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From source file:calendarevent.CalendarEvent.java
/** * @param args the command line arguments *//*from w w w. j ava 2 s . c o m*/ public static void main(String[] args) { // TODO code application logic here /* This has to be replaced with the json data coming from the getJsonData() method Expecting the Json will be in the format from the above methid. */ String jsonString = "{\n" + " \"kind\": \"calendar#events\",\n" + " \"etag\": \"\\\"2DaeHpkENZGECFHdcr5l8tYxjD4/QElT1PHkP9d3G5VSndpdEMlSzKE\\\"\",\n" + " \"summary\": \"PushEvents\",\n" + " \"description\": \"Hackathon\",\n" + " \"updated\": \"2014-03-29T22:35:18.495Z\",\n" + " \"timeZone\": \"Asia/Calcutta\",\n" + " \"accessRole\": \"reader\",\n" + " \"items\": [\n" + " {\n" + " \"kind\": \"calendar#event\",\n" + " \"etag\": \"\\\"2DaeHpkENZGECFHdcr5l8tYxjD4/MTM5NjEyNTQwNzcxMTAwMA\\\"\",\n" + " \"id\": \"q28lprjb8ad3m17955lf1p9d48\",\n" + " \"status\": \"confirmed\",\n" + " \"htmlLink\": \"https://www.google.com/calendar/event?eid=cTI4bHByamI4YWQzbTE3OTU1bGYxcDlkNDggM3RvcjdvamZxaWhlamNqNjduOWw0dDhnMmNAZw\",\n" + " \"created\": \"2014-03-29T20:36:47.000Z\",\n" + " \"updated\": \"2014-03-29T20:36:47.711Z\",\n" + " \"summary\": \"Test API\",\n" + " \"creator\": {\n" + " \"email\": \"vrohitrao@gmail.com\",\n" + " \"displayName\": \"Rohith Vallu\"\n" + " },\n" + " \"organizer\": {\n" + " \"email\": \"3tor7ojfqihejcj67n9l4t8g2c@group.calendar.google.com\",\n" + " \"displayName\": \"PushEvents\",\n" + " \"self\": true\n" + " },\n" + " \"start\": {\n" + " \"dateTime\": \"2014-03-30T02:30:00+05:30\"\n" + " },\n" + " \"end\": {\n" + " \"dateTime\": \"2014-03-30T03:30:00+05:30\"\n" + " },\n" + " \"iCalUID\": \"q28lprjb8ad3m17955lf1p9d48@google.com\",\n" + " \"sequence\": 0\n" + " },\n" + " {\n" + " \"kind\": \"calendar#event\",\n" + " \"etag\": \"\\\"2DaeHpkENZGECFHdcr5l8tYxjD4/MTM5NjEzMjUzMjQxNzAwMA\\\"\",\n" + " \"id\": \"jgpue3stuo3js5qlsodob84voo\",\n" + " \"status\": \"confirmed\",\n" + " \"htmlLink\": \"https://www.google.com/calendar/event?eid=amdwdWUzc3R1bzNqczVxbHNvZG9iODR2b28gM3RvcjdvamZxaWhlamNqNjduOWw0dDhnMmNAZw\",\n" + " \"created\": \"2014-03-29T22:35:32.000Z\",\n" + " \"updated\": \"2014-03-29T22:35:32.417Z\",\n" + " \"summary\": \"Test Events\",\n" + " \"description\": \"Hack!!\",\n" + " \"location\": \"Northeastern University, Huntington Avenue, Boston, MA, United States\",\n" + " \"creator\": {\n" + " \"email\": \"vrohitrao@gmail.com\",\n" + " \"displayName\": \"Rohith Vallu\"\n" + " },\n" + " \"organizer\": {\n" + " \"email\": \"3tor7ojfqihejcj67n9l4t8g2c@group.calendar.google.com\",\n" + " \"displayName\": \"PushEvents\",\n" + " \"self\": true\n" + " },\n" + " \"start\": {\n" + " \"dateTime\": \"2014-03-30T04:30:00+05:30\"\n" + " },\n" + " \"end\": {\n" + " \"dateTime\": \"2014-03-30T19:30:00+05:30\"\n" + " },\n" + " \"visibility\": \"public\",\n" + " \"iCalUID\": \"jgpue3stuo3js5qlsodob84voo@google.com\",\n" + " \"sequence\": 0\n" + " }\n" + " ]\n" + "}"; Gson gson = new Gson(); try { JSONObject jsonData = new JSONObject(jsonString); JSONArray jsonArray = jsonData.getJSONArray("items"); JSONObject eventData; Event event = new Event(); for (int i = 0; i < jsonArray.length(); i++) { System.out.println(jsonArray.get(i).toString()); Items item = gson.fromJson(jsonArray.get(i).toString(), Items.class); event.setSummary(item.getSummary()); event.setLocation(item.getLocation()); /* Will be adding the attendees here ArrayList<EventAttendee> attendees = new ArrayList<EventAttendee>(); attendees.add(new EventAttendee().setEmail("attendeeEmail")); // ... event.setAttendees(attendees); */ Date startDate = new Date(); Date endDate = new Date(startDate.getTime() + 3600000); DateTime start = new DateTime(startDate, TimeZone.getDefault().getDefault().getTimeZone("UTC")); event.setStart(new EventDateTime().setDateTime(start)); DateTime end = new DateTime(endDate, TimeZone.getTimeZone("UTC")); event.setEnd(new EventDateTime().setDateTime(end)); HttpTransport transport = new NetHttpTransport(); JsonFactory jsonFactory = new JacksonFactory(); Calendar.Builder builder = new Calendar.Builder(transport, jsonFactory, null); String clientID = "937140966210.apps.googleusercontent.com"; String redirectURL = "urn:ietf:wg:oauth:2.0:oob"; String clientSecret = "qMFSb_cadYDG7uh3IDXWiMQY"; ArrayList<String> scope = new ArrayList<String>(); scope.add("https://www.googleapis.com/auth/calendar"); String url = new GoogleAuthorizationCodeRequestUrl(clientID, redirectURL, scope).build(); System.out.println("Go to the following link in your browser:"); System.out.println(url); // Read the authorization code from the standard input stream. BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); System.out.println("What is the authorization code?"); String code = in.readLine(); GoogleTokenResponse response = new GoogleAuthorizationCodeTokenRequest(transport, jsonFactory, clientID, clientSecret, redirectURL, code, redirectURL).execute(); GoogleCredential credential = new GoogleCredential().setFromTokenResponse(response); Calendar service = new Calendar.Builder(transport, jsonFactory, credential).build(); Event createdEvent = service.events().insert(item.getSummary(), event).execute(); System.out.println(createdEvent.getId()); } } catch (Exception e) { e.printStackTrace(); } }
From source file:com.genentech.chemistry.openEye.apps.SDFTopologicalIndexer.java
/** * @param args// w w w . j a v a2s. com */ 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); opt.setArgName("fn"); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); opt.setArgName("fn"); 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(); } if (args.length == 0) { System.err.println("Specify at least one index type"); exitWithHelp(options); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); Set<String> selectedIndexes = new HashSet<String>(args.length); if (args.length == 1 && "all".equalsIgnoreCase(args[0])) selectedIndexes = AVAILIndexes; else selectedIndexes.addAll(Arrays.asList(args)); if (!AVAILIndexes.containsAll(selectedIndexes)) { selectedIndexes.removeAll(AVAILIndexes); StringBuilder err = new StringBuilder("Unknown Index types: "); for (String it : selectedIndexes) err.append(it).append(" "); System.err.println(err); exitWithHelp(options); } SDFTopologicalIndexer sdfIndexer = new SDFTopologicalIndexer(outFile, selectedIndexes); sdfIndexer.run(inFile); sdfIndexer.close(); }
From source file:fr.ippon.pamelaChu.test.support.LdapTestServer.java
/** * Main class. We just do a lookup on the server to check that it's available. * <p/>/* w ww. j a v a 2 s. c o m*/ * FIXME : in Eclipse : when running this classes as "Java Application", target/test-classes is not added in the classpath * resulting in a java.lang.ClassNotFoundException ... * * @param args Not used. * @throws Exception */ public static void main(String[] args) throws Exception { FileUtils.deleteDirectory(workingDir); LdapTestServer ads = null; try { // Create the server ads = new LdapTestServer(); ads.start(); // Read an entry Entry result = ads.service.getAdminSession().lookup(new LdapDN("dc=ippon,dc=fr")); // And print it if available System.out.println("Found entry : " + result); } catch (Exception e) { // Ok, we have something wrong going on ... e.printStackTrace(); } System.out.println("Press enter"); new BufferedReader(new InputStreamReader(System.in)).readLine(); ads.stop(); }
From source file:com.example.geomesa.kafka08.KafkaLoadTester.java
public static void main(String[] args) throws Exception { // read command line args for a connection to Kafka CommandLineParser parser = new BasicParser(); Options options = getCommonRequiredOptions(); CommandLine cmd = parser.parse(options, args); String visibility = getVisibility(cmd); if (visibility == null) { System.out.println("visibility: null"); } else {//from www .j a v a 2s . c o m System.out.println("visibility: '" + visibility + "'"); } // create the producer and consumer KafkaDataStore objects Map<String, String> dsConf = getKafkaDataStoreConf(cmd); System.out.println("KDS config: " + dsConf); dsConf.put("isProducer", "true"); DataStore producerDS = DataStoreFinder.getDataStore(dsConf); dsConf.put("isProducer", "false"); DataStore consumerDS = DataStoreFinder.getDataStore(dsConf); // verify that we got back our KafkaDataStore objects properly if (producerDS == null) { throw new Exception("Null producer KafkaDataStore"); } if (consumerDS == null) { throw new Exception("Null consumer KafkaDataStore"); } // create the schema which creates a topic in Kafka // (only needs to be done once) final String sftName = "KafkaStressTest"; final String sftSchema = "name:String,age:Int,step:Double,lat:Double,dtg:Date,*geom:Point:srid=4326"; SimpleFeatureType sft = SimpleFeatureTypes.createType(sftName, sftSchema); // set zkPath to default if not specified String zkPath = (dsConf.get(ZK_PATH) == null) ? "/geomesa/ds/kafka" : dsConf.get(ZK_PATH); SimpleFeatureType preppedOutputSft = KafkaDataStoreHelper.createStreamingSFT(sft, zkPath); // only create the schema if it hasn't been created already if (!Arrays.asList(producerDS.getTypeNames()).contains(sftName)) producerDS.createSchema(preppedOutputSft); System.out.println("Register KafkaDataStore in GeoServer (Press enter to continue)"); System.in.read(); // the live consumer must be created before the producer writes features // in order to read streaming data. // i.e. the live consumer will only read data written after its instantiation SimpleFeatureStore producerFS = (SimpleFeatureStore) producerDS.getFeatureSource(sftName); SimpleFeatureSource consumerFS = consumerDS.getFeatureSource(sftName); // creates and adds SimpleFeatures to the producer every 1/5th of a second System.out.println("Writing features to Kafka... refresh GeoServer layer preview to see changes"); SimpleFeatureBuilder builder = new SimpleFeatureBuilder(sft); Integer numFeats = getLoad(cmd); System.out.println("Building a list of " + numFeats + " SimpleFeatures."); List<SimpleFeature> features = IntStream.range(1, numFeats) .mapToObj(i -> createFeature(builder, i, visibility)).collect(Collectors.toList()); // set variables to estimate feature production rate Long startTime = null; Long featuresSinceStartTime = 0L; int cycle = 0; int cyclesToSkip = 50000 / numFeats; // collect enough features // to get an accurate rate estimate while (true) { // write features features.forEach(feat -> { try { DefaultFeatureCollection featureCollection = new DefaultFeatureCollection(); featureCollection.add(feat); producerFS.addFeatures(featureCollection); } catch (Exception e) { System.out.println("Caught an exception while writing features."); e.printStackTrace(); } updateFeature(feat); }); // count features written Integer consumerSize = consumerFS.getFeatures().size(); cycle++; featuresSinceStartTime += consumerSize; System.out.println("At " + new Date() + " wrote " + consumerSize + " features"); // if we've collected enough features, calculate the rate if (cycle >= cyclesToSkip || startTime == null) { Long endTime = System.currentTimeMillis(); if (startTime != null) { Long diffTime = endTime - startTime; Double rate = (featuresSinceStartTime.doubleValue() * 1000.0) / diffTime.doubleValue(); System.out.printf("%.1f feats/sec (%d/%d)\n", rate, featuresSinceStartTime, diffTime); } cycle = 0; startTime = endTime; featuresSinceStartTime = 0L; } } }
From source file:com.act.biointerpretation.BiointerpretationDriver.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());// w ww. j a v a2s . 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; } if (cl.hasOption(OPTION_CONFIGURATION_FILE)) { List<BiointerpretationStep> steps; File configFile = new File(cl.getOptionValue(OPTION_CONFIGURATION_FILE)); if (!configFile.exists()) { String msg = String.format("Cannot find configuration file at %s", configFile.getAbsolutePath()); LOGGER.error(msg); throw new RuntimeException(msg); } // Read the whole config file. try (InputStream is = new FileInputStream(configFile)) { steps = OBJECT_MAPPER.readValue(is, new TypeReference<List<BiointerpretationStep>>() { }); } catch (IOException e) { LOGGER.error("Caught IO exception when attempting to read configuration file: %s", e.getMessage()); throw e; // Crash after logging if the config file can't be read. } // Ask for explicit confirmation before dropping databases. LOGGER.info("Biointerpretation plan:"); for (BiointerpretationStep step : steps) { crashIfInvalidDBName(step.getReadDBName()); crashIfInvalidDBName(step.getWriteDBName()); LOGGER.info("%s: %s -> %s", step.getOperation(), step.getReadDBName(), step.getWriteDBName()); } LOGGER.warn("WARNING: each DB to be written will be dropped before the writing step commences"); LOGGER.info("Proceed? [y/n]"); String readLine; try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) { readLine = reader.readLine(); } readLine.trim(); if ("y".equalsIgnoreCase(readLine) || "yes".equalsIgnoreCase(readLine)) { LOGGER.info("Biointerpretation plan confirmed, commencing"); for (BiointerpretationStep step : steps) { performOperation(step, true); } LOGGER.info("Biointerpretation plan completed"); } else { LOGGER.info("Biointerpretation plan not confirmed, exiting"); } } else if (cl.hasOption(OPTION_SINGLE_OPERATION)) { if (!cl.hasOption(OPTION_SINGLE_READ_DB) || !cl.hasOption(OPTION_SINGLE_WRITE_DB)) { String msg = "Must specify read and write DB names when performing a single operation"; LOGGER.error(msg); throw new RuntimeException(msg); } BiointerpretationOperation operation; try { operation = BiointerpretationOperation.valueOf(cl.getOptionValue(OPTION_SINGLE_OPERATION)); } catch (IllegalArgumentException e) { LOGGER.error("Caught IllegalArgumentException when trying to parse operation '%s': %s", cl.getOptionValue(OPTION_SINGLE_OPERATION), e.getMessage()); throw e; // Crash if we can't interpret the operation. } String readDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_READ_DB)); String writeDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_WRITE_DB)); performOperation(new BiointerpretationStep(operation, readDB, writeDB), false); } else { String msg = "Must specify either a config file or a single operation to perform."; LOGGER.error(msg); throw new RuntimeException(msg); } }
From source file:com.aestel.chemistry.openEye.fp.Fingerprinter.java
public static void main(String... args) throws IOException { long start = System.currentTimeMillis(); long iCounter = 0; // create command line Options object Options options = new Options(); Option opt = new Option("in", true, "input file [.ism,.sdf,...]"); opt.setRequired(true);//from www. j a va2 s . c om options.addOption(opt); opt = new Option("out", true, "output file .tsv or oe-supported"); opt.setRequired(true); options.addOption(opt); opt = new Option("idTag", true, "field with ID (default title)"); opt.setRequired(false); options.addOption(opt); opt = new Option("fpType", true, "fingerPrintType: maccs|linear7|linear7*4|HashLinear7*4\n" + " maccs: generate maccs keys\n" + " linear7 generate 7 bonds long linear fingerprints (210k known rest hashed)\n" + " linear7*4 linear 7 bonds if more than 4 atoms code atoms as * (5.1k known rest hashed)\n" + " HashLinear7*4: as linear7*4 but hashed to 16k"); opt.setRequired(true); options.addOption(opt); opt = new Option("format", true, "folded512|folded2048|bitList|fragList|none\n" + " folded512/2048: hex encoded 512/2048 bits\n" + " bitList: list of bitpositions\n" + " none: no fp output for use with writeCodeMap"); opt.setRequired(true); options.addOption(opt); opt = new Option("writeCodeMap", false, "Overwrite the codeMap file at the end of processing"); 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 idTag = null; if (cmd.hasOption("idTag")) idTag = cmd.getOptionValue("idTag"); String outformat = cmd.getOptionValue("format").toLowerCase().intern(); if (args.length != 0) { exitWithHelp(options); } String type = cmd.getOptionValue("fpType"); boolean updateDictionaryFile = cmd.hasOption("writeCodeMap"); boolean hashUnknownFrag = true; if (type.equals("HashLinear7*4")) hashUnknownFrag = false; if (type.equals("maccs")) hashUnknownFrag = false; if (updateDictionaryFile) hashUnknownFrag = false; Fingerprinter fprinter = createFingerprinter(type, updateDictionaryFile, hashUnknownFrag); OEMolBase mol = new OEGraphMol(); String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); oemolistream ifs = new oemolistream(inFile); Runtime rt = Runtime.getRuntime(); Outputter out; if (outFile.endsWith(".txt") || outFile.endsWith(".tab")) out = new TabOutputter(fprinter.getMapper(), outFile, outformat); else out = new OEOutputter(fprinter.getMapper(), outFile, type, outformat); while (oechem.OEReadMolecule(ifs, mol)) { iCounter++; Fingerprint fp = fprinter.getFingerprint(mol); String id; if (idTag == null) id = mol.GetTitle(); else id = oechem.OEGetSDData(mol, idTag); if (iCounter % 100 == 0) System.err.print("."); if (iCounter % 4000 == 0) { System.err.printf(" %d %dsec\tt=%d f=%d u=%d m=%d tf=%d\n", iCounter, (System.currentTimeMillis() - start) / 1000, rt.totalMemory() / 1024, rt.freeMemory() / 1024, (rt.totalMemory() - rt.freeMemory()) / 1024, rt.maxMemory() / 1024, (rt.freeMemory() + (rt.maxMemory() - rt.totalMemory())) / 1024); } out.output(id, mol, fp); } System.err.printf("Fingerprinter: Read %d structures in %d sec\n", iCounter, (System.currentTimeMillis() - start) / 1000); if (updateDictionaryFile) fprinter.writeDictionary(); out.close(); fprinter.close(); }
From source file:com.splout.db.dnode.TCPStreamer.java
/** * This main method can be used for testing the TCP interface directly to a * local DNode. Will ask for protocol input from Stdin and print output to * Stdout/*from w ww . j ava2 s . co m*/ */ public static void main(String[] args) throws UnknownHostException, IOException, SerializationException { SploutConfiguration config = SploutConfiguration.get(); Socket clientSocket = new Socket("localhost", config.getInt(DNodeProperties.STREAMING_PORT)); DataInputStream inFromServer = new DataInputStream(new BufferedInputStream(clientSocket.getInputStream())); DataOutputStream outToServer = new DataOutputStream( new BufferedOutputStream(clientSocket.getOutputStream())); BufferedReader reader = new BufferedReader(new InputStreamReader(System.in)); System.out.println("Enter tablespace: "); String tablespace = reader.readLine(); System.out.println("Enter version number: "); long versionNumber = Long.parseLong(reader.readLine()); System.out.println("Enter partition: "); int partition = Integer.parseInt(reader.readLine()); System.out.println("Enter query: "); String query = reader.readLine(); outToServer.writeUTF(tablespace); outToServer.writeLong(versionNumber); outToServer.writeInt(partition); outToServer.writeUTF(query); outToServer.flush(); byte[] buffer = new byte[0]; boolean read; do { read = false; int nBytes = inFromServer.readInt(); if (nBytes > 0) { buffer = new byte[nBytes]; int inRead = inFromServer.read(buffer); if (inRead > 0) { Object[] res = ResultSerializer.deserialize(ByteBuffer.wrap(buffer), Object[].class); read = true; System.out.println(Arrays.toString(res)); } } } while (read); clientSocket.close(); }
From source file:jackrabbit.app.App.java
public static void main(String[] args) { if (args.length == 0 || args.length == 1 && args[0].equals("-h")) { System.out.println("Usage: java -jar ackrabbit-migration-query-tool-" + VERSION + "-jar-with-dependencies.jar " + "--src src --src-conf conf [--src-repo-path path] [--src-user src_user] [--src-passwd src_pw] " + "[--dest-user dest_user] [--dest-passwd dest_pw] [--dest dest] [--dest-conf conf] [--dest-repo-path path] " + "[--cnd cnd] [--node-limit limit] " + "[--query-type type] [--query query]"); System.out.println("\t --src source repository directory"); System.out.println("\t --src-conf source repository configuration file"); System.out.println("\t --src-repo-path path to source node to copy from; default is \"/\""); System.out.println("\t --src-user source repository login"); System.out.println("\t --src-passwd source repository password"); System.out.println("\t --dest destination repository directory"); System.out.println("\t --dest-conf destination repository configuration file"); System.out.println("\t --dest-repo-path path to destination node to copy to; default is \"/\""); System.out.println("\t --dest-user destination repository login"); System.out.println("\t --dest-passwd destination repository password"); System.out.println(//from w w w . j ava2 s . c o m "\t --node-limit size to partition nodes with before copying. If it is not supplied, no partitioning is performed"); System.out.println("\t --cnd common node type definition file"); System.out.println( "\t --query query to run in src. If --query is specified, then --dest, --dest-conf, --dest-repo-path and --cnd will be ignored."); System.out.println("\t --query-type query type (sql, xpath, JCR-SQL2); default is JCR-SQL2"); return; } for (int i = 0; i < args.length; i = i + 2) { if (args[i].equals("--src") && i + 1 < args.length) { srcRepoDir = args[i + 1]; } else if (args[i].equals("--dest") && i + 1 < args.length) { destRepoDir = args[i + 1]; } else if (args[i].equals("--src-conf") && i + 1 < args.length) { srcConf = args[i + 1]; } else if (args[i].equals("--dest-conf") && i + 1 < args.length) { destConf = args[i + 1]; } else if (args[i].equals("--src-repo-path") && i + 1 < args.length) { srcRepoPath = args[i + 1]; } else if (args[i].equals("--dest-repo-path") && i + 1 < args.length) { destRepoPath = args[i + 1]; } else if (args[i].equals("--src-user") && i + 1 < args.length) { srcUser = args[i + 1]; } else if (args[i].equals("--src-passwd") && i + 1 < args.length) { srcPasswd = args[i + 1]; } else if (args[i].equals("--dest-user") && i + 1 < args.length) { destUser = args[i + 1]; } else if (args[i].equals("--dest-passwd") && i + 1 < args.length) { destPasswd = args[i + 1]; } else if (args[i].equals("--node-limit") && i + 1 < args.length) { nodeLimit = Long.parseLong(args[i + 1]); } else if (args[i].equals("--cnd") && i + 1 < args.length) { cndPath = args[i + 1]; } else if (args[i].equals("--query") && i + 1 < args.length) { query = args[i + 1]; } else if (args[i].equals("--query-type") && i + 1 < args.length) { queryType = args[i + 1]; } } boolean missingArgs = false; if (srcRepoDir.isEmpty()) { missingArgs = true; log.error("Please specify the --src option."); } if (destRepoDir.isEmpty() && !destConf.isEmpty()) { missingArgs = true; log.error("Please specify the --dest option."); } if (srcConf.isEmpty()) { missingArgs = true; log.error("Please specify the --src-conf option."); } if (destConf.isEmpty() && !destRepoDir.isEmpty()) { missingArgs = true; log.error("Please specify the --dest-conf option."); } if (missingArgs) return; SimpleCredentials credentials = new SimpleCredentials(srcUser, srcPasswd.toCharArray()); SimpleCredentials destCredentials = new SimpleCredentials(destUser, destPasswd.toCharArray()); JackrabbitRepository dest = null; RepositoryFactory destRf = null; RepositoryFactory srcRf = new RepositoryFactoryImpl(srcConf, srcRepoDir); if (!destConf.isEmpty()) { destRf = new RepositoryFactoryImpl(destConf, destRepoDir); } try { final JackrabbitRepository src = srcRf.getRepository(); SessionFactory srcSf = new SessionFactoryImpl(src, credentials); final Session srcSession = srcSf.getSession(); Runtime.getRuntime().addShutdownHook(new Thread() { public void run() { srcSession.logout(); src.shutdown(); } }); if (destConf.isEmpty()) {//query mode BufferedReader in = new BufferedReader(new InputStreamReader(System.in, "UTF-8")); if (query.isEmpty()) { while (true) { System.out.print(">"); String line = in.readLine(); if (line == null || line.isEmpty() || line.equalsIgnoreCase("quit") || line.equalsIgnoreCase("exit")) { break; } try { runQuery(srcSession, line, queryType); } catch (RepositoryException e) { log.error(e.getMessage(), e); } } } else { try { runQuery(srcSession, query, queryType); } catch (RepositoryException e) { log.error(e.getMessage(), e); } } return; } dest = destRf.getRepository(); SessionFactory destSf = new SessionFactoryImpl(dest, destCredentials); Session destSession = destSf.getSession(); try { RepositoryManager.registerCustomNodeTypes(destSession, cndPath); if (nodeLimit == 0) NodeCopier.copy(srcSession, destSession, srcRepoPath, destRepoPath, true); else NodeCopier.copy(srcSession, destSession, srcRepoPath, destRepoPath, nodeLimit, true); log.info("Copying " + srcSession.getWorkspace().getName() + " to " + destSession.getWorkspace().getName() + " for " + srcRepoDir + " done."); } catch (ParseException e) { log.error(e.getMessage(), e); } catch (IOException e) { log.error(e.getMessage(), e); } catch (PathNotFoundException e) { log.error(e.getMessage(), e); } catch (RepositoryException e) { log.error(e.getMessage(), e); } List<String> destWkspaces = RepositoryManager.getDestinationWorkspaces(srcSession, destSession); for (String workspace : destWkspaces) { Session wsSession = srcSf.getSession(workspace); Session wsDestSession = destSf.getSession(workspace); try { RepositoryManager.registerCustomNodeTypes(wsDestSession, cndPath); if (nodeLimit == 0) NodeCopier.copy(wsSession, wsDestSession, srcRepoPath, destRepoPath, true); else { NodeCopier.copy(wsSession, wsDestSession, srcRepoPath, destRepoPath, nodeLimit, true); } log.info("Copying " + wsSession.getWorkspace().getName() + " to " + wsDestSession.getWorkspace().getName() + " for " + srcRepoDir + " done."); } catch (IOException e) { log.error(e.getMessage(), e); } catch (ParseException e) { log.error(e.getMessage(), e); } catch (PathNotFoundException e) { log.error(e.getMessage(), e); } catch (RepositoryException e) { log.error(e.getMessage(), e); } finally { wsSession.logout(); wsDestSession.logout(); } } } catch (IOException e) { log.error(e.getMessage(), e); } catch (PathNotFoundException e) { log.error(e.getMessage(), e); } catch (RepositoryException e) { log.error(e.getMessage(), e); } finally { if (dest != null) dest.shutdown(); } }
From source file:com.genentech.chemistry.tool.mm.SDFMMMinimize.java
/** * Main function for running on the command line * @param args/*from w ww .ja v a 2 s .co 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.trsst.Command.java
public static void main(String[] argv) { // during alpha period: expire after one week Date builtOn = Common.getBuildDate(); if (builtOn != null) { long weekMillis = 1000 * 60 * 60 * 24 * 7; Date expiry = new Date(builtOn.getTime() + weekMillis); if (new Date().after(expiry)) { System.err.println("Build expired on: " + expiry); System.err.println("Please obtain a more recent build for testing."); System.exit(1);//from www . j a v a 2 s . c o m } else { System.err.println("Build will expire on: " + expiry); } } // experimental tor support boolean wantsTor = false; for (String s : argv) { if ("--tor".equals(s)) { wantsTor = true; break; } } if (wantsTor && !HAS_TOR) { try { log.info("Attempting to connect to tor network..."); Security.addProvider(new BouncyCastleProvider()); JvmGlobalUtil.init(); NetLayer netLayer = NetFactory.getInstance().getNetLayerById(NetLayerIDs.TOR); JvmGlobalUtil.setNetLayerAndNetAddressNameService(netLayer, true); log.info("Connected to tor network"); HAS_TOR = true; } catch (Throwable t) { log.error("Could not connect to tor: exiting", t); System.exit(1); } } // if unspecified, default relay to home.trsst.com if (System.getProperty("com.trsst.server.relays") == null) { System.setProperty("com.trsst.server.relays", "https://home.trsst.com/feed"); } // default to user-friendlier file names String home = System.getProperty("user.home", "."); if (System.getProperty("com.trsst.client.storage") == null) { File client = new File(home, "Trsst Accounts"); System.setProperty("com.trsst.client.storage", client.getAbsolutePath()); } if (System.getProperty("com.trsst.server.storage") == null) { File server = new File(home, "Trsst System Cache"); System.setProperty("com.trsst.server.storage", server.getAbsolutePath()); } // TODO: try to detect if launching from external volume like a flash // drive and store on the local flash drive instead Console console = System.console(); int result; try { if (console == null && argv.length == 0) { argv = new String[] { "serve", "--gui" }; } result = new Command().doBegin(argv, System.out, System.in); // task queue prevents exit unless stopped if (TrsstAdapter.TASK_QUEUE != null) { TrsstAdapter.TASK_QUEUE.cancel(); } } catch (Throwable t) { result = 1; // "general catchall error code" log.error("Unexpected error, exiting.", t); } // if error if (result != 0) { // force exit System.exit(result); } }