List of usage examples for org.apache.commons.cli Option getValue
public String getValue()
null if there is no value. From source file:org.jruyi.launcher.Main.java
private static boolean processCommandLines(String[] args) throws Exception { Options options = new Options(); options.addOption("?", "help", false, null); options.addOption("v", "version", false, null); Option o = new Option("D", true, null); o.setArgs(Option.UNLIMITED_VALUES); options.addOption(o);//from ww w . j a v a2 s. c o m options.addOption("r", "run", true, null); CommandLine line = new PosixParser().parse(options, args); Option[] opts = line.getOptions(); for (Option option : opts) { String opt = option.getOpt(); if (opt.equals("?")) { printHelp(); return false; } else if (opt.equals("v")) { MainHolder.INST.printVersion(); return false; } else if (opt.equals("D")) { handleSystemProps(option.getValues()); } else if (opt.equals("r")) { System.setProperty(JRUYI_INST_NAME, option.getValue().trim()); } else throw new Exception("Unknown option: " + option); } return true; }
From source file:org.ldaptive.cli.AbstractCli.java
/** * Reads the options from the supplied command line and returns a properties * containing those options.//from w ww. j a va 2s.c o m * * @param domain to place property names in * @param line command line * * @return properties for each option and value */ protected Properties getPropertiesFromOptions(final String domain, final CommandLine line) { final Properties props = new Properties(); for (Option o : line.getOptions()) { if (o.hasArg()) { // if provider property, split the value // else add the domain to the ldaptive properties if (o.getOpt().equals(OPT_PROVIDER_PROPERTIES)) { final String[] s = o.getValue().split("="); props.setProperty(s[0], s[1]); } else { props.setProperty(domain + o.getOpt(), o.getValue()); } } } return props; }
From source file:org.mitre.ccv.mapred.CompleteCompositionVectors.java
/** * * The JSO data will be the same as {@link org.mitre.ccv.CompleteMatrix#jsonCompleteMatrix}, but the features * will be in a different order. This version, by default sorts, only by entropy values, whereas the * ccv in-memory version sorts by the k-mer natural order (i.e., lexigraphic). * @param argv//w w w. ja va 2 s . c om * @return * @throws java.lang.Exception */ @Override @SuppressWarnings("static-access") // For OptionBuilder public int run(String[] argv) throws Exception { JobConf conf = new JobConf(getConf()); String cli_title = "CompleteCompositionVectorHadoop"; int start = CalculateKmerCounts.DEFAULT_START; int end = CalculateKmerCounts.DEFAULT_END; int topkmers = 0; String input = null; String output = null; String vectorJsonOutput = null; //String kmerJsonOutput = null; boolean cleanLogs = false; /** create the Options */ Options options = new Options(); /** Hadoop Options */ options.addOption( OptionBuilder.withArgName("number").hasArg(true).withDescription("number of maps").create("m")); options.addOption( OptionBuilder.withArgName("number").hasArg(true).withDescription("number of reducers").create("r")); // org.hadoop.util.GenericOptionsParser should captures this, but it doesn't options.addOption(OptionBuilder.withArgName("property=value").hasArg(true).withValueSeparator() .withDescription("use value for given property").create("D")); /** CompleteCompositionVector Options */ options.addOption(OptionBuilder.withArgName("number").hasArg(true) .withDescription("number of top k-mers to use in calculations").create("topKmers")); options.addOption(OptionBuilder.withArgName("start").hasArg(true).withDescription("starting length of tile") .create("start")); options.addOption(OptionBuilder.withArgName("end").hasArg(true).withDescription("ending length of title") .create("end")); options.addOption(OptionBuilder.hasArg(true).withArgName("file") .withDescription("JSON file to write out k-mers to").create("kmersfile")); options.addOption(OptionBuilder.hasArg(true).withArgName("file") .withDescription("JSON file to write out feature vectors to " + "(Overrides kmersout, only one file will be written).") .create("vectorsfile")); options.addOption(OptionBuilder.withArgName("number").hasArg(true) .withDescription("What preference to use: 0-min 1-median 2-avg(min,med): default is median") .create("prefval")); options.addOption(OptionBuilder.withArgName("help").hasArg(false).withDescription("print this message") .create("help")); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); //GenericOptionsParser gop = new GenericOptionsParser(conf, options, argv); GenericOptionsParser gop = new GenericOptionsParser(conf, argv); String[] remaining_args = gop.getRemainingArgs(); // create the parser CommandLineParser parser = new GnuParser(); //CommandLine line = gop.getCommandLine(); String[] other_args = new String[] {}; try { CommandLine line = parser.parse(options, remaining_args); other_args = line.getArgs(); // Make sure there is a parameter left. if (other_args.length == 0) { System.out.println(cli_title); System.out.println("Missing input path!"); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); return -1; } Option[] opts = line.getOptions(); if (line.hasOption("help")) { System.out.println(cli_title); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); return -1; } // could also use line.iterator() for (Option opt : opts) { if (opt.getOpt().equals("m")) { conf.setNumMapTasks(Integer.parseInt(opt.getValue())); } if (opt.getOpt().equals("r")) { conf.setNumReduceTasks(Integer.parseInt(opt.getValue())); } if (opt.getOpt().equals("D")) { // We can have multiple properties we want to set String[] properties = opt.getValues(); for (String property : properties) { String[] keyval = property.split("="); conf.set(keyval[0], keyval[1]); } } if (opt.getOpt().equals("start")) { start = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("end")) { end = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("topKmers")) { topkmers = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("vectorsfile")) { vectorJsonOutput = opt.getValue(); } } } catch (ParseException e) { LOG.warn("options parsing faild: " + e.getMessage()); System.out.println(cli_title); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); } if (start <= 2) { throw new IllegalArgumentException("Value of 'start' argument must be larger than 2"); } input = other_args[0]; if (other_args.length < 2) { output = input + "_" + FileUtils.getSimpleDate(); } else { output = other_args[2]; } /** * Check output path. Either needs to exist as a directory or not exist */ Path outputPath = new Path(output); FileSystem fs = outputPath.getFileSystem(conf); if (!fs.exists(outputPath)) { fs.mkdirs(outputPath); } else if (fs.exists(outputPath) || !fs.getFileStatus(outputPath).isDir()) { LOG.fatal(String.format("Output directory %s already exists", outputPath.makeQualified(fs))); throw new FileAlreadyExistsException( String.format("Output directory %s already exists", outputPath.makeQualified(fs))); } String outputDir = output + Path.SEPARATOR; int res; /** * Zero, CalculateCompositionVectors */ LOG.info("Starting CalculateCompositionVectors Map-Reduce job"); CalculateCompositionVectors cv = new CalculateCompositionVectors(); res = cv.initJob(conf, start, end, input, outputDir + COMPOSITION_VECTORS, cleanLogs); if (res != 0) { LOG.info("CalculateCompositionVectors returned non-zero result!"); return res; } // We can stop now or continue to reduce dimensionallity using RRE or other means /** * First, CalculateKmerCounts */ LOG.info("Starting CalculateKmerCounts Map-Reduce job"); // FastMap option for CalculateKmers!?! CalculateKmerCounts ckc = new CalculateKmerCounts(); res = ckc.initJob(conf, start, end, input, outputDir + KMER_COUNTS); if (res != 0) { LOG.fatal("CalculateKmerCounts returned non-zero result!"); return res; } /** * Second, TotalSequenceLength */ LOG.info("Starting TotalSequenceLength Map-Reduce job"); TotalSequenceLength tsl = new TotalSequenceLength(); res = tsl.initJob(conf, input, outputDir + TOTAL_LENGTH, cleanLogs); if (res != 0) { LOG.fatal("TotalSequenceLength returned non-zero result!"); return res; } int length = tsl.getCount(conf, outputDir + TOTAL_LENGTH); if (length < 3) { LOG.fatal("TotalSequenceLength returned a total sequence length of less than 3."); return -1; } else { LOG.info(String.format("TotalSequenceLength returned a total sequence length of %d.", length)); } /** * Third, CalculateKmerProbabilities */ LOG.info("Starting CalculateKmerProbabilities Map-Reduce job"); CalculateKmerProbabilities ckp = new CalculateKmerProbabilities(); res = ckp.initJob(conf, start, end, length, outputDir + KMER_COUNTS, outputDir + KMER_PROBABILITIES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerProbabilities returned non-zero result!"); return res; } /** * Fourth, InvertKmerProbabilities */ LOG.info("Starting InvertKmerProbabilities Map-Reduce job"); InvertKmerProbabilities ikp = new InvertKmerProbabilities(); res = ikp.initJob(conf, outputDir + KMER_PROBABILITIES, outputDir + INVERTED_KMER_PROBABILITIES, cleanLogs); if (res != 0) { LOG.fatal("InvertKmerProbabilities returned non-zero result!"); return res; } /** * Fifth, CalculateKmerPiValues */ LOG.info("Starting CalculateKmerPiValues Map-Reduce job"); CalculateKmerPiValues kpv = new CalculateKmerPiValues(); res = kpv.initJob(conf, start, end, outputDir + INVERTED_KMER_PROBABILITIES, outputDir + KMER_PI_VALUES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerPiValues returned non-zero result!"); return res; } /** * Sixth,CalculateKmerRevisedRelativeEntropy */ LOG.info("Starting CalculateKmerRevisedRelativeEntropy Map-Reduce job"); CalculateKmerRevisedRelativeEntropy krre = new CalculateKmerRevisedRelativeEntropy(); res = krre.initJob(conf, outputDir + KMER_PI_VALUES, outputDir + COMPOSITION_VECTORS, outputDir + ENTROPY_VALUES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerRevisedRelativeEntropy returned non-zero result!"); return res; } /** * Seventh, SortKmerRevisedRelativeEntropies */ SortKmerRevisedRelativeEntropies srre = new SortKmerRevisedRelativeEntropies(); res = srre.initJob(conf, outputDir + ENTROPY_VALUES, outputDir + SORTED_ENTROPY_VALUES, cleanLogs); if (res != 0) { LOG.fatal("SortKmerRevisedRelativeEntropies returned non-zero result!"); return res; } /** * Eigth, GenerateFeatureVectors * * Generate a flatten list to add to the cache to be distributed to the map-tasks. */ Path listOutputPath = new Path(outputDir + Integer.toString(topkmers) + KMER_ENTROPY_SET); LOG.info(String.format("Loading %d sorted k-mers from %s to %s", topkmers, outputDir + SORTED_ENTROPY_VALUES, listOutputPath.toString())); int num = CompleteCompositionVectorUtils.flattenKmerEntropySequenceFile(conf, topkmers, outputDir + SORTED_ENTROPY_VALUES, listOutputPath.toString(), cleanLogs); if (num != topkmers) { LOG.fatal(String.format("Requested %d k-mers, but got %d. Using %d", topkmers, num, num)); topkmers = num; } GenerateFeatureVectors fv = new GenerateFeatureVectors(); res = fv.initJob(conf, listOutputPath.toString(), topkmers, outputDir + COMPOSITION_VECTORS, outputDir + FEATURE_VECTORS, cleanLogs); if (res != 0) { LOG.fatal("GenerateFeatureVectors returned non-zero result!"); return res; } /** * Save feature vectors, features (k-mers), and properties to a JSON file. * * The data will be the same as {@link org.mitre.ccv.CompleteMatrix#jsonCompleteMatrix}, but the features * will be in a different order. This version, by default sorts, only by entropy values, whereas the * ccv in-memory version sorts by the k-mer natural order (i.e., lexigraphic). */ if (vectorJsonOutput != null && vectorJsonOutput.length() > 0) { LOG.info("Writing features out to " + vectorJsonOutput); CompleteCompositionVectorUtils.featureVectors2Json(conf, start, end, topkmers, outputDir + SORTED_ENTROPY_VALUES, outputDir + FEATURE_VECTORS, vectorJsonOutput); } LOG.info("All done generating complete composition vectors and feature vectors."); return res; }
From source file:org.obiba.bitwise.client.OpenCommand.java
public boolean execute(Option opt, ClientContext context) { BitwiseStoreUtil bwsUtil = BitwiseStoreUtil.getInstance(); //Extract name of store to be opened String newStoreName = opt.getValue(); //Make sure the store name exists if (!(bwsUtil.exists(newStoreName))) { System.out.println("Specified store name doesn't exist.\n"); return false; }// w w w . ja v a 2s. c o m //Close the currently opened store BitwiseStore currentStore = context.getStore(); if (!(currentStore == null)) { currentStore.endTransaction(); currentStore.close(); } //Open the new store BitwiseStore newStore = bwsUtil.open(newStoreName); newStore.startTransaction(); context.setStore(newStore); System.out.println("Switching to store " + newStoreName + "\n"); return false; }
From source file:org.obiba.bitwise.client.PrintRecordCommand.java
public boolean execute(Option opt, ClientContext context) throws ParseException { String str = opt.getValue(); try {//from w ww. ja va2 s . c o m int index = Integer.valueOf(str); BitwiseStore store = context.getStore(); ResultDisplay rd = new ResultDisplay(); rd.setDisplayType(ResultDisplay.DisplayType.PLAIN); //Filter out template fields for (String field : store.getFieldList()) { // if (field.matches(".*_\\d+")) { // continue; // } rd.addField(field); } rd.putRecord(store, index); System.out.println(rd.getOutput()); } catch (NumberFormatException e) { throw new ParseException(e.getMessage()); } return false; }
From source file:org.obiba.genobyte.cli.DropCommand.java
public boolean execute(Option opt, CliContext context) throws ParseException { String storeName = opt.getValue(); if (context.getStore() != null) { if (context.getStore().getSampleRecordStore().getStore().getName().equals(storeName + "_samples")) { context.getOutput().println("Closing current store."); context.getStore().close();/*from ww w. j av a 2s .c o m*/ context.clear(); } } context.getOutput().println("Deleting store " + storeName + "."); BitwiseDiskUtil.deleteStores(storeName + "_samples", storeName + "_assays"); return false; }
From source file:org.obiba.genobyte.cli.OpenCommand.java
public boolean execute(Option opt, CliContext context) throws ParseException { String storeName = opt.getValue(); if (context.getStore() != null) { context.getOutput().println("Closing current store."); context.getStore().close();/* ww w . j a v a 2 s.com*/ } context.clear(); context.getOutput().println("Opening store " + storeName + "."); GenotypingStore<?, ?, ?, ?> store = open(storeName); if (store == null) { context.getOutput().println("Store " + storeName + " does not exist"); return false; } context.setStore(store); context.setActiveRecordStore(store.getSampleRecordStore()); return false; }
From source file:org.obiba.genobyte.cli.PrintCommand.java
public boolean execute(Option opt, CliContext context) { String str = opt.getValue(); QueryExecution qe = context.getHistory().resolveQuery(str); if (qe != null) { context.getOutput().println("Store: " + qe.getStore().getStore().getName()); context.getOutput().println("Query: " + qe.getQuery()); context.getOutput().println("Count: " + qe.count()); context.getOutput().println("Results: "); if (qe.count() > 0) { int hits = qe.count(); QueryResult qr = qe.getResult(); for (int i = 0; i < hits; i++) { int hit = qr.hit(i); context.getOutput().print(hit + " "); }/*from w w w . ja v a2s. co m*/ context.getOutput().println(""); } else { context.getOutput().println("Query [" + str + "] produced no result. Nothing to print."); } } else { context.getOutput().println("No query result to print. Execute a query first."); } return false; }
From source file:org.obiba.genobyte.cli.PrintRecordCommand.java
public boolean execute(Option opt, CliContext context) throws ParseException { String str = opt.getValue(); try {/*from w w w .ja va 2s . c o m*/ int index = Integer.valueOf(str); GenotypingRecordStore<?, ?, ?> store = context.getActiveRecordStore(); if (store.getStore().getSize() == 0) { context.getOutput().println("Store is empty. To load records, use the --load command."); } else if (index < 0 || index >= store.getStore().getSize()) { context.getOutput().println( "Record index invalid. Value must be between 0 and " + (store.getStore().getSize() - 1)); } else { context.getOutput().println(store.getRecordManager().load(index)); } } catch (NumberFormatException e) { context.getOutput().println("Record index invalid. The argument to this command should be an integer."); } return false; }
From source file:org.obiba.illumina.bitwise.client.CreateStoreCommand.java
public boolean execute(Option opt, CliContext context) throws ParseException { if (context.getStore() != null) { context.getOutput().println("Closing current store."); context.getStore().close();// w ww . j av a 2s.c o m context.clear(); } String name = opt.getValue(); AnnotationStoreSchemaBuilder schemaBuilder = new AnnotationStoreSchemaBuilder(); BitwiseStore samples; BitwiseStore assays; try { String samplesName = name + "_samples"; if (BitwiseStoreUtil.getInstance().exists(samplesName) == true) { context.getOutput().println("A store named " + name + " already exists. Either use the existing store or delete it to create a new store with that name."); return false; } context.getOutput().println("Creating store " + name + "."); samples = BitwiseStoreUtil.getInstance().create(name + "_samples", schemaBuilder.createSchema(Sample.class), 0); assays = BitwiseStoreUtil.getInstance().create(name + "_assays", schemaBuilder.createSchema(Assay.class), 0); } catch (Exception e) { context.getOutput() .println("An unexpected error occured while creating store [" + name + "]: " + e.getMessage()); e.printStackTrace(context.getOutput()); return false; } context.setStore(new InfiniumGenotypingStore(samples, assays)); context.setActiveRecordStore(context.getStore().getSampleRecordStore()); return false; }