Example usage for org.apache.commons.cli CommandLine getOptionValues

List of usage examples for org.apache.commons.cli CommandLine getOptionValues

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Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLine getOptionValues.

Prototype

public String[] getOptionValues(char opt)

Source Link

Document

Retrieves the array of values, if any, of an option.

Usage

From source file:com.github.braully.graph.UtilResultMerge.java

public static void main(String... args) throws Exception {
    Options options = new Options();

    Option input = new Option("i", "input", true, "input file path");
    input.setRequired(false);/*from  w  ww  . ja v  a  2  s .  c  o m*/
    options.addOption(input);

    Option output = new Option("o", "output", true, "output file");
    output.setRequired(false);
    options.addOption(output);

    Option verb = new Option("v", "verbose", false, "verbose");
    output.setRequired(false);
    options.addOption(verb);

    Option exluces = new Option("x", "exclude", true, "exclude operations");
    exluces.setRequired(false);
    options.addOption(exluces);

    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("UtilResult", options);

        System.exit(1);
        return;
    }

    String[] excludes = cmd.getOptionValues("exclude");
    String[] inputs = cmd.getOptionValues("input");
    if (inputs == null) {
        inputs = new String[] {
                "/home/strike/Dropbox/workspace/graph-caratheodory-np3/grafos-processamento/Almost_hypohamiltonian"
                //                "/media/dados/documentos/grafos-processamento/Almost_hypohamiltonian",
                //                "/home/strike/Documentos/grafos-processamento/Cubic",
                //                "/home/strike/Documentos/grafos-processamento/Critical_H-free",
                //                "/home/strike/Documentos/grafos-processamento/Highly_irregular",
                //                "/home/strike/Documentos/grafos-processamento/Hypohamiltonian_graphs",
                //                "/home/strike/Documentos/grafos-processamento/Maximal_triangle-free",
                //                "/home/strike/Documentos/grafos-processamento/Minimal_Ramsey",
                //                "/home/strike/Documentos/grafos-processamento/Strongly_regular",
                //                "/home/strike/Documentos/grafos-processamento/Vertex-transitive",
                //                "/home/strike/Documentos/grafos-processamento/Trees"
        };
        excludes = new String[] { "carathe" };
        verbose = true;
    }

    if (cmd.hasOption(verb.getOpt())) {
        verbose = true;
    }

    if (inputs != null) {
        processInputs(inputs, excludes);
    }
}

From source file:com.act.lcms.db.analysis.BestMoleculesPickerFromLCMSIonAnalysis.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*from w ww. j av  a  2  s. co  m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        HELP_FORMATTER.printHelp(BestMoleculesPickerFromLCMSIonAnalysis.class.getCanonicalName(), HELP_MESSAGE,
                opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(BestMoleculesPickerFromLCMSIonAnalysis.class.getCanonicalName(), HELP_MESSAGE,
                opts, null, true);
        System.exit(1);
    }

    List<String> positiveReplicateResults = new ArrayList<>(
            Arrays.asList(cl.getOptionValues(OPTION_INPUT_FILES)));

    if (cl.hasOption(OPTION_MIN_OF_REPLICATES)) {
        HitOrMissReplicateFilterAndTransformer transformer = new HitOrMissReplicateFilterAndTransformer();

        List<IonAnalysisInterchangeModel> models = positiveReplicateResults.stream().map(file -> {
            try {
                return IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile(file);
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
        }).collect(Collectors.toList());

        IonAnalysisInterchangeModel transformedModel = IonAnalysisInterchangeModel
                .filterAndOperateOnMoleculesFromMultipleReplicateModels(models, transformer);

        printInchisAndIonsToFile(transformedModel, cl.getOptionValue(OPTION_OUTPUT_FILE),
                cl.hasOption(OPTION_JSON_FORMAT));
        return;
    }

    Double minSnrThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_SNR_THRESHOLD));
    Double minIntensityThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_INTENSITY_THRESHOLD));
    Double minTimeThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_TIME_THRESHOLD));

    if (cl.hasOption(OPTION_GET_IONS_SUPERSET)) {
        List<IonAnalysisInterchangeModel> models = positiveReplicateResults.stream().map(file -> {
            try {
                return IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile(file);
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
        }).collect(Collectors.toList());

        IonAnalysisInterchangeModel transformedModel = IonAnalysisInterchangeModel
                .getSupersetOfIonicVariants(models, minSnrThreshold, minIntensityThreshold, minTimeThreshold);

        printInchisAndIonsToFile(transformedModel, cl.getOptionValue(OPTION_OUTPUT_FILE),
                cl.hasOption(OPTION_JSON_FORMAT));
        return;
    }

    if (cl.hasOption(OPTION_THRESHOLD_ANALYSIS)) {

        if (positiveReplicateResults.size() > 1) {
            LOGGER.error("Since this is a threshold analysis, the number of positive replicates should be 1.");
            System.exit(1);
        }

        // We need to set this variable as a final since it is used in a lambda function below.
        final Set<String> ions = new HashSet<>();
        if (cl.hasOption(OPTION_FILTER_BY_IONS)) {
            ions.addAll(Arrays.asList(cl.getOptionValues(OPTION_FILTER_BY_IONS)));
        }

        HitOrMissSingleSampleFilterAndTransformer hitOrMissSingleSampleTransformer = new HitOrMissSingleSampleFilterAndTransformer(
                minIntensityThreshold, minSnrThreshold, minTimeThreshold, ions);

        IonAnalysisInterchangeModel model = IonAnalysisInterchangeModel.filterAndOperateOnMoleculesFromModel(
                IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile(
                        positiveReplicateResults.get(0)),
                hitOrMissSingleSampleTransformer);

        printInchisAndIonsToFile(model, cl.getOptionValue(OPTION_OUTPUT_FILE),
                cl.hasOption(OPTION_JSON_FORMAT));
    }
}

From source file:com.ctriposs.rest4j.tools.snapshot.gen.Rest4JSnapshotExporterCmdLineApp.java

/**
 * @param args rest4jexporter -sourcepath sourcepath -resourcepackages packagenames [-name api_name] [-outdir outdir]
 *//*w  w  w  .  j a v  a  2s.  co  m*/
public static void main(String[] args) {
    CommandLine cl = null;
    try {
        final CommandLineParser parser = new GnuParser();
        cl = parser.parse(OPTIONS, args);
    } catch (ParseException e) {
        System.err.println("Invalid arguments: " + e.getMessage());
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(
                "rest4jexporter -sourcepath sourcepath [-resourcepackages packagenames] [-resourceclasses classnames]"
                        + "[-name api_name] [-outdir outdir]",
                OPTIONS);
        System.exit(0);
    }

    final String resolverPath = System.getProperty(AbstractGenerator.GENERATOR_RESOLVER_PATH);

    try {
        final Rest4JSnapshotExporter exporter = new Rest4JSnapshotExporter();
        exporter.setResolverPath(resolverPath);
        exporter.export(cl.getOptionValue("name"), null, cl.getOptionValues("sourcepath"),
                cl.getOptionValues("resourcepackages"), cl.getOptionValues("resourceClasses"),
                cl.getOptionValue("outdir", "."));
    } catch (Throwable e) {
        log.error("Error writing Snapshot files", e);
        System.out.println("Error writing Snapshot files:\n" + e);
        System.exit(1);
    }
}

From source file:com.linkedin.restli.tools.snapshot.gen.RestLiSnapshotExporterCmdLineApp.java

/**
 * @param args restliexporter -sourcepath sourcepath -resourcepackages packagenames [-name api_name] [-outdir outdir]
 *//*from ww w .jav  a 2  s  .  co m*/
public static void main(String[] args) {
    CommandLine cl = null;
    try {
        final CommandLineParser parser = new GnuParser();
        cl = parser.parse(OPTIONS, args);
    } catch (ParseException e) {
        System.err.println("Invalid arguments: " + e.getMessage());
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(
                "restliexporter -sourcepath sourcepath [-resourcepackages packagenames] [-resourceclasses classnames]"
                        + "[-name api_name] [-outdir outdir]",
                OPTIONS);
        System.exit(0);
    }

    final String resolverPath = System.getProperty(AbstractGenerator.GENERATOR_RESOLVER_PATH);

    try {
        final RestLiSnapshotExporter exporter = new RestLiSnapshotExporter();
        exporter.setResolverPath(resolverPath);
        exporter.export(cl.getOptionValue("name"), null, cl.getOptionValues("sourcepath"),
                cl.getOptionValues("resourcepackages"), cl.getOptionValues("resourceClasses"),
                cl.getOptionValue("outdir", "."),
                AdditionalDocProvidersUtil.findDocProviders(log, cl.hasOption("loadAdditionalDocProviders")));
    } catch (Throwable e) {
        log.error("Error writing Snapshot files", e);
        System.out.println("Error writing Snapshot files:\n" + e);
        System.exit(1);
    }
}

From source file:com.act.biointerpretation.analytics.ReactionCountProvenance.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*w  w w  .  j  a  v a  2  s  .c o m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        LOGGER.error(String.format("Argument parsing failed: %s\n", e.getMessage()));
        HELP_FORMATTER.printHelp(ReactionCountProvenance.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionCountProvenance.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    if (!cl.hasOption(OPTION_OUTPUT_PREFIX)) {
        LOGGER.error("Input -o prefix");
        return;
    }

    List<String> dbs = new ArrayList<>(Arrays.asList(cl.getOptionValues(OPTION_ORDERED_LIST_OF_DBS)));
    ReactionCountProvenance reactionCountProvenance = new ReactionCountProvenance(dbs,
            cl.getOptionValue(OPTION_OUTPUT_PREFIX));
    reactionCountProvenance.run();
    reactionCountProvenance.writeToDisk();
}

From source file:eqtlmappingpipeline.util.ModuleEqtlGeuvadisReplication.java

/**
 * @param args the command line arguments
 *///from w  w  w  . j ava  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<EQTL>> replicationQtls = new QTLTextFile(replicationQtlFilePath, false)
            .readQtlsAsTreeMap();

    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;
        }

        EQTL bestMatch = null;
        double bestMatchR2 = Double.NaN;
        Ld bestMatchLd = null;
        double nextBestR2 = Double.NaN;

        ArrayList<EQTL> sameSnpQtls = replicationQtls.get(chr, pos);

        if (sameSnpQtls != null) {
            for (EQTL sameSnpQtl : sameSnpQtls) {
                if (sameSnpQtl.getProbe().equals(gene)) {
                    bestMatch = sameSnpQtl;
                    bestMatchR2 = 1;
                }
            }
        }

        NavigableMap<Integer, ArrayList<EQTL>> potentionalReplicationQtls = replicationQtls.getChrRange(chr,
                pos - window, true, pos + window, true);

        for (ArrayList<EQTL> potentialReplicationQtls : potentionalReplicationQtls.values()) {

            for (EQTL potentialReplicationQtl : potentialReplicationQtls) {

                if (!potentialReplicationQtl.getProbe().equals(gene)) {
                    continue;
                }

                GeneticVariant potentialReplicationQtlVariant = genotypeData.getSnpVariantByPos(
                        potentialReplicationQtl.getRsChr().toString(), potentialReplicationQtl.getRsChrPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getRsChr().toString() + ":"
                            + potentialReplicationQtl.getRsChrPos());
                    ++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.getZscore();
            replicationAlleleAssessed = bestMatch.getAlleleAssessed();

            if (pos != bestMatch.getRsChrPos()) {

                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.getAlleleAssessed());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getRsChrPos()));
        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:lee.util.jtap.JTapCli.java

/**
 * @param args//from  w  ww  . ja va  2s. c  o  m
 */
public static void main(String[] args) {
    Options options = constructOptions();

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println("Cmd Parsing Error:   " + e.getMessage());
        JTapCli.printHelp(options);
    }
    String resultMessage = "Done.";
    if (cmd.hasOption("dumpkeys")) {
        resultMessage = JTapCli.dumpKeys();
    } else if (cmd.hasOption("dumpall")) {
        resultMessage = JTapCli.dumpAll();
    } else if (cmd.hasOption("s") || cmd.hasOption("session")) {
        HashMap<String, String> argsMap = getMappedArgs(cmd, "host", "bucket", "password", "port");
        resultMessage = ">> " + JTapCli.setSession(argsMap);
    } else if (cmd.hasOption("dk") || cmd.hasOption("deletekey")) {
        resultMessage = JTapCli.deleteKey(cmd.getOptionValues("dk"));
    } else if (cmd.hasOption("gk") || cmd.hasOption("getkey")) {
        resultMessage = JTapCli.dumpKey(cmd.getOptionValues("gk"));
    } else if (cmd.hasOption("cs") || cmd.hasOption("clearsession")) {
        boolean removed = JTapCli.session.delete();
        if (removed) {
            System.out
                    .println("Saved session data has been cleared. To set the values again call with -session");
        }
    } else {
        JTapCli.printHelp(options);
        resultMessage = "";
    }
    System.out.println(resultMessage);
    return;
}

From source file:tuit.java

@SuppressWarnings("ConstantConditions")
public static void main(String[] args) {
    System.out.println(licence);//from   w  w  w  .j a va  2  s . co  m
    //Declare variables
    File inputFile;
    File outputFile;
    File tmpDir;
    File blastnExecutable;
    File properties;
    File blastOutputFile = null;
    //
    TUITPropertiesLoader tuitPropertiesLoader;
    TUITProperties tuitProperties;
    //
    String[] parameters = null;
    //
    Connection connection = null;
    MySQL_Connector mySQL_connector;
    //
    Map<Ranks, TUITCutoffSet> cutoffMap;
    //
    BLASTIdentifier blastIdentifier = null;
    //
    RamDb ramDb = null;

    CommandLineParser parser = new GnuParser();
    Options options = new Options();

    options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)");
    options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)");
    options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)");
    options.addOption(tuit.V, "verbose", false, "Enable verbose output");
    options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output");
    options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases");
    options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases");
    options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy");

    Option option = new Option(tuit.REDUCE, "reduce", true,
            "Pack identical (100% similar sequences) records in the given sample file");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    option = new Option(tuit.COMBINE, "combine", true,
            "Combine a set of given reduction files into an HMP Tree-compatible taxonomy");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    options.addOption(tuit.NORMALIZE, "normalize", false,
            "If used in combination with -combine ensures that the values are normalized by the root value");

    HelpFormatter formatter = new HelpFormatter();

    try {

        //Get TUIT directory
        final File tuitDir = new File(
                new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
                        .getParent());
        final File ramDbFile = new File(tuitDir, tuit.RAM_DB);

        //Setup logger
        Log.getInstance().setLogName("tuit.log");

        //Read command line
        final CommandLine commandLine = parser.parse(options, args, true);

        //Check if the REDUCE option is on
        if (commandLine.hasOption(tuit.REDUCE)) {

            final String[] fileList = commandLine.getOptionValues(tuit.REDUCE);
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "...");
                final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor
                        .fromPath(path);
                ReductorFileOperator.save(nucleotideFastaSequenceReductor,
                        path.resolveSibling(path.getFileName().toString() + ".rdc"));
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Check if COMBINE is on
        if (commandLine.hasOption(tuit.COMBINE)) {
            final boolean normalize = commandLine.hasOption(tuit.NORMALIZE);
            final String[] fileList = commandLine.getOptionValues(tuit.COMBINE);
            //TODO: implement a test for format here

            final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>();
            final TreeFormatter treeFormatter = TreeFormatter
                    .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat());
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "...");
                treeFormatter.loadFromPath(path);
                final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput
                        .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf(".")));
                hmpTreesOutputs.add(output);
                treeFormatter.erase();
            }
            final Path destination;
            if (commandLine.hasOption(OUT)) {
                destination = Paths.get(commandLine.getOptionValue(tuit.OUT));
            } else {
                destination = Paths.get("merge.tcf");
            }
            CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination);
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        if (!commandLine.hasOption(tuit.P)) {
            throw new ParseException("No properties file option found, exiting.");
        } else {
            properties = new File(commandLine.getOptionValue(tuit.P));
        }

        //Load properties
        tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties);
        tuitProperties = tuitPropertiesLoader.getTuitProperties();

        //Create tmp directory and blastn executable
        tmpDir = new File(tuitProperties.getTMPDir().getPath());
        blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath());

        //Check for deploy
        if (commandLine.hasOption(tuit.DEPLOY)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir);
            } else {
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }
        //Check for update
        if (commandLine.hasOption(tuit.UPDATE)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir);
            } else {
                //No need to specify a different way to update the database other than just deploy in case of the RAM database
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Connect to the database
        if (commandLine.hasOption(tuit.USE_DB)) {
            mySQL_connector = MySQL_Connector.newDefaultInstance(
                    "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/",
                    tuitProperties.getDBConnection().getLogin().trim(),
                    tuitProperties.getDBConnection().getPassword().trim());
            mySQL_connector.connectToDatabase();
            connection = mySQL_connector.getConnection();
        } else {
            //Probe for ram database

            if (ramDbFile.exists() && ramDbFile.canRead()) {
                Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map...");
                try {
                    ramDb = RamDb.loadSelfFromFile(ramDbFile);
                } catch (IOException ie) {
                    if (ie instanceof java.io.InvalidClassException)
                        throw new IOException("The RAM-based taxonomic database needs to be updated.");
                }

            } else {
                Log.getInstance().log(Level.SEVERE,
                        "The RAM database either has not been deployed, or is not accessible."
                                + "Please use the --deploy option and check permissions on the TUIT directory. "
                                + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option.");
                return;
            }
        }

        if (commandLine.hasOption(tuit.B)) {
            blastOutputFile = new File(commandLine.getOptionValue(tuit.B));
            if (!blastOutputFile.exists() || !blastOutputFile.canRead()) {
                throw new Exception("BLAST output file either does not exist, or is not readable.");
            } else if (blastOutputFile.isDirectory()) {
                throw new Exception("BLAST output file points to a directory.");
            }
        }
        //Check vital parameters
        if (!commandLine.hasOption(tuit.IN)) {
            throw new ParseException("No input file option found, exiting.");
        } else {
            inputFile = new File(commandLine.getOptionValue(tuit.IN));
            Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log");
        }
        //Correct the output file option if needed
        if (!commandLine.hasOption(tuit.OUT)) {
            outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT);
        } else {
            outputFile = new File(commandLine.getOptionValue(tuit.OUT));
        }

        //Adjust the output level
        if (commandLine.hasOption(tuit.V)) {
            Log.getInstance().setLevel(Level.FINE);
            Log.getInstance().log(Level.INFO, "Using verbose output for the log");
        } else {
            Log.getInstance().setLevel(Level.INFO);
        }
        //Try all files
        if (inputFile != null) {
            if (!inputFile.exists() || !inputFile.canRead()) {
                throw new Exception("Input file either does not exist, or is not readable.");
            } else if (inputFile.isDirectory()) {
                throw new Exception("Input file points to a directory.");
            }
        }

        if (!properties.exists() || !properties.canRead()) {
            throw new Exception("Properties file either does not exist, or is not readable.");
        } else if (properties.isDirectory()) {
            throw new Exception("Properties file points to a directory.");
        }

        //Create blast parameters
        final StringBuilder stringBuilder = new StringBuilder();
        for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) {
            stringBuilder.append(database.getUse());
            stringBuilder.append(" ");//Gonna insert an extra space for the last database
        }
        String remote;
        String entrez_query;
        if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) {
            remote = "-remote";
            entrez_query = "-entrez_query";
            parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query,
                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue",
                    tuitProperties.getBLASTNParameters().getExpect().getValue() };
        } else {
            if (!commandLine.hasOption(tuit.B)) {
                if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .startsWith("NOT")
                        || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                                .startsWith("ALL")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist",
                            TUITFileOperatorHelper.restrictToEntrez(tmpDir,
                                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()
                                            .toUpperCase().replace("NOT", "OR"))
                                    .getAbsolutePath(),
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .equals("")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads",
                            tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(),
                            /*"-gilist", TUITFileOperatorHelper.restrictToEntrez(
                            tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!!
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                }
            }
        }
        //Prepare a cutoff Map
        if (tuitProperties.getSpecificationParameters() != null
                && tuitProperties.getSpecificationParameters().size() > 0) {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size());
            for (SpecificationParameters specificationParameters : tuitProperties
                    .getSpecificationParameters()) {
                cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()),
                        TUITCutoffSet.newDefaultInstance(
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getPIdentCutoff().getValue()),
                                Double.parseDouble(specificationParameters.getCutoffSet()
                                        .getQueryCoverageCutoff().getValue()),
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getAlpha().getValue())));
            }
        } else {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>();
        }
        final TUITFileOperatorHelper.OutputFormat format;
        if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) {
            format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK;
        } else {
            format = TUITFileOperatorHelper.OutputFormat.TUIT;
        }

        try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator
                .newInstance(format, cutoffMap);) {
            nucleotideFastaTUITFileOperator.setInputFile(inputFile);
            nucleotideFastaTUITFileOperator.setOutputFile(outputFile);
            final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep();
            final boolean cleanup;
            if (cleanupString.equals("no")) {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted.");
                cleanup = true;
            } else {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept.");
                cleanup = false;
            }
            //Create blast identifier
            ExecutorService executorService = Executors.newSingleThreadExecutor();
            if (commandLine.hasOption(tuit.USE_DB)) {

                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection,
                            cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }

            } else {
                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup, ramDb);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup, ramDb);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            }
            Future<?> runnableFuture = executorService.submit(blastIdentifier);
            runnableFuture.get();
            executorService.shutdown();
        }
    } catch (ParseException pe) {
        Log.getInstance().log(Level.SEVERE, (pe.getMessage()));
        formatter.printHelp("tuit", options);
    } catch (SAXException saxe) {
        Log.getInstance().log(Level.SEVERE, saxe.getMessage());
    } catch (FileNotFoundException fnfe) {
        Log.getInstance().log(Level.SEVERE, fnfe.getMessage());
    } catch (TUITPropertyBadFormatException tpbfe) {
        Log.getInstance().log(Level.SEVERE, tpbfe.getMessage());
    } catch (ClassCastException cce) {
        Log.getInstance().log(Level.SEVERE, cce.getMessage());
    } catch (JAXBException jaxbee) {
        Log.getInstance().log(Level.SEVERE,
                "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema.");
    } catch (ClassNotFoundException cnfe) {
        //Probably won't happen unless the library deleted from the .jar
        Log.getInstance().log(Level.SEVERE, cnfe.getMessage());
        //cnfe.printStackTrace();
    } catch (SQLException sqle) {
        Log.getInstance().log(Level.SEVERE,
                "A database communication error occurred with the following message:\n" + sqle.getMessage());
        //sqle.printStackTrace();
        if (sqle.getMessage().contains("Access denied for user")) {
            Log.getInstance().log(Level.SEVERE, "Please use standard database login: "
                    + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password);
        }
    } catch (Exception e) {
        Log.getInstance().log(Level.SEVERE, e.getMessage());
        e.printStackTrace();
    } finally {
        if (connection != null) {
            try {
                connection.close();
            } catch (SQLException sqle) {
                Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle);
            }
        }
        Log.getInstance().log(Level.FINE, "Task done, exiting...");
    }
}

From source file:es.eucm.ead.exporter.ExporterMain.java

@SuppressWarnings("all")
public static void main(String args[]) {

    Options options = new Options();

    Option help = new Option("h", "help", false, "print this message");
    Option quiet = new Option("q", "quiet", false, "be extra quiet");
    Option verbose = new Option("v", "verbose", false, "be extra verbose");

    Option legacy = OptionBuilder.withArgName("s> <t").hasArgs(3)
            .withDescription(//  w  w  w . j a v  a 2 s.c  o m
                    "source is a version 1.x game; must specify\n" + "<simplify> if 'true', simplifies result\n"
                            + "<translate> if 'true', enables translation")
            .withLongOpt("import").create("i");

    Option war = OptionBuilder.withArgName("web-base").hasArg()
            .withDescription("WAR packaging (web app); " + "must specify\n<web-base> the base WAR directory")
            .withLongOpt("war").create("w");

    Option jar = OptionBuilder.withDescription("JAR packaging (desktop)").withLongOpt("jar").create("j");

    Option apk = OptionBuilder.withArgName("props> <adk> <d").hasArgs(3)
            .withDescription("APK packaging (android); must specify \n" + "<props> (a properties file) \n"
                    + "<adk> (location of the ADK to use) \n" + "<deploy> ('true' to install & deploy)")
            .withLongOpt("apk").create("a");

    // EAD option
    Option ead = OptionBuilder.withDescription("EAD packaging (eAdventure)").withLongOpt("ead").create("e");

    options.addOption(legacy);
    options.addOption(help);
    options.addOption(quiet);
    options.addOption(verbose);
    options.addOption(jar);
    options.addOption(war);
    options.addOption(apk);
    options.addOption(ead);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException pe) {
        System.err.println("Error parsing command-line: " + pe.getMessage());
        showHelp(options);
        return;
    }

    // general options

    String[] extras = cmd.getArgs();

    if (cmd.hasOption(help.getOpt()) || extras.length < 2) {
        showHelp(options);
        return;
    }
    if (cmd.hasOption(verbose.getOpt())) {
        verbosity = Verbose;
    }
    if (cmd.hasOption(quiet.getOpt())) {
        verbosity = Quiet;
    }

    // import

    String source = extras[0];

    // optional import step
    if (cmd.hasOption(legacy.getOpt())) {
        String[] values = cmd.getOptionValues(legacy.getOpt());

        AdventureConverter converter = new AdventureConverter();
        if (values.length > 0 && values[0].equalsIgnoreCase("true")) {
            converter.setEnableSimplifications(true);
        }
        if (values.length > 1 && values[1].equalsIgnoreCase("true")) {
            converter.setEnableTranslations(true);
        }

        // set source for next steps to import-target
        source = converter.convert(source, null);
    }

    if (cmd.hasOption(jar.getOpt())) {
        if (checkFilesExist(cmd, options, source)) {
            JarExporter e = new JarExporter();
            e.export(source, extras[1], verbosity.equals(Quiet) ? new QuietStream() : System.err);
        }
    } else if (cmd.hasOption(apk.getOpt())) {
        String[] values = cmd.getOptionValues(apk.getOpt());
        if (checkFilesExist(cmd, options, values[0], values[1], source)) {
            AndroidExporter e = new AndroidExporter();
            Properties props = new Properties();
            File propsFile = new File(values[0]);
            try {
                props.load(new FileReader(propsFile));
                props.setProperty(AndroidExporter.SDK_HOME,
                        props.getProperty(AndroidExporter.SDK_HOME, values[1]));
            } catch (IOException ioe) {
                System.err.println("Could not load properties from " + propsFile.getAbsolutePath());
                return;
            }
            e.export(source, extras[1], props, values.length > 2 && values[2].equalsIgnoreCase("true"));
        }
    } else if (cmd.hasOption(war.getOpt())) {
        if (checkFilesExist(cmd, options, extras[0])) {
            WarExporter e = new WarExporter();
            e.setWarPath(cmd.getOptionValue(war.getOpt()));
            e.export(source, extras[1]);
        }
    } else if (cmd.hasOption(ead.getOpt())) {
        String destiny = extras[1];
        if (!destiny.endsWith(".ead")) {
            destiny += ".ead";
        }
        FileUtils.zip(new File(destiny), new File(source));
    } else {
        showHelp(options);
    }
}

From source file:com.picdrop.security.SecureStoreMain.java

static public void main(String[] args)
        throws ParseException, IOException, FileNotFoundException, NoSuchAlgorithmException,
        CertificateException, KeyStoreException, KeyStoreException, InterruptedException {

    CommandLineParser cliP = new DefaultParser();

    Options ops = generateBasicOptions();
    CommandLine cli = cliP.parse(ops, args);
    HelpFormatter hlp = new HelpFormatter();

    SecureStore ss;/*  w w  w . j  av a  2  s . c  om*/
    String path = ".";

    try {
        if (cli.hasOption("help")) {
            hlp.printHelp("SecureStore", ops);
            System.exit(0);
        }

        if (cli.hasOption("keystore")) {
            path = cli.getOptionValue("keystore", ".");
        }

        if (cli.hasOption("create")) {
            ss = new SecureStore(path, false);
            ss.createKeyStore();
            System.exit(0);
        } else {
            ss = new SecureStore(path, true);
        }

        if (cli.hasOption("list")) {
            Enumeration<String> en = ss.listAlias();
            while (en.hasMoreElements()) {
                System.out.println(en.nextElement());
            }
            System.exit(0);
        }

        if (cli.hasOption("store")) {
            ss.storeValue(cli.getOptionValues("store")[0], cli.getOptionValues("store")[1]);
            ss.writeStore();
            System.exit(0);
        }

        if (cli.hasOption("clear")) {
            ss.deleteValue(cli.getOptionValue("clear"));
            ss.writeStore();
            System.exit(0);
        }
    } finally {
        hlp.printHelp("SecureStore", ops);
        System.exit(0);
    }
}