List of usage examples for org.apache.commons.cli PosixParser PosixParser
PosixParser
From source file:javadepchecker.Main.java
/** * @param args the command line arguments *///from www .j av a 2 s. com public static void main(String[] args) throws IOException { int exit = 0; try { CommandLineParser parser = new PosixParser(); Options options = new Options(); options.addOption("h", "help", false, "print help"); options.addOption("i", "image", true, "image directory"); options.addOption("v", "verbose", false, "print verbose output"); CommandLine line = parser.parse(options, args); String[] files = line.getArgs(); if (line.hasOption("h") || files.length == 0) { HelpFormatter h = new HelpFormatter(); h.printHelp("java-dep-check [-i <image] <package.env>+", options); } else { image = line.getOptionValue("i", ""); for (String arg : files) { if (line.hasOption('v')) { System.out.println("Checking " + arg); } if (!checkPkg(new File(arg))) { exit = 1; } } } } catch (ParseException ex) { Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex); } System.exit(exit); }
From source file:de.unileipzig.ub.scroller.Main.java
public static void main(String[] args) throws IOException { Options options = new Options(); // add t option options.addOption("h", "help", false, "display this help"); // elasticsearch options options.addOption("t", "host", true, "elasticsearch hostname (default: 0.0.0.0)"); options.addOption("p", "port", true, "transport port (that's NOT the http port, default: 9300)"); options.addOption("c", "cluster", true, "cluster name (default: elasticsearch_mdma)"); options.addOption("i", "index", true, "index to use"); options.addOption("f", "filter", true, "filter(s) - e.g. meta.kind=title"); options.addOption("j", "junctor", true, "values: and, or (default: and)"); options.addOption("n", "notice-every", true, "show speed after every N items"); options.addOption("v", "verbose", false, "be verbose"); // options.addOption("z", "end-of-message", true, "sentinel to print to stdout, once the regular input finished (default: EOM)"); CommandLineParser parser = new PosixParser(); CommandLine cmd = null;/*from w w w. jav a 2s. com*/ try { cmd = parser.parse(options, args); } catch (ParseException ex) { logger.error(ex); System.exit(1); } // process options if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("scroller", options, true); System.exit(0); } String endOfMessage = "EOM"; boolean verbose = false; if (cmd.hasOption("verbose")) { verbose = true; } if (!cmd.hasOption("i")) { System.err.println("error: no index specified"); System.exit(1); } long noticeEvery = 10000; if (cmd.hasOption("n")) { noticeEvery = Long.parseLong(cmd.getOptionValue("n")); } // ES options String[] hosts = new String[] { "0.0.0.0" }; int port = 9300; String clusterName = "elasticsearch_mdma"; int bulkSize = 3000; if (cmd.hasOption("host")) { hosts = cmd.getOptionValues("host"); } if (cmd.hasOption("port")) { port = Integer.parseInt(cmd.getOptionValue("port")); } if (cmd.hasOption("cluster")) { clusterName = cmd.getOptionValue("cluster"); } // Index String indexName = cmd.getOptionValue("index"); Map<String, String> filterMap = new HashMap<String, String>(); if (cmd.hasOption("filter")) { try { filterMap = getMapForKeys(cmd.getOptionValues("filter")); } catch (ParseException pe) { System.err.println(pe); System.exit(1); } } Collection<HashMap> filterList = new ArrayList<HashMap>(); if (cmd.hasOption("filter")) { try { filterList = getFilterList(cmd.getOptionValues("filter")); } catch (ParseException pe) { System.err.println(pe); System.exit(1); } } // ES Client final Settings settings = ImmutableSettings.settingsBuilder().put("cluster.name", "elasticsearch_mdma") .put("client.transport.ping_timeout", "60s").build(); final TransportClient client = new TransportClient(settings); for (String host : hosts) { client.addTransportAddress(new InetSocketTransportAddress(host, port)); } // build the query String junctor = "and"; if (cmd.hasOption("j")) { junctor = cmd.getOptionValue("j"); } // ArrayList<TermFilterBuilder> filters = new ArrayList<TermFilterBuilder>(); // if (filterMap.size() > 0) { // for (Map.Entry<String, String> entry : filterMap.entrySet()) { // filters.add(new TermFilterBuilder(entry.getKey(), entry.getValue())); // } // } ArrayList<TermFilterBuilder> filters = new ArrayList<TermFilterBuilder>(); if (filterList.size() > 0) { for (HashMap map : filterList) { for (Object obj : map.entrySet()) { Map.Entry entry = (Map.Entry) obj; filters.add(new TermFilterBuilder(entry.getKey().toString(), entry.getValue().toString())); } } } FilterBuilder fb = null; if (junctor.equals("and")) { AndFilterBuilder afb = new AndFilterBuilder(); for (TermFilterBuilder tfb : filters) { afb.add(tfb); } fb = afb; } if (junctor.equals("or")) { OrFilterBuilder ofb = new OrFilterBuilder(); for (TermFilterBuilder tfb : filters) { ofb.add(tfb); } fb = ofb; } // TermFilterBuilder tfb0 = new TermFilterBuilder("meta.kind", "title"); // TermFilterBuilder tfb1 = new TermFilterBuilder("meta.timestamp", "201112081240"); // // AndFilterBuilder afb0 = new AndFilterBuilder(tfb0, tfb1); QueryBuilder qb0 = null; if (filterMap.isEmpty()) { qb0 = matchAllQuery(); } else { qb0 = filteredQuery(matchAllQuery(), fb); } // sorting // FieldSortBuilder sortBuilder = new FieldSortBuilder("meta.timestamp"); // sortBuilder.order(SortOrder.DESC); // FilteredQueryBuilder fqb0 = filteredQuery(matchAllQuery(), tfb0); final CountResponse countResponse = client.prepareCount(indexName).setQuery(qb0).execute().actionGet(); final long total = countResponse.getCount(); SearchResponse scrollResp = client.prepareSearch(indexName).setSearchType(SearchType.SCAN) .setScroll(new TimeValue(60000)).setQuery(qb0) // .addSort(sortBuilder) // sort has no effect on scroll type (see: https://github.com/CPAN-API/cpan-api/issues/172) .setSize(1000) //1000 hits per shard will be returned for each scroll .execute().actionGet(); //Scroll until no hits are returned System.err.println("[Scroller] query: " + qb0.toString()); System.err.println("[Scroller] took: " + scrollResp.getTookInMillis() + "ms"); System.err.println("[Scroller] docs found: " + total); long counter = 0; long start = System.currentTimeMillis(); while (true) { scrollResp = client.prepareSearchScroll(scrollResp.getScrollId()).setScroll(new TimeValue(600000)) .execute().actionGet(); if (scrollResp.getHits().hits().length == 0) { break; } for (SearchHit hit : scrollResp.getHits()) { System.out.println(hit.sourceAsString()); counter += 1; if (counter % noticeEvery == 0) { final double elapsed = (System.currentTimeMillis() - start) / 1000; final double speed = counter / elapsed; final long eta = (long) ((elapsed / counter) * (total - counter) * 1000); System.err.println( counter + "/" + total + " records recvd @ speed " + String.format("%1$,.1f", speed) + " r/s eta: " + DurationFormatUtils.formatDurationWords(eta, false, false)); } } } System.out.close(); // System.out.println(endOfMessage); }
From source file:de.ipbhalle.metfrag.main.CommandLineTool.java
/** * @param args/*from ww w . ja va 2s .c o m*/ * @throws Exception */ public static void main(String[] args) { CommandLineParser parser = new PosixParser(); // create the Options Options options = new Options(); options.addOption("d", "database", true, "database: " + Databases.getString() + " (default: kegg)"); options.addOption("l", "localdb", true, "use a local database together with a settings file for candidate search (default: not used) note: only usable if pubchem database is selected (-d)"); options.addOption("a", "mzabs", true, "allowed absolute (Da) mass deviation of fragment and peak masses (default: 0.01)"); options.addOption("p", "mzppm", true, "allowed relative (ppm) mass deviation of fragment and peak masses (default: 10)"); options.addOption("s", "searchppm", true, "relative (ppm) mass deviation used for candidate search in given compound database (-d) (default: 10; not used by default if sdf database is selected (-d))\n"); options.addOption("n", "exactmass", true, "neutral mass of measured compound used for candidate search in database (-d) (mandatory)"); options.addOption("b", "biological", false, "only consider compounds including CHNOPS atoms (not used by default)"); options.addOption("i", "databaseids", true, "database ids of compounds used for in silico fragmentation (separated by ,) (not used by default; not used if sdf database is selected (-d)) note: given ids must be valid ids of given database (-d)"); options.addOption("t", "treedepth", true, "treedepth used for in silico fragmentation (default: 2) note: high values result in high computation time"); options.addOption("M", "mode", true, "mode used for measured ms/ms spectrum:\n" + Modes.getString() + "(default: 3)"); options.addOption("f", "formula", true, "molecular formula of measured compound used for candidate search in database (-d) (not used by default; not used if sdf database is selected (-d))"); options.addOption("B", "breakrings", false, "allow splitting of aromatic rings of candidate structures during in silico fragmentation (not used by default)"); options.addOption("F", "storefragments", false, "store in silico generated fragments of candidate molecules (not used by default)"); options.addOption("R", "resultspath", true, "directory where result files are stored (default: /tmp)"); options.addOption("L", "sdffile", true, "location of the local sdf file (mandatory if sdf database (-d) is selected)"); options.addOption("h", "help", false, "print help"); options.addOption("D", "spectrumfile", true, "file containing peak data (mandatory) note: commandline options overwrite parameters given in the spectrum data file"); options.addOption("T", "threads", true, "number of threads used for fragment calculation (default: number of available cpu cores)"); options.addOption("c", "chemspidertoken", true, "Token for ChemSpider database search (not used by default; only necessary (mandatory) if ChemSpider database (-d) is selected)"); options.addOption("v", "verbose", false, "get more output information during the processing (not used by default)"); options.addOption("S", "samplename", true, "name of the sample measured (mandatory) note: result files are stored with given value"); options.addOption("P", "saveparameters", false, "save used parameters (not used by default)"); options.addOption("e", "printexamplespecfile", false, "print an example spectrum data file (not used by default)"); options.addOption("C", "charge", true, "charge used in combination with mode (-M):\n" + Charges.getString() + " (default: 1)"); options.addOption("r", "range", true, "range of candidates that will be processed: N (first N), M-N (from M to N), M- (from M), -N (till N); if N is greater than the number of candidates it will be set accordingly"); // parse the command line arguments CommandLine line = null; try { line = parser.parse(options, args); } catch (ParseException e1) { System.out.println(e1.getMessage()); System.out.println("Error: Could not parse option parameters."); System.out.println("Use help -h (--help) for information."); System.exit(1); } if (line == null) { System.out.println("Error: Could not parse option parameters."); System.out.println("Use help -h (--help) for information."); System.exit(1); } if (checkInitialParamsPresent(line, options)) System.exit(0); if (!checkSpectrumFile(line)) { System.out.println("Error: Option parameters are not set correctly."); System.out.println("Use help -h (--help) for information."); System.exit(1); } if (!parseSpectrumFile(spectrumfile)) { System.out.println("Error: Could not correctly parse the spectrum data file."); System.out.println("Use help -h (--help) for information."); System.exit(1); } int successfulSet = setParameters(line, options); if (successfulSet == 2) System.exit(0); if (successfulSet != 0) { System.out.println("Error: Option parameters are not set correctly."); System.out.println("Use help -h (--help) for information."); System.exit(1); } boolean successfulChecked = true; if (successfulSet == 0) successfulChecked = checkParameters(); if (saveParametersIsSet) { try { BufferedWriter bwriter = new BufferedWriter(new FileWriter(new File( resultspath + System.getProperty("file.separator") + "parameters_" + sampleName + ".txt"))); bwriter.write(getParameters()); bwriter.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } try { boolean isPositive = true; if (charge.getValue() == 2) isPositive = false; spec = new WrapperSpectrum(peaksString, mode.getValueWithOffset(), exactMass.getValue(), isPositive); } catch (Exception e) { System.out.println("Error: Could not parse spectrum correctly. Check the given peak list."); System.exit(1); } if (!successfulChecked) { System.out.println("Error: Option parameters are not set correctly."); System.out.println("Use help -h (--help) for information."); System.exit(1); } List<MetFragResult> results = null; String pathToStoreFrags = ""; if (storeFragments) pathToStoreFrags = resultspath; //run metfrag when all checks were successful if (usesdf) { try { if (verbose) { System.out.println("start fragmenter with local database"); System.out.println("using database " + database); } results = MetFrag.startConvenienceSDF(spec, mzabs.getValue(), mzppm.getValue(), searchppm.getValue(), true, breakRings, treeDepth.getValue(), true, true, true, false, Integer.MAX_VALUE, true, sdfFile, "", null, searchppmIsSet, pathToStoreFrags, numberThreads.getValue(), verbose, sampleName, onlyBiologicalCompounds); } catch (Exception e) { System.out.println("Error: " + e.getMessage()); System.out.println("Error: Could not perform in silico fragmentation step."); System.exit(1); } } else { try { if (verbose) { if (!localdbIsSet) System.out.println("start fragmenter with web database"); else System.out.println("start fragmenter with local database"); System.out.println("using database " + database); } results = MetFrag.startConvenience(database, databaseIDs, formula, exactMass.getValue(), spec, useProxy, mzabs.getValue(), mzppm.getValue(), searchppm.getValue(), true, breakRings, treeDepth.getValue(), true, false, true, false, startindex.getValue(), endindex.getValue(), true, pathToStoreFrags, numberThreads.getValue(), chemSpiderToken, verbose, sampleName, localdb, onlyBiologicalCompounds, dblink, dbuser, dbpass, uniquebyinchi); } catch (Exception e) { e.printStackTrace(); System.out.println("Error: " + e.getMessage()); System.out.println("Error: Could not perform in silico fragmentation step."); System.exit(1); } } saveResults(results); }
From source file:com.genentech.chemistry.openEye.apps.enumerate.SDFEnumerator.java
public static void main(String... args) throws IOException { Options options = new Options(); Option opt = new Option("out", true, "output file oe-supported"); opt.setRequired(true);//from w w w . j a va 2s . co m options.addOption(opt); opt = new Option("hydrogenExplicit", false, "Use explicit hydrogens"); options.addOption(opt); opt = new Option("correctValences", false, "Correct valences after the enumeration"); options.addOption(opt); opt = new Option("regenerate2D", false, "Regenerate 2D coordinates for the products"); options.addOption(opt); opt = new Option("reactAllSites", false, "Generate a product for each match in a reagent."); options.addOption(opt); opt = new Option("randomFraction", true, "Only output a fraction of the products."); options.addOption(opt); opt = new Option("maxAtoms", true, "Only output products with <= maxAtoms."); options.addOption(opt); opt = new Option("notReacted", true, "Output file for reagents that didn't produce at leaste one output molecule, useful for debugging SMIRKS."); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp("", options); } args = cmd.getArgs(); if (args.length < 2) { exitWithHelp("Transformation and/or reagentFiles missing", options); } String smirks = args[0]; if (new File(smirks).canRead()) smirks = IOUtil.fileToString(smirks).trim(); if (!smirks.contains(">>")) smirks = scaffoldToSmirks(smirks); String[] reagentSmiOrFiles = Arrays.copyOfRange(args, 1, args.length); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String outFile = cmd.getOptionValue("out"); OELibraryGen lg = new OELibraryGen(); lg.Init(smirks); if (!lg.IsValid()) exitWithHelp("Invalid Transform: " + smirks, options); lg.SetExplicitHydrogens(cmd.hasOption("hydrogenExplicit")); lg.SetValenceCorrection(cmd.hasOption("correctValences")); lg.SetRemoveUnmappedFragments(true); boolean regenerate2D = cmd.hasOption("regenerate2D"); boolean reactAllSites = cmd.hasOption("reactAllSites"); String unreactedFile = null; if (cmd.hasOption("notReacted")) { unreactedFile = cmd.getOptionValue("notReacted"); } double randomFract = 2; if (cmd.hasOption("randomFraction")) randomFract = Double.parseDouble(cmd.getOptionValue("randomFraction")); int maxAtoms = 0; if (cmd.hasOption("maxAtoms")) maxAtoms = Integer.parseInt(cmd.getOptionValue("maxAtoms")); SDFEnumerator en = new SDFEnumerator(lg, reactAllSites, reagentSmiOrFiles); en.generateLibrary(outFile, maxAtoms, randomFract, regenerate2D, unreactedFile); en.delete(); }
From source file:com.cyberway.issue.io.Arc2Warc.java
/** * Command-line interface to Arc2Warc.//from w ww . ja v a 2 s.c om * * @param args Command-line arguments. * @throws ParseException Failed parse of the command line. * @throws IOException * @throws java.text.ParseException */ public static void main(String[] args) throws ParseException, IOException, java.text.ParseException { Options options = new Options(); options.addOption(new Option("h", "help", false, "Prints this message and exits.")); options.addOption(new Option("f", "force", false, "Force overwrite of target file.")); PosixParser parser = new PosixParser(); CommandLine cmdline = parser.parse(options, args, false); List cmdlineArgs = cmdline.getArgList(); Option[] cmdlineOptions = cmdline.getOptions(); HelpFormatter formatter = new HelpFormatter(); // If no args, print help. if (cmdlineArgs.size() <= 0) { usage(formatter, options, 0); } // Now look at options passed. boolean force = false; for (int i = 0; i < cmdlineOptions.length; i++) { switch (cmdlineOptions[i].getId()) { case 'h': usage(formatter, options, 0); break; case 'f': force = true; break; default: throw new RuntimeException("Unexpected option: " + +cmdlineOptions[i].getId()); } } // If no args, print help. if (cmdlineArgs.size() != 2) { usage(formatter, options, 0); } (new Arc2Warc()).transform(new File(cmdlineArgs.get(0).toString()), new File(cmdlineArgs.get(1).toString()), force); }
From source file:net.bobah.mail.Dupes.java
public static void main(String[] args) throws Exception { installDefaultUncaughtExceptionHandler(log); final CommandLineParser parser = new PosixParser(); final Options options = new Options() .addOption("j", "threads", true, "number of parallel threads to use for analyzing") .addOption("hash", true, "hash function to use, possible values: " + Arrays.toString(Hashes.values())) .addOption("dir", true, "add directory to search"); final CommandLine cmdline = parser.parse(options, args); final int threads = Integer.valueOf( cmdline.getOptionValue("threads", String.valueOf(Runtime.getRuntime().availableProcessors()))); final HashFunction hash = Hashes.valueOf(cmdline.getOptionValue("hash", "adler32")).hashfunc; final File[] dirs = Collections2 .transform(Arrays.asList(cmdline.getOptionValues("dir")), new Function<String, File>() { @Override//from w w w .ja va 2 s. co m public File apply(String from) { return new File(from); } }).toArray(new File[] {}); log.info("hash: {}, threads: {}, dirs: {} in total", hash, threads, dirs.length); try { new Dupes(threads, hash, dirs).run(); } finally { Utils.shutdownLogger(); } }
From source file:com.ict.dtube.tools.command.MQAdminStartup.java
public static void main(String[] args) { System.setProperty(RemotingCommand.RemotingVersionKey, Integer.toString(MQVersion.CurrentVersion)); try {/*from www . j ava 2 s.c o m*/ initLogback(); switch (args.length) { case 0: printHelp(); break; case 2: if (args[0].equals("help")) { SubCommand cmd = findSubCommand(args[1]); if (cmd != null) { Options options = ServerUtil.buildCommandlineOptions(new Options()); options = cmd.buildCommandlineOptions(options); if (options != null) { ServerUtil.printCommandLineHelp("mqadmin " + cmd.commandName(), options); } } else { System.out.println("The sub command \'" + args[1] + "\' not exist."); } break; } case 1: default: SubCommand cmd = findSubCommand(args[0]); if (cmd != null) { // mainargs?args? String[] subargs = parseSubArgs(args); // ? Options options = ServerUtil.buildCommandlineOptions(new Options()); final CommandLine commandLine = ServerUtil.parseCmdLine("mqadmin " + cmd.commandName(), subargs, cmd.buildCommandlineOptions(options), new PosixParser()); if (null == commandLine) { System.exit(-1); return; } if (commandLine.hasOption('n')) { String namesrvAddr = commandLine.getOptionValue('n'); System.setProperty(MixAll.NAMESRV_ADDR_PROPERTY, namesrvAddr); } cmd.execute(commandLine, options); } else { System.out.println("The sub command \'" + args[0] + "\' not exist."); } break; } } catch (Exception e) { e.printStackTrace(); } }
From source file:eqtlmappingpipeline.util.ModuleEqtWestraReplication.java
/** * @param args the command line arguments *//*from w ww . j a v a 2s.c om*/ 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:com.cws.esolutions.security.main.PasswordUtility.java
public static void main(final String[] args) { final String methodName = PasswordUtility.CNAME + "#main(final String[] args)"; if (DEBUG) {// w w w .j a v a 2 s . c om DEBUGGER.debug("Value: {}", methodName); } if (args.length == 0) { HelpFormatter usage = new HelpFormatter(); usage.printHelp(PasswordUtility.CNAME, options, true); System.exit(1); } BufferedReader bReader = null; BufferedWriter bWriter = null; try { // load service config first !! SecurityServiceInitializer.initializeService(PasswordUtility.SEC_CONFIG, PasswordUtility.LOG_CONFIG, false); if (DEBUG) { DEBUGGER.debug("Options options: {}", options); for (String arg : args) { DEBUGGER.debug("Value: {}", arg); } } CommandLineParser parser = new PosixParser(); CommandLine commandLine = parser.parse(options, args); if (DEBUG) { DEBUGGER.debug("CommandLineParser parser: {}", parser); DEBUGGER.debug("CommandLine commandLine: {}", commandLine); DEBUGGER.debug("CommandLine commandLine.getOptions(): {}", (Object[]) commandLine.getOptions()); DEBUGGER.debug("CommandLine commandLine.getArgList(): {}", commandLine.getArgList()); } final SecurityConfigurationData secConfigData = PasswordUtility.svcBean.getConfigData(); final SecurityConfig secConfig = secConfigData.getSecurityConfig(); final PasswordRepositoryConfig repoConfig = secConfigData.getPasswordRepo(); final SystemConfig systemConfig = secConfigData.getSystemConfig(); if (DEBUG) { DEBUGGER.debug("SecurityConfigurationData secConfig: {}", secConfigData); DEBUGGER.debug("SecurityConfig secConfig: {}", secConfig); DEBUGGER.debug("RepositoryConfig secConfig: {}", repoConfig); DEBUGGER.debug("SystemConfig systemConfig: {}", systemConfig); } if (commandLine.hasOption("encrypt")) { if ((StringUtils.isBlank(repoConfig.getPasswordFile())) || (StringUtils.isBlank(repoConfig.getSaltFile()))) { System.err.println("The password/salt files are not configured. Entries will not be stored!"); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } final String entryName = commandLine.getOptionValue("entry"); final String username = commandLine.getOptionValue("username"); final String password = commandLine.getOptionValue("password"); final String salt = RandomStringUtils.randomAlphanumeric(secConfig.getSaltLength()); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); DEBUGGER.debug("String password: {}", password); DEBUGGER.debug("String salt: {}", salt); } final String encodedSalt = PasswordUtils.base64Encode(salt); final String encodedUserName = PasswordUtils.base64Encode(username); final String encryptedPassword = PasswordUtils.encryptText(password, salt, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); final String encodedPassword = PasswordUtils.base64Encode(encryptedPassword); if (DEBUG) { DEBUGGER.debug("String encodedSalt: {}", encodedSalt); DEBUGGER.debug("String encodedUserName: {}", encodedUserName); DEBUGGER.debug("String encodedPassword: {}", encodedPassword); } if (commandLine.hasOption("store")) { try { new File(passwordFile.getParent()).mkdirs(); new File(saltFile.getParent()).mkdirs(); boolean saltFileExists = (saltFile.exists()) ? true : saltFile.createNewFile(); if (DEBUG) { DEBUGGER.debug("saltFileExists: {}", saltFileExists); } // write the salt out first if (!(saltFileExists)) { throw new IOException("Unable to create salt file"); } boolean passwordFileExists = (passwordFile.exists()) ? true : passwordFile.createNewFile(); if (!(passwordFileExists)) { throw new IOException("Unable to create password file"); } if (commandLine.hasOption("replace")) { File[] files = new File[] { saltFile, passwordFile }; if (DEBUG) { DEBUGGER.debug("File[] files: {}", (Object) files); } for (File file : files) { if (DEBUG) { DEBUGGER.debug("File: {}", file); } String currentLine = null; File tmpFile = new File(FileUtils.getTempDirectory() + "/" + "tmpFile"); if (DEBUG) { DEBUGGER.debug("File tmpFile: {}", tmpFile); } bReader = new BufferedReader(new FileReader(file)); bWriter = new BufferedWriter(new FileWriter(tmpFile)); while ((currentLine = bReader.readLine()) != null) { if (!(StringUtils.equals(currentLine.trim().split(",")[0], entryName))) { bWriter.write(currentLine + System.getProperty("line.separator")); bWriter.flush(); } } bWriter.close(); FileUtils.deleteQuietly(file); FileUtils.copyFile(tmpFile, file); FileUtils.deleteQuietly(tmpFile); } } FileUtils.writeStringToFile(saltFile, entryName + "," + encodedUserName + "," + encodedSalt + System.getProperty("line.separator"), true); FileUtils.writeStringToFile(passwordFile, entryName + "," + encodedUserName + "," + encodedPassword + System.getProperty("line.separator"), true); } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); } } System.out.println("Entry Name " + entryName + " stored."); } if (commandLine.hasOption("decrypt")) { String saltEntryName = null; String saltEntryValue = null; String decryptedPassword = null; String passwordEntryName = null; if ((StringUtils.isEmpty(commandLine.getOptionValue("entry")) && (StringUtils.isEmpty(commandLine.getOptionValue("username"))))) { throw new ParseException("No entry or username was provided to decrypt."); } if (StringUtils.isEmpty(commandLine.getOptionValue("username"))) { throw new ParseException("no entry provided to decrypt"); } String entryName = commandLine.getOptionValue("entry"); String username = commandLine.getOptionValue("username"); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } if ((!(saltFile.canRead())) || (!(passwordFile.canRead()))) { throw new IOException( "Unable to read configured password/salt file. Please check configuration and/or permissions."); } for (String lineEntry : FileUtils.readLines(saltFile, systemConfig.getEncoding())) { saltEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String saltEntryName: {}", saltEntryName); } if (StringUtils.equals(saltEntryName, entryName)) { saltEntryValue = PasswordUtils.base64Decode(lineEntry.split(",")[2]); break; } } if (StringUtils.isEmpty(saltEntryValue)) { throw new SecurityException("No entries were found that matched the provided information"); } for (String lineEntry : FileUtils.readLines(passwordFile, systemConfig.getEncoding())) { passwordEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String passwordEntryName: {}", passwordEntryName); } if (StringUtils.equals(passwordEntryName, saltEntryName)) { String decodedPassword = PasswordUtils.base64Decode(lineEntry.split(",")[2]); decryptedPassword = PasswordUtils.decryptText(decodedPassword, saltEntryValue, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); break; } } if (StringUtils.isEmpty(decryptedPassword)) { throw new SecurityException("No entries were found that matched the provided information"); } System.out.println(decryptedPassword); } else if (commandLine.hasOption("encode")) { System.out.println(PasswordUtils.base64Encode((String) commandLine.getArgList().get(0))); } else if (commandLine.hasOption("decode")) { System.out.println(PasswordUtils.base64Decode((String) commandLine.getArgList().get(0))); } } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); System.err.println("An error occurred during processing: " + iox.getMessage()); System.exit(1); } catch (ParseException px) { ERROR_RECORDER.error(px.getMessage(), px); System.err.println("An error occurred during processing: " + px.getMessage()); System.exit(1); } catch (SecurityException sx) { ERROR_RECORDER.error(sx.getMessage(), sx); System.err.println("An error occurred during processing: " + sx.getMessage()); System.exit(1); } catch (SecurityServiceException ssx) { ERROR_RECORDER.error(ssx.getMessage(), ssx); System.exit(1); } finally { try { if (bReader != null) { bReader.close(); } if (bWriter != null) { bReader.close(); } } catch (IOException iox) { } } System.exit(0); }
From source file:eu.scape_project.droid_identify.DroidIdentification.java
public static void main(String[] args) throws ParseException, IOException, InterruptedException, ClassNotFoundException { CommandLineParser cmdParser = new PosixParser(); DroidCliOptions droidCliOpts = new DroidCliOptions(); appConfig = new DroidCliConfig(); CommandLine cmd = cmdParser.parse(droidCliOpts.options, args); if ((args.length == 0) || (cmd.hasOption(droidCliOpts.HELP_OPT))) { droidCliOpts.exit("Help", 0); } else {//from w w w . ja va2 s. co m droidCliOpts.initOptions(cmd, appConfig); DroidIdentification tc = new DroidIdentification(); if (appConfig.isLocal()) { tc.startApplication(); } else { tc.startHadoopJob(); } } }