasta que un objeto llegue. ObjectInputStream entrada = new ObjectInputStream(clienteNuevo.getInputStream()); JSONObject request = (JSONObject) entrada.readObject(); String b = (String) request.get("id"); //hacer una query a la base de datos con la palabra que se quiere obtener BasicDBObject query = new BasicDBObject("palabra", b); DBCursor cursor = collection.find(query); ArrayList<DocumentosDB> lista_doc = new ArrayList<>(); // de la query tomo el campo documentos y los agrego a una lista try { while (cursor.hasNext()) { //System.out.println(cursor.next()); BasicDBList campo_documentos = (BasicDBList) cursor.next().get("documentos"); // en el for voy tomando uno por uno los elementos en el campo documentos for (Iterator<Object> it = campo_documentos.iterator(); it.hasNext();) { BasicDBObject dbo = (BasicDBObject) it.next(); //DOC tiene id y frecuencia DocumentosDB doc = new DocumentosDB(); doc.makefn2(dbo); //int id = (int)doc.getId_documento(); //int f = (int)doc.getFrecuencia(); lista_doc.add(doc); //******************************************* //******************************************** //QUERY A LA COLECCION DE TEXTOS /* BasicDBObject query_textos = new BasicDBObject("id", doc.getId_documento());//query DBCursor cursor_textos = collection_textos.find(query_textos); try { while (cursor_textos.hasNext()) { DBObject obj = cursor_textos.next(); String titulo = (String) obj.get("titulo"); titulo = titulo + "\n\n"; String texto = (String) obj.get("texto"); String texto_final = titulo + texto; aux = texto_final; lista_textos.add(texto_final); } } finally { cursor_textos.close(); }*/ //System.out.println(doc.getId_documento()); //System.out.println(doc.getFrecuencia()); } // end for } //end while query } finally { cursor.close(); } // ordeno la lista de menor a mayor Collections.sort(lista_doc, new Comparator<DocumentosDB>() { @Override public int compare(DocumentosDB o1, DocumentosDB o2) { //throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. return o1.getFrecuencia().compareTo(o2.getFrecuencia()); } }); int tam = lista_doc.size() - 1; for (int j = tam; j >= 0; j--) { BasicDBObject query_textos = new BasicDBObject("id", (int) lista_doc.get(j).getId_documento().intValue());//query DBCursor cursor_textos = collection_textos.find(query_textos);// lo busco try { while (cursor_textos.hasNext()) { DBObject obj = cursor_textos.next(); String titulo = "*******************************"; titulo += (String) obj.get("titulo"); int f = (int) lista_doc.get(j).getFrecuencia().intValue(); String strinf = Integer.toString(f); titulo += "******************************* frecuencia:" + strinf; titulo = titulo + "\n\n"; String texto = (String) obj.get("texto"); String texto_final = titulo + texto + "\n\n"; aux = aux + texto_final; //lista_textos.add(texto_final); } } finally { cursor_textos.close(); } } //actualizar el cache try { Socket cliente_cache = new Socket("localhost", 4500); // nos conectamos con el servidor ObjectOutputStream mensaje_cache = new ObjectOutputStream(cliente_cache.getOutputStream()); // get al output del servidor, que es cliente : socket del cliente q se conecto al server JSONObject actualizacion_cache = new JSONObject(); actualizacion_cache.put("actualizacion", 1); actualizacion_cache.put("busqueda", b); actualizacion_cache.put("respuesta", aux); mensaje_cache.writeObject(actualizacion_cache); // envio el msj al servidor } catch (Exception ex) { } //RESPONDER DESDE EL SERVIDORIndex al FRONT ObjectOutputStream resp = new ObjectOutputStream(clienteNuevo.getOutputStream());// obtengo el output del cliente para mandarle un msj resp.writeObject(aux); System.out.println("msj enviado desde el servidor"); } } catch (IOException ex) { Logger.getLogger(MainServidor.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:edu.harvard.i2b2.patientMapping.serviceClient.IMQueryClient.java
public static void main(String[] args) throws Exception { PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String conceptPath = new String( "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"); ArrayList<String> paths = new ArrayList<String>(); // paths.add(conceptPath); conceptPath = new String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); paths.add(conceptPath); // conceptPath = new // String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); // paths.add(conceptPath); ArrayList<String> ppaths = new ArrayList<String>(); conceptPath = new String("\\Providers\\BWH"); // ppaths.add(conceptPath); String xmlStr = pdoFactory.requestXmlMessage(null, "1545", new Integer(1), new Integer(20), false); String result = sendSetKeyQueryRequestREST(xmlStr); // FileWriter fwr = new FileWriter("c:\\testdir\\response.txt"); // fwr.write(result); log.debug(result);//from w w w . j ava2s .co m PDOItem set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"; set.hasValueDisplayProperty = true; PDOValueModel valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 8.4; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.4; valdp.right = 8.9; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.9; valdp.right = 10.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.0; valdp.right = 10.6; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.6; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; TimelineRow row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Calcium (Group:CA)"; ArrayList<TimelineRow> rows = new ArrayList<TimelineRow>(); rows.add(row); set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"; set.hasValueDisplayProperty = true; valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 1.0; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 1.0; valdp.right = 19.0; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 19.0; valdp.right = 34.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 34.0; valdp.right = 82.0; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 82.0; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Gamma Glutamyltrans (Group:GGT)"; rows.add(row); // testWritelld(result, rows, true); testWriteTableFile(result); }
From source file:edu.cmu.lti.oaqa.knn4qa.apps.ExtractDataAndQueryAsSparseVectors.java
public static void main(String[] args) { String optKeys[] = { CommonParams.MAX_NUM_QUERY_PARAM, MAX_NUM_DATA_PARAM, CommonParams.MEMINDEX_PARAM, IN_QUERIES_PARAM, OUT_QUERIES_PARAM, OUT_DATA_PARAM, TEXT_FIELD_PARAM, TEST_QTY_PARAM, }; String optDescs[] = { CommonParams.MAX_NUM_QUERY_DESC, MAX_NUM_DATA_DESC, CommonParams.MEMINDEX_DESC, IN_QUERIES_DESC, OUT_QUERIES_DESC, OUT_DATA_DESC, TEXT_FIELD_DESC, TEST_QTY_DESC }; boolean hasArg[] = { true, true, true, true, true, true, true, true }; ParamHelper prmHlp = null;/*from w w w . j a va2 s.c o m*/ try { prmHlp = new ParamHelper(args, optKeys, optDescs, hasArg); CommandLine cmd = prmHlp.getCommandLine(); Options opt = prmHlp.getOptions(); int maxNumQuery = Integer.MAX_VALUE; String tmpn = cmd.getOptionValue(CommonParams.MAX_NUM_QUERY_PARAM); if (tmpn != null) { try { maxNumQuery = Integer.parseInt(tmpn); } catch (NumberFormatException e) { UsageSpecify(CommonParams.MAX_NUM_QUERY_PARAM, opt); } } int maxNumData = Integer.MAX_VALUE; tmpn = cmd.getOptionValue(MAX_NUM_DATA_PARAM); if (tmpn != null) { try { maxNumData = Integer.parseInt(tmpn); } catch (NumberFormatException e) { UsageSpecify(MAX_NUM_DATA_PARAM, opt); } } String memIndexPref = cmd.getOptionValue(CommonParams.MEMINDEX_PARAM); if (null == memIndexPref) { UsageSpecify(CommonParams.MEMINDEX_PARAM, opt); } String textField = cmd.getOptionValue(TEXT_FIELD_PARAM); if (null == textField) { UsageSpecify(TEXT_FIELD_PARAM, opt); } textField = textField.toLowerCase(); int fieldId = -1; for (int i = 0; i < FeatureExtractor.mFieldNames.length; ++i) if (FeatureExtractor.mFieldNames[i].compareToIgnoreCase(textField) == 0) { fieldId = i; break; } if (-1 == fieldId) { Usage("Wrong field index, should be one of the following: " + String.join(",", FeatureExtractor.mFieldNames), opt); } InMemForwardIndex indx = new InMemForwardIndex( FeatureExtractor.indexFileName(memIndexPref, FeatureExtractor.mFieldNames[fieldId])); BM25SimilarityLucene bm25simil = new BM25SimilarityLucene(FeatureExtractor.BM25_K1, FeatureExtractor.BM25_B, indx); String inQueryFile = cmd.getOptionValue(IN_QUERIES_PARAM); String outQueryFile = cmd.getOptionValue(OUT_QUERIES_PARAM); if ((inQueryFile == null) != (outQueryFile == null)) { Usage("You should either specify both " + IN_QUERIES_PARAM + " and " + OUT_QUERIES_PARAM + " or none of them", opt); } String outDataFile = cmd.getOptionValue(OUT_DATA_PARAM); tmpn = cmd.getOptionValue(TEST_QTY_PARAM); int testQty = 0; if (tmpn != null) { try { testQty = Integer.parseInt(tmpn); } catch (NumberFormatException e) { UsageSpecify(TEST_QTY_PARAM, opt); } } ArrayList<DocEntry> testDocEntries = new ArrayList<DocEntry>(); ArrayList<DocEntry> testQueryEntries = new ArrayList<DocEntry>(); ArrayList<TrulySparseVector> testDocVectors = new ArrayList<TrulySparseVector>(); ArrayList<TrulySparseVector> testQueryVectors = new ArrayList<TrulySparseVector>(); if (outDataFile != null) { BufferedWriter out = new BufferedWriter( new OutputStreamWriter(CompressUtils.createOutputStream(outDataFile))); ArrayList<DocEntryExt> docEntries = indx.getDocEntries(); for (int id = 0; id < Math.min(maxNumData, docEntries.size()); ++id) { DocEntry e = docEntries.get(id).mDocEntry; TrulySparseVector v = bm25simil.getDocSparseVector(e, false); if (id < testQty) { testDocEntries.add(e); testDocVectors.add(v); } outputVector(out, v); } out.close(); } Splitter splitOnSpace = Splitter.on(' ').trimResults().omitEmptyStrings(); if (outQueryFile != null) { BufferedReader inpText = new BufferedReader( new InputStreamReader(CompressUtils.createInputStream(inQueryFile))); BufferedWriter out = new BufferedWriter( new OutputStreamWriter(CompressUtils.createOutputStream(outQueryFile))); String queryText = XmlHelper.readNextXMLIndexEntry(inpText); for (int queryQty = 0; queryText != null && queryQty < maxNumQuery; queryText = XmlHelper .readNextXMLIndexEntry(inpText), queryQty++) { Map<String, String> queryFields = null; // 1. Parse a query try { queryFields = XmlHelper.parseXMLIndexEntry(queryText); } catch (Exception e) { System.err.println("Parsing error, offending QUERY:\n" + queryText); throw new Exception("Parsing error."); } String fieldText = queryFields.get(FeatureExtractor.mFieldsSOLR[fieldId]); if (fieldText == null) { fieldText = ""; } ArrayList<String> tmpa = new ArrayList<String>(); for (String s : splitOnSpace.split(fieldText)) tmpa.add(s); DocEntry e = indx.createDocEntry(tmpa.toArray(new String[tmpa.size()])); TrulySparseVector v = bm25simil.getDocSparseVector(e, true); if (queryQty < testQty) { testQueryEntries.add(e); testQueryVectors.add(v); } outputVector(out, v); } out.close(); } int testedQty = 0, diffQty = 0; // Now let's do some testing for (int iq = 0; iq < testQueryEntries.size(); ++iq) { DocEntry queryEntry = testQueryEntries.get(iq); TrulySparseVector queryVector = testQueryVectors.get(iq); for (int id = 0; id < testDocEntries.size(); ++id) { DocEntry docEntry = testDocEntries.get(id); TrulySparseVector docVector = testDocVectors.get(id); float val1 = bm25simil.compute(queryEntry, docEntry); float val2 = TrulySparseVector.scalarProduct(queryVector, docVector); ++testedQty; if (Math.abs(val1 - val2) > 1e5) { System.err.println( String.format("Potential mismatch BM25=%f <-> scalar product=%f", val1, val2)); ++diffQty; } } } if (testedQty > 0) System.out.println(String.format("Tested %d Mismatched %d", testedQty, diffQty)); } catch (ParseException e) { Usage("Cannot parse arguments: " + e, prmHlp != null ? prmHlp.getOptions() : null); e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); System.err.println("Terminating due to an exception: " + e); System.exit(1); } }