Example usage for java.io File getAbsolutePath

List of usage examples for java.io File getAbsolutePath

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Introduction

In this page you can find the example usage for java.io File getAbsolutePath.

Prototype

public String getAbsolutePath()

Source Link

Document

Returns the absolute pathname string of this abstract pathname.

Usage

From source file:mase.jbot.PresetCreator.java

public static void main(String[] args) throws Exception {
    if (args.length != 3) {
        System.out.println("PresetCreator [preset file] [controller file] [name tag]");
        System.exit(1);/*ww  w .  jav a  2s.  c  o m*/
    }

    File preset = new File(args[0]);
    File cont = new File(args[1]);
    File tag = new File(args[2]);

    PersistentSolution sol = SolutionPersistence.readSolution(new FileInputStream(cont));
    GroupController contr = sol.getController();
    if (contr instanceof HomogeneousGroupController) {
        AgentController ac = contr.getAgentControllers(1)[0];
        File newFile = new File(preset.getAbsolutePath().replace(".conf", "") + "-" + tag + ".conf");
        FileUtils.copyFile(preset, newFile);
        NEATAgentController nac = (NEATAgentController) ac;
        double[] w = NEATSerializer.serializeToArray(nac.getNetwork());
        fillWeights(newFile, w);
    } else {
        AgentController[] acs = contr.getAgentControllers(0);
        for (int i = 0; i < acs.length; i++) {
            File newFile = new File(
                    preset.getAbsolutePath().replace(".conf", "") + "-" + tag + "-" + i + ".conf");
            FileUtils.copyFile(preset, newFile);
            NEATAgentController nac = (NEATAgentController) acs[i];
            double[] w = NEATSerializer.serializeToArray(nac.getNetwork());
            fillWeights(newFile, w);
        }
    }
}

From source file:fr.inria.edelweiss.kgdqp.core.CentralizedInferrencing.java

public static void main(String args[])
        throws ParseException, EngineException, InterruptedException, IOException {

    List<String> endpoints = new ArrayList<String>();
    String queryPath = null;//ww w  . ja  va2  s. c  o m
    boolean rulesSelection = false;
    File rulesDir = null;
    File ontDir = null;

    /////////////////
    Graph graph = Graph.create();
    QueryProcess exec = QueryProcess.create(graph);

    Options options = new Options();
    Option helpOpt = new Option("h", "help", false, "print this message");
    //        Option queryOpt = new Option("q", "query", true, "specify the sparql query file");
    //        Option endpointOpt = new Option("e", "endpoint", true, "a federated sparql endpoint URL");
    Option versionOpt = new Option("v", "version", false, "print the version information and exit");
    Option rulesOpt = new Option("r", "rulesDir", true, "directory containing the inference rules");
    Option ontOpt = new Option("o", "ontologiesDir", true,
            "directory containing the ontologies for rules selection");
    //        Option locOpt = new Option("c", "centralized", false, "performs centralized inferences");
    Option dataOpt = new Option("l", "load", true, "data file or directory to be loaded");
    //        Option selOpt = new Option("s", "rulesSelection", false, "if set to true, only the applicable rules are run");
    //        options.addOption(queryOpt);
    //        options.addOption(endpointOpt);
    options.addOption(helpOpt);
    options.addOption(versionOpt);
    options.addOption(rulesOpt);
    options.addOption(ontOpt);
    //        options.addOption(selOpt);
    //        options.addOption(locOpt);
    options.addOption(dataOpt);

    String header = "Corese/KGRAM rule engine experiment command line interface";
    String footer = "\nPlease report any issue to alban.gaignard@cnrs.fr, olivier.corby@inria.fr";

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);
    if (cmd.hasOption("h")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("kgdqp", header, options, footer, true);
        System.exit(0);
    }
    if (cmd.hasOption("o")) {
        rulesSelection = true;
        String ontDirPath = cmd.getOptionValue("o");
        ontDir = new File(ontDirPath);
        if (!ontDir.isDirectory()) {
            logger.warn(ontDirPath + " is not a valid directory path.");
            System.exit(0);
        }
    }
    if (!cmd.hasOption("r")) {
        logger.info("You must specify a path for inference rules directory !");
        System.exit(0);
    }

    if (cmd.hasOption("l")) {
        String[] dataPaths = cmd.getOptionValues("l");
        for (String path : dataPaths) {
            Load ld = Load.create(graph);
            ld.load(path);
            logger.info("Loaded " + path);
        }
    }

    if (cmd.hasOption("v")) {
        logger.info("version 3.0.4-SNAPSHOT");
        System.exit(0);
    }

    String rulesDirPath = cmd.getOptionValue("r");
    rulesDir = new File(rulesDirPath);
    if (!rulesDir.isDirectory()) {
        logger.warn(rulesDirPath + " is not a valid directory path.");
        System.exit(0);
    }

    // Local rules graph initialization
    Graph rulesG = Graph.create();
    Load ld = Load.create(rulesG);

    if (rulesSelection) {
        // Ontology loading
        if (ontDir.isDirectory()) {
            for (File o : ontDir.listFiles()) {
                logger.info("Loading " + o.getAbsolutePath());
                ld.load(o.getAbsolutePath());
            }
        }
    }

    // Rules loading
    if (rulesDir.isDirectory()) {
        for (File r : rulesDir.listFiles()) {
            logger.info("Loading " + r.getAbsolutePath());
            ld.load(r.getAbsolutePath());
        }
    }

    // Rule engine initialization
    RuleEngine ruleEngine = RuleEngine.create(graph);
    ruleEngine.set(exec);
    ruleEngine.setOptimize(true);
    ruleEngine.setConstructResult(true);
    ruleEngine.setTrace(true);

    StopWatch sw = new StopWatch();
    logger.info("Federated graph size : " + graph.size());
    logger.info("Rules graph size : " + rulesG.size());

    // Rule selection
    logger.info("Rules selection");
    QueryProcess localKgram = QueryProcess.create(rulesG);
    ArrayList<String> applicableRules = new ArrayList<String>();
    sw.start();
    String rulesSelQuery = "";
    if (rulesSelection) {
        rulesSelQuery = pertinentRulesQuery;
    } else {
        rulesSelQuery = allRulesQuery;
    }
    Mappings maps = localKgram.query(rulesSelQuery);
    logger.info("Rules selected in " + sw.getTime() + " ms");
    logger.info("Applicable rules : " + maps.size());

    // Selected rule loading
    for (Mapping map : maps) {
        IDatatype dt = (IDatatype) map.getValue("?res");
        String rule = dt.getLabel();
        //loading rule in the rule engine
        //            logger.info("Adding rule : ");
        //            System.out.println("-------");
        //            System.out.println(rule);
        //            System.out.println("");
        //            if (! rule.toLowerCase().contains("sameas")) {
        applicableRules.add(rule);
        ruleEngine.addRule(rule);
        //            }
    }

    // Rules application on distributed sparql endpoints
    logger.info("Rules application (" + applicableRules.size() + " rules)");
    ExecutorService threadPool = Executors.newCachedThreadPool();
    RuleEngineThread ruleThread = new RuleEngineThread(ruleEngine);
    sw.reset();
    sw.start();

    //        ruleEngine.process();
    threadPool.execute(ruleThread);
    threadPool.shutdown();

    //monitoring loop
    while (!threadPool.isTerminated()) {
        //            System.out.println("******************************");
        //            System.out.println(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter));
        //            System.out.println("Rule engine running for " + sw.getTime() + " ms");
        //            System.out.println("Federated graph size : " + graph.size());
        System.out.println(sw.getTime() + " , " + graph.size());
        Thread.sleep(5000);
    }

    logger.info("Federated graph size : " + graph.size());
    //        logger.info(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter));

    //        TripleFormat f = TripleFormat.create(graph, true);
    //        f.write("/tmp/gAll.ttl");

}

From source file:act.installer.pubchem.PubchemSynonymFinder.java

public static void main(String[] args) throws Exception {
    org.apache.commons.cli.Options opts = new org.apache.commons.cli.Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/* w  ww .  j a v  a2 s . c  o  m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH));
    if (!rocksDBFile.isDirectory()) {
        System.err.format("Index directory does not exist or is not a directory at '%s'",
                rocksDBFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    List<String> compoundIds = null;
    if (cl.hasOption(OPTION_PUBCHEM_COMPOUND_ID)) {
        compoundIds = Collections.singletonList(cl.getOptionValue(OPTION_PUBCHEM_COMPOUND_ID));
    } else if (cl.hasOption(OPTION_IDS_FILE)) {
        File idsFile = new File(cl.getOptionValue(OPTION_IDS_FILE));
        if (!idsFile.exists()) {
            System.err.format("Cannot find Pubchem CIDs file at %s", idsFile.getAbsolutePath());
            HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                    true);
            System.exit(1);
        }

        compoundIds = getCIDsFromFile(idsFile);

        if (compoundIds.size() == 0) {
            System.err.format("Found zero Pubchem CIDs to process in file at '%s', exiting",
                    idsFile.getAbsolutePath());
            HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                    true);
            System.exit(1);
        }
    } else {
        System.err.format("Must specify one of '%s' or '%s'; index is too big to print all synonyms.",
                OPTION_PUBCHEM_COMPOUND_ID, OPTION_IDS_FILE);
        HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    // Run a quick check to warn users of malformed ids.
    compoundIds.forEach(x -> {
        if (!PC_CID_PATTERN.matcher(x).matches()) { // Use matches() for complete matching.
            LOGGER.warn("Specified compound id does not match expected format: %s", x);
        }
    });

    LOGGER.info("Opening DB and searching for %d Pubchem CIDs", compoundIds.size());
    Pair<RocksDB, Map<PubchemTTLMerger.COLUMN_FAMILIES, ColumnFamilyHandle>> dbAndHandles = null;
    Map<String, PubchemSynonyms> results = new LinkedHashMap<>(compoundIds.size());
    try {
        dbAndHandles = PubchemTTLMerger.openExistingRocksDB(rocksDBFile);
        RocksDB db = dbAndHandles.getLeft();
        ColumnFamilyHandle cidToSynonymsCfh = dbAndHandles.getRight()
                .get(PubchemTTLMerger.COLUMN_FAMILIES.CID_TO_SYNONYMS);

        for (String cid : compoundIds) {
            PubchemSynonyms synonyms = null;
            byte[] val = db.get(cidToSynonymsCfh, cid.getBytes(UTF8));
            if (val != null) {
                ObjectInputStream oi = new ObjectInputStream(new ByteArrayInputStream(val));
                // We're relying on our use of a one-value-type per index model here so we can skip the instanceof check.
                synonyms = (PubchemSynonyms) oi.readObject();
            } else {
                LOGGER.warn("No synonyms available for compound id '%s'", cid);
            }
            results.put(cid, synonyms);
        }
    } finally {
        if (dbAndHandles != null) {
            dbAndHandles.getLeft().close();
        }
    }

    try (OutputStream outputStream = cl.hasOption(OPTION_OUTPUT)
            ? new FileOutputStream(cl.getOptionValue(OPTION_OUTPUT))
            : System.out) {
        OBJECT_MAPPER.writerWithDefaultPrettyPrinter().writeValue(outputStream, results);
        new OutputStreamWriter(outputStream).append('\n');
    }
    LOGGER.info("Done searching for Pubchem synonyms");
}

From source file:Pathway2RDFv2.java

public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException,
        ServiceException, ClassNotFoundException, IDMapperException, ParseException {

    int softwareVersion = 0;
    int schemaVersion = 0;
    int latestRevision = 0;

    BioDataSource.init();/*from  w  w  w.j  ava  2  s .c  o m*/
    Class.forName("org.bridgedb.rdb.IDMapperRdb");
    File dir = new File("/Users/andra/Downloads/bridge");
    File[] bridgeDbFiles = dir.listFiles();
    IDMapperStack mapper = new IDMapperStack();
    for (File bridgeDbFile : bridgeDbFiles) {
        System.out.println(bridgeDbFile.getAbsolutePath());
        mapper.addIDMapper("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath());
    }

    Model bridgeDbmodel = ModelFactory.createDefaultModel();
    InputStream in = new FileInputStream("/tmp/BioDataSource.ttl");
    bridgeDbmodel.read(in, "", "TURTLE");

    WikiPathwaysClient client = new WikiPathwaysClient(
            new URL("http://www.wikipathways.org/wpi/webservice/webservice.php"));

    basicCalls.printMemoryStatus();

    //Map wikipathway organisms to NCBI organisms
    HashMap<String, String> organismTaxonomy = wpRelatedCalls.getOrganismsTaxonomyMapping();
    //HashMap<String, String> miriamSources = new HashMap<String, String>();
    //      HashMap<String, Str ing> miriamLinks = basicCalls.getMiriamUriBridgeDb();

    //Document wikiPathwaysDom = basicCalls.openXmlFile(args[0]);
    Document wikiPathwaysDom = basicCalls.openXmlFile("/tmp/WpGPML.xml");

    //initiate the Jena model to be populated
    Model model = ModelFactory.createDefaultModel();
    Model voidModel = ModelFactory.createDefaultModel();

    voidModel.setNsPrefix("xsd", XSD.getURI());
    voidModel.setNsPrefix("void", Void.getURI());
    voidModel.setNsPrefix("wprdf", "http://rdf.wikipathways.org/");
    voidModel.setNsPrefix("pav", Pav.getURI());
    voidModel.setNsPrefix("prov", Prov.getURI());
    voidModel.setNsPrefix("dcterms", DCTerms.getURI());
    voidModel.setNsPrefix("biopax", Biopax_level3.getURI());
    voidModel.setNsPrefix("gpml", Gpml.getURI());
    voidModel.setNsPrefix("wp", Wp.getURI());
    voidModel.setNsPrefix("foaf", FOAF.getURI());
    voidModel.setNsPrefix("hmdb", "http://identifiers.org/hmdb/");
    voidModel.setNsPrefix("freq", Freq.getURI());
    voidModel.setNsPrefix("dc", DC.getURI());
    setModelPrefix(model);

    //Populate void.ttl
    Calendar now = Calendar.getInstance();
    Literal nowLiteral = voidModel.createTypedLiteral(now);
    Literal titleLiteral = voidModel.createLiteral("WikiPathways-RDF VoID Description", "en");
    Literal descriptionLiteral = voidModel
            .createLiteral("This is the VoID description for a WikiPathwyas-RDF dataset.", "en");
    Resource voidBase = voidModel.createResource("http://rdf.wikipathways.org/");
    Resource identifiersOrg = voidModel.createResource("http://identifiers.org");
    Resource wpHomeBase = voidModel.createResource("http://www.wikipathways.org/");
    Resource authorResource = voidModel
            .createResource("http://semantics.bigcat.unimaas.nl/figshare/search_author.php?author=waagmeester");
    Resource apiResource = voidModel
            .createResource("http://www.wikipathways.org/wpi/webservice/webservice.php");
    Resource mainDatadump = voidModel.createResource("http://rdf.wikipathways.org/wpContent.ttl.gz");
    Resource license = voidModel.createResource("http://creativecommons.org/licenses/by/3.0/");
    Resource instituteResource = voidModel.createResource("http://dbpedia.org/page/Maastricht_University");
    voidBase.addProperty(RDF.type, Void.Dataset);
    voidBase.addProperty(DCTerms.title, titleLiteral);
    voidBase.addProperty(DCTerms.description, descriptionLiteral);
    voidBase.addProperty(FOAF.homepage, wpHomeBase);
    voidBase.addProperty(DCTerms.license, license);
    voidBase.addProperty(Void.uriSpace, voidBase);
    voidBase.addProperty(Void.uriSpace, identifiersOrg);
    voidBase.addProperty(Pav.importedBy, authorResource);
    voidBase.addProperty(Pav.importedFrom, apiResource);
    voidBase.addProperty(Pav.importedOn, nowLiteral);
    voidBase.addProperty(Void.dataDump, mainDatadump);
    voidBase.addProperty(Voag.frequencyOfChange, Freq.Irregular);
    voidBase.addProperty(Pav.createdBy, authorResource);
    voidBase.addProperty(Pav.createdAt, instituteResource);
    voidBase.addLiteral(Pav.createdOn, nowLiteral);
    voidBase.addProperty(DCTerms.subject, Biopax_level3.Pathway);
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/ncbigene/2678"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/pubmed/15215856"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/hmdb/HMDB02005"));
    voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://rdf.wikipathways.org/WP15"));
    voidBase.addProperty(Void.exampleResource,
            voidModel.createResource("http://identifiers.org/obo.chebi/17242"));

    for (String organism : organismTaxonomy.values()) {
        voidBase.addProperty(DCTerms.subject,
                voidModel.createResource("http://dbpedia.org/page/" + organism.replace(" ", "_")));
    }
    voidBase.addProperty(Void.vocabulary, Biopax_level3.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Wp.getURI()));
    voidBase.addProperty(Void.vocabulary, voidModel.createResource(Gpml.getURI()));
    voidBase.addProperty(Void.vocabulary, FOAF.NAMESPACE);
    voidBase.addProperty(Void.vocabulary, Pav.NAMESPACE);
    //Custom Properties
    String baseUri = "http://rdf.wikipathways.org/";
    NodeList pathwayElements = wikiPathwaysDom.getElementsByTagName("Pathway");

    //BioDataSource.init();
    for (int i = 0; i < pathwayElements.getLength(); i++) {
        Model pathwayModel = createPathwayModel();
        String wpId = pathwayElements.item(i).getAttributes().getNamedItem("identifier").getTextContent();
        String revision = pathwayElements.item(i).getAttributes().getNamedItem("revision").getTextContent();
        String pathwayOrganism = "";
        if (pathwayElements.item(i).getAttributes().getNamedItem("Organism") != null)
            pathwayOrganism = pathwayElements.item(i).getAttributes().getNamedItem("Organism").getTextContent()
                    .trim();
        if (Integer.valueOf(revision) > latestRevision) {
            latestRevision = Integer.valueOf(revision);
        }
        File f = new File("/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl");
        System.out.println(f.getName());
        if (!f.exists()) {

            Resource voidPwResource = wpRelatedCalls.addVoidTriples(voidModel, voidBase,
                    pathwayElements.item(i), client);
            Resource pwResource = wpRelatedCalls.addPathwayLevelTriple(pathwayModel, pathwayElements.item(i),
                    organismTaxonomy);

            // Get the comments
            NodeList commentElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Comment");
            wpRelatedCalls.addCommentTriples(pathwayModel, pwResource, commentElements, wpId, revision);
            // Get the Groups
            NodeList groupElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Group");
            for (int n = 0; n < groupElements.getLength(); n++) {
                wpRelatedCalls.addGroupTriples(pathwayModel, pwResource, groupElements.item(n), wpId, revision);
            }
            // Get all the Datanodes
            NodeList dataNodesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("DataNode");
            for (int j = 0; j < dataNodesElement.getLength(); j++) {
                wpRelatedCalls.addDataNodeTriples(pathwayModel, pwResource, dataNodesElement.item(j), wpId,
                        revision, bridgeDbmodel, mapper);
            }
            // Get all the lines
            NodeList linesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Line");
            for (int k = 0; k < linesElement.getLength(); k++) {
                wpRelatedCalls.addLineTriples(pathwayModel, pwResource, linesElement.item(k), wpId, revision);
            }
            //Get all the labels
            NodeList labelsElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Label");
            for (int l = 0; l < labelsElement.getLength(); l++) {
                wpRelatedCalls.addLabelTriples(pathwayModel, pwResource, labelsElement.item(l), wpId, revision);
            }
            NodeList referenceElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXref");
            for (int m = 0; m < referenceElements.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements.item(m), wpId,
                        revision);
            }
            NodeList referenceElements2 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:publicationXref");
            for (int m = 0; m < referenceElements2.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements2.item(m), wpId,
                        revision);
            }
            NodeList referenceElements3 = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:PublicationXRef");
            for (int m = 0; m < referenceElements3.getLength(); m++) {
                wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements3.item(m), wpId,
                        revision);
            }

            NodeList ontologyElements = ((Element) pathwayElements.item(i))
                    .getElementsByTagName("bp:openControlledVocabulary");
            for (int n = 0; n < ontologyElements.getLength(); n++) {
                wpRelatedCalls.addPathwayOntologyTriples(pathwayModel, pwResource, ontologyElements.item(n));
            }
            System.out.println(wpId);
            basicCalls.saveRDF2File(pathwayModel, "/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl",
                    "TURTLE");

            model.add(pathwayModel);
            pathwayModel.removeAll();
        }
    }
    Date myDate = new Date();
    SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd");
    String myDateString = sdf.format(myDate);
    FileUtils.writeStringToFile(new File("latestVersion.txt"),
            "v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString);
    basicCalls.saveRDF2File(model, "/tmp/wpContent_v" + schemaVersion + "." + softwareVersion + "."
            + latestRevision + "_" + myDateString + ".ttl", "TURTLE");
    basicCalls.saveRDF2File(voidModel, "/tmp/void.ttl", "TURTLE");
}

From source file:com.osrdata.etltoolbox.fileloader.Main.java

/**
 * Main entry point into the application.
 * @param args command line argunemtns//from w w  w  . j  a  va 2s  .  c om
 */
public static void main(String[] args) {
    Options options = new Options();
    options.addOption(new Option("s", "spec", true, "Source-to-target specification file"));
    options.addOption(new Option("d", "directory", true, "Source directory to load"));
    options.addOption(new Option("f", "file", true, "File to perform operation on"));
    options.addOption(new Option("r", "replace", false, "Replace previously loaded data"));
    options.addOption(new Option("t", "trace", true, "Trace records processed at specified interval"));

    CommandLineParser parser = new BasicParser();

    try {
        CommandLine line = parser.parse(options, args);

        if (line.hasOption("spec") && (line.hasOption("directory") || line.hasOption("file"))) {
            FileLoader loader = new FileLoader(line);

            loader.init();

            if (line.hasOption("file")) {
                loader.load(new File(line.getOptionValue("file")));
            } else if (line.hasOption("directory")) {
                File directory = new File(line.getOptionValue("directory"));

                if (directory.isDirectory()) {
                    File[] files = directory.listFiles();

                    for (File file : files) {
                        loader.load(file);
                    }
                } else {
                    log.fatal(directory.getAbsolutePath() + " does not appear to be a directory.");
                }
            }
        } else {
            usage();
        }
    } catch (ParseException e) {
        usage();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:FaceRatios.java

@SuppressWarnings("serial")
public static void main(String[] args) {
    int r = FSDK.ActivateLibrary(FACE_SDK_LICENSE);
    if (r == FSDK.FSDKE_OK) {
        FSDK.Initialize();/*ww  w . jav  a  2  s . co m*/
        FSDK.SetFaceDetectionParameters(true, true, 384);

        Map<String, Map<String, ArrayList<Double>>> faceProperties = new HashMap<>();

        for (String directory : new File(FACE_DIRECTORY).list()) {
            if (new File(FACE_DIRECTORY + directory).isDirectory()) {
                Map<String, ArrayList<Double>> properties = new HashMap<String, ArrayList<Double>>() {
                    {
                        for (String property : propertyNames)
                            put(property, new ArrayList<Double>());
                    }
                };

                File[] files = new File(FACE_DIRECTORY + directory).listFiles();
                System.out.println("Analyzing " + directory + " with " + files.length + " files\n");
                for (File file : files) {
                    if (file.isFile()) {
                        HImage imageHandle = new HImage();
                        FSDK.LoadImageFromFileW(imageHandle, file.getAbsolutePath());

                        FSDK.TFacePosition.ByReference facePosition = new FSDK.TFacePosition.ByReference();
                        if (FSDK.DetectFace(imageHandle, facePosition) == FSDK.FSDKE_OK) {
                            FSDK_Features.ByReference facialFeatures = new FSDK_Features.ByReference();
                            FSDK.DetectFacialFeaturesInRegion(imageHandle, (FSDK.TFacePosition) facePosition,
                                    facialFeatures);

                            Point[] featurePoints = new Point[FSDK.FSDK_FACIAL_FEATURE_COUNT];
                            for (int i = 0; i < FSDK.FSDK_FACIAL_FEATURE_COUNT; i++) {
                                featurePoints[i] = new Point(0, 0);
                                featurePoints[i].x = facialFeatures.features[i].x;
                                featurePoints[i].y = facialFeatures.features[i].y;
                            }

                            double eyeDistance = featureDistance(featurePoints, FeatureID.LEFT_EYE,
                                    FeatureID.RIGHT_EYE);
                            double rightEyeSize = featureDistance(featurePoints,
                                    FeatureID.RIGHT_EYE_INNER_CORNER, FeatureID.RIGHT_EYE_OUTER_CORNER);
                            double leftEyeSize = featureDistance(featurePoints, FeatureID.LEFT_EYE_INNER_CORNER,
                                    FeatureID.LEFT_EYE_OUTER_CORNER);
                            double averageEyeSize = (rightEyeSize + leftEyeSize) / 2;

                            double mouthLength = featureDistance(featurePoints, FeatureID.MOUTH_RIGHT_CORNER,
                                    FeatureID.MOUTH_LEFT_CORNER);
                            double mouthHeight = featureDistance(featurePoints, FeatureID.MOUTH_BOTTOM,
                                    FeatureID.MOUTH_TOP);
                            double noseHeight = featureDistance(featurePoints, FeatureID.NOSE_BOTTOM,
                                    FeatureID.NOSE_BRIDGE);
                            double chinHeight = featureDistance(featurePoints, FeatureID.CHIN_BOTTOM,
                                    FeatureID.MOUTH_BOTTOM);

                            double chinToBridgeHeight = featureDistance(featurePoints, FeatureID.CHIN_BOTTOM,
                                    FeatureID.NOSE_BRIDGE);

                            double faceContourLeft = (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getY()
                                    - featurePoints[FeatureID.FACE_CONTOUR2.getIndex()].getY())
                                    / (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getX()
                                            - featurePoints[FeatureID.FACE_CONTOUR2.getIndex()].getX());
                            double faceContourRight = (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getY()
                                    - featurePoints[FeatureID.FACE_CONTOUR12.getIndex()].getY())
                                    / (featurePoints[FeatureID.CHIN_BOTTOM.getIndex()].getX()
                                            - featurePoints[FeatureID.FACE_CONTOUR12.getIndex()].getX());

                            double bridgeLeftEyeDistance = featureDistance(featurePoints,
                                    FeatureID.LEFT_EYE_INNER_CORNER, FeatureID.NOSE_BRIDGE);
                            double bridgeRightEyeDistance = featureDistance(featurePoints,
                                    FeatureID.RIGHT_EYE_INNER_CORNER, FeatureID.NOSE_BRIDGE);

                            properties.get("eyeSize/eyeDistance").add(averageEyeSize / eyeDistance);
                            properties.get("eyeSizeDisparity")
                                    .add(Math.abs(leftEyeSize - rightEyeSize) / averageEyeSize);
                            properties.get("bridgeToEyeDisparity")
                                    .add(Math.abs(bridgeLeftEyeDistance - bridgeRightEyeDistance)
                                            / ((bridgeLeftEyeDistance + bridgeRightEyeDistance) / 2));
                            properties.get("eyeDistance/mouthLength").add(eyeDistance / mouthLength);
                            properties.get("eyeDistance/noseHeight").add(eyeDistance / noseHeight);
                            properties.get("eyeSize/mouthLength").add(eyeDistance / mouthLength);
                            properties.get("eyeSize/noseHeight").add(eyeDistance / noseHeight);
                            properties.get("mouthLength/mouthHeight").add(mouthLength / mouthHeight);
                            properties.get("chinHeight/noseHeight").add(chinHeight / noseHeight);
                            properties.get("chinHeight/chinToBridgeHeight")
                                    .add(chinHeight / chinToBridgeHeight);
                            properties.get("noseHeight/chinToBridgeHeight")
                                    .add(noseHeight / chinToBridgeHeight);
                            properties.get("mouthHeight/chinToBridgeHeight")
                                    .add(mouthHeight / chinToBridgeHeight);
                            properties.get("faceCountourAngle")
                                    .add(Math.toDegrees(Math.atan((faceContourLeft - faceContourRight)
                                            / (1 + faceContourLeft * faceContourRight))));
                        }

                        FSDK.FreeImage(imageHandle);
                    }
                }

                System.out.format("%32s\t%8s\t%8s\t%3s%n", "Property", "", "", "c");
                System.out.println(new String(new char[76]).replace("\0", "-"));

                ArrayList<Entry<String, ArrayList<Double>>> propertyList = new ArrayList<>(
                        properties.entrySet());
                Collections.sort(propertyList, new Comparator<Entry<String, ArrayList<Double>>>() {
                    @Override
                    public int compare(Entry<String, ArrayList<Double>> arg0,
                            Entry<String, ArrayList<Double>> arg1) {
                        DescriptiveStatistics dStats0 = new DescriptiveStatistics(listToArray(arg0.getValue()));
                        DescriptiveStatistics dStats1 = new DescriptiveStatistics(listToArray(arg1.getValue()));
                        return new Double(dStats0.getStandardDeviation() / dStats0.getMean())
                                .compareTo(dStats1.getStandardDeviation() / dStats1.getMean());
                    }
                });

                for (Entry<String, ArrayList<Double>> property : propertyList) {
                    DescriptiveStatistics dStats = new DescriptiveStatistics(listToArray(property.getValue()));
                    System.out.format("%32s\t%4f\t%4f\t%3s%n", property.getKey(), dStats.getMean(),
                            dStats.getStandardDeviation(),
                            Math.round(dStats.getStandardDeviation() / dStats.getMean() * 100) + "%");
                }

                System.out.println("\n");
                faceProperties.put(directory, properties);
            }
        }

        for (String propertyName : propertyNames) {
            DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset();
            for (Entry<String, Map<String, ArrayList<Double>>> face : faceProperties.entrySet()) {
                dataset.add(face.getValue().get(propertyName), "Default Series", face.getKey());
            }

            PropertyBoxWhisker plot = new PropertyBoxWhisker(propertyName, dataset);
            plot.pack();
            plot.setVisible(true);
        }
    }
}

From source file:com.norconex.collector.http.HttpCollector.java

/**
 * Invokes the HTTP Collector from the command line.  
 * @param args Invoke it once without any arguments to get a 
 *    list of command-line options.//from   w  w w  .ja va2 s .com
 */
public static void main(String[] args) {
    CommandLine cmd = parseCommandLineArguments(args);
    String action = cmd.getOptionValue(ARG_ACTION);
    File configFile = new File(cmd.getOptionValue(ARG_CONFIG));
    File varFile = null;
    if (cmd.hasOption(ARG_VARIABLES)) {
        varFile = new File(cmd.getOptionValue(ARG_VARIABLES));
    }

    try {
        HttpCollector conn = new HttpCollector(configFile, varFile);
        if (ARG_ACTION_START.equalsIgnoreCase(action)) {
            conn.crawl(false);
        } else if (ARG_ACTION_RESUME.equalsIgnoreCase(action)) {
            conn.crawl(true);
        } else if (ARG_ACTION_STOP.equalsIgnoreCase(action)) {
            conn.stop();
        }
    } catch (Exception e) {
        File errorFile = new File("./error-" + System.currentTimeMillis() + ".log");
        System.err.println("\n\nAn ERROR occured:\n\n" + e.getLocalizedMessage());
        System.err.println(
                "\n\nDetails of the error has been stored at: " + errorFile.getAbsolutePath() + "\n\n");
        try {
            PrintWriter w = new PrintWriter(errorFile);
            e.printStackTrace(w);
            w.flush();
            w.close();
        } catch (FileNotFoundException e1) {
            throw new HttpCollectorException("Cannot write error file.", e1);
        }
    }
}

From source file:com.opendesign.utils.ThumbnailManager.java

public static void main(String[] args) {

    //      //product ? 
    //      saveThumbDesignWorkMedium(thumbnailPath); //? ??
    //      saveThumbDesignWorkLarge(thumbnailPath); //? ??
    //      //from  w ww  .ja  v a2  s.  com
    //      //project ?
    //      saveThumbDesignWorkMedium(thumbnailPath); //? ??
    //      saveThumbProjectWorkMedium(thumbnailPath); //? ??
    //      
    //      //work ?
    //      saveThumbProjectWorkSmall(thumbnailPath); //? ??
    //      saveThumbProjectWorkLarge(thumbnailPath); //? ??

    File productFolder = new File(
            "/Users/windfall/Desktop/00_working/02_?/02_01_OpenDesign/02_01_100_temp/km_upload/product");

    int updated = 0;
    int total = 0;
    for (File image : productFolder.listFiles()) {
        if (image != null) {

            System.out.println("resizing " + image.getAbsolutePath());
            saveThumbDesignWorkMedium(image.getAbsolutePath()); //? ??
            saveThumbDesignWorkLarge(image.getAbsolutePath()); //? ??
            updated++;

        } else {
            System.out.println("Fail=" + image);
        }
        total++;
    }

    System.out.println("Product Files=[" + total + "] updated=[" + updated + "]");

    updated = 0;
    total = 0;
    File projectFolder = new File(
            "/Users/windfall/Desktop/00_working/02_?/02_01_OpenDesign/02_01_100_temp/km_upload/project");

    for (File image : projectFolder.listFiles()) {
        if (image != null) {

            System.out.println("resizing " + image.getAbsolutePath());
            saveThumbDesignWorkMedium(image.getAbsolutePath()); //? ??
            saveThumbProjectWorkMedium(image.getAbsolutePath()); //? ??
            updated++;

        } else {
            System.out.println("Fail=" + image);
        }
        total++;
    }

    System.out.println("Project Files=[" + total + "] updated=[" + updated + "]");

    updated = 0;
    total = 0;

    File workFolder = new File(
            "/Users/windfall/Desktop/00_working/02_?/02_01_OpenDesign/02_01_100_temp/km_upload/project_work_file");

    for (File image : workFolder.listFiles()) {
        if (image != null) {

            System.out.println("resizing " + image.getAbsolutePath());
            saveThumbProjectWorkSmall(image.getAbsolutePath()); //? ??
            saveThumbProjectWorkLarge(image.getAbsolutePath()); //? ??
            updated++;

        } else {
            System.out.println("Fail=" + image);
        }
        total++;
    }

    System.out.println("Work Files=[" + total + "] updated=[" + updated + "]");

}

From source file:com.act.biointerpretation.l2expansion.L2ExpansionDriver.java

public static void main(String[] args) throws Exception {

    // Build command line parser.
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//from  w  w w .j  a va 2 s.  c  om
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        LOGGER.error("Argument parsing failed: %s", e.getMessage());
        HELP_FORMATTER.printHelp(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    // Print help.
    if (cl.hasOption(OPTION_HELP)) {
        HELP_FORMATTER.printHelp(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    // Get output files.
    String outputPath = cl.getOptionValue(OPTION_OUTPUT_PATH);
    File outputFile = new File(outputPath);
    if (outputFile.isDirectory() || outputFile.exists()) {
        LOGGER.error("Supplied output file is a directory or already exists.");
        System.exit(1);
    }
    outputFile.createNewFile();
    File inchiOutputFile = new File(outputPath + ".inchis");
    if (inchiOutputFile.isDirectory() || inchiOutputFile.exists()) {
        LOGGER.error("Supplied inchi output file is a directory or already exists.");
        System.exit(1);
    }
    inchiOutputFile.createNewFile();

    Optional<OutputStream> maybeProgressStream = Optional.empty();
    if (cl.hasOption(OPTION_PROGRESS_PATH)) {
        String progressPath = cl.getOptionValue(OPTION_PROGRESS_PATH);
        File progressFile = new File(progressPath);
        LOGGER.info("Writing incremental results to file at %s", progressFile.getAbsolutePath());
        if (progressFile.isDirectory() || progressFile.exists()) {
            LOGGER.error("Supplied progress file is a directory or already exists.");
            System.exit(1);
        }
        maybeProgressStream = Optional.of(new FileOutputStream(progressFile));
    }

    // Get metabolite list
    L2InchiCorpus inchiCorpus = getInchiCorpus(cl, OPTION_METABOLITES);
    LOGGER.info("%d substrate inchis.", inchiCorpus.getInchiList().size());

    Integer maxMass = NO_MASS_THRESHOLD;
    if (cl.hasOption(OPTION_MASS_THRESHOLD)) {
        maxMass = Integer.parseInt(cl.getOptionValue(OPTION_MASS_THRESHOLD));
        LOGGER.info("Filtering out substrates with mass more than %d daltons.", maxMass);
    }
    inchiCorpus.filterByMass(maxMass);
    LOGGER.info("%d substrate inchis that are importable as molecules.", inchiCorpus.getInchiList().size());

    PredictionGenerator generator = new AllPredictionsGenerator(new ReactionProjector());

    L2Expander expander = buildExpander(cl, inchiCorpus, generator);
    L2PredictionCorpus predictionCorpus = expander.getPredictions(maybeProgressStream);

    LOGGER.info("Done with L2 expansion. Produced %d predictions.", predictionCorpus.getCorpus().size());

    LOGGER.info("Writing corpus to file.");
    predictionCorpus.writePredictionsToJsonFile(outputFile);
    L2InchiCorpus productInchis = new L2InchiCorpus(predictionCorpus.getUniqueProductInchis());
    productInchis.writeToFile(inchiOutputFile);
    LOGGER.info("L2ExpansionDriver complete!");
}

From source file:fr.inria.edelweiss.kgdqp.core.CentralizedInferrencingNoSpin.java

public static void main(String args[])
        throws ParseException, EngineException, InterruptedException, IOException, LoadException {

    List<String> endpoints = new ArrayList<String>();
    String queryPath = null;/*w w w  .  j ava2 s .co m*/
    boolean rulesSelection = false;
    File rulesDir = null;
    File ontDir = null;

    /////////////////
    Graph graph = Graph.create();
    QueryProcess exec = QueryProcess.create(graph);

    Options options = new Options();
    Option helpOpt = new Option("h", "help", false, "print this message");
    //        Option queryOpt = new Option("q", "query", true, "specify the sparql query file");
    //        Option endpointOpt = new Option("e", "endpoint", true, "a federated sparql endpoint URL");
    Option versionOpt = new Option("v", "version", false, "print the version information and exit");
    Option rulesOpt = new Option("r", "rulesDir", true, "directory containing the inference rules");
    Option ontOpt = new Option("o", "ontologiesDir", true,
            "directory containing the ontologies for rules selection");
    //        Option locOpt = new Option("c", "centralized", false, "performs centralized inferences");
    Option dataOpt = new Option("l", "load", true, "data file or directory to be loaded");
    //        Option selOpt = new Option("s", "rulesSelection", false, "if set to true, only the applicable rules are run");
    //        options.addOption(queryOpt);
    //        options.addOption(endpointOpt);
    options.addOption(helpOpt);
    options.addOption(versionOpt);
    options.addOption(rulesOpt);
    options.addOption(ontOpt);
    //        options.addOption(selOpt);
    //        options.addOption(locOpt);
    options.addOption(dataOpt);

    String header = "Corese/KGRAM rule engine experiment command line interface";
    String footer = "\nPlease report any issue to alban.gaignard@cnrs.fr, olivier.corby@inria.fr";

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);
    if (cmd.hasOption("h")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("kgdqp", header, options, footer, true);
        System.exit(0);
    }
    if (cmd.hasOption("o")) {
        rulesSelection = true;
        String ontDirPath = cmd.getOptionValue("o");
        ontDir = new File(ontDirPath);
        if (!ontDir.isDirectory()) {
            logger.warn(ontDirPath + " is not a valid directory path.");
            System.exit(0);
        }
    }
    if (!cmd.hasOption("r")) {
        logger.info("You must specify a path for inference rules directory !");
        System.exit(0);
    }

    if (cmd.hasOption("l")) {
        String[] dataPaths = cmd.getOptionValues("l");
        for (String path : dataPaths) {
            Load ld = Load.create(graph);
            ld.load(path);
            logger.info("Loaded " + path);
        }
    }

    if (cmd.hasOption("v")) {
        logger.info("version 3.0.4-SNAPSHOT");
        System.exit(0);
    }

    String rulesDirPath = cmd.getOptionValue("r");
    rulesDir = new File(rulesDirPath);
    if (!rulesDir.isDirectory()) {
        logger.warn(rulesDirPath + " is not a valid directory path.");
        System.exit(0);
    }

    // Local rules graph initialization
    Graph rulesG = Graph.create();
    Load ld = Load.create(rulesG);

    if (rulesSelection) {
        // Ontology loading
        if (ontDir.isDirectory()) {
            for (File o : ontDir.listFiles()) {
                logger.info("Loading " + o.getAbsolutePath());
                ld.load(o.getAbsolutePath());
            }
        }
    }

    // Rules loading
    if (rulesDir.isDirectory()) {
        for (File r : rulesDir.listFiles()) {
            if (r.getAbsolutePath().endsWith(".rq")) {
                logger.info("Loading " + r.getAbsolutePath());
                //                ld.load(r.getAbsolutePath());

                //                    byte[] encoded = Files.readAllBytes(Paths.get(r.getAbsolutePath()));
                //                    String construct = new String(encoded, "UTF-8"); //StandardCharsets.UTF_8);

                FileInputStream f = new FileInputStream(r);
                QueryLoad ql = QueryLoad.create();
                String construct = ql.read(f);
                f.close();

                SPINProcess sp = SPINProcess.create();
                String spinConstruct = sp.toSpin(construct);

                ld.load(new ByteArrayInputStream(spinConstruct.getBytes()), Load.TURTLE_FORMAT);
                logger.info("Rules graph size : " + rulesG.size());

            }
        }
    }

    // Rule engine initialization
    RuleEngine ruleEngine = RuleEngine.create(graph);
    ruleEngine.set(exec);
    ruleEngine.setOptimize(true);
    ruleEngine.setConstructResult(true);
    ruleEngine.setTrace(true);

    StopWatch sw = new StopWatch();
    logger.info("Federated graph size : " + graph.size());
    logger.info("Rules graph size : " + rulesG.size());

    // Rule selection
    logger.info("Rules selection");
    QueryProcess localKgram = QueryProcess.create(rulesG);
    ArrayList<String> applicableRules = new ArrayList<String>();
    sw.start();
    String rulesSelQuery = "";
    if (rulesSelection) {
        rulesSelQuery = pertinentRulesQuery;
    } else {
        rulesSelQuery = allRulesQuery;
    }
    Mappings maps = localKgram.query(rulesSelQuery);
    logger.info("Rules selected in " + sw.getTime() + " ms");
    logger.info("Applicable rules : " + maps.size());

    // Selected rule loading
    for (Mapping map : maps) {
        IDatatype dt = (IDatatype) map.getValue("?res");
        String rule = dt.getLabel();
        //loading rule in the rule engine
        //            logger.info("Adding rule : ");
        //            System.out.println("-------");
        //            System.out.println(rule);
        //            System.out.println("");
        //            if (! rule.toLowerCase().contains("sameas")) {
        applicableRules.add(rule);
        ruleEngine.addRule(rule);
        //            }
    }

    // Rules application on distributed sparql endpoints
    logger.info("Rules application (" + applicableRules.size() + " rules)");
    ExecutorService threadPool = Executors.newCachedThreadPool();
    RuleEngineThread ruleThread = new RuleEngineThread(ruleEngine);
    sw.reset();
    sw.start();

    //        ruleEngine.process();
    threadPool.execute(ruleThread);
    threadPool.shutdown();

    //monitoring loop
    while (!threadPool.isTerminated()) {
        //            System.out.println("******************************");
        //            System.out.println(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter));
        //            System.out.println("Rule engine running for " + sw.getTime() + " ms");
        //            System.out.println("Federated graph size : " + graph.size());
        System.out.println(sw.getTime() + " , " + graph.size());
        Thread.sleep(5000);
    }

    logger.info("Federated graph size : " + graph.size());
    //        logger.info(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter));

    //        TripleFormat f = TripleFormat.create(graph, true);
    //        f.write("/tmp/gAll.ttl");
}