List of usage examples for java.lang String equals
public boolean equals(Object anObject)
From source file:edu.umass.cs.gigapaxos.paxospackets.RequestPacket.java
public static void main(String[] args) throws UnsupportedEncodingException, UnknownHostException { Util.assertAssertionsEnabled(); int numReqs = 25; RequestPacket[] reqs = new RequestPacket[numReqs]; RequestPacket req = new RequestPacket("asd" + 999, true); for (int i = 0; i < numReqs; i++) { reqs[i] = new RequestPacket("asd" + i, true); }//from w w w. j a v a 2 s. co m System.out.println("Decision size estimate = " + SIZE_ESTIMATE); req.latchToBatch(reqs); String reqStr = req.toString(); try { RequestPacket reqovered = new RequestPacket(req.toJSONObject()); String reqoveredStr = reqovered.toString(); assert (reqStr.equals(reqoveredStr)); System.out.println("batchSize = " + reqovered.batched.length); // System.out.println(reqovered.batched[3]); System.out.println(samplePValue); System.out.println(reqs[1]); System.out.println(new RequestPacket(reqs[1].toBytes())); System.out.println(req); System.out.println(reqovered = new RequestPacket(req.toBytes())); assert (req.toString().equals(reqovered.toString())); } catch (JSONException e) { e.printStackTrace(); } }
From source file:agilejson.Base64.java
/** * Main program. Used for testing.//from w ww . java 2s. c o m * * Encodes or decodes two files from the command line * * @param args command arguments */ public final static void main(String[] args) { if (args.length < 3) { usage("Not enough arguments."); } else { String flag = args[0]; String infile = args[1]; String outfile = args[2]; if (flag.equals("-e")) { // encode encodeFileToFile(infile, outfile); } else if (flag.equals("-d")) { // decode decodeFileToFile(infile, outfile); } else { usage("Unknown flag: " + flag); } } }
From source file:com.healthmarketscience.rmiio.RemoteStreamServerTest.java
public static void main(String[] args) throws Exception { int argc = 0; String appType = null; if (args.length > argc) { appType = args[argc++];// ww w . j av a 2s .co m } // create sub-argument list int subArgsLength = ((args.length > argc) ? (args.length - argc) : 0); String[] subArgs = new String[subArgsLength]; if (subArgsLength > 0) { System.arraycopy(args, argc, subArgs, 0, subArgsLength); } List<AccumulateRemoteStreamMonitor<?>> monitors = new ArrayList<AccumulateRemoteStreamMonitor<?>>(); List<Throwable> clientExceptions = new ArrayList<Throwable>(); if (appType.equals("-server")) { FileServer.main(subArgs); } else if (appType.equals("-client")) { FileClient.main(subArgs); } else if (appType.equals("-test")) { mainTest(subArgs, clientExceptions, null); } else { LOG.debug("First argument must be '-server' or 'client'"); System.exit(1); } if (!clientExceptions.isEmpty()) { LOG.debug("Client exceptions: " + clientExceptions); } }
From source file:edu.brown.costmodel.SingleSitedCostModel.java
/** * MAIN!/*w ww .ja va2s. c o m*/ * * @param vargs * @throws Exception */ public static void main(String[] vargs) throws Exception { ArgumentsParser args = ArgumentsParser.load(vargs); args.require(ArgumentsParser.PARAM_CATALOG, ArgumentsParser.PARAM_WORKLOAD, ArgumentsParser.PARAM_PARTITION_PLAN); assert (args.workload.getTransactionCount() > 0) : "No transactions were loaded from " + args.workload_path; if (args.hasParam(ArgumentsParser.PARAM_CATALOG_HOSTS)) { ClusterConfiguration cc = new ClusterConfiguration(args.getParam(ArgumentsParser.PARAM_CATALOG_HOSTS)); args.updateCatalog(FixCatalog.addHostInfo(args.catalog, cc), null); } // Enable compact output final boolean table_output = (args.getOptParams().contains("table")); // If given a PartitionPlan, then update the catalog File pplan_path = new File(args.getParam(ArgumentsParser.PARAM_PARTITION_PLAN)); PartitionPlan pplan = new PartitionPlan(); pplan.load(pplan_path.getAbsolutePath(), args.catalog_db); if (args.getBooleanParam(ArgumentsParser.PARAM_PARTITION_PLAN_REMOVE_PROCS, false)) { for (Procedure catalog_proc : pplan.proc_entries.keySet()) { pplan.setNullProcParameter(catalog_proc); } // FOR } if (args.getBooleanParam(ArgumentsParser.PARAM_PARTITION_PLAN_RANDOM_PROCS, false)) { for (Procedure catalog_proc : pplan.proc_entries.keySet()) { pplan.setRandomProcParameter(catalog_proc); } // FOR } pplan.apply(args.catalog_db); System.out.println("Applied PartitionPlan '" + pplan_path + "' to catalog\n" + pplan); System.out.print(StringUtil.DOUBLE_LINE); // if (!table_output) { // // } // } else if (!table_output) { // System.err.println("PartitionPlan file '" + pplan_path + // "' does not exist. Ignoring..."); // } if (args.hasParam(ArgumentsParser.PARAM_PARTITION_PLAN_OUTPUT)) { String output = args.getParam(ArgumentsParser.PARAM_PARTITION_PLAN_OUTPUT); if (output.equals("-")) output = pplan_path.getAbsolutePath(); pplan.save(output); System.out.println("Saved PartitionPlan to '" + output + "'"); } System.out.flush(); // TODO: REMOVE STORED PROCEDURE ROUTING FOR SCHISM long singlepartition = 0; long multipartition = 0; long total = 0; SingleSitedCostModel costmodel = new SingleSitedCostModel(args.catalog_db); Collection<Integer> all_partitions = CatalogUtil.getAllPartitionIds(args.catalog_db); // costmodel.setEntropyWeight(4.0); // costmodel.setJavaExecutionWeightEnabled(true); // costmodel.setJavaExecutionWeight(100); // XXX: 2011-10-28 costmodel.setCachingEnabled(true); Histogram<String> hist = new Histogram<String>(); for (int i = 0; i < 2; i++) { ProfileMeasurement time = new ProfileMeasurement("costmodel").start(); hist.clear(); for (AbstractTraceElement<? extends CatalogType> element : args.workload) { if (element instanceof TransactionTrace) { total++; TransactionTrace xact = (TransactionTrace) element; boolean is_singlesited = costmodel.processTransaction(args.catalog_db, xact, null).singlesited; if (is_singlesited) { singlepartition++; hist.put(xact.getCatalogItemName()); } else { multipartition++; if (!hist.contains(xact.getCatalogItemName())) hist.put(xact.getCatalogItemName(), 0); } } } // FOR System.err.println("ESTIMATE TIME: " + time.stop().getTotalThinkTimeSeconds()); break; // XXX } // FOR // long total_partitions_touched_txns = // costmodel.getTxnPartitionAccessHistogram().getSampleCount(); // long total_partitions_touched_queries = // costmodel.getQueryPartitionAccessHistogram().getSampleCount(); Histogram<Integer> h = null; if (!table_output) { System.out.println("Workload Procedure Histogram:"); System.out.println(StringUtil.addSpacers(args.workload.getProcedureHistogram().toString())); System.out.print(StringUtil.DOUBLE_LINE); System.out.println("SinglePartition Procedure Histogram:"); System.out.println(StringUtil.addSpacers(hist.toString())); System.out.print(StringUtil.DOUBLE_LINE); System.out.println("Java Execution Histogram:"); h = costmodel.getJavaExecutionHistogram(); h.setKeepZeroEntries(true); h.putAll(all_partitions, 0); System.out.println(StringUtil.addSpacers(h.toString())); System.out.print(StringUtil.DOUBLE_LINE); System.out.println("Transaction Partition Histogram:"); h = costmodel.getTxnPartitionAccessHistogram(); h.setKeepZeroEntries(true); h.putAll(all_partitions, 0); System.out.println(StringUtil.addSpacers(h.toString())); System.out.print(StringUtil.DOUBLE_LINE); System.out.println("Query Partition Touch Histogram:"); h = costmodel.getQueryPartitionAccessHistogram(); h.setKeepZeroEntries(true); h.putAll(all_partitions, 0); System.out.println(StringUtil.addSpacers(h.toString())); System.out.print(StringUtil.DOUBLE_LINE); } Map<String, Object> maps[] = new Map[2]; int idx = 0; ListOrderedMap<String, Object> m = null; // Execution Cost m = new ListOrderedMap<String, Object>(); m.put("SINGLE-PARTITION", singlepartition); m.put("MULTI-PARTITION", multipartition); m.put("TOTAL", total + " [" + singlepartition / (double) total + "]"); m.put("PARTITIONS TOUCHED (TXNS)", costmodel.getTxnPartitionAccessHistogram().getSampleCount()); m.put("PARTITIONS TOUCHED (QUERIES)", costmodel.getQueryPartitionAccessHistogram().getSampleCount()); maps[idx++] = m; // Utilization m = new ListOrderedMap<String, Object>(); costmodel.getJavaExecutionHistogram().setKeepZeroEntries(false); int active_partitions = costmodel.getJavaExecutionHistogram().getValueCount(); m.put("ACTIVE PARTITIONS", active_partitions); m.put("IDLE PARTITIONS", (all_partitions.size() - active_partitions)); // System.out.println("Partitions Touched By Queries: " + // total_partitions_touched_queries); Histogram<Integer> entropy_h = costmodel.getJavaExecutionHistogram(); m.put("JAVA SKEW", SkewFactorUtil.calculateSkew(all_partitions.size(), entropy_h.getSampleCount(), entropy_h)); entropy_h = costmodel.getTxnPartitionAccessHistogram(); m.put("TRANSACTION SKEW", SkewFactorUtil.calculateSkew(all_partitions.size(), entropy_h.getSampleCount(), entropy_h)); // TimeIntervalCostModel<SingleSitedCostModel> timecostmodel = new // TimeIntervalCostModel<SingleSitedCostModel>(args.catalog_db, // SingleSitedCostModel.class, 1); // timecostmodel.estimateCost(args.catalog_db, args.workload); // double entropy = timecostmodel.getLastEntropyCost() m.put("UTILIZATION", (costmodel.getJavaExecutionHistogram().getValueCount() / (double) all_partitions.size())); maps[idx++] = m; System.out.println(StringUtil.formatMaps(maps)); }
From source file:com.serena.rlc.provider.tfs.client.TFSClient.java
static public void main(String[] args) { TFSClient tfs = new TFSClient(null, "https://digitalparkingsolutions.visualstudio.com", "1.0", "https://digitalparkingsolutions.vsrm.visualstudio.com", "3.0-preview.1", "2.0", "DefaultCollection", "kevinalee", "67popgoaxbdm2ducvhaf54fgmtzbouronq22rfdb6fddt542c3va"); Project firstProj = null;//from w ww . j a va2s. co m Query firstQuery = null; WorkItem firstWorkItem = null; ReleaseDefinition firstReleaseDefinition = null; Release firstRelease = null; Environment firstEnvironment = null; BuildDefinition firstBuildDefinition = null; BuildQueue firstBuildQueue = null; Build firstBuild = null; System.out.println("Retrieving TFS Projects..."); List<Project> projects = null; try { projects = tfs.getProjects(); for (Project p : projects) { if (firstProj == null) firstProj = p; System.out.println("Found Project: " + p.getTitle()); System.out.println("Description: " + p.getDescription()); System.out.println("URL: " + p.getUrl()); } } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Retrieving TFS Queries..."); List<Query> queries = null; try { queries = tfs.getQueries(firstProj.getId(), "Shared Queries"); for (Query q : queries) { if (firstQuery == null) firstQuery = q; System.out.println("Found Query: " + q.getTitle()); System.out.println("Path: " + q.getPath()); System.out.println("URL: " + q.getUrl()); } } catch (TFSClientException e) { System.out.print(e.toString()); } for (Query query : queries) { System.out.println("Retrieving Work Items for Query: " + query.getTitle()); if (query.getIsFolder()) continue; List<WorkItem> workItems = null; try { workItems = tfs.getWorkItems(query.getId(), "", 2); if (workItems != null) { for (WorkItem wi : workItems) { if (firstWorkItem == null) firstWorkItem = wi; System.out.println("Found Work Item: " + wi.getId()); System.out.println("Title: " + wi.getTitle()); System.out.println("Description: " + wi.getDescription()); System.out.println("Severity: " + wi.getSeverity()); } } } catch (TFSClientException e) { System.out.print(e.toString()); } } System.out.println("Retrieving Work Item: " + firstWorkItem.getId() + "..."); try { WorkItem wi = tfs.getWorkItem(firstWorkItem.getId()); System.out.println("Found Work Item: " + wi.getId()); System.out.println("Title: " + wi.getTitle()); System.out.println("State: " + wi.getState()); System.out.println("Severity: " + wi.getSeverity()); System.out.println("Type: " + wi.getType()); System.out.println("Project: " + wi.getProject()); } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Retrieving TFS Release Definitions..."); List<ReleaseDefinition> releaseDefinitions = null; try { releaseDefinitions = tfs.getReleaseDefinitions(firstProj.getId()); for (ReleaseDefinition rd : releaseDefinitions) { if (firstReleaseDefinition == null) firstReleaseDefinition = rd; System.out.println("Found Release Definition: " + rd.getId() + " - " + rd.getTitle()); System.out.println("URL: " + rd.getUrl()); } } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Retrieving TFS Releases..."); List<Release> releases = null; try { releases = tfs.getReleases(firstProj.getId(), firstReleaseDefinition.getId()); for (Release r : releases) { if (firstRelease == null) firstRelease = r; System.out.println("Found Release: " + r.getId() + " - " + r.getTitle()); System.out.println("Status: " + r.getState()); for (Environment e : r.getEnvironments()) { if (firstEnvironment == null) { firstEnvironment = e; } System.out.println("with Environment: " + e.getId() + " - " + e.getTitle()); } } } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Deploying Release " + firstRelease.getTitle() + " to " + firstEnvironment.getTitle()); try { Release release = tfs.deployRelease(firstProj.getId(), firstRelease.getId(), firstEnvironment.getId()); System.out.println("Release " + release.getTitle() + " has status: " + release.getState()); } catch (TFSClientException e) { System.out.print(e.toString()); } int pollCount = 0; String deployStatus = null; while (pollCount < 100) { try { Thread.sleep(6000); deployStatus = tfs.getReleaseEnvironmentStatus(firstProj.getId(), firstRelease.getId(), firstEnvironment.getId()); System.out.println("Environment Deployment Status = " + deployStatus); } catch (TFSClientException e) { logger.debug("Error checking release status ({}) - {}", firstRelease.getId(), e.getMessage()); } catch (InterruptedException e) { } if (deployStatus != null && (deployStatus.equals("succeeded") || deployStatus.equals("rejected") || deployStatus.equals("failed"))) { break; } pollCount++; } if (deployStatus != null && deployStatus.equals("succeeded")) { System.out.println("Release " + firstRelease.getTitle() + " has succeeded"); } else { System.out.println("Release " + firstRelease.getTitle() + " has failed/rejected or its status cannot be retrieved."); } System.out.println("Retrieving TFS Build Definitions..."); List<BuildDefinition> buildDefinitions = null; try { buildDefinitions = tfs.getBuildDefinitions(firstProj.getId(), ""); for (BuildDefinition bd : buildDefinitions) { if (firstBuildDefinition == null) firstBuildDefinition = bd; System.out.println("Found Build Definition: " + bd.getId() + " - " + bd.getTitle()); System.out.println("URL: " + bd.getUrl()); } } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Retrieving TFS Build Queues..."); List<BuildQueue> buildQueues = null; try { buildQueues = tfs.getBuildQueues("buildController", ""); for (BuildQueue bq : buildQueues) { if (firstBuildQueue == null) firstBuildQueue = bq; System.out.println("Found Build Queue: " + bq.getId() + " - " + bq.getTitle()); System.out.println("URL: " + bq.getUrl()); } } catch (TFSClientException e) { System.out.print(e.toString()); } System.out.println("Retrieving TFS Builds..."); List<Build> builds = null; try { builds = tfs.getBuilds(firstProj.getId(), firstBuildDefinition.getId(), "", "", 50); for (Build b : builds) { if (firstBuild == null) firstBuild = b; System.out.println("Found Build: " + b.getId() + " - " + b.getBuildNumber()); System.out.println("Status: " + b.getState()); System.out.println("Result: " + b.getBuildResult()); } } catch (TFSClientException e) { System.out.print(e.toString()); } Build queuedBuild = null; System.out.println("Queuing Build for Definition " + firstBuildDefinition.getTitle()); try { queuedBuild = tfs.queueBuild(firstProj.getId(), firstBuildDefinition.getId(), firstBuildQueue.getId(), null); System.out.println("Build " + queuedBuild.getBuildNumber() + " has status: " + queuedBuild.getState()); } catch (TFSClientException e) { System.out.print(e.toString()); } pollCount = 0; String buildStatus = null; String buildResult = null; while (pollCount < 100) { try { Thread.sleep(6000); Build tmpBuild = tfs.getBuild(firstProj.getId(), queuedBuild.getId()); buildStatus = tmpBuild.getState(); System.out.println("Build Status = " + buildStatus); System.out.println("Build Result = " + buildResult); } catch (TFSClientException e) { logger.debug("Error checking build status ({}) - {}", queuedBuild.getId(), e.getMessage()); } catch (InterruptedException e) { } if (buildStatus != null && buildStatus.equals("completed")) { break; } pollCount++; } if (buildStatus != null && buildStatus.equals("completed")) { System.out.println("Build " + queuedBuild.getId() + " has completed with result " + buildResult); } else { System.out.println("Build " + queuedBuild.getId() + " result cannot be retrieved."); } }
From source file:com.adobe.aem.demomachine.RegExp.java
public static void main(String[] args) throws IOException { String fileName = null;//from w w w. j a va 2s. c o m String regExp = null; String position = null; String value = "n/a"; List<String> allMatches = new ArrayList<String>(); // Command line options for this tool Options options = new Options(); options.addOption("f", true, "Filename"); options.addOption("r", true, "RegExp"); options.addOption("p", true, "Position"); CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("f")) { fileName = cmd.getOptionValue("f"); } if (cmd.hasOption("f")) { regExp = cmd.getOptionValue("r"); } if (cmd.hasOption("p")) { position = cmd.getOptionValue("p"); } if (fileName == null || regExp == null || position == null) { System.out.println("Command line parameters: -f fileName -r regExp -p position"); System.exit(-1); } } catch (ParseException ex) { logger.error(ex.getMessage()); } String content = readFile(fileName, Charset.defaultCharset()); if (content != null) { Matcher m = Pattern.compile(regExp).matcher(content); while (m.find()) { String group = m.group(); int pos = group.indexOf(".zip"); if (pos > 0) { group = group.substring(0, pos); } logger.debug("RegExp: " + m.group() + " found returning " + group); allMatches.add(group); } if (allMatches.size() > 0) { if (position.equals("first")) { value = allMatches.get(0); } if (position.equals("last")) { value = allMatches.get(allMatches.size() - 1); } } } System.out.println(value); }
From source file:ca.uqac.dim.mapreduce.ltl.LTLValidation.java
/** * Program entry point.//from www . java 2 s .c o m * @param args Command-line arguments */ @SuppressWarnings("static-access") public static void main(String[] args) { // Define and process command line arguments Options options = new Options(); HelpFormatter help_formatter = new HelpFormatter(); Option opt; options.addOption("h", "help", false, "Show help"); opt = OptionBuilder.withArgName("property").hasArg() .withDescription("Property to verify, enclosed in double quotes").create("p"); options.addOption(opt); opt = OptionBuilder.withArgName("filename").hasArg().withDescription("Input filename").create("i"); options.addOption(opt); opt = OptionBuilder.withArgName("x").hasArg() .withDescription("Set verbosity level to x (default: 0 = quiet)").create("v"); options.addOption(opt); opt = OptionBuilder.withArgName("ParserType").hasArg().withDescription("Parser type (Dom or Sax)") .create("t"); options.addOption(opt); opt = OptionBuilder.withLongOpt("redirection").withArgName("x").hasArg() .withDescription("Set the redirection file for the System.out").create("r"); options.addOption(opt); CommandLine c_line = parseCommandLine(options, args); String redirectionFile = ""; //Contains a redirection file for the output if (c_line.hasOption("redirection")) { try { redirectionFile = c_line.getOptionValue("redirection"); PrintStream ps; ps = new PrintStream(redirectionFile); System.setOut(ps); } catch (FileNotFoundException e) { System.out.println("Redirection error !!!"); e.printStackTrace(); } } if (!c_line.hasOption("p") || !c_line.hasOption("i") | c_line.hasOption("h")) { help_formatter.printHelp(app_name, options); System.exit(1); } assert c_line.hasOption("p"); assert c_line.hasOption("i"); String trace_filename = c_line.getOptionValue("i"); String trace_format = getExtension(trace_filename); String property_str = c_line.getOptionValue("p"); String ParserType = ""; if (c_line.hasOption("t")) { ParserType = c_line.getOptionValue("t"); } else { System.err.println("No Parser Type in Arguments"); System.exit(ERR_ARGUMENTS); } if (c_line.hasOption("v")) m_verbosity = Integer.parseInt(c_line.getOptionValue("v")); // Obtain the property to verify and break into subformulas Operator property = null; try { int preset = Integer.parseInt(property_str); property = new Edoc2012Presets().property(preset); } catch (NumberFormatException e) { try { property = Operator.parseFromString(property_str); } catch (Operator.ParseException pe) { System.err.println("ERROR: parsing"); System.exit(1); } } Set<Operator> subformulas = property.getSubformulas(); // Initialize first collector depending on input file format int max_loops = property.getDepth(); int max_tuples_total = 0, total_tuples_total = 0; long time_begin = System.nanoTime(); TraceCollector initial_collector = null; { File in_file = new File(trace_filename); if (trace_format.compareToIgnoreCase(".txt") == 0) { initial_collector = new CharacterTraceCollector(in_file, subformulas); } else if (trace_format.compareToIgnoreCase(".xml") == 0) { if (ParserType.equals("Dom")) { initial_collector = new XmlDomTraceCollector(in_file, subformulas); } else if (ParserType.equals("Sax")) { initial_collector = new XmlSaxTraceCollector(in_file, subformulas); } else { initial_collector = new XmlSaxTraceCollector(in_file, subformulas); } } } if (initial_collector == null) { System.err.println("ERROR: unrecognized input format"); System.exit(1); } // Start workflow int trace_len = initial_collector.getTraceLength(); InCollector<Operator, LTLTupleValue> loop_collector = initial_collector; print(System.out, property.toString(), 2); print(System.out, loop_collector.toString(), 3); for (int i = 0; i < max_loops; i++) { print(System.out, "Loop " + i, 2); LTLSequentialWorkflow w = new LTLSequentialWorkflow(new LTLMapper(subformulas), new LTLReducer(subformulas, trace_len), loop_collector); loop_collector = w.run(); max_tuples_total += w.getMaxTuples(); total_tuples_total += w.getTotalTuples(); if (m_verbosity >= 3) { print(System.out, loop_collector.toString(), 3); } } boolean result = getVerdict(loop_collector, property); long time_end = System.nanoTime(); if (result) print(System.out, "Formula is true", 1); else print(System.out, "Formula is false", 1); long time_total = (time_end - time_begin) / 1000000; System.out.println(trace_len + "," + max_tuples_total + "," + total_tuples_total + "," + time_total); }
From source file:net.massbank.validator.RecordValidator.java
public static void main(String[] args) { RequestDummy request;//w w w . ja va 2s . c om PrintStream out = System.out; Options lvOptions = new Options(); lvOptions.addOption("h", "help", false, "show this help."); lvOptions.addOption("r", "recdata", true, "points to the recdata directory containing massbank records. Reads all *.txt files in there."); CommandLineParser lvParser = new BasicParser(); CommandLine lvCmd = null; try { lvCmd = lvParser.parse(lvOptions, args); if (lvCmd.hasOption('h')) { printHelp(lvOptions); return; } } catch (org.apache.commons.cli.ParseException pvException) { System.out.println(pvException.getMessage()); } String recDataPath = lvCmd.getOptionValue("recdata"); // --------------------------------------------- // ???? // --------------------------------------------- final String baseUrl = MassBankEnv.get(MassBankEnv.KEY_BASE_URL); final String dbRootPath = "./"; final String dbHostName = MassBankEnv.get(MassBankEnv.KEY_DB_HOST_NAME); final String tomcatTmpPath = "."; final String tmpPath = (new File(tomcatTmpPath + sdf.format(new Date()))).getPath() + File.separator; GetConfig conf = new GetConfig(baseUrl); int recVersion = 2; String selDbName = ""; Object up = null; // Was: file Upload boolean isResult = true; String upFileName = ""; boolean upResult = false; DatabaseAccess db = null; try { // ---------------------------------------------------- // ??? // ---------------------------------------------------- // if (FileUpload.isMultipartContent(request)) { // (new File(tmpPath)).mkdir(); // String os = System.getProperty("os.name"); // if (os.indexOf("Windows") == -1) { // isResult = FileUtil.changeMode("777", tmpPath); // if (!isResult) { // out.println(msgErr("[" + tmpPath // + "] chmod failed.")); // return; // } // } // up = new FileUpload(request, tmpPath); // } // ---------------------------------------------------- // ?DB???? // ---------------------------------------------------- List<String> dbNameList = Arrays.asList(conf.getDbName()); ArrayList<String> dbNames = new ArrayList<String>(); dbNames.add(""); File[] dbDirs = (new File(dbRootPath)).listFiles(); if (dbDirs != null) { for (File dbDir : dbDirs) { if (dbDir.isDirectory()) { int pos = dbDir.getName().lastIndexOf("\\"); String dbDirName = dbDir.getName().substring(pos + 1); pos = dbDirName.lastIndexOf("/"); dbDirName = dbDirName.substring(pos + 1); if (dbNameList.contains(dbDirName)) { // DB???massbank.conf???DB???? dbNames.add(dbDirName); } } } } if (dbDirs == null || dbNames.size() == 0) { out.println(msgErr("[" + dbRootPath + "] directory not exist.")); return; } Collections.sort(dbNames); // ---------------------------------------------------- // ? // ---------------------------------------------------- // if (FileUpload.isMultipartContent(request)) { // HashMap<String, String[]> reqParamMap = new HashMap<String, // String[]>(); // reqParamMap = up.getRequestParam(); // if (reqParamMap != null) { // for (Map.Entry<String, String[]> req : reqParamMap // .entrySet()) { // if (req.getKey().equals("ver")) { // try { // recVersion = Integer // .parseInt(req.getValue()[0]); // } catch (NumberFormatException nfe) { // } // } else if (req.getKey().equals("db")) { // selDbName = req.getValue()[0]; // } // } // } // } else { // if (request.getParameter("ver") != null) { // try { // recVersion = Integer.parseInt(request // .getParameter("ver")); // } catch (NumberFormatException nfe) { // } // } // selDbName = request.getParameter("db"); // } // if (selDbName == null || selDbName.equals("") // || !dbNames.contains(selDbName)) { // selDbName = dbNames.get(0); // } // --------------------------------------------- // // --------------------------------------------- out.println("Database: "); for (int i = 0; i < dbNames.size(); i++) { String dbName = dbNames.get(i); out.print("dbName"); if (dbName.equals(selDbName)) { out.print(" selected"); } if (i == 0) { out.println("------------------"); } else { out.println(dbName); } } out.println("Record Version : "); out.println(recVersion); out.println("Record Archive :"); // --------------------------------------------- // // --------------------------------------------- // HashMap<String, Boolean> upFileMap = up.doUpload(); // if (upFileMap != null) { // for (Map.Entry<String, Boolean> e : upFileMap.entrySet()) { // upFileName = e.getKey(); // upResult = e.getValue(); // break; // } // if (upFileName.equals("")) { // out.println(msgErr("please select file.")); // isResult = false; // } else if (!upResult) { // out.println(msgErr("[" + upFileName // + "] upload failed.")); // isResult = false; // } else if (!upFileName.endsWith(ZIP_EXTENSION) // && !upFileName.endsWith(MSBK_EXTENSION)) { // out.println(msgErr("please select [" // + UPLOAD_RECDATA_ZIP // + "] or [" // + UPLOAD_RECDATA_MSBK + "].")); // up.deleteFile(upFileName); // isResult = false; // } // } else { // out.println(msgErr("server error.")); // isResult = false; // } // up.deleteFileItem(); // if (!isResult) { // return; // } // --------------------------------------------- // ??? // --------------------------------------------- // final String upFilePath = (new File(tmpPath + File.separator // + upFileName)).getPath(); // isResult = FileUtil.unZip(upFilePath, tmpPath); // if (!isResult) { // out.println(msgErr("[" // + upFileName // + "] extraction failed. possibility of time-out.")); // return; // } // --------------------------------------------- // ?? // --------------------------------------------- final String recPath = (new File(dbRootPath + File.separator + selDbName)).getPath(); File tmpRecDir = new File(recDataPath); if (!tmpRecDir.isDirectory()) { tmpRecDir.mkdirs(); } // --------------------------------------------- // ??? // --------------------------------------------- // data? // final String recDataPath = (new File(tmpPath + File.separator // + RECDATA_DIR_NAME)).getPath() // + File.separator; // // if (!(new File(recDataPath)).isDirectory()) { // if (upFileName.endsWith(ZIP_EXTENSION)) { // out.println(msgErr("[" // + RECDATA_DIR_NAME // + "] directory is not included in the up-loading file.")); // } else if (upFileName.endsWith(MSBK_EXTENSION)) { // out.println(msgErr("The uploaded file is not record data.")); // } // return; // } // --------------------------------------------- // DB // --------------------------------------------- // db = new DatabaseAccess(dbHostName, selDbName); // isResult = db.open(); // if (!isResult) { // db.close(); // out.println(msgErr("not connect to database.")); // return; // } // --------------------------------------------- // ?? // --------------------------------------------- TreeMap<String, String> resultMap = validationRecord(db, out, recDataPath, recPath, recVersion); if (resultMap.size() == 0) { return; } // --------------------------------------------- // ? // --------------------------------------------- isResult = dispResult(out, resultMap); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } finally { if (db != null) { db.close(); } File tmpDir = new File(tmpPath); if (tmpDir.exists()) { FileUtil.removeDir(tmpDir.getPath()); } } }
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 ava2 s .co 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:DokeosConverter.java
public static void main(String[] arguments) throws Exception { CommandLineParser commandLineParser = new PosixParser(); CommandLine commandLine = commandLineParser.parse(OPTIONS, arguments); int port = SocketOpenOfficeConnection.DEFAULT_PORT; if (commandLine.hasOption(OPTION_PORT.getOpt())) { port = Integer.parseInt(commandLine.getOptionValue(OPTION_PORT.getOpt())); }// w ww .ja v a 2 s . c o m String outputFormat = null; if (commandLine.hasOption(OPTION_OUTPUT_FORMAT.getOpt())) { outputFormat = commandLine.getOptionValue(OPTION_OUTPUT_FORMAT.getOpt()); } boolean verbose = false; if (commandLine.hasOption(OPTION_VERBOSE.getOpt())) { verbose = true; } String dokeosMode = "woogie"; if (commandLine.hasOption(OPTION_DOKEOS_MODE.getOpt())) { dokeosMode = commandLine.getOptionValue(OPTION_DOKEOS_MODE.getOpt()); } int width = 800; if (commandLine.hasOption(OPTION_WIDTH.getOpt())) { width = Integer.parseInt(commandLine.getOptionValue(OPTION_WIDTH.getOpt())); } int height = 600; if (commandLine.hasOption(OPTION_HEIGHT.getOpt())) { height = Integer.parseInt(commandLine.getOptionValue(OPTION_HEIGHT.getOpt())); } String[] fileNames = commandLine.getArgs(); if ((outputFormat == null && fileNames.length != 2 && dokeosMode != null) || fileNames.length < 1) { String syntax = "convert [options] input-file output-file; or\n" + "[options] -f output-format input-file [input-file...]"; HelpFormatter helpFormatter = new HelpFormatter(); helpFormatter.printHelp(syntax, OPTIONS); System.exit(EXIT_CODE_TOO_FEW_ARGS); } OpenOfficeConnection connection = new DokeosSocketOfficeConnection(port); try { if (verbose) { System.out.println("-- connecting to OpenOffice.org on port " + port); } connection.connect(); } catch (ConnectException officeNotRunning) { System.err.println( "ERROR: connection failed. Please make sure OpenOffice.org is running and listening on port " + port + "."); System.exit(EXIT_CODE_CONNECTION_FAILED); } try { // choose the good constructor to deal with the conversion DocumentConverter converter; if (dokeosMode.equals("oogie")) { converter = new OogieDocumentConverter(connection, new DokeosDocumentFormatRegistry(), width, height); } else if (dokeosMode.equals("woogie")) { converter = new WoogieDocumentConverter(connection, new DokeosDocumentFormatRegistry(), width, height); } else { converter = new OpenOfficeDocumentConverter(connection); } if (outputFormat == null) { File inputFile = new File(fileNames[0]); File outputFile = new File(fileNames[1]); convertOne(converter, inputFile, outputFile, verbose); } else { for (int i = 0; i < fileNames.length; i++) { File inputFile = new File(fileNames[i]); File outputFile = new File(FilenameUtils.getFullPath(fileNames[i]) + FilenameUtils.getBaseName(fileNames[i]) + "." + outputFormat); convertOne(converter, inputFile, outputFile, verbose); } } } catch (com.artofsolving.jodconverter.openoffice.connection.OpenOfficeException e) { connection.disconnect(); System.err.println("ERROR: conversion failed."); System.exit(EXIT_CODE_CONVERSION_FAILED); } finally { if (verbose) { System.out.println("-- disconnecting"); } connection.disconnect(); } }