Example usage for org.apache.commons.cli CommandLineParser parse

Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLineParser parse.

Prototype

CommandLine parse(Options options, String[] arguments) throws ParseException;

Source Link

Document

Parse the arguments according to the specified options.

Usage

From source file:com.act.biointerpretation.mechanisminspection.ReactionValidator.java

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

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

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

    NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));
    MechanisticValidator validator = new MechanisticValidator(api);
    validator.init();

    Map<Integer, List<Ero>> results = validator
            .validateOneReaction(Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));

    if (results == null) {
        System.out.format("ERROR: validation results are null.\n");
    } else if (results.size() == 0) {
        System.out.format("No matching EROs were found for the specified reaction.\n");
    } else {
        for (Map.Entry<Integer, List<Ero>> entry : results.entrySet()) {
            List<String> eroIds = entry.getValue().stream().map(x -> x.getId().toString())
                    .collect(Collectors.toList());
            System.out.format("%d: %s\n", entry.getKey(), StringUtils.join(eroIds, ", "));
        }
    }
}

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From source file:com.ctriposs.rest4j.tools.idlgen.Rest4JResourceModelExporterCmdLineApp.java

/**
 * @param args rest4jexporter -sourcepath sourcepath -resourcepackages packagenames [-name api_name] [-outdir outdir]
 *///from  w  w w .  j  ava 2s. c o m
public static void main(String[] args) {
    //    args = new String[] {"-name", "groups",
    //                         "-resourcepackages", "com.ctriposs.groups.server.rest1.impl com.ctriposs.groups.server.rest2.impl ",
    //                         "-resourceclasses", "com.ctriposs.groups.server.restX.impl.FooResource",
    //                         "-sourcepath", "src/main/java",
    //                         "-outdir", "src/codegen/idl",
    //                         "-split"};

    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);
    }

    try {
        new Rest4JResourceModelExporter().export(cl.getOptionValue("name"), null,
                cl.getOptionValues("sourcepath"), cl.getOptionValues("resourcepackages"),
                cl.getOptionValues("resourceclasses"), cl.getOptionValue("outdir", "."));
    } catch (Throwable e) {
        log.error("Error writing IDL files", e);
        System.exit(1);
    }
}

---

From source file:it.serasoft.pdi.PDITools.java

public static void main(String[] args) throws Exception {

    Options opts = new Options();

    opts.addOption("report", false, "Generate a report documenting the procedures under analysis");

    opts.addOption("follow", true, "Values: directory, links, none");
    opts.addOption("outDir", true, "Path to output directory where we will write eventual output files");
    opts.addOption("srcDir", true, "Path to base directory containing the PDI processes source");

    CommandLineParser parser = new DefaultParser();
    CommandLine cmdLine = parser.parse(opts, args);

    String outDir = cmdLine.hasOption("outDir") ? cmdLine.getOptionValue("outDir") : null;
    String srcDir = cmdLine.hasOption("srcDir") ? cmdLine.getOptionValue("srcDir") : null;
    String follow = cmdLine.hasOption("follow") ? cmdLine.getOptionValue("follow") : FOLLOW_DIR;
    // Follow links between procedures only if required and recurseSubdir = false (DEFAULT)
    boolean recurseDir = follow.equals(FOLLOW_DIR);
    boolean followLinks = follow.equals(FOLLOW_PROCLINKS);

    startReadingDir(srcDir, recurseDir, followLinks);
}

---

From source file:name.ikysil.beanpathdsl.codegen.CLI.java

/**
 * @param args the command line arguments
 *//*from  w w w.  j  a  v a2  s  .c o m*/
public static void main(String[] args) {
    final Options options = buildOptions();
    try {
        CommandLineParser parser = new DefaultParser();
        CommandLine cmdLine = parser.parse(options, args);
        if (cmdLine.hasOption("h")) {
            usage(options);
            System.exit(1);
        }
        Configuration configuration = new Configuration();
        if (cmdLine.hasOption("s")) {
            configuration.setOutputDirectory(cmdLine.getOptionValue("s"));
        }
        if (cmdLine.hasOption("c")) {
            configuration.setOutputCharset(Charset.forName(cmdLine.getOptionValue("c")));
        }
        if (cmdLine.hasOption("cnp")) {
            configuration.setClassNamePrefix(cmdLine.getOptionValue("cnp"));
        }
        if (cmdLine.hasOption("cns")) {
            configuration.setClassNameSuffix(cmdLine.getOptionValue("cns"));
        }
        if (cmdLine.hasOption("pnp")) {
            configuration.setPackageNamePrefix(cmdLine.getOptionValue("pnp"));
        }
        if (cmdLine.hasOption("pns")) {
            configuration.setPackageNameSuffix(cmdLine.getOptionValue("pns"));
        }
        new CodeGen(configuration).process();
    } catch (ParseException ex) {
        System.err.println(String.format("Can not parse arguments: %s", ex.getMessage()));
        usage(options);
    }
}

---

From source file:com.act.biointerpretation.cofactorremoval.ReactionCofactorRemover.java

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

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

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

    NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));

    CofactorRemover cofactorRemover = new CofactorRemover(api);
    cofactorRemover.init();

    Pair<Reaction, Reaction> results = cofactorRemover
            .removeCofactorsFromOneReaction(Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));

    System.out.format("Reaction before processing:\n");
    printReport(results.getLeft());
    System.out.println();
    System.out.format("Reaction after processing:\n");
    printReport(results.getRight());
    System.out.println();
}

---

From source file:graphgen.GraphGen.java

/**
 * @param args the command line arguments
 *///from w  w  w .j  a  v  a2  s . c  o m
public static void main(String[] args) {
    Options options = new Options();
    HelpFormatter formatter = new HelpFormatter();

    options.addOption(OPTION_EDGES, true, OPTION_EDGES_MSG);
    options.addOption(OPTION_NODES, true, OPTION_NODES_MSG);
    options.addOption(OPTION_OUTPUT, true, OPTION_OUTPUT_MSG);

    CommandLineParser parser = new BasicParser();
    try {
        CommandLine cmd = parser.parse(options, args);
        int edgeCount = Integer.valueOf(cmd.getOptionValue(OPTION_EDGES));
        int nodeCount = Integer.valueOf(cmd.getOptionValue(OPTION_NODES));
        String outputFile = cmd.getOptionValue(OPTION_OUTPUT);

        if ((nodeCount < edgeCount) || (outputFile != null)) {
            String graph = generateGraph(nodeCount, edgeCount);
            saveGraph(graph, outputFile);
        } else {
            formatter.printHelp(HELP_NAME, options);
        }

    } catch (NumberFormatException | ParseException e) {
        formatter.printHelp(HELP_NAME, options);
    } catch (IllegalArgumentException | FileNotFoundException e) {
        System.err.println(e.getMessage());
    }
}

---

From source file:dk.statsbiblioteket.jpar2.filecompare.FileCompare.java

/**
 * Main method. //  w  ww  . j  a  v a2s.  c  om
 * @param args
 */
public static void main(String[] args) {

    Options options = new Options();
    options.addOption("s", "slices", true, "The number of slices to use in the comparison");

    CommandLineParser parser = new PosixParser();
    try {
        CommandLine cmd = parser.parse(options, args);
        args = cmd.getArgs();
        if (!cmd.hasOption("s") || args.length != 2) {
            System.exit(2);
        }
        int slices = Integer.parseInt(cmd.getOptionValue("s").trim());

        File f1 = new File(args[0]);
        File f2 = new File(args[1]);
        if (f1.length() == f2.length()) {
            int sliceSize = (int) (f1.length() / slices);//rounding here...

            DataFile df1 = new DataFile(f1, sliceSize);
            DataFile df2 = new DataFile(f2, sliceSize);

            List<Integer> defectIndexes = df1.compareWithIndex(df2);

            for (int index : defectIndexes) {
                System.out.println("index " + index + ", from " + index * sliceSize + " to "
                        + (index + 1) * sliceSize + " is defect");
            }
            if (defectIndexes.size() == 0) {
                System.out.println("Files are identical");
            }

        } else {
            System.out.println("Files differ in length, cannot help you");
        }
    } catch (ParseException e) {
        e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
    } catch (IOException e) {
        e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
    }

}

---

From source file:com.act.lcms.db.io.report.IonAnalysisInterchangeModelOperations.java

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

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

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

    if (cl.hasOption(OPTION_LOG_DISTRIBUTION)) {
        IonAnalysisInterchangeModel model = new IonAnalysisInterchangeModel();
        model.loadResultsFromFile(new File(cl.getOptionValue(OPTION_INPUT_FILE)));
        Map<Pair<Double, Double>, Integer> rangeToCount = model
                .computeLogFrequencyDistributionOfMoleculeCountToMetric(
                        IonAnalysisInterchangeModel.METRIC.valueOf(cl.getOptionValue(OPTION_LOG_DISTRIBUTION)));

        try (BufferedWriter predictionWriter = new BufferedWriter(
                new FileWriter(new File(OPTION_OUTPUT_FILE)))) {
            for (Map.Entry<Pair<Double, Double>, Integer> entry : rangeToCount.entrySet()) {
                String value = String.format("%f,%d", entry.getKey().getLeft(), entry.getValue());
                predictionWriter.write(value);
                predictionWriter.newLine();
            }
        }
    }
}

---

From source file:com.dattack.dbping.cli.PingCli.java

/**
 * The <code>main</code> method.
 *
 * @param args//w  w w . j  av  a2s.c  o  m
 *            the program arguments
 */
public static void main(final String[] args) {

    final Options options = createOptions();

    try {
        final CommandLineParser parser = new DefaultParser();
        final CommandLine cmd = parser.parse(options, args);
        final String[] filenames = cmd.getOptionValues(FILE_OPTION);
        final String[] taskNames = cmd.getOptionValues(TASK_NAME_OPTION);

        HashSet<String> hs = null;
        if (taskNames != null) {
            hs = new HashSet<>(Arrays.asList(taskNames));
        }

        final PingEngine ping = new PingEngine();
        ping.execute(filenames, hs);

    } catch (@SuppressWarnings("unused") final ParseException e) {
        showUsage(options);
    } catch (final ConfigurationException | DattackParserException e) {
        System.err.println(e.getMessage());
    }
}

---

From source file:de.drippinger.serviceExtractor.CLIEntry.java

public static void main(String... args) {

    Banner.printBanner();//  w  ww .  j  ava  2  s  . c om

    try {

        CommandLineParser parser = new DefaultParser();
        CommandLine cmd = parser.parse(createOptions(), args);
        RunParameter parameter = null;

        if (cmd.hasOption("h")) {
            printHelp();
        } else if (cmd.hasOption("c")) {
            parameter = extractParameterFromConfigFile(cmd);
        } else {
            parameter = extractParameterFromCommandline(cmd);
        }

        if (parameter != null && parameter.hasSufficientData()) {
            parameter.printParameter();
            // TODO Do main stuff
        } else {
            log.warn("Not sufficient parameters provided. exiting");
        }

    } catch (ParseException | ExtractorException e) {
        log.error(e.toString());
    }
}

---

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