List of usage examples for java.lang Exception getMessage
public String getMessage()
From source file:MainClass.java
public static void main(String argv[]) { int start = 1; int end = -1; int optind;// w ww. j a v a 2s.c om for (optind = 0; optind < argv.length; optind++) { if (argv[optind].equals("-T")) { // protocol protocol = argv[++optind]; } else if (argv[optind].equals("-H")) { // host host = argv[++optind]; } else if (argv[optind].equals("-U")) { // user user = argv[++optind]; } else if (argv[optind].equals("-P")) { // password password = argv[++optind]; } else if (argv[optind].equals("-L")) { url = argv[++optind]; } else if (argv[optind].equals("-s")) { // Source mbox src = argv[++optind]; } else if (argv[optind].equals("-d")) { // Destination mbox dest = argv[++optind]; } else if (argv[optind].equals("-x")) { // Expunge ? expunge = true; } else if (argv[optind].equals("--")) { optind++; break; } else if (argv[optind].startsWith("-")) { System.out.println("Usage: mover [-T protocol] [-H host] [-U user] [-P password] [-L url] [-v]"); System.out.println("\t[-s source mbox] [-d destination mbox] [-x] [msgnum1] [msgnum2]"); System.out.println("\t The -x option => EXPUNGE deleted messages"); System.out.println("\t msgnum1 => start of message-range; msgnum2 => end of message-range"); System.exit(1); } else { break; } } if (optind < argv.length) start = Integer.parseInt(argv[optind++]); // start msg if (optind < argv.length) end = Integer.parseInt(argv[optind++]); // end msg try { // Get a Properties object Properties props = System.getProperties(); // Get a Session object Session session = Session.getInstance(props, null); // Get a Store object Store store = null; if (url != null) { URLName urln = new URLName(url); store = session.getStore(urln); store.connect(); } else { if (protocol != null) store = session.getStore(protocol); else store = session.getStore(); // Connect if (host != null || user != null || password != null) store.connect(host, user, password); else store.connect(); } // Open source Folder Folder folder = store.getFolder(src); if (folder == null || !folder.exists()) { System.out.println("Invalid folder: " + folder.getName()); System.exit(1); } folder.open(Folder.READ_WRITE); int count = folder.getMessageCount(); if (count == 0) { // No messages in the source folder System.out.println(folder.getName() + " is empty"); // Close folder, store and return folder.close(false); store.close(); return; } // Open destination folder, create if reqd Folder dfolder = store.getFolder(dest); if (!dfolder.exists()) dfolder.create(Folder.HOLDS_MESSAGES); if (end == -1) end = count; // Get the message objects to copy Message[] msgs = folder.getMessages(start, end); System.out.println("Moving " + msgs.length + " messages"); if (msgs.length != 0) { folder.copyMessages(msgs, dfolder); folder.setFlags(msgs, new Flags(Flags.Flag.DELETED), true); // Dump out the Flags of the moved messages, to insure that // all got deleted for (int i = 0; i < msgs.length; i++) { if (!msgs[i].isSet(Flags.Flag.DELETED)) System.out.println("Message # " + msgs[i] + " not deleted"); } } // Close folders and store folder.close(expunge); store.close(); } catch (MessagingException mex) { Exception ex = mex; do { System.out.println(ex.getMessage()); if (ex instanceof MessagingException) ex = ((MessagingException) ex).getNextException(); else ex = null; } while (ex != null); } }
From source file:org.dspace.app.cris.batch.ScriptDeleteRP.java
/** * Batch script to delete a RP. See the technical documentation for further * details./*from ww w. jav a 2s. c om*/ */ public static void main(String[] args) { log.info("#### START DELETE: -----" + new Date() + " ----- ####"); Context dspaceContext = null; ApplicationContext context = null; try { dspaceContext = new Context(); dspaceContext.turnOffAuthorisationSystem(); DSpace dspace = new DSpace(); ApplicationService applicationService = dspace.getServiceManager() .getServiceByName("applicationService", ApplicationService.class); CommandLineParser parser = new PosixParser(); Options options = new Options(); options.addOption("h", "help", false, "help"); options.addOption("r", "researcher", true, "RP id to delete"); options.addOption("s", "silent", false, "no interactive mode"); CommandLine line = parser.parse(options, args); if (line.hasOption('h')) { HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("ScriptHKURPDelete \n", options); System.out.println("\n\nUSAGE:\n ScriptHKURPDelete -r <id> \n"); System.out.println("Please note: add -s for no interactive mode"); System.exit(0); } Integer rpId = null; boolean delete = false; boolean silent = line.hasOption('s'); Item[] items = null; if (line.hasOption('r')) { rpId = ResearcherPageUtils.getRealPersistentIdentifier(line.getOptionValue("r"), ResearcherPage.class); ResearcherPage rp = applicationService.get(ResearcherPage.class, rpId); if (rp == null) { if (!silent) { System.out.println("RP not exist...exit"); } log.info("RP not exist...exit"); System.exit(0); } log.info("Use browse indexing"); BrowseIndex bi = BrowseIndex.getBrowseIndex(plugInBrowserIndex); // now start up a browse engine and get it to do the work for us BrowseEngine be = new BrowseEngine(dspaceContext); String authKey = ResearcherPageUtils.getPersistentIdentifier(rp); // set up a BrowseScope and start loading the values into it BrowserScope scope = new BrowserScope(dspaceContext); scope.setBrowseIndex(bi); // scope.setOrder(order); scope.setFilterValue(authKey); scope.setAuthorityValue(authKey); scope.setResultsPerPage(Integer.MAX_VALUE); scope.setBrowseLevel(1); BrowseInfo binfo = be.browse(scope); log.debug("Find " + binfo.getResultCount() + "item(s) for the reseracher " + authKey); items = binfo.getItemResults(dspaceContext); if (!silent && rp != null) { System.out.println(MESSAGE_ONE); // interactive mode System.out.println("Attempting to remove Researcher Page:"); System.out.println("StaffNo:" + rp.getSourceID()); System.out.println("FullName:" + rp.getFullName()); System.out .println("the researcher has " + items.length + " relation(s) with item(s) in the HUB"); System.out.println(); System.out.println(QUESTION_ONE); InputStreamReader isr = new InputStreamReader(System.in); BufferedReader reader = new BufferedReader(isr); String answer = reader.readLine(); if (answer.equals("yes")) { delete = true; } else { System.out.println("Exit without delete"); log.info("Exit without delete"); System.exit(0); } } else { delete = true; } } else { System.out.println("\n\nUSAGE:\n ScriptHKURPDelete <-v> -r <RPid> \n"); System.out.println("-r option is mandatory"); log.error("-r option is mandatory"); System.exit(1); } if (delete) { if (!silent) { System.out.println("Deleting..."); } log.info("Deleting..."); cleanAuthority(dspaceContext, items, rpId); applicationService.delete(ResearcherPage.class, rpId); dspaceContext.complete(); } if (!silent) { System.out.println("Ok...Bye"); } } catch (Exception e) { log.error(e.getMessage(), e); throw new RuntimeException(e.getMessage(), e); } finally { if (dspaceContext != null && dspaceContext.isValid()) { dspaceContext.abort(); } if (context != null) { context.publishEvent(new ContextClosedEvent(context)); } } log.info("#### END: -----" + new Date() + " ----- ####"); System.exit(0); }
From source file:com.genentech.chemistry.openEye.apps.SDFTorsionScanner.java
/** * @param args/*from w ww . j a v a 2s . c o m*/ */ 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 filename."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_STARTTorsion, true, "The torsion in your inMol will be rotated by this value for the first job"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_TORSIONIncrement, true, "Incremnt each subsequent conformation by this step size"); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_NSTEPS, true, "Number of conformations to create"); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_BONDFILE, true, "The file containing the bond atoms that define the torsion."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_MINIMIZE, false, "Minimize conformer at each step using MMFFs. If maxConfsPerStep is > 1, " + "all confs will be mimimized and the lowest E will be output."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_CONSTRIANT, true, "One of strong (90), medium (45), weak(20), none or a floating point number" + " to specify the tethered constraint strength for -minimize (def=strong)"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_MAXCONFS_PER_STEP, true, "While holding the torsion fixed, maximum number of conformations of free atoms to generat. default=1"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_COREFILE, true, "Outputfile to store guessed core."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_TORSIONS_ATOM_TAG, true, "Name of sdf tag which will contain the indices of atoms that define the torsion."); opt.setRequired(true); 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 bondFile = cmd.getOptionValue(OPT_BONDFILE); String coreFilename = cmd.getOptionValue(OPT_COREFILE); String torsionAtomsTag = cmd.getOptionValue(OPT_TORSIONS_ATOM_TAG); int nSteps = Integer.parseInt(cmd.getOptionValue(OPT_NSTEPS)); int nStartTor = Integer.parseInt(cmd.getOptionValue(OPT_STARTTorsion)); int nTorIncr = Integer.parseInt(cmd.getOptionValue(OPT_TORSIONIncrement)); int nMaxConfsPerStep = 1; if (cmd.hasOption(OPT_MAXCONFS_PER_STEP)) { nMaxConfsPerStep = Integer.parseInt(cmd.getOptionValue(OPT_MAXCONFS_PER_STEP)); } String constraintStrength = cmd.getOptionValue(OPT_CONSTRIANT); boolean doMinimize = cmd.hasOption(OPT_MINIMIZE); SDFTorsionScanner torGenerator = new SDFTorsionScanner(bondFile, coreFilename, torsionAtomsTag, nSteps, nStartTor, nTorIncr, nMaxConfsPerStep, doMinimize, constraintStrength); torGenerator.run(inFile, outFile, coreFilename); }
From source file:it.sardegnaricerche.voiceid.sr.Voiceid.java
public static void main(String[] args) { logger.info("Voiceid main method"); logger.info("First argument: '" + args[0] + "'"); long startTime = System.currentTimeMillis(); Voiceid voiceid = null;//from w w w . ja v a 2 s . c om GMMVoiceDB db = null; try { db = new GMMVoiceDB(args[1], new UBMModel(args[0])); File f = new File(args[2]); voiceid = new Voiceid(db, f, new LIUMStandardDiarizator()); voiceid.extractClusters(); voiceid.matchClusters(); // voiceid.toWav(); // voiceid.printClusters(); JSONObject obj = voiceid.toJson(); for (VCluster c : voiceid.getClusters()) { logger.info("" + c.getSample().getResource().getAbsolutePath()); } // FileWriter fstream = new // FileWriter(f.getAbsolutePath().replaceFirst("[.][^.]+$", "") + // ".json"); String filename = Utils.getBasename(f) + ".json"; FileWriter fstream = new FileWriter(filename); BufferedWriter out = new BufferedWriter(fstream); out.write(obj.toString()); // Close the output stream out.close(); // voiceid.makeAllModels(); } catch (IOException e) { logger.severe(e.getMessage()); } catch (Exception ex) { logger.severe(ex.getMessage()); } long endTime = System.currentTimeMillis(); long duration = endTime - startTime; logger.info("Exit (" + ((float) duration / 1000) + " s)"); // logger.info("Max Threads: " + (int) db.maxThreads); }
From source file:GetAppInfo.java
/** * @param args// w w w .ja v a 2s.co m */ public static void main(String[] args) { if (args.length != 4) { System.out.println("Usage :\n" + "java -jar this_jar_name confpath query_str startIndex numbers"); System.exit(1); } String confpath = args[0]; GetAppConfig conf = new GetAppConfig(confpath); String email = conf.getUserID(); String password = conf.getPassword(); String query = args[1]; final int startIndex = Integer.parseInt(args[2]); final int numbers = Integer.parseInt(args[3]); String androidid = conf.getDeviceID(); if (email.equals("")) { System.out.println("Error: Failed to get UserID."); System.exit(2); } else if (password.equals("")) { System.out.println("Error: Failed to get Password."); System.exit(3); } else if (androidid.equals("")) { System.out.println("Error: Failed to get DeviceID."); System.exit(4); } System.out.println("query: " + query); MarketSession session = new MarketSession(); session.getContext().setAndroidId(androidid); Locale locale = new Locale("ja", "JP"); session.setLocale(locale); session.setOperator("NTT DOCOMO", "44010"); session.getContext().setDeviceAndSdkVersion("passion:8"); try { session.login(email, password, androidid); } catch (Exception e) { System.out.println("Error: failed to login.: " + e.getMessage()); System.exit(1); } AppsRequest appsRequest = AppsRequest.newBuilder().setQuery(query).setStartIndex(startIndex) .setEntriesCount(numbers).setWithExtendedInfo(true).build(); Callback<AppsResponse> callback = new Callback<AppsResponse>() { @Override public void onResult(ResponseContext context, AppsResponse response) { int totalcnt, cnt; JsonFactory factory = new JsonFactory(); try { JsonGenerator generator = factory.createGenerator(new FileWriter(new File("pkginfo.json"))); generator.writeStartObject(); //generator.setRootValueSeparator(new SerializedString("\n")); if (response != null) { totalcnt = response.getEntriesCount(); cnt = response.getAppCount(); System.out.println("startIndex = " + startIndex); System.out.println("entriesCount = " + numbers); System.out.println("totalcount = " + totalcnt); System.out.println("count = " + cnt); generator.writeNumberField("startIndex", startIndex); generator.writeNumberField("entriesCount", numbers); generator.writeNumberField("total", totalcnt); generator.writeNumberField("count", cnt); generator.writeRaw("\n"); } else { cnt = -1; } generator.writeFieldName("dataset"); generator.writeStartArray(); if (cnt > 0) { for (int i = 0; ((i < cnt) && (i < numbers)); i++) { generator.writeStartObject(); generator.writeNumberField("num", i + startIndex); System.out.println( "------------------------------------------------------------------------------------"); int counter = i + startIndex; System.out.println(counter + ":"); System.out.println( "------------------------------------------------------------------------------------"); generator.writeStringField("title", response.getApp(i).getTitle()); generator.writeStringField("appType", "" + response.getApp(i).getAppType()); generator.writeStringField("category", response.getApp(i).getExtendedInfo().getCategory()); generator.writeStringField("rating", response.getApp(i).getRating()); generator.writeNumberField("ratingCount", response.getApp(i).getRatingsCount()); generator.writeStringField("countText", response.getApp(i).getExtendedInfo().getDownloadsCountText()); generator.writeStringField("creatorId", response.getApp(i).getCreatorId()); generator.writeStringField("id", response.getApp(i).getId()); generator.writeStringField("packageName", response.getApp(i).getPackageName()); generator.writeStringField("version", response.getApp(i).getVersion()); generator.writeNumberField("versionCode", response.getApp(i).getVersionCode()); generator.writeStringField("price", response.getApp(i).getPrice()); generator.writeNumberField("priceMicros", response.getApp(i).getPriceMicros()); generator.writeStringField("priceCurrency", response.getApp(i).getPriceCurrency()); generator.writeStringField("contactWebsite", response.getApp(i).getExtendedInfo().getContactWebsite()); generator.writeNumberField("screenshotsCount", response.getApp(i).getExtendedInfo().getScreenshotsCount()); generator.writeNumberField("installSize", response.getApp(i).getExtendedInfo().getInstallSize()); generator.writeStringField("permissionIdList", "" + response.getApp(i).getExtendedInfo().getPermissionIdList()); generator.writeStringField("promotoText", response.getApp(i).getExtendedInfo().getPromoText()); generator.writeStringField("description", response.getApp(i).getExtendedInfo().getDescription()); System.out.println("title: " + response.getApp(i).getTitle()); System.out.println("appType: " + response.getApp(i).getAppType()); System.out.println("category: " + response.getApp(i).getExtendedInfo().getCategory()); System.out.println("rating: " + response.getApp(i).getRating()); System.out.println("ratingsCount: " + response.getApp(i).getRatingsCount()); System.out .println("count: " + response.getApp(i).getExtendedInfo().getDownloadsCount()); System.out.println( "countText: " + response.getApp(i).getExtendedInfo().getDownloadsCountText()); System.out.println("creator: " + response.getApp(i).getCreator()); System.out.println("creatorId: " + response.getApp(i).getCreatorId()); System.out.println("id: " + response.getApp(i).getId()); System.out.println("packageName: " + response.getApp(i).getPackageName()); System.out.println("version: " + response.getApp(i).getVersion()); //System.out.println("contactEmail: " + response.getApp(i).getExtendedInfo().getContactEmail()); //System.out.println("contactPhone: " + response.getApp(i).getExtendedInfo().getContactPhone()); System.out.println( "installSize: " + response.getApp(i).getExtendedInfo().getInstallSize()); generator.writeEndObject(); generator.writeRaw("\n"); } } else if (cnt == 0) { System.out.println("no hit"); } else { System.out.println("Bad Reqeust"); } generator.writeEndArray(); generator.writeEndObject(); generator.close(); } catch (Exception e) { System.out.println("Error: pkginfo(): " + e.getMessage()); } } // onResult() }; session.append(appsRequest, callback); session.flush(); }
From source file:edu.msu.cme.rdp.readseq.utils.ResampleSeqFile.java
public static void main(String[] args) throws IOException { int numOfSelection = 0; int subregion_length = 0; try {// w ww . j a va2 s . c om CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("num-selection")) { numOfSelection = Integer.parseInt(line.getOptionValue("num-selection")); if (numOfSelection < 1) { throw new Exception("num-selection should be at least 1"); } } if (line.hasOption("subregion_length")) { subregion_length = Integer.parseInt(line.getOptionValue("subregion_length")); if (subregion_length < 1) { throw new Exception("subregion_length should be at least 1"); } } args = line.getArgs(); if (args.length != 2) { throw new Exception("Incorrect number of command line arguments"); } ResampleSeqFile.select(args[0], args[1], numOfSelection, subregion_length); } catch (Exception e) { new HelpFormatter().printHelp(120, "ResampleSeqFile [options] <infile(dir)> <outdir>", "", options, ""); System.out.println("ERROR: " + e.getMessage()); return; } }
From source file:com.moss.appsnap.server.AppSnapServer.java
public static void main(String[] args) throws Exception { System.setProperty("org.mortbay.log.class", Slf4jLog.class.getName()); File log4jConfigFile = new File("log4j.xml"); if (log4jConfigFile.exists()) { DOMConfigurator.configureAndWatch(log4jConfigFile.getAbsolutePath(), 1000); } else {// ww w . j a v a 2 s.com BasicConfigurator.configure(); Logger.getRootLogger().setLevel(Level.INFO); } ServerConfiguration config; JAXBContext context = JAXBContext.newInstance(ServerConfiguration.class, VeracityId.class); JAXBHelper helper = new JAXBHelper(context); Logger log = Logger.getLogger(AppSnapServer.class); File[] configPaths = new File[] { new File("settings.xml"), new File(new File(System.getProperty("user.home")), ".appsnap-server.xml"), new File("/etc/appsnap-server.xml") }; File configFile = null; for (File next : configPaths) { if (next.exists()) { configFile = next; } } if (configFile == null) { log.warn("No config file found."); for (int x = configPaths.length - 1; x >= 0; x--) { File next = configPaths[x]; log.warn("Attempting to create default config file at " + next.getAbsolutePath()); ServerConfiguration defaults = new ServerConfiguration(); defaults.idProofRecipie( new PasswordProofRecipie(new SimpleId("mr-admin-dude"), "my-super-secret-password")); try { helper.writeToFile(helper.writeToXmlString(defaults), next); log.warn("done"); break; } catch (Exception e) { log.warn("Error writing file: " + e.getMessage(), e); } } System.exit(1); return; } else { log.info("Reading configuration from " + configFile.getAbsolutePath()); config = helper.readFromFile(configFile); } ProxyFactory proxyFactory = new ProxyFactory(new HessianProxyProvider()); try { new AppSnapServer(config, proxyFactory); } catch (Exception e) { e.printStackTrace(); System.out.println("Unexpected Error. Shutting Down."); System.exit(1); } }
From source file:importer.handler.post.stages.SAXSplitter.java
public static void main(String[] args) { if (args.length == 1) { File f = new File(args[0]); byte[] data = new byte[(int) f.length()]; try {/*from w w w . ja v a2 s .c o m*/ FileInputStream fis = new FileInputStream(f); fis.read(data); SAXSplitter ss = new SAXSplitter(); JSONArray jArr = ss.scan(new String(data, "UTF-8")); String jStr = jArr.toJSONString(); System.out.println(jStr.replaceAll("\\\\/", "/")); } catch (Exception e) { System.out.println(e.getMessage()); } } }
From source file:org.eclipse.lyo.client.oslc.samples.RTCFormSample.java
/** * Login to the RTC server and perform some OSLC actions * @param args/*from w ww .j a va2s .c om*/ * @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 RTCFormSample -url https://exmple.com:9443/ccm -user ADMIN -password ADMIN -project \"JKE Banking (Change 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 ChangeManagement catalog //RTC contains a service provider for CM and SCM, so we need to indicate our interest in CM JazzRootServicesHelper helper = new JazzRootServicesHelper(webContextUrl, OSLCConstants.OSLC_CM_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 ChangeManagement 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_CM_V2, OSLCConstants.CM_CHANGE_REQUEST_TYPE); //SCENARIO A: Run a query for all open ChangeRequests with OSLC paging of 10 items per //page turned on and list the members of the result OslcQueryParameters queryParams = new OslcQueryParameters(); queryParams.setWhere("oslc_cm:closed=false"); queryParams.setSelect("dcterms:identifier,dcterms:title,oslc_cm:status"); 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 ChangeRequest selecting only certain //attributes and then print it as raw XML. Change the dcterms:identifier below to match a //real workitem in your RTC project area OslcQueryParameters queryParams2 = new OslcQueryParameters(); queryParams2.setWhere("dcterms:identifier=\"10\""); queryParams2.setSelect( "dcterms:identifier,dcterms:title,dcterms:creator,dcterms:created,oslc_cm:status"); OslcQuery query2 = new OslcQuery(client, queryCapability, queryParams2); OslcQueryResult result2 = query2.submit(); ClientResponse rawResponse = result2.getRawResponse(); processRawResponse(rawResponse); rawResponse.consumeContent(); //SCENARIO C: RTC Workitem creation and update ChangeRequest changeRequest = new ChangeRequest(); changeRequest.setTitle("Implement accessibility in Pet Store application"); changeRequest.setDescription( "Image elements must provide a description in the 'alt' attribute for consumption by screen readers."); changeRequest.addTestedByTestCase(new Link(new URI("http://qmprovider/testcase/1"), "Accessibility verification using a screen reader")); changeRequest.addDctermsType("task"); //Get the Creation Factory URL for change requests so that we can create one String changeRequestCreation = client.lookupCreationFactory(serviceProviderUrl, OSLCConstants.OSLC_CM_V2, changeRequest.getRdfTypes()[0].toString()); //Create the change request ClientResponse creationResponse = client.createResource(changeRequestCreation, changeRequest, OslcMediaType.APPLICATION_RDF_XML, OslcMediaType.APPLICATION_RDF_XML); String changeRequestLocation = creationResponse.getHeaders().getFirst(HttpHeaders.LOCATION); creationResponse.consumeContent(); System.out.println("Change Request created a location " + changeRequestLocation); //Get the change request from the service provider and update its title property changeRequest = client.getResource(changeRequestLocation, OslcMediaType.APPLICATION_RDF_XML) .getEntity(ChangeRequest.class); changeRequest.setTitle(changeRequest.getTitle() + " (updated)"); //Create a partial update URL so that only the title will be updated. //Assuming (for readability) that the change request URL does not already contain a '?' String updateUrl = changeRequest.getAbout() + "?oslc.properties=dcterms:title"; //Update the change request at the service provider ClientResponse updateResponse = client.updateResource(updateUrl, changeRequest, OslcMediaType.APPLICATION_RDF_XML, OslcMediaType.APPLICATION_RDF_XML); updateResponse.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:com.genentech.chemistry.openEye.apps.SDFEStateCalculator.java
/** * @param args// w w w .j av a 2s.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_ESTATE_COUNT, false, "Output the the counts (occurrence) for each E-state atom group." + " E-state counts will be output if no output option is specified"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_SUM, false, "Output the sum of the E-state indices for each E-state atom group" + " in addition to the output of the" + " E-state atom groups."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_SYMBOL, false, "Output the E-state atom group symbol"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_UNASSIGNED_ATOMS, false, "Output atoms in the given molecules that" + " could not be assigned to an E-state atom group"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_UNASSIGNED_COUNT, false, "Output the number of atoms in the given molecules that" + " could not be assigned to an E-state atom group"); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_ESTATE_INDICE, false, "Output the E-state indice of all atoms in the given molecule" + " in one field."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_SMARTS, true, "Description of the group of interest. If specified, the" + " E-state indice of atoms matching the SMARTS are output" + " in separated fields."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_PRINT_DETAILS, false, "Output the details of the calculation to stderr"); 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 smarts = cmd.getOptionValue(OPT_SMARTS); boolean outputESIndex = cmd.hasOption(OPT_ESTATE_INDICE); boolean outputESCount = cmd.hasOption(OPT_ESTATE_COUNT); boolean outputESSum = cmd.hasOption(OPT_ESTATE_SUM); boolean outputESSymbol = cmd.hasOption(OPT_ESTATE_SYMBOL); boolean outputUnkCount = cmd.hasOption(OPT_UNASSIGNED_COUNT); boolean outputUnkAtoms = cmd.hasOption(OPT_UNASSIGNED_ATOMS); boolean printDetails = cmd.hasOption(OPT_PRINT_DETAILS); SDFEStateCalculator calculator = new SDFEStateCalculator(outFile); if (!outputESCount && !outputESSum && !outputUnkCount && !outputESSymbol && !outputESIndex && (smarts == null || smarts.length() == 0)) outputESCount = true; try { calculator.prepare(outputESCount, outputESSum, outputESSymbol, outputUnkCount, outputUnkAtoms, outputESIndex, smarts, printDetails); calculator.run(inFile); } finally { calculator.close(); } }