List of usage examples for java.lang Exception getMessage
public String getMessage()
From source file:org.eclipse.lyo.client.oslc.samples.RQMFormSample.java
/** * Login to the RQM server and perform some OSLC actions * @param args//from w ww.j ava 2 s .c o m * @throws ParseException */ public static void main(String[] args) throws ParseException { Options options = new Options(); options.addOption("url", true, "url"); options.addOption("user", true, "user ID"); options.addOption("password", true, "password"); options.addOption("project", true, "project area"); CommandLineParser cliParser = new GnuParser(); //Parse the command line CommandLine cmd = cliParser.parse(options, args); if (!validateOptions(cmd)) { logger.severe( "Syntax: java <class_name> -url https://<server>:port/<context>/ -user <user> -password <password> -project \"<project_area>\""); logger.severe( "Example: java RQMFormSample -url https://exmple.com:9443/ccm -user ADMIN -password ADMIN -project \"JKE Banking (Quality Management)\""); return; } String webContextUrl = cmd.getOptionValue("url"); String user = cmd.getOptionValue("user"); String passwd = cmd.getOptionValue("password"); String projectArea = cmd.getOptionValue("project"); try { //STEP 1: Initialize a Jazz rootservices helper and indicate we're looking for the QualityManagement catalog //RQM contains both Quality and Change Management providers, so need to look for QM specifically JazzRootServicesHelper helper = new JazzRootServicesHelper(webContextUrl, OSLCConstants.OSLC_QM_V2); //STEP 2: Create a new Form Auth client with the supplied user/password JazzFormAuthClient client = helper.initFormClient(user, passwd); //STEP 3: Login in to Jazz Server if (client.formLogin() == HttpStatus.SC_OK) { //STEP 4: Get the URL of the OSLC QualityManagement catalog String catalogUrl = helper.getCatalogUrl(); //STEP 5: Find the OSLC Service Provider for the project area we want to work with String serviceProviderUrl = client.lookupServiceProviderUrl(catalogUrl, projectArea); //STEP 6: Get the Query Capabilities URL so that we can run some OSLC queries String queryCapability = client.lookupQueryCapability(serviceProviderUrl, OSLCConstants.OSLC_QM_V2, OSLCConstants.QM_TEST_RESULT_QUERY); //SCENARIO A: Run a query for all TestResults with a status of passed with OSLC paging of 10 items per //page turned on and list the members of the result OslcQueryParameters queryParams = new OslcQueryParameters(); queryParams.setWhere("oslc_qm:status=\"com.ibm.rqm.execution.common.state.passed\""); OslcQuery query = new OslcQuery(client, queryCapability, 10, queryParams); OslcQueryResult result = query.submit(); boolean processAsJavaObjects = true; processPagedQueryResults(result, client, processAsJavaObjects); System.out.println("\n------------------------------\n"); //SCENARIO B: Run a query for a specific TestResult selecting only certain //attributes and then print it as raw XML. Change the dcterms:title below to match a //real TestResult in your RQM project area OslcQueryParameters queryParams2 = new OslcQueryParameters(); queryParams2 .setWhere("dcterms:title=\"Consistent_display_of_currency_Firefox_DB2_WAS_Windows_S1\""); queryParams2.setSelect( "dcterms:identifier,dcterms:title,dcterms:creator,dcterms:created,oslc_qm:status"); OslcQuery query2 = new OslcQuery(client, queryCapability, queryParams2); OslcQueryResult result2 = query2.submit(); ClientResponse rawResponse = result2.getRawResponse(); processRawResponse(rawResponse); rawResponse.consumeContent(); //SCENARIO C: RQM TestCase creation and update TestCase testcase = new TestCase(); testcase.setTitle("Accessibility verification using a screen reader"); testcase.setDescription( "This test case uses a screen reader application to ensure that the web browser content fully complies with accessibility standards"); testcase.addTestsChangeRequest(new Link(new URI("http://cmprovider/changerequest/1"), "Implement accessibility in Pet Store application")); //Get the Creation Factory URL for test cases so that we can create a test case String testcaseCreation = client.lookupCreationFactory(serviceProviderUrl, OSLCConstants.OSLC_QM_V2, testcase.getRdfTypes()[0].toString()); //Create the test case ClientResponse creationResponse = client.createResource(testcaseCreation, testcase, OslcMediaType.APPLICATION_RDF_XML); creationResponse.consumeContent(); String testcaseLocation = creationResponse.getHeaders().getFirst(HttpHeaders.LOCATION); System.out.println("Test Case created a location " + testcaseLocation); //Get the test case from the service provider and update its title property testcase = client.getResource(testcaseLocation, OslcMediaType.APPLICATION_RDF_XML) .getEntity(TestCase.class); testcase.setTitle(testcase.getTitle() + " (updated)"); //Create a partial update URL so that only the title will be updated. //Assuming (for readability) that the test case URL does not already contain a '?' String updateUrl = testcase.getAbout() + "?oslc.properties=dcterms:title"; //Update the test case at the service provider client.updateResource(updateUrl, testcase, OslcMediaType.APPLICATION_RDF_XML).consumeContent(); } } catch (RootServicesException re) { logger.log(Level.SEVERE, "Unable to access the Jazz rootservices document at: " + webContextUrl + "/rootservices", re); } catch (Exception e) { logger.log(Level.SEVERE, e.getMessage(), e); } }
From source file:es.tid.cosmos.platform.injection.server.InjectionServerMain.java
/** * //ww w .j ava 2 s . c o m * @param args * @throws ConfigurationException */ public static void main(String[] args) throws ConfigurationException { ServerCommandLine commandLine = new ServerCommandLine(); try { commandLine.parse(args); } catch (ParseException e) { commandLine.printUsage(); System.exit(1); } // try catch String externalConfiguration = DEFAULT_EXTERNAL_CONFIGURATION; if (commandLine.hasConfigFile()) { externalConfiguration = commandLine.getConfigFile(); } // if Configuration config; try { config = new Configuration(new File(externalConfiguration).toURI().toURL()); } catch (Exception ex) { config = new Configuration(InjectionServerMain.class.getResource(INTERNAL_CONFIGURATION)); } // try catch try { InjectionServer server = new InjectionServer(config); server.setupSftpServer(); } catch (Exception ex) { LOG.error(ex.getMessage(), ex); System.exit(1); } // try catch }
From source file:com.genentech.chemistry.tool.align.SDFAlign.java
public static void main(String... args) { Options options = new Options(); Option opt = new Option("in", true, "input sd file"); opt.setRequired(true);/*w w w . ja v a 2s .c o m*/ options.addOption(opt); opt = new Option("out", true, "output file"); opt.setRequired(true); options.addOption(opt); opt = new Option("method", true, "fss|sss|MCS|clique (default mcs)."); options.addOption(opt); opt = new Option("ref", true, "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported"); options.addOption(opt); opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image."); options.addOption(opt); opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output."); options.addOption(opt); opt = new Option("atomMatch", true, "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n" + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n" + "Queryfeatures are considered only if default is used."); options.addOption(opt); opt = new Option("bondMatch", true, "Sequence of none|default specifing how bonds are matched cf. oe document."); options.addOption(opt); opt = new Option("keepCoreHydrogens", false, "If not specified the hydrigen atoms are removed from the core."); options.addOption(opt); opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd."); options.addOption(opt); opt = new Option("doNotOptimize", false, "If specified the RMSD is computed without moving optimizing the overlay."); options.addOption(opt); opt = new Option("quiet", false, "Reduced warining messages"); options.addOption(opt); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { exitWithHelp(e.getMessage(), options); } if (cmd.getArgs().length > 0) exitWithHelp("To many arguments", options); // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms int atomExpr = OEExprOpts.DefaultAtoms; int bondExpr = OEExprOpts.DefaultBonds; String atomMatch = cmd.getOptionValue("atomMatch"); if (atomMatch == null) atomMatch = ""; atomMatch = '|' + atomMatch.toLowerCase() + '|'; String bondMatch = cmd.getOptionValue("bondMatch"); if (bondMatch == null) bondMatch = ""; bondMatch = '|' + bondMatch.toLowerCase() + '|'; String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String refFile = cmd.getOptionValue("ref"); String method = cmd.getOptionValue("method"); String rmsdTag = cmd.getOptionValue("rmsdTag"); String oMol = cmd.getOptionValue("outputMol"); boolean doMirror = cmd.hasOption("mirror"); boolean doOptimize = !cmd.hasOption("doNotOptimize"); boolean quiet = cmd.hasOption("quiet"); OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase()); if (atomMatch.startsWith("|none")) atomExpr = 0; if (atomMatch.contains("|hcount|")) atomExpr |= OEExprOpts.HCount; if (atomMatch.contains("|noAromatic|")) atomExpr &= (~OEExprOpts.Aromaticity); if (bondMatch.startsWith("|none")) bondExpr = 0; ArrayList<OEMol> refmols = new ArrayList<OEMol>(); if (refFile != null) { oemolistream reffs = new oemolistream(refFile); if (!is3DFormat(reffs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); reffs.SetFormat(OEFormat.MDL); int aromodel = OEIFlavor.Generic.OEAroModelOpenEye; int qflavor = reffs.GetFlavor(reffs.GetFormat()); reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel)); OEMol rmol = new OEMol(); while (oechem.OEReadMDLQueryFile(reffs, rmol)) { if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); rmol = new OEMol(); } rmol.delete(); if (refmols.size() == 0) throw new Error("reference file had no entries"); reffs.close(); } oemolistream fitfs = new oemolistream(inFile); if (!is3DFormat(fitfs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); oemolostream ofs = new oemolostream(outFile); if (!is3DFormat(ofs.GetFormat())) oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates"); AlignInterface aligner = null; OEGraphMol fitmol = new OEGraphMol(); if (oechem.OEReadMolecule(fitfs, fitmol)) { if (refmols.size() == 0) { OEMol rmol = new OEMol(fitmol); if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); } if ("sss".equalsIgnoreCase(method)) { aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("clique".equalsIgnoreCase(method)) { aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("fss".equalsIgnoreCase(method)) { if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch")) exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options); aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror); } else { aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } do { aligner.align(fitmol); oechem.OEWriteMolecule(ofs, fitmol); } while (oechem.OEReadMolecule(fitfs, fitmol)); } fitmol.delete(); if (aligner != null) aligner.close(); for (OEMolBase mol : refmols) mol.delete(); fitfs.close(); ofs.close(); }
From source file:se.berazy.api.examples.App.java
/** * Operation examples./* ww w. j a va2 s . co m*/ * @param args */ public static void main(String[] args) { Scanner scanner = null; try { client = new BookkeepingClient(); System.out.println("Choose operation to invoke:\n"); System.out.println("1. Create invoice"); System.out.println("2. Credit invoice"); scanner = new Scanner(System.in); while (scanner.hasNextLine()) { String line = scanner.nextLine(); line = (line != null) ? line.trim().toLowerCase() : ""; if (line.equals("1")) { outPutResponse(createInvoice()); } else if (line.equals("2")) { outPutResponse(creditInvoice()); } else if (line.equals("q") || line.equals("quit") || line.equals("exit")) { System.exit(0); } else { System.out.println("\nPlease choose an operation from 1-7."); } } scanner.close(); } catch (Exception ex) { System.out.println(String.format( "\nAn exception occured, press CTRL+C to exit or enter 'q', 'quit' or 'exit'.\n\nException: %s %s", ex.getMessage(), ex.getStackTrace())); } finally { if (scanner != null) { scanner.close(); } } }
From source file:com.genentech.chemistry.openEye.apps.enumerate.SDFEnumerator.java
public static void main(String... args) throws IOException { Options options = new Options(); Option opt = new Option("out", true, "output file oe-supported"); opt.setRequired(true);//from ww w.j av a 2 s . c o m options.addOption(opt); opt = new Option("hydrogenExplicit", false, "Use explicit hydrogens"); options.addOption(opt); opt = new Option("correctValences", false, "Correct valences after the enumeration"); options.addOption(opt); opt = new Option("regenerate2D", false, "Regenerate 2D coordinates for the products"); options.addOption(opt); opt = new Option("reactAllSites", false, "Generate a product for each match in a reagent."); options.addOption(opt); opt = new Option("randomFraction", true, "Only output a fraction of the products."); options.addOption(opt); opt = new Option("maxAtoms", true, "Only output products with <= maxAtoms."); options.addOption(opt); opt = new Option("notReacted", true, "Output file for reagents that didn't produce at leaste one output molecule, useful for debugging SMIRKS."); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp("", options); } args = cmd.getArgs(); if (args.length < 2) { exitWithHelp("Transformation and/or reagentFiles missing", options); } String smirks = args[0]; if (new File(smirks).canRead()) smirks = IOUtil.fileToString(smirks).trim(); if (!smirks.contains(">>")) smirks = scaffoldToSmirks(smirks); String[] reagentSmiOrFiles = Arrays.copyOfRange(args, 1, args.length); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String outFile = cmd.getOptionValue("out"); OELibraryGen lg = new OELibraryGen(); lg.Init(smirks); if (!lg.IsValid()) exitWithHelp("Invalid Transform: " + smirks, options); lg.SetExplicitHydrogens(cmd.hasOption("hydrogenExplicit")); lg.SetValenceCorrection(cmd.hasOption("correctValences")); lg.SetRemoveUnmappedFragments(true); boolean regenerate2D = cmd.hasOption("regenerate2D"); boolean reactAllSites = cmd.hasOption("reactAllSites"); String unreactedFile = null; if (cmd.hasOption("notReacted")) { unreactedFile = cmd.getOptionValue("notReacted"); } double randomFract = 2; if (cmd.hasOption("randomFraction")) randomFract = Double.parseDouble(cmd.getOptionValue("randomFraction")); int maxAtoms = 0; if (cmd.hasOption("maxAtoms")) maxAtoms = Integer.parseInt(cmd.getOptionValue("maxAtoms")); SDFEnumerator en = new SDFEnumerator(lg, reactAllSites, reagentSmiOrFiles); en.generateLibrary(outFile, maxAtoms, randomFract, regenerate2D, unreactedFile); en.delete(); }
From source file:com.xlson.standalonewar.Starter.java
/** * @param args the command line arguments *///from w w w .j a va 2s . c o m public static void main(String[] args) { try { defaultProperties = new PropertiesConfiguration( Starter.class.getClassLoader().getResource("webserver.properties").toURI().toURL()); appendClasspath(defaultProperties.getList("webserver.extraClasspath")); config = loadConfig(); final String PROP_NAME_WEBSERVER_TIMEOUT = defaultProperties.getString("PROP_NAME_WEBSERVER_TIMEOUT", "webserver.timeout"); int timeout = Integer.parseInt(getString(PROP_NAME_WEBSERVER_TIMEOUT, "0")); start(); if (timeout != 0) { Thread.sleep(timeout); stop(); } } catch (Exception ex) { logger.error("error", ex); System.err.println(ex.getMessage()); System.exit(-1); } }
From source file:com.genentech.chemistry.tool.mm.SDFMMMinimize.java
/** * Main function for running on the command line * @param args//from w w w . ja v a 2s . c o m */ public static void main(String... args) throws IOException { // Get the available options from the programs Map<String, List<String>> allowedProgramsAndForceFields = getAllowedProgramsAndForceFields(); Map<String, List<String>> allowedProgramsAndSolvents = getAllowedProgramsAndSolvents(); // 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); StringBuilder programOptions = new StringBuilder("Program to use for minimization. Choices are\n"); for (String program : allowedProgramsAndForceFields.keySet()) { programOptions.append("\n*** -program " + program + " ***\n"); String forcefields = ""; for (String option : allowedProgramsAndForceFields.get(program)) { forcefields += option + " "; } programOptions.append("-forcefield " + forcefields + "\n"); String solvents = ""; for (String option : allowedProgramsAndSolvents.get(program)) { solvents += option + " "; } programOptions.append("-solvent " + solvents + "\n"); } opt = new Option(OPT_PROGRAM, true, programOptions.toString()); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_FORCEFIELD, true, "Forcefield options. See -program for choices"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_SOLVENT, true, "Solvent options. See -program for choices"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_FIXED_ATOM_TAG, true, "SD tag name which contains the atom numbers to be held fixed."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_FIX_TORSION, true, "true/false. if true, the atoms in fixedAtomTag contains 4 indices of atoms defining a torsion angle to be held fixed"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_WORKING_DIR, true, "Working directory to put files."); 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 (args.length != 0) { System.err.println("Unknown arguments" + args); exitWithHelp(options); } 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 fixedAtomTag = cmd.getOptionValue(OPT_FIXED_ATOM_TAG); boolean fixTorsion = (cmd.getOptionValue(OPT_FIX_TORSION) != null && cmd.getOptionValue(OPT_FIX_TORSION).equalsIgnoreCase("true")); String programName = cmd.getOptionValue(OPT_PROGRAM); String forcefield = cmd.getOptionValue(OPT_FORCEFIELD); String solvent = cmd.getOptionValue(OPT_SOLVENT); String workDir = cmd.getOptionValue(OPT_WORKING_DIR); if (workDir == null || workDir.trim().length() == 0) workDir = "."; // Create a minimizer SDFMMMinimize minimizer = new SDFMMMinimize(); minimizer.setMethod(programName, forcefield, solvent); minimizer.run(inFile, outFile, fixedAtomTag, fixTorsion, workDir); minimizer.close(); System.err.println("Minimization complete."); }
From source file:com.marklogic.contentpump.ContentPump.java
public static void main(String[] args) throws Exception { if (args.length == 0) { printUsage();// www .ja v a2 s .c o m System.exit(1); } String[] expandedArgs = null; int rc = 1; try { expandedArgs = OptionsFileUtil.expandArguments(args); rc = runCommand(expandedArgs); } catch (Exception ex) { LOG.error("Error while expanding arguments", ex); System.err.println(ex.getMessage()); System.err.println("Try 'mlcp help' for usage."); } System.exit(rc); }
From source file:edu.msu.cme.rdp.seqmatch.cli.SeqmatchCheckRevSeq.java
public static void main(String[] args) throws Exception { String trainingFile = null;//from w w w .j a va 2 s . c o m String queryFile = null; String outputFile = null; PrintWriter revOutputWriter = new PrintWriter(System.out); PrintStream correctedQueryOut = System.out; String traineeDesc = null; int numOfResults = 20; boolean checkReverse = false; float diffScoreCutoff = CheckReverseSeq.DIFF_SCORE_CUTOFF; String format = "txt"; // default try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("c")) { checkReverse = true; } if (line.hasOption("t")) { trainingFile = line.getOptionValue("t"); } else { throw new Exception("training file must be specified"); } if (line.hasOption("q")) { queryFile = line.getOptionValue("q"); } else { throw new Exception("query file must be specified"); } if (line.hasOption("o")) { outputFile = line.getOptionValue("o"); } else { throw new Exception("output file must be specified"); } if (line.hasOption("r")) { revOutputWriter = new PrintWriter(line.getOptionValue("r")); } if (line.hasOption("s")) { correctedQueryOut = new PrintStream(line.getOptionValue("s")); } if (line.hasOption("d")) { diffScoreCutoff = Float.parseFloat(line.getOptionValue("d")); } if (line.hasOption("h")) { traineeDesc = line.getOptionValue("h"); } if (line.hasOption("n")) { numOfResults = Integer.parseInt(line.getOptionValue("n")); } if (line.hasOption("f")) { format = line.getOptionValue("f"); if (!format.equals("tab") && !format.equals("dbformat") && !format.equals("xml")) { throw new IllegalArgumentException("Only dbformat, tab or xml format available"); } } } catch (Exception e) { System.out.println("Command Error: " + e.getMessage()); new HelpFormatter().printHelp(120, "SeqmatchCheckRevSeq", "", options, "", true); return; } SeqmatchCheckRevSeq theObj = new SeqmatchCheckRevSeq(); if (!checkReverse) { theObj.doUserLibMatch(queryFile, trainingFile, outputFile, numOfResults, format, traineeDesc); } else { theObj.checkRevSeq(queryFile, trainingFile, outputFile, revOutputWriter, correctedQueryOut, diffScoreCutoff, format, traineeDesc); } }
From source file:com.microsoft.azure.management.network.samples.ManageInternalLoadBalancer.java
/** * Main entry point.//from ww w .j a v a 2 s. c o m * @param args parameters.\ */ public static void main(String[] args) { try { //============================================================= // Authenticate final File credFile = new File(System.getenv("AZURE_AUTH_LOCATION")); Azure azure = Azure.configure().withLogLevel(LogLevel.BODY).authenticate(credFile) .withDefaultSubscription(); // Print selected subscription System.out.println("Selected subscription: " + azure.subscriptionId()); runSample(azure); } catch (Exception e) { System.out.println(e.getMessage()); e.printStackTrace(); } }