Example usage for java.lang Exception getMessage

Introduction

In this page you can find the example usage for java.lang Exception getMessage.

Prototype

public String getMessage() 

Source Link

Document

Returns the detail message string of this throwable.

Usage

From source file:alluxio.cli.AlluxioFrameworkIntegrationTest.java

/**
 * @param args arguments/*from ww w  .  jav a 2 s.co m*/
 * @throws Exception if an exception occurs
 */
public static void main(String[] args) throws Exception {
    AlluxioFrameworkIntegrationTest test = new AlluxioFrameworkIntegrationTest();
    JCommander jc = new JCommander(test);
    jc.setProgramName(AlluxioFrameworkIntegrationTest.class.getName());
    try {
        jc.parse(args);
    } catch (Exception e) {
        LOG.error(e.getMessage());
        jc.usage();
        System.exit(1);
    }
    if (test.mHelp) {
        jc.usage();
    } else {
        test.run();
    }
}

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From source file:com.gordcorp.jira2db.App.java

public static void main(String[] args) throws Exception {
    File log4jFile = new File("log4j.xml");
    if (log4jFile.exists()) {
        DOMConfigurator.configure("log4j.xml");
    }/*from ww w.ja v  a 2s .  c om*/

    Option help = new Option("h", "help", false, "print this message");

    @SuppressWarnings("static-access")
    Option project = OptionBuilder.withLongOpt("project").withDescription("Only sync Jira project PROJECT")
            .hasArg().withArgName("PROJECT").create();

    @SuppressWarnings("static-access")
    Option property = OptionBuilder.withArgName("property=value").hasArgs(2).withValueSeparator()
            .withDescription("use value for given property").create("D");

    @SuppressWarnings("static-access")
    Option testJira = OptionBuilder.withLongOpt("test-jira")
            .withDescription("Test the connection to Jira and print the results").create();

    @SuppressWarnings("static-access")
    Option forever = OptionBuilder.withLongOpt("forever")
            .withDescription("Will continue polling Jira and syncing forever").create();

    Options options = new Options();
    options.addOption(help);
    options.addOption(project);
    options.addOption(property);
    options.addOption(testJira);
    options.addOption(forever);

    CommandLineParser parser = new GnuParser();
    try {

        CommandLine line = parser.parse(options, args);

        if (line.hasOption(help.getOpt())) {
            printHelp(options);
            return;
        }

        // Overwrite the properties file with command line arguments
        if (line.hasOption("D")) {
            String[] values = line.getOptionValues("D");
            for (int i = 0; i < values.length; i = i + 2) {
                String key = values[i];
                // If user does not provide a value for this property, use
                // an empty string
                String value = "";
                if (i + 1 < values.length) {
                    value = values[i + 1];
                }

                log.info("Setting key=" + key + " value=" + value);
                PropertiesWrapper.set(key, value);
            }

        }

        if (line.hasOption("test-jira")) {
            testJira();
        } else {
            JiraSynchroniser jira = new JiraSynchroniser();

            if (line.hasOption("project")) {

                jira.setProjects(Arrays.asList(new String[] { line.getOptionValue("project") }));
            }

            if (line.hasOption("forever")) {
                jira.syncForever();
            } else {
                jira.syncAll();
            }
        }
    } catch (ParseException exp) {

        log.error("Parsing failed: " + exp.getMessage());
    } catch (Exception e) {
        log.error(e.getMessage(), e);
    }
}

---

From source file:com.aerospike.examples.Main.java

/**
 * Main entry point.// w  w  w . j  ava 2 s .  co  m
 */
public static void main(String[] args) {

    try {
        Options options = new Options();
        options.addOption("h", "host", true, "Server hostname (default: localhost)");
        options.addOption("p", "port", true, "Server port (default: 3000)");
        options.addOption("U", "user", true, "User name");
        options.addOption("P", "password", true, "Password");
        options.addOption("n", "namespace", true, "Namespace (default: test)");
        options.addOption("s", "set", true, "Set name. Use 'empty' for empty set (default: demoset)");
        options.addOption("g", "gui", false, "Invoke GUI to selectively run tests.");
        options.addOption("d", "debug", false, "Run in debug mode.");
        options.addOption("u", "usage", false, "Print usage.");

        CommandLineParser parser = new PosixParser();
        CommandLine cl = parser.parse(options, args, false);

        if (args.length == 0 || cl.hasOption("u")) {
            logUsage(options);
            return;
        }
        Parameters params = parseParameters(cl);
        String[] exampleNames = cl.getArgs();

        if ((exampleNames.length == 0) && (!cl.hasOption("g"))) {
            logUsage(options);
            return;
        }

        // Check for all.
        for (String exampleName : exampleNames) {
            if (exampleName.equalsIgnoreCase("all")) {
                exampleNames = ExampleNames;
                break;
            }
        }

        if (cl.hasOption("d")) {
            Log.setLevel(Level.DEBUG);
        }

        if (cl.hasOption("g")) {
            GuiDisplay.startGui(params);
        } else {
            Console console = new Console();
            runExamples(console, params, exampleNames);
        }
    } catch (Exception ex) {
        System.out.println(ex.getMessage());
        ex.printStackTrace();
    }
}

---

From source file:fedora.client.Uploader.java

/**
 * Test this class by uploading the given file three times. First, with the
 * provided credentials, as an InputStream. Second, with the provided
 * credentials, as a File. Third, with bogus credentials, as a File.
 */// w w w  . j a v  a  2s  .  c o  m
public static void main(String[] args) {
    try {
        if (args.length == 5 || args.length == 6) {
            String protocol = args[0];
            int port = Integer.parseInt(args[1]);
            String user = args[2];
            String password = args[3];
            String fileName = args[4];

            String context = Constants.FEDORA_DEFAULT_APP_CONTEXT;

            if (args.length == 6 && !args[5].equals("")) {
                context = args[5];
            }

            Uploader uploader = new Uploader(protocol, port, context, user, password);
            File f = new File(fileName);
            System.out.println(uploader.upload(new FileInputStream(f)));
            System.out.println(uploader.upload(f));
            uploader = new Uploader(protocol, port, context, user + "test", password);
            System.out.println(uploader.upload(f));
        } else {
            System.err.println("Usage: Uploader host port user password file [context]");
        }
    } catch (Exception e) {
        System.err.println("ERROR: " + e.getMessage());
    }
}

---

From source file:edu.msu.cme.rdp.framebot.stat.TaxonAbundance.java

/**
 * this class group the nearest matches by phylum/class, or by match 
 * @param args/*  ww w .j a va2s  . com*/
 * @throws Exception 
 */
public static void main(String[] args) throws Exception {
    HashMap<String, Double> coveragetMap = null;
    double identity = 0.0;
    try {
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption("seqCoverage")) {
            String coveragefile = line.getOptionValue("seqCoverage");
            coveragetMap = parseKmerCoverage(coveragefile);
        }
        if (line.hasOption("identity")) {
            identity = Double.parseDouble(line.getOptionValue("identity"));
            if (identity < 0 || identity > 100) {
                throw new IllegalArgumentException("identity cutoff should be in the range of 0 and 100");
            }
        }

        args = line.getArgs();
        if (args.length != 3) {
            throw new Exception("");
        }

    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(80, "[options] <FrameBot Alignment file or Dir> <seqLineage> <out file> ",
                "", options,
                "seqLineage: a tab-delimited file with ref seqID and lineage, or fasta of ref seq with lineage as the descrption"
                        + "\nframeBot alignment file or Dir: frameBot alignment files "
                        + "\noutfile: output with the nearest match count group by phylum/class; and by match name");
    }
    TaxonAbundance.mapAbundance(new File(args[0]), new File(args[1]), args[2], coveragetMap, identity);
}

---

From source file:edu.msu.cme.rdp.probematch.cli.PrimerMatch.java

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

    PrintStream out = new PrintStream(System.out);
    int maxDist = Integer.MAX_VALUE;

    try {/*from www .ja va  2 s.c  o m*/
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption("outFile")) {
            out = new PrintStream(new File(line.getOptionValue("outFile")));
        }
        if (line.hasOption("maxDist")) {
            maxDist = Integer.valueOf(line.getOptionValue("maxDist"));
        }
        args = line.getArgs();

        if (args.length != 2) {
            throw new Exception("Unexpected number of command line arguments");
        }
    } catch (Exception e) {
        System.err.println("Error: " + e.getMessage());
        new HelpFormatter().printHelp("PrimerMatch <primer_list | primer_file> <seq_file>", options);
        return;
    }

    List<PatternBitMask64> primers = new ArrayList();
    if (new File(args[0]).exists()) {
        File primerFile = new File(args[0]);
        SequenceFormat seqformat = SeqUtils.guessFileFormat(primerFile);

        if (seqformat.equals(SequenceFormat.FASTA)) {
            SequenceReader reader = new SequenceReader(primerFile);
            Sequence seq;

            while ((seq = reader.readNextSequence()) != null) {
                primers.add(new PatternBitMask64(seq.getSeqString(), true, seq.getSeqName()));
            }
            reader.close();
        } else {
            BufferedReader reader = new BufferedReader(new FileReader(args[0]));
            String line;

            while ((line = reader.readLine()) != null) {
                line = line.trim();
                if (!line.equals("")) {
                    primers.add(new PatternBitMask64(line, true));
                }
            }
            reader.close();
        }
    } else {
        for (String primer : args[0].split(",")) {
            primers.add(new PatternBitMask64(primer, true));
        }
    }

    SeqReader seqReader = new SequenceReader(new File(args[1]));
    Sequence seq;
    String primerRegion;

    out.println("#seqname\tdesc\tprimer_index\tprimer_name\tposition\tmismatches\tseq_primer_region");
    while ((seq = seqReader.readNextSequence()) != null) {
        for (int index = 0; index < primers.size(); index++) {
            PatternBitMask64 primer = primers.get(index);
            BitVector64Result results = BitVector64.process(seq.getSeqString().toCharArray(), primer, maxDist);

            for (BitVector64Match result : results.getResults()) {
                primerRegion = seq.getSeqString().substring(
                        Math.max(0, result.getPosition() - primer.getPatternLength()), result.getPosition());

                if (result.getPosition() < primer.getPatternLength()) {
                    for (int pad = result.getPosition(); pad < primer.getPatternLength(); pad++) {
                        primerRegion = "x" + primerRegion;
                    }
                }

                out.println(seq.getSeqName() + "\t" + seq.getDesc() + "\t" + (index + 1) + "\t"
                        + primer.getPrimerName() + "\t" + result.getPosition() + "\t" + result.getScore() + "\t"
                        + primerRegion);
            }
        }
    }
    out.close();
    seqReader.close();
}

---

From source file:com.yahoo.athenz.example.zts.tls.client.ZTSAWSCredsClient.java

public static void main(String[] args) {

    // parse our command line to retrieve required input

    CommandLine cmd = parseCommandLine(args);

    final String domainName = cmd.getOptionValue("domain").toLowerCase();
    final String roleName = cmd.getOptionValue("role").toLowerCase();
    final String ztsUrl = cmd.getOptionValue("ztsurl");
    final String keyPath = cmd.getOptionValue("key");
    final String certPath = cmd.getOptionValue("cert");
    final String trustStorePath = cmd.getOptionValue("trustStorePath");
    final String trustStorePassword = cmd.getOptionValue("trustStorePassword");

    // we are going to setup our service private key and
    // certificate into a ssl context that we can use with
    // our zts client

    try {//from   w w w .  j  av  a2  s  . c  om
        KeyRefresher keyRefresher = Utils.generateKeyRefresher(trustStorePath, trustStorePassword, certPath,
                keyPath);
        SSLContext sslContext = Utils.buildSSLContext(keyRefresher.getKeyManagerProxy(),
                keyRefresher.getTrustManagerProxy());

        // obtain temporary credential provider for our domain and role

        AWSCredentialsProviderImpl awsCredProvider = new AWSCredentialsProviderImpl(ztsUrl, sslContext,
                domainName, roleName);

        // retrieve and display aws temporary creds. Typically you just pass
        // the AWSCredentialsProvider object to any AWS api that requires it.
        // for example, when creating an AWS S3 client
        //      AmazonS3 s3client = AmazonS3ClientBuilder.standard()
        //          .withCredentials(awsCredProvider).withClientConfiguration(cltConf)
        //          .withRegion(getRegion()).build();

        retrieveAWSTempCreds(awsCredProvider);

        // once we're done with our api and we no longer need our
        // provider we need to make sure to close it

        awsCredProvider.close();

    } catch (Exception ex) {
        System.out.println("Exception: " + ex.getMessage());
        ex.printStackTrace();
        System.exit(1);
    }
}

---

From source file:genql.CLIRunner.java

public static void main(String[] args) {
    Options options = setupOptions();/*w ww.ja  va  2s  .  c om*/
    CommandLineParser parser = new BasicParser();
    try {
        //            for (int i = 0; i < args.length; i++) {
        //                System.out.println(args[i]);
        //            }
        CommandLine line = parser.parse(options, args);
        if (line.hasOption('e')) {
            isEval = true;
        }
        if (line.hasOption('g')) {
            isGen = true;
        }
        if (line.hasOption('d')) {
            corpusDir = line.getOptionValue('d');
        }
        if (line.hasOption('n')) {
            qcount = Integer.parseInt(line.getOptionValue('n'));
        } else {
            qcount = 10;
        }
        if (line.hasOption('o')) {
            outputFile = line.getOptionValue('o');
        }
        if (line.hasOption('g')) {
            groundTruthQueryFile = line.getOptionValue('g');
        }
        if (line.hasOption('q')) {
            generatedQueryFile = line.getOptionValue('q');
        }
        if (line.hasOption('m')) {
            min_query_len = Integer.parseInt(line.getOptionValue('m'));
        } else {
            min_query_len = 2;
        }
        if (line.hasOption('x')) {
            max_query_len = Integer.parseInt(line.getOptionValue('x'));
        } else {
            max_query_len = 7;
        }
        if (line.hasOption('h')) {
            printHelpAndExit(options);
        }

        if (isGen) {
            MainApp.gen(corpusDir, outputFile, qcount, min_query_len, max_query_len);
        } else if (isEval) {
            final String intermediateResults = corpusDir + "/temp";
            new File(intermediateResults).mkdir();
            MainApp.eval(corpusDir, generatedQueryFile, groundTruthQueryFile, intermediateResults,
                    min_query_len, max_query_len);
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        System.err.println("Unexpected exception: " + ex.getMessage());
        System.exit(1);
    }
}

---

From source file:com.genentech.chemistry.openEye.apps.SDFALogP.java

/**
 * @param args//from   www  . ja  v a2 s.c  om
 */
public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option(OPT_INFILE, true,
            "input file oe-supported Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_SMARTS_FILE, true, "Optional: to overwrite atom type definition file.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_PRINT_COUNTS, false,
            "If set the count of each atom type is added to the output file.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_VALIDATE_ASSIGNMENT, false,
            "Print warning if no atomtype matches an atom in a candidte molecule.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_SUPRESS_ZERO, false, "If given atom type counts with count=0 will not be added.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_NEUTRALIZE, true, "y|n to neutralize molecule if possible (default=y)");
    opt.setRequired(false);
    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 (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    String smartsFile = cmd.getOptionValue(OPT_SMARTS_FILE);
    boolean outputCount = cmd.hasOption(OPT_PRINT_COUNTS);
    boolean outputZero = !cmd.hasOption(OPT_SUPRESS_ZERO);
    boolean neutralize = !"n".equalsIgnoreCase(cmd.getOptionValue(OPT_NEUTRALIZE));
    boolean ValidateAssignment = cmd.hasOption(OPT_VALIDATE_ASSIGNMENT);

    SDFALogP sdfALogP = new SDFALogP(smartsFile, outFile, outputZero, neutralize, ValidateAssignment);

    sdfALogP.run(inFile, outputCount);
    sdfALogP.close();
}

---

From source file:net.modelbased.proasense.storage.registry.StorageRegistrySensorDataTestClient.java

public static void main(String[] args) {
    // Get client properties from properties file
    //        StorageRegistrySensorDataTestClient client = new StorageRegistrySensorDataTestClient();
    //        client.loadClientProperties();

    // Hardcoded client properties (simple test client)
    String STORAGE_REGISTRY_SERVICE_URL = "http://192.168.84.34:8080/storage-registry";

    // Default HTTP client and common properties for requests
    HttpClient client = new DefaultHttpClient();
    StringBuilder requestUrl = null;
    List<NameValuePair> params = null;
    String queryString = null;/*from  ww  w  .ja v  a  2s  .  c  o  m*/

    // Default HTTP response and common properties for responses
    HttpResponse response = null;
    ResponseHandler<String> handler = null;
    int status = 0;
    String body = null;

    // Query for sensor list
    requestUrl = new StringBuilder(STORAGE_REGISTRY_SERVICE_URL);
    requestUrl.append("/query/sensor/list");

    try {
        HttpGet query21 = new HttpGet(requestUrl.toString());
        query21.setHeader("Content-type", "application/json");
        response = client.execute(query21);

        // Check status code
        status = response.getStatusLine().getStatusCode();
        if (status != 200) {
            throw new RuntimeException("Failed! HTTP error code: " + status);
        }

        // Get body
        handler = new BasicResponseHandler();
        body = handler.handleResponse(response);

        System.out.println("SENSOR LIST: " + body);
    } catch (Exception e) {
        System.out.println(e.getClass().getName() + ": " + e.getMessage());
    }

    // Query for sensor properties
    requestUrl = new StringBuilder(STORAGE_REGISTRY_SERVICE_URL);
    requestUrl.append("/query/sensor/properties");

    params = new LinkedList<NameValuePair>();
    params.add(new BasicNameValuePair("sensorId", "visualInspection"));

    queryString = URLEncodedUtils.format(params, "utf-8");
    requestUrl.append("?");
    requestUrl.append(queryString);

    try {
        HttpGet query22 = new HttpGet(requestUrl.toString());
        query22.setHeader("Content-type", "application/json");
        response = client.execute(query22);

        // Check status code
        status = response.getStatusLine().getStatusCode();
        if (status != 200) {
            throw new RuntimeException("Failed! HTTP error code: " + status);
        }

        // Get body
        handler = new BasicResponseHandler();
        body = handler.handleResponse(response);

        System.out.println("SENSOR PROPERTIES: " + body);
    } catch (Exception e) {
        System.out.println(e.getClass().getName() + ": " + e.getMessage());
    }
}

---

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