List of usage examples for org.apache.commons.cli Option UNLIMITED_VALUES
int UNLIMITED_VALUES
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From source file:edu.nyu.vida.data_polygamy.relationship_computation.Relationship.java
/** * @param args/* w w w .j a va 2 s . c o m*/ * @throws ParseException */ @SuppressWarnings({ "deprecation" }) public static void main(String[] args) throws IOException, InterruptedException, ClassNotFoundException { Options options = new Options(); Option forceOption = new Option("f", "force", false, "force the computation of the relationship " + "even if files already exist"); forceOption.setRequired(false); options.addOption(forceOption); Option scoreOption = new Option("sc", "score", true, "set threhsold for relationship score"); scoreOption.setRequired(false); scoreOption.setArgName("SCORE THRESHOLD"); options.addOption(scoreOption); Option strengthOption = new Option("st", "strength", true, "set threhsold for relationship strength"); strengthOption.setRequired(false); strengthOption.setArgName("STRENGTH THRESHOLD"); options.addOption(strengthOption); Option completeRandomizationOption = new Option("c", "complete-randomization", false, "use complete randomization when performing significance tests"); completeRandomizationOption.setRequired(false); options.addOption(completeRandomizationOption); Option idOption = new Option("id", "ids", false, "output id instead of names for datasets and attributes"); idOption.setRequired(false); options.addOption(idOption); Option g1Option = new Option("g1", "first-group", true, "set first group of datasets"); g1Option.setRequired(true); g1Option.setArgName("FIRST GROUP"); g1Option.setArgs(Option.UNLIMITED_VALUES); options.addOption(g1Option); Option g2Option = new Option("g2", "second-group", true, "set second group of datasets"); g2Option.setRequired(false); g2Option.setArgName("SECOND GROUP"); g2Option.setArgs(Option.UNLIMITED_VALUES); options.addOption(g2Option); Option machineOption = new Option("m", "machine", true, "machine identifier"); machineOption.setRequired(true); machineOption.setArgName("MACHINE"); machineOption.setArgs(1); options.addOption(machineOption); Option nodesOption = new Option("n", "nodes", true, "number of nodes"); nodesOption.setRequired(true); nodesOption.setArgName("NODES"); nodesOption.setArgs(1); options.addOption(nodesOption); Option s3Option = new Option("s3", "s3", false, "data on Amazon S3"); s3Option.setRequired(false); options.addOption(s3Option); Option awsAccessKeyIdOption = new Option("aws_id", "aws-id", true, "aws access key id; " + "this is required if the execution is on aws"); awsAccessKeyIdOption.setRequired(false); awsAccessKeyIdOption.setArgName("AWS-ACCESS-KEY-ID"); awsAccessKeyIdOption.setArgs(1); options.addOption(awsAccessKeyIdOption); Option awsSecretAccessKeyOption = new Option("aws_key", "aws-id", true, "aws secrect access key; " + "this is required if the execution is on aws"); awsSecretAccessKeyOption.setRequired(false); awsSecretAccessKeyOption.setArgName("AWS-SECRET-ACCESS-KEY"); awsSecretAccessKeyOption.setArgs(1); options.addOption(awsSecretAccessKeyOption); Option bucketOption = new Option("b", "s3-bucket", true, "bucket on s3; " + "this is required if the execution is on aws"); bucketOption.setRequired(false); bucketOption.setArgName("S3-BUCKET"); bucketOption.setArgs(1); options.addOption(bucketOption); Option helpOption = new Option("h", "help", false, "display this message"); helpOption.setRequired(false); options.addOption(helpOption); Option removeOption = new Option("r", "remove-not-significant", false, "remove relationships that are not" + "significant from the final output"); removeOption.setRequired(false); options.addOption(removeOption); HelpFormatter formatter = new HelpFormatter(); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { formatter.printHelp("hadoop jar data-polygamy.jar " + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship", options, true); System.exit(0); } if (cmd.hasOption("h")) { formatter.printHelp("hadoop jar data-polygamy.jar " + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship", options, true); System.exit(0); } boolean s3 = cmd.hasOption("s3"); String s3bucket = ""; String awsAccessKeyId = ""; String awsSecretAccessKey = ""; if (s3) { if ((!cmd.hasOption("aws_id")) || (!cmd.hasOption("aws_key")) || (!cmd.hasOption("b"))) { System.out.println( "Arguments 'aws_id', 'aws_key', and 'b'" + " are mandatory if execution is on AWS."); formatter.printHelp( "hadoop jar data-polygamy.jar " + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship", options, true); System.exit(0); } s3bucket = cmd.getOptionValue("b"); awsAccessKeyId = cmd.getOptionValue("aws_id"); awsSecretAccessKey = cmd.getOptionValue("aws_key"); } boolean snappyCompression = false; boolean bzip2Compression = false; String machine = cmd.getOptionValue("m"); int nbNodes = Integer.parseInt(cmd.getOptionValue("n")); Configuration s3conf = new Configuration(); if (s3) { s3conf.set("fs.s3.awsAccessKeyId", awsAccessKeyId); s3conf.set("fs.s3.awsSecretAccessKey", awsSecretAccessKey); s3conf.set("bucket", s3bucket); } Path path = null; FileSystem fs = FileSystem.get(new Configuration()); ArrayList<String> shortDataset = new ArrayList<String>(); ArrayList<String> firstGroup = new ArrayList<String>(); ArrayList<String> secondGroup = new ArrayList<String>(); HashMap<String, String> datasetAgg = new HashMap<String, String>(); boolean removeNotSignificant = cmd.hasOption("r"); boolean removeExistingFiles = cmd.hasOption("f"); boolean completeRandomization = cmd.hasOption("c"); boolean hasScoreThreshold = cmd.hasOption("sc"); boolean hasStrengthThreshold = cmd.hasOption("st"); boolean outputIds = cmd.hasOption("id"); String scoreThreshold = hasScoreThreshold ? cmd.getOptionValue("sc") : ""; String strengthThreshold = hasStrengthThreshold ? cmd.getOptionValue("st") : ""; // all datasets ArrayList<String> all_datasets = new ArrayList<String>(); if (s3) { path = new Path(s3bucket + FrameworkUtils.datasetsIndexDir); fs = FileSystem.get(path.toUri(), s3conf); } else { path = new Path(fs.getHomeDirectory() + "/" + FrameworkUtils.datasetsIndexDir); } BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(path))); String line = br.readLine(); while (line != null) { all_datasets.add(line.split("\t")[0]); line = br.readLine(); } br.close(); if (s3) fs.close(); String[] all_datasets_array = new String[all_datasets.size()]; all_datasets.toArray(all_datasets_array); String[] firstGroupCmd = cmd.getOptionValues("g1"); String[] secondGroupCmd = cmd.hasOption("g2") ? cmd.getOptionValues("g2") : all_datasets_array; addDatasets(firstGroupCmd, firstGroup, shortDataset, datasetAgg, path, fs, s3conf, s3, s3bucket); addDatasets(secondGroupCmd, secondGroup, shortDataset, datasetAgg, path, fs, s3conf, s3, s3bucket); if (shortDataset.size() == 0) { System.out.println("No datasets to process."); System.exit(0); } if (firstGroup.isEmpty()) { System.out.println("No indices from datasets in G1."); System.exit(0); } if (secondGroup.isEmpty()) { System.out.println("No indices from datasets in G2."); System.exit(0); } // getting dataset ids String datasetNames = ""; String datasetIds = ""; HashMap<String, String> datasetId = new HashMap<String, String>(); Iterator<String> it = shortDataset.iterator(); while (it.hasNext()) { datasetId.put(it.next(), null); } if (s3) { path = new Path(s3bucket + FrameworkUtils.datasetsIndexDir); fs = FileSystem.get(path.toUri(), s3conf); } else { path = new Path(fs.getHomeDirectory() + "/" + FrameworkUtils.datasetsIndexDir); } br = new BufferedReader(new InputStreamReader(fs.open(path))); line = br.readLine(); while (line != null) { String[] dt = line.split("\t"); all_datasets.add(dt[0]); if (datasetId.containsKey(dt[0])) { datasetId.put(dt[0], dt[1]); datasetNames += dt[0] + ","; datasetIds += dt[1] + ","; } line = br.readLine(); } br.close(); if (s3) fs.close(); datasetNames = datasetNames.substring(0, datasetNames.length() - 1); datasetIds = datasetIds.substring(0, datasetIds.length() - 1); it = shortDataset.iterator(); while (it.hasNext()) { String dataset = it.next(); if (datasetId.get(dataset) == null) { System.out.println("No dataset id for " + dataset); System.exit(0); } } String firstGroupStr = ""; String secondGroupStr = ""; for (String dataset : firstGroup) { firstGroupStr += datasetId.get(dataset) + ","; } for (String dataset : secondGroup) { secondGroupStr += datasetId.get(dataset) + ","; } firstGroupStr = firstGroupStr.substring(0, firstGroupStr.length() - 1); secondGroupStr = secondGroupStr.substring(0, secondGroupStr.length() - 1); String relationshipsDir = ""; if (outputIds) { relationshipsDir = FrameworkUtils.relationshipsIdsDir; } else { relationshipsDir = FrameworkUtils.relationshipsDir; } FrameworkUtils.createDir(s3bucket + relationshipsDir, s3conf, s3); String random = completeRandomization ? "complete" : "restricted"; String indexInputDirs = ""; String noRelationship = ""; HashSet<String> dirs = new HashSet<String>(); String dataset1; String dataset2; String datasetId1; String datasetId2; for (int i = 0; i < firstGroup.size(); i++) { for (int j = 0; j < secondGroup.size(); j++) { if (Integer.parseInt(datasetId.get(firstGroup.get(i))) < Integer .parseInt(datasetId.get(secondGroup.get(j)))) { dataset1 = firstGroup.get(i); dataset2 = secondGroup.get(j); } else { dataset1 = secondGroup.get(j); dataset2 = firstGroup.get(i); } datasetId1 = datasetId.get(dataset1); datasetId2 = datasetId.get(dataset2); if (dataset1.equals(dataset2)) continue; String correlationOutputFileName = s3bucket + relationshipsDir + "/" + dataset1 + "-" + dataset2 + "/"; if (removeExistingFiles) { FrameworkUtils.removeFile(correlationOutputFileName, s3conf, s3); } if (!FrameworkUtils.fileExists(correlationOutputFileName, s3conf, s3)) { dirs.add(s3bucket + FrameworkUtils.indexDir + "/" + dataset1); dirs.add(s3bucket + FrameworkUtils.indexDir + "/" + dataset2); } else { noRelationship += datasetId1 + "-" + datasetId2 + ","; } } } if (dirs.isEmpty()) { System.out.println("All the relationships were already computed."); System.out.println("Use -f in the beginning of the command line to force the computation."); System.exit(0); } for (String dir : dirs) { indexInputDirs += dir + ","; } Configuration conf = new Configuration(); Machine machineConf = new Machine(machine, nbNodes); String jobName = "relationship" + "-" + random; String relationshipOutputDir = s3bucket + relationshipsDir + "/tmp/"; FrameworkUtils.removeFile(relationshipOutputDir, s3conf, s3); for (int i = 0; i < shortDataset.size(); i++) { conf.set("dataset-" + datasetId.get(shortDataset.get(i)) + "-agg", datasetAgg.get(shortDataset.get(i))); } for (int i = 0; i < shortDataset.size(); i++) { conf.set("dataset-" + datasetId.get(shortDataset.get(i)) + "-agg-size", Integer.toString(datasetAgg.get(shortDataset.get(i)).split(",").length)); } conf.set("dataset-keys", datasetIds); conf.set("dataset-names", datasetNames); conf.set("first-group", firstGroupStr); conf.set("second-group", secondGroupStr); conf.set("complete-random", String.valueOf(completeRandomization)); conf.set("output-ids", String.valueOf(outputIds)); conf.set("complete-random-str", random); conf.set("main-dataset-id", datasetId.get(shortDataset.get(0))); conf.set("remove-not-significant", String.valueOf(removeNotSignificant)); if (noRelationship.length() > 0) { conf.set("no-relationship", noRelationship.substring(0, noRelationship.length() - 1)); } if (hasScoreThreshold) { conf.set("score-threshold", scoreThreshold); } if (hasStrengthThreshold) { conf.set("strength-threshold", strengthThreshold); } conf.set("mapreduce.tasktracker.map.tasks.maximum", String.valueOf(machineConf.getMaximumTasks())); conf.set("mapreduce.tasktracker.reduce.tasks.maximum", String.valueOf(machineConf.getMaximumTasks())); conf.set("mapreduce.jobtracker.maxtasks.perjob", "-1"); conf.set("mapreduce.reduce.shuffle.parallelcopies", "20"); conf.set("mapreduce.input.fileinputformat.split.minsize", "0"); conf.set("mapreduce.task.io.sort.mb", "200"); conf.set("mapreduce.task.io.sort.factor", "100"); conf.set("mapreduce.task.timeout", "2400000"); if (s3) { machineConf.setMachineConfiguration(conf); conf.set("fs.s3.awsAccessKeyId", awsAccessKeyId); conf.set("fs.s3.awsSecretAccessKey", awsSecretAccessKey); conf.set("bucket", s3bucket); } if (snappyCompression) { conf.set("mapreduce.map.output.compress", "true"); conf.set("mapreduce.map.output.compress.codec", "org.apache.hadoop.io.compress.SnappyCodec"); //conf.set("mapreduce.output.fileoutputformat.compress.codec", "org.apache.hadoop.io.compress.SnappyCodec"); } if (bzip2Compression) { conf.set("mapreduce.map.output.compress", "true"); conf.set("mapreduce.map.output.compress.codec", "org.apache.hadoop.io.compress.BZip2Codec"); //conf.set("mapreduce.output.fileoutputformat.compress.codec", "org.apache.hadoop.io.compress.BZip2Codec"); } Job job = new Job(conf); job.setJobName(jobName); job.setMapOutputKeyClass(PairAttributeWritable.class); job.setMapOutputValueClass(TopologyTimeSeriesWritable.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(Text.class); job.setMapperClass(CorrelationMapper.class); job.setReducerClass(CorrelationReducer.class); job.setNumReduceTasks(machineConf.getNumberReduces()); job.setInputFormatClass(SequenceFileInputFormat.class); //job.setOutputFormatClass(TextOutputFormat.class); LazyOutputFormat.setOutputFormatClass(job, TextOutputFormat.class); FileInputFormat.setInputDirRecursive(job, true); FileInputFormat.setInputPaths(job, indexInputDirs.substring(0, indexInputDirs.length() - 1)); FileOutputFormat.setOutputPath(job, new Path(relationshipOutputDir)); job.setJarByClass(Relationship.class); long start = System.currentTimeMillis(); job.submit(); job.waitForCompletion(true); System.out.println(jobName + "\t" + (System.currentTimeMillis() - start)); // moving files to right place for (int i = 0; i < firstGroup.size(); i++) { for (int j = 0; j < secondGroup.size(); j++) { if (Integer.parseInt(datasetId.get(firstGroup.get(i))) < Integer .parseInt(datasetId.get(secondGroup.get(j)))) { dataset1 = firstGroup.get(i); dataset2 = secondGroup.get(j); } else { dataset1 = secondGroup.get(j); dataset2 = firstGroup.get(i); } if (dataset1.equals(dataset2)) continue; String from = s3bucket + relationshipsDir + "/tmp/" + dataset1 + "-" + dataset2 + "/"; String to = s3bucket + relationshipsDir + "/" + dataset1 + "-" + dataset2 + "/"; FrameworkUtils.renameFile(from, to, s3conf, s3); } } }
From source file:com.enioka.jqm.tools.Main.java
/** * Startup method for the packaged JAR/*from w ww . j av a 2 s . c o m*/ * * @param args * 0 is node name */ @SuppressWarnings("static-access") public static void main(String[] args) { Helpers.setLogFileName("cli"); Option o00 = OptionBuilder.withArgName("nodeName").hasArg().withDescription("name of the JQM node to start") .isRequired().create("startnode"); Option o01 = OptionBuilder.withDescription("display help").withLongOpt("help").create("h"); Option o11 = OptionBuilder.withArgName("applicationname").hasArg() .withDescription("name of the application to launch").isRequired().create("enqueue"); Option o21 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("path of the XML configuration file to import").isRequired() .create("importjobdef"); Option o31 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("export all queue definitions into an XML file").isRequired() .create("exportallqueues"); OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("export some queue definitions into an XML file").isRequired() .create("exportqueuefile"); OptionBuilder.withArgName("queues").hasArg().withDescription("queues to export").withValueSeparator(',') .isRequired().create("queue"); Option o51 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("import all queue definitions from an XML file").isRequired() .create("importqueuefile"); Option o61 = OptionBuilder.withArgName("nodeName").hasArg() .withDescription("creates a JQM node of this name, or updates it if it exists. Implies -u.") .isRequired().create("createnode"); Option o71 = OptionBuilder.withDescription("display JQM engine version").withLongOpt("version").create("v"); Option o81 = OptionBuilder.withDescription("upgrade JQM database").withLongOpt("upgrade").create("u"); Option o91 = OptionBuilder.withArgName("jobInstanceId").hasArg() .withDescription("get job instance status by ID").isRequired().withLongOpt("getstatus").create("g"); Option o101 = OptionBuilder.withArgName("password").hasArg() .withDescription("creates or resets root admin account password").isRequired().withLongOpt("root") .create("r"); Option o111 = OptionBuilder.withArgName("option").hasArg() .withDescription( "ws handling. Possible values are: enable, disable, ssl, nossl, internalpki, externalapi") .isRequired().withLongOpt("gui").create("w"); Option o121 = OptionBuilder.withArgName("id[,logfilepath]").hasArg().withDescription("single launch mode") .isRequired().withLongOpt("gui").create("s"); Option o131 = OptionBuilder.withArgName("resourcefile").hasArg() .withDescription("resource parameter file to use. Default is resources.xml") .withLongOpt("resources").create("p"); Option o141 = OptionBuilder.withArgName("login,password,role1,role2,...").hasArgs(Option.UNLIMITED_VALUES) .withValueSeparator(',') .withDescription("Create or update a JQM account. Roles must exist beforehand.").create("U"); Options options = new Options(); OptionGroup og1 = new OptionGroup(); og1.setRequired(true); og1.addOption(o00); og1.addOption(o01); og1.addOption(o11); og1.addOption(o21); og1.addOption(o31); og1.addOption(o51); og1.addOption(o61); og1.addOption(o71); og1.addOption(o81); og1.addOption(o91); og1.addOption(o101); og1.addOption(o111); og1.addOption(o121); og1.addOption(o141); options.addOptionGroup(og1); OptionGroup og2 = new OptionGroup(); og2.addOption(o131); options.addOptionGroup(og2); HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(160); try { // Parse arguments CommandLineParser parser = new BasicParser(); CommandLine line = parser.parse(options, args); // Other db connection? if (line.getOptionValue(o131.getOpt()) != null) { jqmlogger.info("Using resource XML file " + line.getOptionValue(o131.getOpt())); Helpers.resourceFile = line.getOptionValue(o131.getOpt()); } // Set db connection Helpers.registerJndiIfNeeded(); // Enqueue if (line.getOptionValue(o11.getOpt()) != null) { enqueue(line.getOptionValue(o11.getOpt())); } // Get status if (line.getOptionValue(o91.getOpt()) != null) { getStatus(Integer.parseInt(line.getOptionValue(o91.getOpt()))); } // Import XML else if (line.getOptionValue(o21.getOpt()) != null) { importJobDef(line.getOptionValue(o21.getOpt())); } // Start engine else if (line.getOptionValue(o00.getOpt()) != null) { startEngine(line.getOptionValue(o00.getOpt())); } // Export all Queues else if (line.getOptionValue(o31.getOpt()) != null) { exportAllQueues(line.getOptionValue(o31.getOpt())); } // Import queues else if (line.getOptionValue(o51.getOpt()) != null) { importQueues(line.getOptionValue(o51.getOpt())); } // Create node else if (line.getOptionValue(o61.getOpt()) != null) { createEngine(line.getOptionValue(o61.getOpt())); } // Upgrade else if (line.hasOption(o81.getOpt())) { upgrade(); } // Help else if (line.hasOption(o01.getOpt())) { formatter.printHelp("java -jar jqm-engine.jar", options, true); } // Version else if (line.hasOption(o71.getOpt())) { jqmlogger.info("Engine version: " + Helpers.getMavenVersion()); } // Root password else if (line.hasOption(o101.getOpt())) { root(line.getOptionValue(o101.getOpt())); } // Web options else if (line.hasOption(o111.getOpt())) { ws(line.getOptionValue(o111.getOpt())); } // Web options else if (line.hasOption(o121.getOpt())) { single(line.getOptionValue(o121.getOpt())); } // User handling else if (line.hasOption(o141.getOpt())) { user(line.getOptionValues(o141.getOpt())); } } catch (ParseException exp) { jqmlogger.fatal("Could not read command line: " + exp.getMessage()); formatter.printHelp("java -jar jqm-engine.jar", options, true); return; } }
From source file:com.basistech.ninja.Train.java
/** * Command line interface to train a model. * * <pre>/*from w ww . ja v a2 s . c o m*/ * usage: Train [options] * --batch-size <arg> batch size (default = 10) * --epochs <arg> epochs (default = 5) * --examples <arg> input examples file (required) * --layer-sizes <arg> layer sizes, including input/output, e.g. 3 4 2 (required) * --learning-rate <arg> learning-rate (default = 0.7) * --model <arg> output model file (required) * </pre> * * @param args command line arguments * @throws IOException */ public static void main(String[] args) throws IOException { String defaultBatchSize = "10"; String deafaultEpochs = "5"; String defaultLearningRate = "0.7"; Options options = new Options(); Option option; option = new Option(null, "examples", true, "input examples file (required)"); option.setRequired(true); options.addOption(option); option = new Option(null, "model", true, "output model file (required)"); option.setRequired(true); options.addOption(option); option = new Option(null, "layer-sizes", true, "layer sizes, including input/output, e.g. 3 4 2 (required)"); option.setRequired(true); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(null, "batch-size", true, String.format("batch size (default = %s)", defaultBatchSize)); options.addOption(option); option = new Option(null, "epochs", true, String.format("epochs (default = %s)", deafaultEpochs)); options.addOption(option); option = new Option(null, "learning-rate", true, String.format("learning-rate (default = %s)", defaultLearningRate)); options.addOption(option); CommandLineParser parser = new GnuParser(); CommandLine cmdline = null; try { cmdline = parser.parse(options, args); } catch (org.apache.commons.cli.ParseException e) { System.err.println(e.getMessage()); usage(options); System.exit(1); } String[] remaining = cmdline.getArgs(); if (remaining == null) { usage(options); System.exit(1); } List<Integer> layerSizes = Lists.newArrayList(); for (String s : cmdline.getOptionValues("layer-sizes")) { layerSizes.add(Integer.parseInt(s)); } File examplesFile = new File(cmdline.getOptionValue("examples")); Train that = new Train(layerSizes, examplesFile); int batchSize = Integer.parseInt(cmdline.getOptionValue("batch-size", defaultBatchSize)); int epochs = Integer.parseInt(cmdline.getOptionValue("epochs", deafaultEpochs)); double learningRate = Double.parseDouble(cmdline.getOptionValue("learning-rate", defaultLearningRate)); File modelFile = new File(cmdline.getOptionValue("model")); that.train(batchSize, epochs, learningRate, modelFile); }
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);/* www .j a v a2 s . co m*/ //Declare variables File inputFile; File outputFile; File tmpDir; File blastnExecutable; File properties; File blastOutputFile = null; // TUITPropertiesLoader tuitPropertiesLoader; TUITProperties tuitProperties; // String[] parameters = null; // Connection connection = null; MySQL_Connector mySQL_connector; // Map<Ranks, TUITCutoffSet> cutoffMap; // BLASTIdentifier blastIdentifier = null; // RamDb ramDb = null; CommandLineParser parser = new GnuParser(); Options options = new Options(); options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)"); options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)"); options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)"); options.addOption(tuit.V, "verbose", false, "Enable verbose output"); options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output"); options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases"); options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases"); options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy"); Option option = new Option(tuit.REDUCE, "reduce", true, "Pack identical (100% similar sequences) records in the given sample file"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(tuit.COMBINE, "combine", true, "Combine a set of given reduction files into an HMP Tree-compatible taxonomy"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); options.addOption(tuit.NORMALIZE, "normalize", false, "If used in combination with -combine ensures that the values are normalized by the root value"); HelpFormatter formatter = new HelpFormatter(); try { //Get TUIT directory final File tuitDir = new File( new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()) .getParent()); final File ramDbFile = new File(tuitDir, tuit.RAM_DB); //Setup logger Log.getInstance().setLogName("tuit.log"); //Read command line final CommandLine commandLine = parser.parse(options, args, true); //Check if the REDUCE option is on if (commandLine.hasOption(tuit.REDUCE)) { final String[] fileList = commandLine.getOptionValues(tuit.REDUCE); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "..."); final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor .fromPath(path); ReductorFileOperator.save(nucleotideFastaSequenceReductor, path.resolveSibling(path.getFileName().toString() + ".rdc")); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check if COMBINE is on if (commandLine.hasOption(tuit.COMBINE)) { final boolean normalize = commandLine.hasOption(tuit.NORMALIZE); final String[] fileList = commandLine.getOptionValues(tuit.COMBINE); //TODO: implement a test for format here final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>(); final TreeFormatter treeFormatter = TreeFormatter .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat()); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "..."); treeFormatter.loadFromPath(path); final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf("."))); hmpTreesOutputs.add(output); treeFormatter.erase(); } final Path destination; if (commandLine.hasOption(OUT)) { destination = Paths.get(commandLine.getOptionValue(tuit.OUT)); } else { destination = Paths.get("merge.tcf"); } CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination); Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } if (!commandLine.hasOption(tuit.P)) { throw new ParseException("No properties file option found, exiting."); } else { properties = new File(commandLine.getOptionValue(tuit.P)); } //Load properties tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties); tuitProperties = tuitPropertiesLoader.getTuitProperties(); //Create tmp directory and blastn executable tmpDir = new File(tuitProperties.getTMPDir().getPath()); blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath()); //Check for deploy if (commandLine.hasOption(tuit.DEPLOY)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir); } else { NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check for update if (commandLine.hasOption(tuit.UPDATE)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir); } else { //No need to specify a different way to update the database other than just deploy in case of the RAM database NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Connect to the database if (commandLine.hasOption(tuit.USE_DB)) { mySQL_connector = MySQL_Connector.newDefaultInstance( "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/", tuitProperties.getDBConnection().getLogin().trim(), tuitProperties.getDBConnection().getPassword().trim()); mySQL_connector.connectToDatabase(); connection = mySQL_connector.getConnection(); } else { //Probe for ram database if (ramDbFile.exists() && ramDbFile.canRead()) { Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map..."); try { ramDb = RamDb.loadSelfFromFile(ramDbFile); } catch (IOException ie) { if (ie instanceof java.io.InvalidClassException) throw new IOException("The RAM-based taxonomic database needs to be updated."); } } else { Log.getInstance().log(Level.SEVERE, "The RAM database either has not been deployed, or is not accessible." + "Please use the --deploy option and check permissions on the TUIT directory. " + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option."); return; } } if (commandLine.hasOption(tuit.B)) { blastOutputFile = new File(commandLine.getOptionValue(tuit.B)); if (!blastOutputFile.exists() || !blastOutputFile.canRead()) { throw new Exception("BLAST output file either does not exist, or is not readable."); } else if (blastOutputFile.isDirectory()) { throw new Exception("BLAST output file points to a directory."); } } //Check vital parameters if (!commandLine.hasOption(tuit.IN)) { throw new ParseException("No input file option found, exiting."); } else { inputFile = new File(commandLine.getOptionValue(tuit.IN)); Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log"); } //Correct the output file option if needed if (!commandLine.hasOption(tuit.OUT)) { outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT); } else { outputFile = new File(commandLine.getOptionValue(tuit.OUT)); } //Adjust the output level if (commandLine.hasOption(tuit.V)) { Log.getInstance().setLevel(Level.FINE); Log.getInstance().log(Level.INFO, "Using verbose output for the log"); } else { Log.getInstance().setLevel(Level.INFO); } //Try all files if (inputFile != null) { if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Input file either does not exist, or is not readable."); } else if (inputFile.isDirectory()) { throw new Exception("Input file points to a directory."); } } if (!properties.exists() || !properties.canRead()) { throw new Exception("Properties file either does not exist, or is not readable."); } else if (properties.isDirectory()) { throw new Exception("Properties file points to a directory."); } //Create blast parameters final StringBuilder stringBuilder = new StringBuilder(); for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) { stringBuilder.append(database.getUse()); stringBuilder.append(" ");//Gonna insert an extra space for the last database } String remote; String entrez_query; if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) { remote = "-remote"; entrez_query = "-entrez_query"; parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue() }; } else { if (!commandLine.hasOption(tuit.B)) { if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("NOT") || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("ALL")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist", TUITFileOperatorHelper.restrictToEntrez(tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue() .toUpperCase().replace("NOT", "OR")) .getAbsolutePath(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .equals("")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), /*"-gilist", TUITFileOperatorHelper.restrictToEntrez( tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!! "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } } } //Prepare a cutoff Map if (tuitProperties.getSpecificationParameters() != null && tuitProperties.getSpecificationParameters().size() > 0) { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size()); for (SpecificationParameters specificationParameters : tuitProperties .getSpecificationParameters()) { cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()), TUITCutoffSet.newDefaultInstance( Double.parseDouble( specificationParameters.getCutoffSet().getPIdentCutoff().getValue()), Double.parseDouble(specificationParameters.getCutoffSet() .getQueryCoverageCutoff().getValue()), Double.parseDouble( specificationParameters.getCutoffSet().getAlpha().getValue()))); } } else { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(); } final TUITFileOperatorHelper.OutputFormat format; if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) { format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK; } else { format = TUITFileOperatorHelper.OutputFormat.TUIT; } try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator .newInstance(format, cutoffMap);) { nucleotideFastaTUITFileOperator.setInputFile(inputFile); nucleotideFastaTUITFileOperator.setOutputFile(outputFile); final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep(); final boolean cleanup; if (cleanupString.equals("no")) { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted."); cleanup = true; } else { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept."); cleanup = false; } //Create blast identifier ExecutorService executorService = Executors.newSingleThreadExecutor(); if (commandLine.hasOption(tuit.USE_DB)) { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } else { try { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } else { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } else { try { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } Future<?> runnableFuture = executorService.submit(blastIdentifier); runnableFuture.get(); executorService.shutdown(); } } catch (ParseException pe) { Log.getInstance().log(Level.SEVERE, (pe.getMessage())); formatter.printHelp("tuit", options); } catch (SAXException saxe) { Log.getInstance().log(Level.SEVERE, saxe.getMessage()); } catch (FileNotFoundException fnfe) { Log.getInstance().log(Level.SEVERE, fnfe.getMessage()); } catch (TUITPropertyBadFormatException tpbfe) { Log.getInstance().log(Level.SEVERE, tpbfe.getMessage()); } catch (ClassCastException cce) { Log.getInstance().log(Level.SEVERE, cce.getMessage()); } catch (JAXBException jaxbee) { Log.getInstance().log(Level.SEVERE, "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema."); } catch (ClassNotFoundException cnfe) { //Probably won't happen unless the library deleted from the .jar Log.getInstance().log(Level.SEVERE, cnfe.getMessage()); //cnfe.printStackTrace(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "A database communication error occurred with the following message:\n" + sqle.getMessage()); //sqle.printStackTrace(); if (sqle.getMessage().contains("Access denied for user")) { Log.getInstance().log(Level.SEVERE, "Please use standard database login: " + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password); } } catch (Exception e) { Log.getInstance().log(Level.SEVERE, e.getMessage()); e.printStackTrace(); } finally { if (connection != null) { try { connection.close(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle); } } Log.getInstance().log(Level.FINE, "Task done, exiting..."); } }
From source file:com.example.dlp.Redact.java
/** Command line application to redact strings, images using the Data Loss Prevention API. */ public static void main(String[] args) throws Exception { OptionGroup optionsGroup = new OptionGroup(); optionsGroup.setRequired(true);/*from w w w . j a v a 2 s . c om*/ Option stringOption = new Option("s", "string", true, "redact string"); optionsGroup.addOption(stringOption); Option fileOption = new Option("f", "file path", true, "redact input file path"); optionsGroup.addOption(fileOption); Options commandLineOptions = new Options(); commandLineOptions.addOptionGroup(optionsGroup); Option minLikelihoodOption = Option.builder("minLikelihood").hasArg(true).required(false).build(); commandLineOptions.addOption(minLikelihoodOption); Option replaceOption = Option.builder("r").longOpt("replace string").hasArg(true).required(false).build(); commandLineOptions.addOption(replaceOption); Option infoTypesOption = Option.builder("infoTypes").hasArg(true).required(false).build(); infoTypesOption.setArgs(Option.UNLIMITED_VALUES); commandLineOptions.addOption(infoTypesOption); Option outputFilePathOption = Option.builder("o").hasArg(true).longOpt("outputFilePath").required(false) .build(); commandLineOptions.addOption(outputFilePathOption); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(commandLineOptions, args); } catch (ParseException e) { System.out.println(e.getMessage()); formatter.printHelp(Redact.class.getName(), commandLineOptions); System.exit(1); return; } String replacement = cmd.getOptionValue(replaceOption.getOpt(), "_REDACTED_"); List<InfoType> infoTypesList = new ArrayList<>(); String[] infoTypes = cmd.getOptionValues(infoTypesOption.getOpt()); if (infoTypes != null) { for (String infoType : infoTypes) { infoTypesList.add(InfoType.newBuilder().setName(infoType).build()); } } Likelihood minLikelihood = Likelihood.valueOf( cmd.getOptionValue(minLikelihoodOption.getOpt(), Likelihood.LIKELIHOOD_UNSPECIFIED.name())); // string inspection if (cmd.hasOption("s")) { String source = cmd.getOptionValue(stringOption.getOpt()); redactString(source, replacement, minLikelihood, infoTypesList); } else if (cmd.hasOption("f")) { String filePath = cmd.getOptionValue(fileOption.getOpt()); String outputFilePath = cmd.getOptionValue(outputFilePathOption.getOpt()); redactImage(filePath, minLikelihood, infoTypesList, outputFilePath); } }
From source file:com.samsung.sjs.Compiler.java
@SuppressWarnings("static-access") public static void main(String[] args) throws IOException, SolverException, InterruptedException { boolean debug = false; boolean use_gc = true; CompilerOptions.Platform p = CompilerOptions.Platform.Native; CompilerOptions opts = null;// w w w.ja v a 2 s . c o m boolean field_opts = false; boolean typecheckonly = false; boolean showconstraints = false; boolean showconstraintsolution = false; String[] decls = null; String[] links = null; String[] objs = null; boolean guest = false; boolean stop_at_c = false; String external_compiler = null; boolean encode_vals = false; boolean x32 = false; boolean validate = true; boolean interop = false; boolean boot_interop = false; boolean oldExpl = false; String explanationStrategy = null; boolean efl = false; Options options = new Options(); options.addOption("debugcompiler", false, "Enable compiler debug spew"); //options.addOption("o", true, "Set compiler output file (must be .c)"); options.addOption(OptionBuilder //.withArgName("o") .withLongOpt("output-file").withDescription("Output file (must be .c)").hasArg().withArgName("file") .create("o")); options.addOption(OptionBuilder.withLongOpt("target") .withDescription("Select target platform: 'native' or 'web'").hasArg().create()); options.addOption(OptionBuilder.withLongOpt("gc") .withDescription("Disable GC: param is 'on' (default) or 'off'").hasArg().create()); options.addOption(OptionBuilder .withDescription("Enable field access optimizations: param is 'true' (default) or 'false'").hasArg() .create("Xfields")); options.addOption(OptionBuilder .withDescription("Compile for encoded values. TEMPORARY. For testing interop codegen").hasArg() .create("XEncodedValues")); options.addOption(OptionBuilder.withLongOpt("typecheck-only") .withDescription("Only typecheck the file, don't compile").create()); options.addOption(OptionBuilder.withLongOpt("show-constraints") .withDescription("Show constraints generated during type inference").create()); options.addOption(OptionBuilder.withLongOpt("show-constraint-solution") .withDescription("Show solution to type inference constraints").create()); options.addOption(OptionBuilder.withLongOpt("extra-decls") .withDescription("Specify extra declaration files, comma-separated").hasArg() .withValueSeparator(',').create()); options.addOption(OptionBuilder.withLongOpt("native-libs") .withDescription("Specify extra linkage files, comma-separated").hasArg().withValueSeparator(',') .create()); Option extraobjs = OptionBuilder.withLongOpt("extra-objs") .withDescription("Specify extra .c/.cpp files, comma-separated").hasArg().withValueSeparator(',') .create(); extraobjs.setArgs(Option.UNLIMITED_VALUES); options.addOption(extraobjs); options.addOption(OptionBuilder.withLongOpt("guest-runtime") .withDescription( "Emit code to be called by another runtime (i.e., main() is written in another language).") .create()); options.addOption(OptionBuilder.withLongOpt("only-c") .withDescription("Generate C code, but do not attempt to compile it").create()); options.addOption(OptionBuilder.withLongOpt("c-compiler") .withDescription("Disable GC: param is 'on' (default) or 'off'").hasArg().create("cc")); options.addOption(OptionBuilder.withLongOpt("runtime-src") .withDescription("Specify path to runtime system source").hasArg().create()); options.addOption(OptionBuilder.withLongOpt("ext-path") .withDescription("Specify path to external dependency dir (GC, etc.)").hasArg().create()); options.addOption(OptionBuilder.withLongOpt("skip-validation") .withDescription("Run the backend without validating the results of type inference").create()); options.addOption(OptionBuilder.withLongOpt("m32").withDescription("Force 32-bit compilation").create()); options.addOption(OptionBuilder.withLongOpt("Xbootinterop") .withDescription("Programs start with global interop dirty flag set (experimental)").create()); options.addOption(OptionBuilder.withLongOpt("Xinterop") .withDescription("Enable (experimental) interoperability backend").create()); options.addOption(OptionBuilder.withDescription("C compiler default optimization level").create("O")); options.addOption(OptionBuilder.withDescription("C compiler optimization level 0").create("O0")); options.addOption(OptionBuilder.withDescription("C compiler optimization level 1").create("O1")); options.addOption(OptionBuilder.withDescription("C compiler optimization level 2").create("O2")); options.addOption(OptionBuilder.withDescription("C compiler optimization level 3").create("O3")); options.addOption( OptionBuilder.withLongOpt("oldExpl").withDescription("Use old error explanations").create()); String explanationStrategyHelp = "default: " + FixingSetFinder.defaultStrategy() + "; other choices: " + FixingSetFinder.strategyNames().stream().filter(s -> !s.equals(FixingSetFinder.defaultStrategy())) .collect(Collectors.joining(", ")); options.addOption(OptionBuilder.withLongOpt("explanation-strategy") .withDescription("Error explanation strategy to use (" + explanationStrategyHelp + ')').hasArg() .create()); options.addOption( OptionBuilder.withLongOpt("efl").withDescription("Set up efl environment in main()").create()); try { CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); String[] newargs = cmd.getArgs(); if (newargs.length != 1) { throw new ParseException("Invalid number of arguments"); } String sourcefile = newargs[0]; if (!sourcefile.endsWith(".js")) { throw new ParseException("Invalid file extension on input file: " + sourcefile); } String gc = cmd.getOptionValue("gc", "on"); if (gc.equals("on")) { use_gc = true; } else if (gc.equals("off")) { use_gc = false; } else { throw new ParseException("Invalid GC option: " + gc); } String fields = cmd.getOptionValue("Xfields", "true"); if (fields.equals("true")) { field_opts = true; } else if (fields.equals("false")) { field_opts = false; } else { throw new ParseException("Invalid field optimization option: " + fields); } String encoding = cmd.getOptionValue("XEncodedValues", "false"); if (encoding.equals("true")) { encode_vals = true; } else if (encoding.equals("false")) { encode_vals = false; } else { throw new ParseException("Invalid value encoding option: " + encode_vals); } String plat = cmd.getOptionValue("target", "native"); if (plat.equals("native")) { p = CompilerOptions.Platform.Native; } else if (plat.equals("web")) { p = CompilerOptions.Platform.Web; } else { throw new ParseException("Invalid target platform: " + plat); } if (cmd.hasOption("cc")) { external_compiler = cmd.getOptionValue("cc"); } if (cmd.hasOption("skip-validation")) { validate = false; } if (cmd.hasOption("typecheck-only")) { typecheckonly = true; } if (cmd.hasOption("show-constraints")) { showconstraints = true; } if (cmd.hasOption("show-constraint-solution")) { showconstraintsolution = true; } if (cmd.hasOption("debugcompiler")) { debug = true; } if (cmd.hasOption("m32")) { x32 = true; } if (cmd.hasOption("Xinterop")) { interop = true; } if (cmd.hasOption("Xbootinterop")) { boot_interop = true; if (!interop) { System.err.println("WARNING: --Xbootinterop enabled without --Xinterop (no effect)"); } } if (cmd.hasOption("oldExpl")) { oldExpl = true; } if (cmd.hasOption("explanation-strategy")) { explanationStrategy = cmd.getOptionValue("explanation-strategy"); } String output = cmd.getOptionValue("o"); if (output == null) { output = sourcefile.replaceFirst(".js$", ".c"); } else { if (!output.endsWith(".c")) { throw new ParseException("Invalid file extension on output file: " + output); } } String runtime_src = cmd.getOptionValue("runtime-src"); String ext_path = cmd.getOptionValue("ext-path"); if (ext_path == null) { ext_path = new File(".").getCanonicalPath() + "/external"; } if (cmd.hasOption("extra-decls")) { decls = cmd.getOptionValues("extra-decls"); } if (cmd.hasOption("native-libs")) { links = cmd.getOptionValues("native-libs"); } if (cmd.hasOption("extra-objs")) { objs = cmd.getOptionValues("extra-objs"); } if (cmd.hasOption("guest-runtime")) { guest = true; } if (cmd.hasOption("only-c")) { stop_at_c = true; } if (cmd.hasOption("efl")) { efl = true; } int coptlevel = -1; // default optimization if (cmd.hasOption("O3")) { coptlevel = 3; } else if (cmd.hasOption("O2")) { coptlevel = 2; } else if (cmd.hasOption("O1")) { coptlevel = 1; } else if (cmd.hasOption("O0")) { coptlevel = 0; } else if (cmd.hasOption("O")) { coptlevel = -1; } else { coptlevel = 3; } if (!Files.exists(Paths.get(sourcefile))) { System.err.println("File " + sourcefile + " was not found."); throw new FileNotFoundException(sourcefile); } String cwd = new java.io.File(".").getCanonicalPath(); opts = new CompilerOptions(p, sourcefile, debug, output, use_gc, external_compiler == null ? "clang" : external_compiler, external_compiler == null ? "emcc" : external_compiler, cwd + "/a.out", // emcc automatically adds .js new File(".").getCanonicalPath(), true, field_opts, showconstraints, showconstraintsolution, runtime_src, encode_vals, x32, oldExpl, explanationStrategy, efl, coptlevel); if (guest) { opts.setGuestRuntime(); } if (interop) { opts.enableInteropMode(); } if (boot_interop) { opts.startInInteropMode(); } opts.setExternalDeps(ext_path); if (decls != null) { for (String s : decls) { Path fname = FileSystems.getDefault().getPath(s); opts.addDeclarationFile(fname); } } if (links != null) { for (String s : links) { Path fname = FileSystems.getDefault().getPath(s); opts.addLinkageFile(fname); } } if (objs == null) { objs = new String[0]; } } catch (Exception e) { System.err.println(e.getMessage()); e.printStackTrace(); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("sjsc", options); } if (opts != null) { // This typechecks, and depending on flags, also generates C compile(opts, typecheckonly, validate); // don't worry about type validation on command line for now if (!typecheckonly && !stop_at_c) { int ret = 0; // Kept around for debugging 32-bit... if (p == CompilerOptions.Platform.Native) { if (opts.m32()) { String[] x = new String[2]; x[0] = "-m32"; x[1] = opts.getExternalDeps() + "/gc/x86/lib/libgc.a"; ret = clang_compile(opts, objs, x); } else { ret = clang_compile(opts, objs, new String[0]); } } else { ret = emcc_compile(opts, objs, new String[0]); } // If clang failed, propagate the failure outwards if (ret != 0) { System.exit(ret); } } } }
From source file:at.ac.tuwien.inso.subcat.miner.MinerRunner.java
public static void main(String[] args) { Options options = new Options(); options.addOption("h", "help", false, "Show this options"); options.addOption("m", "miner-help", false, "Show miner specific options"); options.addOption("d", "db", true, "The database to process (required)"); options.addOption("p", "project", true, "The project ID to process"); options.addOption("P", "list-projects", false, "List all registered projects"); options.addOption("v", "verbose", false, "Show details"); options.addOption(null, "bug-repo", true, "Bug Repository URL"); options.addOption(null, "bug-product", true, "Bug Product Name"); options.addOption(null, "bug-tracker", true, "Bug Tracker name (e.g. bugzilla)"); options.addOption(null, "bug-account", true, "Bug account name"); options.addOption(null, "bug-passwd", true, "Bug account password"); options.addOption(null, "bug-enable-untrusted", false, "Accept untrusted certificates"); options.addOption(null, "bug-threads", true, "Thread count used in bug miners"); options.addOption(null, "bug-cooldown-time", true, "Bug cooldown time"); options.addOption(null, "bug-miner-option", true, "Bug miner specific option. Format: <option-name>:value"); options.addOption(null, "bug-update", false, "Mine all changes since the last run"); options.getOption("bug-miner-option").setArgs(Option.UNLIMITED_VALUES); options.addOption(null, "src-path", true, "Local source repository path"); options.addOption(null, "src-remote", true, "Remote address"); options.addOption(null, "src-passwd", true, "Source repository account password"); options.addOption(null, "src-account", true, "Source repository account name"); options.addOption(null, "src-miner-option", true, "Source miner specific option. Format: <option-name>:value"); options.getOption("src-miner-option").setArgs(Option.UNLIMITED_VALUES); final Reporter reporter = new Reporter(true); reporter.startTimer();/*from w w w . j ava 2 s . c o m*/ boolean printTraces = false; Settings settings = new Settings(); ModelPool pool = null; CommandLineParser parser = new PosixParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("postprocessor", options); return; } if (cmd.hasOption("miner-help")) { init(); for (MetaData meta : registeredMiner) { System.out.println(meta.name()); for (Entry<String, ParamType> opt : meta.getSpecificParams().entrySet()) { System.out.println(" - " + opt.getKey() + " (" + opt.getValue() + ")"); } } return; } if (cmd.hasOption("db") == false) { reporter.error("miner", "Option --db is required"); reporter.printSummary(); return; } printTraces = cmd.hasOption("verbose"); pool = new ModelPool(cmd.getOptionValue("db"), 2); if (cmd.hasOption("list-projects")) { Model model = pool.getModel(); for (Project proj : model.getProjects()) { System.out.println(" " + proj.getId() + ": " + proj.getDate()); } model.close(); return; } Project project; Model model = pool.getModel(); boolean hasSrcInfos = false; boolean hasBugInfos = false; if (cmd.hasOption("project")) { try { int projId = Integer.parseInt(cmd.getOptionValue("project")); project = model.getProject(projId); } catch (NumberFormatException e) { reporter.error("post-processor", "Invalid project ID"); reporter.printSummary(); return; } if (project == null) { reporter.error("post-processor", "Invalid project ID"); reporter.printSummary(); return; } List<String> flags = model.getFlags(project); hasBugInfos = flags.contains(Model.FLAG_BUG_INFO); hasSrcInfos = flags.contains(Model.FLAG_SRC_INFO); } else { project = model.addProject(new Date(), null, settings.bugTrackerName, settings.bugRepository, settings.bugProductName, null); } model.close(); // // Source Repository Mining: // settings.srcLocalPath = cmd.getOptionValue("src-path"); settings.srcRemote = cmd.getOptionValue("src-remote"); settings.srcRemotePw = cmd.getOptionValue("src-passwd"); settings.srcRemoteUser = cmd.getOptionValue("src-account"); if (settings.srcRemotePw == null || settings.srcRemoteUser == null) { if (settings.srcRemotePw != null) { reporter.error("miner", "--src-passwd should only be used in combination with --src-account"); reporter.printSummary(); return; } else if (settings.srcRemoteUser != null) { reporter.error("miner", "--src-account should only be used in combination with --src-passwd"); reporter.printSummary(); return; } } if (settings.srcRemoteUser != null && settings.srcRemote == null) { reporter.error("miner", "--src-account should only be used in combination with --src-remote"); reporter.printSummary(); return; } if (settings.srcLocalPath != null && hasSrcInfos) { reporter.error("miner", "Source repository updates are not supported yet."); reporter.printSummary(true); return; } // // Bug Repository Mining: // settings.bugRepository = cmd.getOptionValue("bug-repo"); settings.bugProductName = cmd.getOptionValue("bug-product"); settings.bugTrackerName = cmd.getOptionValue("bug-tracker"); settings.bugEnableUntrustedCertificates = cmd.hasOption("bug-enable-untrusted"); settings.bugLoginUser = cmd.getOptionValue("bug-account"); settings.bugLoginPw = cmd.getOptionValue("bug-passwd"); settings.bugUpdate = cmd.hasOption("bug-update"); boolean includeBugs = false; if (settings.bugUpdate) { if (project.getBugTracker() == null || project.getDomain() == null) { reporter.error("miner", "flag --bug-update is requires previously mined bugs. Use --bug-repository, --bug-product and --bug-tracker."); reporter.printSummary(true); return; } if (settings.bugTrackerName != null) { reporter.warning("miner", "flag --bug-tracker without effect"); } if (settings.bugProductName != null) { reporter.warning("miner", "flag --bug-product without effect"); } if (settings.bugRepository != null) { reporter.warning("miner", "flag --bug-repository without effect"); } settings.bugTrackerName = project.getBugTracker(); settings.bugProductName = project.getProduct(); settings.bugRepository = project.getDomain(); includeBugs = true; } else if (settings.bugRepository != null && settings.bugProductName != null && settings.bugTrackerName != null) { if (hasBugInfos == false) { // The user is trying to append bug tracker information to a existing project. } else if (!settings.bugTrackerName.equalsIgnoreCase(project.getBugTracker()) || !settings.bugProductName.equalsIgnoreCase(project.getProduct()) || !settings.bugRepository.equalsIgnoreCase(project.getDomain())) { reporter.error("miner", "There are already previously mined bugs for this project. Use --bug-update to update the database."); reporter.printSummary(true); return; } if (settings.bugRepository == null) { reporter.error("miner", "flag --bug-repository is required"); reporter.printSummary(true); return; } if (settings.bugProductName == null) { reporter.error("miner", "flag --bug-product is required"); reporter.printSummary(true); return; } includeBugs = true; } if (includeBugs) { if (settings.bugLoginPw == null || settings.bugLoginUser == null) { if (settings.bugLoginPw != null) { reporter.error("miner", "--bug-passwd should only be used in combination with --bug-account"); reporter.printSummary(); return; } else if (settings.bugLoginUser != null) { reporter.error("miner", "--bug-account should only be used in combination with --bug-passwd"); reporter.printSummary(); return; } } if (cmd.hasOption("bug-threads")) { try { settings.bugThreads = Integer.parseInt(cmd.getOptionValue("bug-threads")); } catch (Exception e) { reporter.error("miner", "--bug-threads: Invalid parameter type"); reporter.printSummary(); return; } } if (cmd.hasOption("bug-cooldown-time")) { try { settings.bugCooldownTime = Integer.parseInt(cmd.getOptionValue("bug-cooldown-time")); } catch (Exception e) { reporter.error("miner", "--bug-cooldown-time: Invalid parameter type"); reporter.printSummary(); return; } } if (cmd.hasOption("bug-miner-option")) { for (String str : cmd.getOptionValues("bug-miner-option")) { addSpecificParameter(settings.bugSpecificParams, str); } } if (cmd.hasOption("src-miner-option")) { for (String str : cmd.getOptionValues("src-miner-option")) { addSpecificParameter(settings.srcSpecificParams, str); } } } else { if (settings.bugLoginPw != null) { reporter.error("miner", "--bug-passwd should only be used in combination with --bug-account"); reporter.printSummary(); return; } if (settings.bugLoginUser != null) { reporter.error("miner", "--bug-account should only be used in combination with --bug-account"); reporter.printSummary(); return; } if (settings.bugRepository != null) { reporter.error("miner", "--bug-repo should only be used in combination with --bug-product and --bug-tracker"); reporter.printSummary(); return; } if (settings.bugProductName != null) { reporter.error("miner", "--bug-product should only be used in combination with --bug-repo and --bug-tracker"); reporter.printSummary(); return; } if (settings.bugTrackerName != null) { reporter.error("miner", "--bug-tracker should only be used in combination with --bug-repo and --bug-product"); reporter.printSummary(); return; } if (settings.bugEnableUntrustedCertificates) { reporter.error("miner", "--bug-enable-untrusted should only be used in combination with --bug-repo, --bug-tracker and --bug-product"); reporter.printSummary(); return; } if (settings.bugUpdate) { reporter.error("miner", "--bug-update should only be used in combination with --bug-repo, --bug-tracker and --bug-product"); reporter.printSummary(); return; } if (cmd.hasOption("bug-threads")) { reporter.error("miner", "--bug-threads should only be used in combination with --bug-repo, --bug-tracker and --bug-product"); reporter.printSummary(); return; } if (cmd.hasOption("bug-cooldown-time")) { reporter.error("miner", "--bug-cooldown-time should only be used in combination with --bug-repo, --bug-tracker and --bug-product"); reporter.printSummary(); return; } if (cmd.hasOption("bug-miner-option")) { reporter.error("miner", "--bug-miner-option should only be used in combination with --bug-repo, --bug-tracker and --bug-product"); reporter.printSummary(); return; } } // // Run: // MinerRunner runner = new MinerRunner(pool, project, settings, reporter); if (cmd.hasOption("verbose")) { runner.addListener(new MinerListener() { private Map<Miner, Integer> totals = new HashMap<Miner, Integer>(); @Override public void start(Miner miner) { } @Override public void end(Miner miner) { } @Override public void stop(Miner miner) { } @Override public void tasksTotal(Miner miner, int count) { totals.put(miner, count); } @Override public void tasksProcessed(Miner miner, int processed) { Integer total = totals.get(miner); reporter.note(miner.getName(), "status: " + processed + "/" + ((total == null) ? "0" : total)); } }); } runner.run(); } catch (ParameterException e) { reporter.error(e.getMiner().getName(), e.getMessage()); } catch (ParseException e) { reporter.error("miner", "Parsing failed: " + e.getMessage()); if (printTraces == true) { e.printStackTrace(); } } catch (ClassNotFoundException e) { reporter.error("miner", "Failed to create a database connection: " + e.getMessage()); if (printTraces == true) { e.printStackTrace(); } } catch (SQLException e) { reporter.error("miner", "Failed to create a database connection: " + e.getMessage()); if (printTraces == true) { e.printStackTrace(); } } catch (MinerException e) { reporter.error("miner", "Mining Error: " + e.getMessage()); if (printTraces == true) { e.printStackTrace(); } } finally { if (pool != null) { pool.close(); } } reporter.printSummary(true); }
From source file:io.hops.tensorflow.CommonArguments.java
protected static Options createOptions() { Options opts = new Options(); opts.addOption(PYTHON, true, "Path to custom Python binary, if not set the default will be " + "used"); opts.addOption(ARGS, true,/*from w ww . j ava 2 s . com*/ "Command line args for the application. Multiple args can be separated by empty space."); opts.getOption(ARGS).setArgs(Option.UNLIMITED_VALUES); opts.addOption(WORKERS, true, "Number of workers"); opts.addOption(PSES, true, "Number of parameter servers"); opts.addOption(ENV, true, "Environment for Python application. Specified as env_key=env_val pairs"); opts.addOption(TENSORBOARD, false, "Enable TensorBoard, one for each worker"); opts.addOption(MEMORY, true, "Amount of memory in MB to be requested to run the TF application"); opts.addOption(VCORES, true, "Amount of virtual cores to be requested to run the TF application"); opts.addOption(GPUS, true, "Amount of GPUs for each TF application container"); opts.addOption(PROTOCOL, true, "Specify the protocol parameter for tf.train.Server()"); // opts.addOption(PRIORITY, true, "Priority for the Python application containers"); opts.addOption(ALLOCATION_TIMEOUT, true, "Container allocation timeout in seconds"); opts.addOption(DEBUG, false, "Dump out debug information"); opts.addOption(HELP, false, "Print usage"); return opts; }
From source file:com.zimbra.common.localconfig.LocalConfigUpgrade.java
private static Options getAllOptions() { Options options = new Options(); options.addOption(O_HELP, "help", false, "print usage"); options.addOption(O_CONFIG, "config", true, "path to localconfig.xml"); options.addOption(O_TAG, "tag", true, "backup and tag with this suffix"); Option bugOpt = new Option(O_BUG, "bug", true, "bug number this upgrade is for (multiple allowed)"); bugOpt.setArgs(Option.UNLIMITED_VALUES); options.addOption(bugOpt);/*from w w w. j av a2 s. c o m*/ return options; }
From source file:com.emc.ecs.util.OptionBuilder.java
public OptionBuilder hasArgs() { argNum = Option.UNLIMITED_VALUES; return this; }