Example usage for java.util Map containsKey

List of usage examples for java.util Map containsKey

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Introduction

In this page you can find the example usage for java.util Map containsKey.

Prototype

boolean containsKey(Object key);

Source Link

Document

Returns true if this map contains a mapping for the specified key.

Usage

From source file:net.ontopia.topicmaps.cmdlineutils.rdbms.RDBMSIndexTool.java

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

    // Initialize logging
    CmdlineUtils.initializeLogging();/* ww  w .j av a2  s .  com*/

    // Register logging options
    CmdlineOptions options = new CmdlineOptions("RDBMSIndexTool", argv);
    CmdlineUtils.registerLoggingOptions(options);

    // Parse command line options
    try {
        options.parse();
    } catch (CmdlineOptions.OptionsException e) {
        System.err.println("Error: " + e.getMessage());
        System.exit(1);
    }

    // Get command line arguments
    String[] args = options.getArguments();

    if (args.length != 1) {
        usage();
        System.exit(3);
    }

    // load database schema project
    ClassLoader cloader = RDBMSIndexTool.class.getClassLoader();
    InputStream istream = cloader.getResourceAsStream("net/ontopia/topicmaps/impl/rdbms/config/schema.xml");
    Project dbp = DatabaseProjectReader.loadProject(istream);

    // open database connection
    String propfile = args[0];
    ConnectionFactoryIF cf = new DefaultConnectionFactory(PropertyUtils.loadProperties(new File(propfile)),
            true);

    Connection conn = cf.requestConnection();
    try {
        DatabaseMetaData dbm = conn.getMetaData();
        boolean downcase = dbm.storesLowerCaseIdentifiers();

        Map extra_indexes = new TreeMap();
        Map missing_indexes = new TreeMap();

        Iterator tables = dbp.getTables().iterator();
        while (tables.hasNext()) {
            Table table = (Table) tables.next();
            String table_name = (downcase ? table.getName().toLowerCase() : table.getName());
            //! System.out.println("T :"  + table_name);

            // get primary keys from database
            Map pkeys = getPrimaryKeys(table_name, dbm);

            // get indexes from database
            Map indexes = getIndexes(table_name, dbm);

            Map dindexes = new HashMap();
            if (table.getPrimaryKeys() != null) {
                String pkey = table_name + '(' + StringUtils.join(table.getPrimaryKeys(), ',') + ')';
                if (!pkeys.containsKey(pkey))
                    System.out.println("PKM: " + pkey);
            }

            Iterator iter = table.getIndexes().iterator();
            while (iter.hasNext()) {
                Index index = (Index) iter.next();
                String i = table_name + '(' + StringUtils.join(index.getColumns(), ',') + ')';
                String index_name = (downcase ? index.getName().toLowerCase() : index.getName());
                dindexes.put(i, index_name);
            }

            Set extra = new HashSet(indexes.keySet());
            extra.removeAll(dindexes.keySet());
            extra.removeAll(pkeys.keySet());
            if (!extra.isEmpty()) {
                Iterator i = extra.iterator();
                while (i.hasNext()) {
                    Object k = i.next();
                    extra_indexes.put(k, indexes.get(k));
                }
            }

            Set missing = new HashSet(dindexes.keySet());
            missing.addAll(pkeys.keySet());
            missing.removeAll(indexes.keySet());
            if (!missing.isEmpty()) {
                Iterator i = missing.iterator();
                while (i.hasNext()) {
                    Object k = i.next();
                    missing_indexes.put(k, dindexes.get(k));
                }
            }

        }
        if (!extra_indexes.isEmpty())
            System.out.println("/* --- Extra indexes ----------------------------------------- */");
        Iterator eiter = extra_indexes.keySet().iterator();
        while (eiter.hasNext()) {
            Object k = eiter.next();
            System.out.println("drop index " + extra_indexes.get(k) + "; /* " + k + " */");
        }

        if (!missing_indexes.isEmpty())
            System.out.println("/* --- Missing indexes---------------------------------------- */");
        Iterator miter = missing_indexes.keySet().iterator();
        while (miter.hasNext()) {
            Object k = miter.next();
            System.out.println("create index " + missing_indexes.get(k) + " on " + k + ";");
        }

    } finally {
        conn.rollback();
        conn.close();
    }

}

From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step5bGoldLabelStatistics.java

@SuppressWarnings("unchecked")
public static void main(String[] args) throws Exception {
    String inputDir = args[0];/*w  w w.j  a v  a2 s  .  c  o  m*/

    Collection<File> files = IOHelper.listXmlFiles(new File(inputDir));

    int totalPairsWithReasonSameAsGold = 0;

    DescriptiveStatistics ds = new DescriptiveStatistics();

    DescriptiveStatistics statsPerTopic = new DescriptiveStatistics();

    Map<String, Integer> goldDataDistribution = new HashMap<>();

    int totalGoldReasonTokens = 0;

    for (File file : files) {
        List<AnnotatedArgumentPair> argumentPairs = (List<AnnotatedArgumentPair>) XStreamTools.getXStream()
                .fromXML(file);

        int pairsPerTopicCounter = 0;

        for (AnnotatedArgumentPair annotatedArgumentPair : argumentPairs) {
            String goldLabel = annotatedArgumentPair.getGoldLabel();

            int sameInOnePair = 0;

            if (goldLabel != null) {
                if (!goldDataDistribution.containsKey(goldLabel)) {
                    goldDataDistribution.put(goldLabel, 0);
                }

                goldDataDistribution.put(goldLabel, goldDataDistribution.get(goldLabel) + 1);

                // get gold reason statistics
                for (AnnotatedArgumentPair.MTurkAssignment assignment : annotatedArgumentPair.mTurkAssignments) {
                    String label = assignment.getValue();

                    if (goldLabel.equals(label)) {
                        sameInOnePair++;

                        totalGoldReasonTokens += assignment.getReason().split("\\W+").length;
                    }
                }

                pairsPerTopicCounter++;
            }

            ds.addValue(sameInOnePair);
            totalPairsWithReasonSameAsGold += sameInOnePair;

        }

        statsPerTopic.addValue(pairsPerTopicCounter);
    }

    System.out.println("Total reasons matching gold " + totalPairsWithReasonSameAsGold);
    System.out.println(ds);

    int totalPairs = 0;
    for (Integer pairs : goldDataDistribution.values()) {
        totalPairs += pairs;
    }

    System.out.println(goldDataDistribution);
    System.out.println(goldDataDistribution.values());
    System.out.println("Total pairs: " + totalPairs);

    System.out.println("Stats per topic: " + statsPerTopic);
    System.out.println("Total gold reason tokens: " + totalGoldReasonTokens);

}

From source file:de.tudarmstadt.ukp.experiments.dip.wp1.documents.Step7CollectMTurkResults.java

public static void main(String[] args) throws Exception {
    // input dir - list of xml query containers
    // /home/user-ukp/research/data/dip/wp1-documents/step4-boiler-plate/
    File inputDir = new File(args[0] + "/");

    // MTurk result file

    // output dir
    File outputDir = new File(args[2]);
    if (!outputDir.exists()) {
        outputDir.mkdirs();//w  w w .j  a  va  2  s  .  c  o  m

    }

    // Folder with success files
    File mturkSuccessDir = new File(args[1]);

    Collection<File> files = FileUtils.listFiles(mturkSuccessDir, new String[] { "result" }, false);
    if (files.isEmpty()) {
        throw new IllegalArgumentException("Input folder is empty. " + mturkSuccessDir);
    }

    HashMap<String, List<MTurkAnnotation>> mturkAnnotations = new HashMap<>();

    // parsing all CSV files
    for (File mturkCSVResultFile : files) {
        System.out.println("Parsing " + mturkCSVResultFile.getName());

        MTurkOutputReader outputReader = new MTurkOutputReader(
                new HashSet<>(Arrays.asList("annotation", "workerid")), mturkCSVResultFile);

        // for fixing broken data input: for each hit, collect all sentence IDs
        Map<String, SortedSet<String>> hitSentences = new HashMap<>();

        // first iteration: collect the sentences
        for (Map<String, String> record : outputReader) {
            String hitID = record.get("hitid");
            if (!hitSentences.containsKey(hitID)) {
                hitSentences.put(hitID, new TreeSet<>());
            }

            String relevantSentences = record.get("Answer.relevant_sentences");
            String irrelevantSentences = record.get("Answer.irrelevant_sentences");

            if (relevantSentences != null) {
                hitSentences.get(hitID).addAll(Arrays.asList(relevantSentences.split(",")));
            }

            if (irrelevantSentences != null) {
                hitSentences.get(hitID).addAll(Arrays.asList(irrelevantSentences.split(",")));
            }
        }

        // and now second iteration
        for (Map<String, String> record : outputReader) {
            String hitID = record.get("hitid");
            String annotatorID = record.get("workerid");
            String acceptTime = record.get("assignmentaccepttime");
            String submitTime = record.get("assignmentsubmittime");
            String relevantSentences = record.get("Answer.relevant_sentences");
            String irrelevantSentences = record.get("Answer.irrelevant_sentences");
            String reject = record.get("reject");
            String filename[];
            String comment;
            String clueWeb;
            String[] relevant = {};
            String[] irrelevant = {};

            filename = record.get("annotation").split("_");
            String fileXml = filename[0];
            clueWeb = filename[1].trim();
            comment = record.get("Answer.comment");

            if (relevantSentences != null) {
                relevant = relevantSentences.split(",");
            }

            if (irrelevantSentences != null) {
                irrelevant = irrelevantSentences.split(",");
            }

            // sanitizing data: if both relevant and irrelevant are empty, that's a bug
            // we're gonna look up all sentences from this HIT and treat this assignment
            // as if there were only irrelevant ones
            if (relevant.length == 0 && irrelevant.length == 0) {
                SortedSet<String> strings = hitSentences.get(hitID);
                irrelevant = new String[strings.size()];
                strings.toArray(irrelevant);
            }

            if (reject != null) {
                System.out.println(" HIT " + hitID + " annotated by " + annotatorID + " was rejected ");
            } else {
                /*
                // relevant sentences is a comma-delimited string,
                // this regular expression is rather strange
                // it must contain digits, it might be that there is only one space or a comma or some other char
                // digits are the sentence ids. if relevant sentences do not contain digits then it is wrong
                if (relevantSentences.matches("^\\D*$") &&
                    irrelevantSentences.matches("^\\D*$")) {
                try {
                    throw new IllegalStateException(
                            "No annotations found for HIT " + hitID + " in " +
                                    fileXml + " for document " + clueWeb);
                }
                catch (IllegalStateException ex) {
                    ex.printStackTrace();
                }
                        
                }
                */
                MTurkAnnotation mturkAnnotation;
                try {
                    mturkAnnotation = new MTurkAnnotation(hitID, annotatorID, acceptTime, submitTime, comment,
                            clueWeb, relevant, irrelevant);
                } catch (IllegalArgumentException ex) {
                    throw new IllegalArgumentException("Record: " + record, ex);
                }

                List<MTurkAnnotation> listOfAnnotations = mturkAnnotations.get(fileXml);

                if (listOfAnnotations == null) {
                    listOfAnnotations = new ArrayList<>();
                }
                listOfAnnotations.add(mturkAnnotation);
                mturkAnnotations.put(fileXml, listOfAnnotations);
            }

        }
        //            parser.close();
    }

    // Debugging: output number of HITs of a query
    System.out.println("Accepted HITs for a query:");
    for (Map.Entry e : mturkAnnotations.entrySet()) {
        ArrayList<MTurkAnnotation> a = (ArrayList<MTurkAnnotation>) e.getValue();
        System.out.println(e.getKey() + " " + a.size());
    }

    for (File f : FileUtils.listFiles(inputDir, new String[] { "xml" }, false)) {
        QueryResultContainer queryResultContainer = QueryResultContainer
                .fromXML(FileUtils.readFileToString(f, "utf-8"));
        String fileName = f.getName();
        List<MTurkAnnotation> listOfAnnotations = mturkAnnotations.get(fileName);

        if (listOfAnnotations == null || listOfAnnotations.isEmpty()) {
            throw new IllegalStateException("No annotations for " + f.getName());
        }

        for (QueryResultContainer.SingleRankedResult rankedResults : queryResultContainer.rankedResults) {
            for (MTurkAnnotation mtAnnotation : listOfAnnotations) {
                String clueWeb = mtAnnotation.clueWeb;
                if (rankedResults.clueWebID.equals(clueWeb)) {
                    List<QueryResultContainer.MTurkRelevanceVote> mTurkRelevanceVotes = rankedResults.mTurkRelevanceVotes;
                    QueryResultContainer.MTurkRelevanceVote relevanceVote = new QueryResultContainer.MTurkRelevanceVote();
                    String annotatorID = mtAnnotation.annotatorID;
                    String hitID = mtAnnotation.hitID;
                    String acceptTime = mtAnnotation.acceptTime;
                    String submitTime = mtAnnotation.submitTime;
                    String comment = mtAnnotation.comment;
                    String[] relevant = mtAnnotation.relevant;
                    String[] irrelevant = mtAnnotation.irrelevant;
                    relevanceVote.turkID = annotatorID.trim();
                    relevanceVote.hitID = hitID.trim();
                    relevanceVote.acceptTime = acceptTime.trim();
                    relevanceVote.submitTime = submitTime.trim();
                    relevanceVote.comment = comment != null ? comment.trim() : null;
                    if (relevant.length == 0 && irrelevant.length == 0) {
                        try {
                            throw new IllegalStateException("the length of the annotations is 0"
                                    + rankedResults.clueWebID + " for HIT " + relevanceVote.hitID);
                        } catch (IllegalStateException e) {
                            e.printStackTrace();
                        }
                    }
                    for (String r : relevant) {
                        String sentenceId = r.trim();
                        if (!sentenceId.isEmpty() && sentenceId.matches("\\d+")) {
                            QueryResultContainer.SingleSentenceRelevanceVote singleSentenceVote = new QueryResultContainer.SingleSentenceRelevanceVote();
                            singleSentenceVote.sentenceID = sentenceId;
                            singleSentenceVote.relevant = "true";
                            relevanceVote.singleSentenceRelevanceVotes.add(singleSentenceVote);
                        }
                    }
                    for (String r : irrelevant) {
                        String sentenceId = r.trim();
                        if (!sentenceId.isEmpty() && sentenceId.matches("\\d+")) {
                            QueryResultContainer.SingleSentenceRelevanceVote singleSentenceVote = new QueryResultContainer.SingleSentenceRelevanceVote();
                            singleSentenceVote.sentenceID = sentenceId;
                            singleSentenceVote.relevant = "false";
                            relevanceVote.singleSentenceRelevanceVotes.add(singleSentenceVote);
                        }
                    }
                    mTurkRelevanceVotes.add(relevanceVote);
                }
            }

        }
        File outputFile = new File(outputDir, f.getName());
        FileUtils.writeStringToFile(outputFile, queryResultContainer.toXML(), "utf-8");
        System.out.println("Finished " + outputFile);
    }

}

From source file:com.act.lcms.db.io.PrintConstructInfo.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*w  ww. j  a v a 2s .  com*/
    }

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

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

    File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY));
    if (!lcmsDir.isDirectory()) {
        System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    try (DB db = DB.openDBFromCLI(cl)) {
        System.out.print("Loading/updating LCMS scan files into DB\n");
        ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir);

        String construct = cl.getOptionValue(OPTION_CONSTRUCT);
        List<LCMSWell> lcmsWells = LCMSWell.getInstance().getByConstructID(db, construct);
        Collections.sort(lcmsWells, new Comparator<LCMSWell>() {
            @Override
            public int compare(LCMSWell o1, LCMSWell o2) {
                return o1.getId().compareTo(o2.getId());
            }
        });

        Set<String> uniqueMSIDs = new HashSet<>();
        Map<Integer, Plate> platesById = new HashMap<>();

        System.out.format("\n\n-- Construct %s --\n\n", construct);

        List<ChemicalAssociatedWithPathway> pathwayChems = ChemicalAssociatedWithPathway.getInstance()
                .getChemicalsAssociatedWithPathwayByConstructId(db, construct);
        System.out.print("Chemicals associated with pathway:\n");
        System.out.format("  %-8s%-15s%-45s\n", "index", "kind", "chemical");
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            System.out.format("  %-8d%-15s%-45s\n", chem.getIndex(), chem.getKind(), chem.getChemical());
        }

        System.out.print("\nLCMS wells:\n");
        System.out.format("  %-15s%-6s%-15s%-15s%-15s\n", "barcode", "well", "msid", "fed", "lcms_count");
        for (LCMSWell well : lcmsWells) {
            uniqueMSIDs.add(well.getMsid());

            Plate p = platesById.get(well.getPlateId());
            if (p == null) {
                // TODO: migrate Plate to be a subclass of BaseDBModel.
                p = Plate.getPlateById(db, well.getPlateId());
                platesById.put(p.getId(), p);
            }

            String chem = well.getChemical();
            List<ScanFile> scanFiles = ScanFile.getScanFileByPlateIDRowAndColumn(db, p.getId(),
                    well.getPlateRow(), well.getPlateColumn());

            System.out.format("  %-15s%-6s%-15s%-15s%-15d\n", p.getBarcode(), well.getCoordinatesString(),
                    well.getMsid(), chem == null || chem.isEmpty() ? "--" : chem, scanFiles.size());
            System.out.flush();
        }

        List<Integer> plateIds = Arrays.asList(platesById.keySet().toArray(new Integer[platesById.size()]));
        Collections.sort(plateIds);
        System.out.print("\nAppears in plates:\n");
        for (Integer id : plateIds) {
            Plate p = platesById.get(id);
            System.out.format("  %s: %s\n", p.getBarcode(), p.getName());
        }

        List<String> msids = Arrays.asList(uniqueMSIDs.toArray(new String[uniqueMSIDs.size()]));
        Collections.sort(msids);
        System.out.format("\nMSIDS: %s\n", StringUtils.join(msids, ", "));

        Set<String> availableNegativeControls = new HashSet<>();
        for (Map.Entry<Integer, Plate> entry : platesById.entrySet()) {
            List<LCMSWell> wells = LCMSWell.getInstance().getByPlateId(db, entry.getKey());
            for (LCMSWell well : wells) {
                if (!construct.equals(well.getComposition())) {
                    availableNegativeControls.add(well.getComposition());
                }
            }
        }

        // Print available standards for each step w/ plate barcodes and coordinates.
        System.out.format("\nAvailable Standards:\n");
        Map<Integer, Plate> plateCache = new HashMap<>();
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            List<StandardWell> matchingWells = StandardWell.getInstance().getStandardWellsByChemical(db,
                    chem.getChemical());
            for (StandardWell well : matchingWells) {
                if (!plateCache.containsKey(well.getPlateId())) {
                    Plate p = Plate.getPlateById(db, well.getPlateId());
                    plateCache.put(p.getId(), p);
                }
            }
            Map<Integer, List<StandardWell>> standardWellsByPlateId = new HashMap<>();
            for (StandardWell well : matchingWells) {
                List<StandardWell> plateWells = standardWellsByPlateId.get(well.getPlateId());
                if (plateWells == null) {
                    plateWells = new ArrayList<>();
                    standardWellsByPlateId.put(well.getPlateId(), plateWells);
                }
                plateWells.add(well);
            }
            List<Pair<String, Integer>> plateBarcodes = new ArrayList<>(plateCache.size());
            for (Plate p : plateCache.values()) {
                if (p.getBarcode() == null) {
                    plateBarcodes.add(Pair.of("(no barcode)", p.getId()));
                } else {
                    plateBarcodes.add(Pair.of(p.getBarcode(), p.getId()));
                }
            }
            Collections.sort(plateBarcodes);
            System.out.format("  %s:\n", chem.getChemical());
            for (Pair<String, Integer> barcodePair : plateBarcodes) {
                // TODO: hoist this whole sorting/translation step into a utility class.
                List<StandardWell> wells = standardWellsByPlateId.get(barcodePair.getRight());
                if (wells == null) {
                    // Don't print plates that don't apply to this chemical, which can happen because we're caching the plates.
                    continue;
                }
                Collections.sort(wells, new Comparator<StandardWell>() {
                    @Override
                    public int compare(StandardWell o1, StandardWell o2) {
                        int c = o1.getPlateRow().compareTo(o2.getPlateRow());
                        if (c != 0)
                            return c;
                        return o1.getPlateColumn().compareTo(o2.getPlateColumn());
                    }
                });
                List<String> descriptions = new ArrayList<>(wells.size());
                for (StandardWell well : wells) {
                    descriptions.add(String.format("%s in %s%s", well.getCoordinatesString(), well.getMedia(),
                            well.getConcentration() == null ? ""
                                    : String.format(" c. %f", well.getConcentration())));
                }
                System.out.format("    %s: %s\n", barcodePair.getLeft(), StringUtils.join(descriptions, ", "));
            }
        }

        List<String> negativeControlStrains = Arrays
                .asList(availableNegativeControls.toArray(new String[availableNegativeControls.size()]));
        Collections.sort(negativeControlStrains);
        System.out.format("\nAvailable negative controls: %s\n", StringUtils.join(negativeControlStrains, ","));
        System.out.print("\n----------\n");
        System.out.print("\n\n");
    }
}

From source file:mase.MaseEvolve.java

public static void main(String[] args) throws Exception {
    File outDir = getOutDir(args);
    boolean force = Arrays.asList(args).contains(FORCE);
    if (!outDir.exists()) {
        outDir.mkdirs();/*from  www  . j  a v a  2s  .co  m*/
    } else if (!force) {
        System.out.println("Folder already exists: " + outDir.getAbsolutePath() + ". Waiting 5 sec.");
        try {
            Thread.sleep(5000);
        } catch (InterruptedException ex) {
        }
    }

    // Get config file
    Map<String, String> pars = readParams(args);

    // Copy config to outdir
    try {
        File rawConfig = writeConfig(args, pars, outDir, false);
        File destiny = new File(outDir, DEFAULT_CONFIG);
        destiny.delete();
        FileUtils.moveFile(rawConfig, new File(outDir, DEFAULT_CONFIG));
    } catch (Exception ex) {
        ex.printStackTrace();
    }

    // JBOT INTEGRATION: copy jbot config file to the outdir
    // Does nothing when jbot is not used
    if (pars.containsKey("problem.jbot-config")) {
        File jbot = new File(pars.get("problem.jbot-config"));
        FileUtils.copyFile(jbot, new File(outDir, jbot.getName()));
    }

    // Write config to system temp file
    File config = writeConfig(args, pars, outDir, true);
    // Launch
    launchExperiment(config);
}

From source file:de.mycrobase.jcloudapp.Main.java

public static void main(String[] args) throws Exception {
    try {/*from  w  w  w . j av a2s.c  o m*/
        // borrowed from https://github.com/cmur2/gloudapp
        ImageNormal = ImageIO.read(Main.class.getResourceAsStream("gloudapp.png"));
        ImageWorking = ImageIO.read(Main.class.getResourceAsStream("gloudapp_working.png"));
        IconNormal = new ImageIcon(ImageNormal.getScaledInstance(64, 64, Image.SCALE_SMOOTH));
        IconLarge = new ImageIcon(ImageNormal);
    } catch (IOException ex) {
        showErrorDialog("Could not load images!\n" + ex);
        System.exit(1);
    }

    URI serviceUrl = URI.create("http://my.cl.ly:80/");
    File storage = getStorageFile();

    if (storage.exists() && storage.isFile()) {
        Yaml yaml = new Yaml();
        try {
            Map<String, String> m = (Map<String, String>) yaml.load(new FileInputStream(storage));
            // avoid NPE by implicitly assuming the presence of a service URL
            if (m.containsKey("service_url")) {
                serviceUrl = URI.create(m.get("service_url"));
            }
        } catch (IOException ex) {
            showErrorDialog("Loading settings from .cloudapp-cli failed: " + ex);
            System.exit(1);
        }
    }

    Main app = new Main(serviceUrl);
    app.login(args);
    app.run();
}

From source file:com.termmed.sampling.ConceptsWithMoreThanThreeRoleGroups.java

/**
 * The main method./*from   w  w w.ja  v  a  2s .c o  m*/
 *
 * @param args the arguments
 * @throws Exception the exception
 */
public static void main(String[] args) throws Exception {
    System.out.println("Starting...");
    Map<String, Set<String>> groupsMap = new HashMap<String, Set<String>>();
    File relsFile = new File(
            "/Users/alo/Downloads/SnomedCT_RF2Release_INT_20160131-1/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20160131.txt");
    BufferedReader br2 = new BufferedReader(new FileReader(relsFile));
    String line2;
    int count2 = 0;
    while ((line2 = br2.readLine()) != null) {
        // process the line.
        count2++;
        if (count2 % 10000 == 0) {
            //System.out.println(count2);
        }
        List<String> columns = Arrays.asList(line2.split("\t", -1));
        if (columns.size() >= 6) {
            if (columns.get(2).equals("1") && !columns.get(6).equals("0")) {
                if (!groupsMap.containsKey(columns.get(4))) {
                    groupsMap.put(columns.get(4), new HashSet<String>());
                }
                groupsMap.get(columns.get(4)).add(columns.get(6));
            }
        }
    }
    System.out.println("Relationship groups loaded");
    Gson gson = new Gson();
    System.out.println("Reading JSON 1");
    File crossoverFile1 = new File("/Users/alo/Downloads/crossover_role_to_group.json");
    String contents = FileUtils.readFileToString(crossoverFile1, "utf-8");
    Type collectionType = new TypeToken<Collection<ControlResultLine>>() {
    }.getType();
    List<ControlResultLine> lineObject = gson.fromJson(contents, collectionType);
    Set<String> crossovers1 = new HashSet<String>();
    for (ControlResultLine loopResult : lineObject) {
        crossovers1.add(loopResult.conceptId);
    }
    System.out.println("Crossovers 1 loaded, " + lineObject.size() + " Objects");

    System.out.println("Reading JSON 2");
    File crossoverFile2 = new File("/Users/alo/Downloads/crossover_group_to_group.json");
    String contents2 = FileUtils.readFileToString(crossoverFile2, "utf-8");
    List<ControlResultLine> lineObject2 = gson.fromJson(contents2, collectionType);
    Set<String> crossovers2 = new HashSet<String>();
    for (ControlResultLine loopResult : lineObject2) {
        crossovers2.add(loopResult.conceptId);
    }
    System.out.println("Crossovers 2 loaded, " + lineObject2.size() + " Objects");

    Set<String> foundConcepts = new HashSet<String>();
    int count3 = 0;
    BufferedWriter writer = new BufferedWriter(
            new FileWriter(new File("ConceptsWithMoreThanThreeRoleGroups.csv")));
    ;
    for (String loopConcept : groupsMap.keySet()) {
        if (groupsMap.get(loopConcept).size() > 3) {
            writer.write(loopConcept);
            writer.newLine();
            foundConcepts.add(loopConcept);
            count3++;
        }
    }
    writer.close();
    System.out.println("Found " + foundConcepts.size() + " concepts");

    int countCrossover1 = 0;
    for (String loopConcept : foundConcepts) {
        if (crossovers1.contains(loopConcept)) {
            countCrossover1++;
        }
    }
    System.out.println(countCrossover1 + " are present in crossover_role_to_group");

    int countCrossover2 = 0;
    for (String loopConcept : foundConcepts) {
        if (crossovers2.contains(loopConcept)) {
            countCrossover2++;
        }
    }
    System.out.println(countCrossover2 + " are present in crossover_group_to_group");

    System.out.println("Done");
}

From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step4MTurkOutputCollector.java

@SuppressWarnings("unchecked")
public static void main(String[] args) throws Exception {
    String inputDirWithArgumentPairs = args[0];

    File[] resultFiles;/*  ww w  .ja  va2 s .  co m*/

    if (args[1].contains("*")) {
        File path = new File(args[1]);
        File directory = path.getParentFile();
        String regex = path.getName().replaceAll("\\*", "");

        List<File> files = new ArrayList<>(FileUtils.listFiles(directory, new String[] { regex }, false));
        resultFiles = new File[files.size()];
        for (int i = 0; i < files.size(); i++) {
            resultFiles[i] = files.get(i);
        }
    } else {
        // result file is a comma-separated list of CSV files from MTurk
        String[] split = args[1].split(",");
        resultFiles = new File[split.length];
        for (int i = 0; i < split.length; i++) {
            resultFiles[i] = new File(split[i]);
        }
    }

    File outputDir = new File(args[2]);

    if (!outputDir.exists()) {
        if (!outputDir.mkdirs()) {
            throw new IOException("Cannot create directory " + outputDir);
        }
    }

    // error if output folder not empty to prevent any confusion by mixing files
    if (!FileUtils.listFiles(outputDir, null, false).isEmpty()) {
        throw new IllegalArgumentException("Output dir " + outputDir + " is not empty");
    }

    // collected assignments with empty reason for rejections
    Set<String> assignmentsWithEmptyReason = new HashSet<>();

    // parse with first line as header
    MTurkOutputReader mTurkOutputReader = new MTurkOutputReader(resultFiles);

    Collection<File> files = FileUtils.listFiles(new File(inputDirWithArgumentPairs), new String[] { "xml" },
            false);

    if (files.isEmpty()) {
        throw new IOException("No xml files found in " + inputDirWithArgumentPairs);
    }

    // statistics: how many hits with how many assignments ; hit ID / assignments
    Map<String, Map<String, Integer>> assignmentsPerHits = new HashMap<>();

    // collect accept/reject statistics
    for (Map<String, String> record : mTurkOutputReader) {
        boolean wasRejected = "Rejected".equals(record.get("assignmentstatus"));
        String hitID = record.get("hitid");
        String hitTypeId = record.get("hittypeid");

        if (!wasRejected) {
            // update statistics
            if (!assignmentsPerHits.containsKey(hitTypeId)) {
                assignmentsPerHits.put(hitTypeId, new HashMap<String, Integer>());
            }

            if (!assignmentsPerHits.get(hitTypeId).containsKey(hitID)) {
                assignmentsPerHits.get(hitTypeId).put(hitID, 0);
            }

            assignmentsPerHits.get(hitTypeId).put(hitID, assignmentsPerHits.get(hitTypeId).get(hitID) + 1);
        }
    }

    // statistics: how many hits with how many assignments ; hit ID / assignments
    Map<String, Integer> approvedAssignmentsPerHit = new HashMap<>();
    Map<String, Integer> rejectedAssignmentsPerHit = new HashMap<>();

    // collect accept/reject statistics
    for (Map<String, String> record : mTurkOutputReader) {
        boolean approved = "Approved".equals(record.get("assignmentstatus"));
        boolean rejected = "Rejected".equals(record.get("assignmentstatus"));
        String hitID = record.get("hitid");

        if (approved) {
            // update statistics
            if (!approvedAssignmentsPerHit.containsKey(hitID)) {
                approvedAssignmentsPerHit.put(hitID, 0);
            }

            approvedAssignmentsPerHit.put(hitID, approvedAssignmentsPerHit.get(hitID) + 1);
        } else if (rejected) {
            // update statistics
            if (!rejectedAssignmentsPerHit.containsKey(hitID)) {
                rejectedAssignmentsPerHit.put(hitID, 0);
            }

            rejectedAssignmentsPerHit.put(hitID, rejectedAssignmentsPerHit.get(hitID) + 1);
        } else {
            throw new IllegalStateException(
                    "Unknown state: " + record.get("assignmentstatus") + " HITID: " + hitID);
        }
    }

    //        System.out.println("Approved: " + approvedAssignmentsPerHit);
    //        System.out.println("Rejected: " + rejectedAssignmentsPerHit);

    System.out.println("Approved (values): " + new HashSet<>(approvedAssignmentsPerHit.values()));
    System.out.println("Rejected (values): " + new HashSet<>(rejectedAssignmentsPerHit.values()));
    // rejection statistics
    int totalRejected = 0;
    for (Map.Entry<String, Integer> rejectionEntry : rejectedAssignmentsPerHit.entrySet()) {
        totalRejected += rejectionEntry.getValue();
    }

    System.out.println("Total rejections: " + totalRejected);

    /*
    // generate .success files for adding more annotations
    for (File resultFile : resultFiles) {
    String hitTypeID = mTurkOutputReader.getHitTypeIdForFile().get(resultFile);
            
    // assignments for that hittypeid (= file)
    Map<String, Integer> assignments = assignmentsPerHits.get(hitTypeID);
            
    prepareUpdateHITsFiles(assignments, hitTypeID, resultFile);
    }
    */

    int totalSavedPairs = 0;

    // load all previously prepared argument pairs
    for (File file : files) {
        List<ArgumentPair> argumentPairs = (List<ArgumentPair>) XStreamTools.getXStream().fromXML(file);

        List<AnnotatedArgumentPair> annotatedArgumentPairs = new ArrayList<>();

        for (ArgumentPair argumentPair : argumentPairs) {
            AnnotatedArgumentPair annotatedArgumentPair = new AnnotatedArgumentPair(argumentPair);

            // is there such an answer?
            String key = "Answer." + argumentPair.getId();

            // iterate only if there is such column to save time
            if (mTurkOutputReader.getColumnNames().contains(key)) {
                // now find the results
                for (Map<String, String> record : mTurkOutputReader) {
                    if (record.containsKey(key)) {
                        // extract the values
                        AnnotatedArgumentPair.MTurkAssignment assignment = new AnnotatedArgumentPair.MTurkAssignment();

                        boolean wasRejected = "Rejected".equals(record.get("assignmentstatus"));

                        // only non-rejected (if required)
                        if (!wasRejected) {
                            String hitID = record.get("hitid");
                            String workerID = record.get("workerid");
                            String assignmentId = record.get("assignmentid");
                            try {
                                assignment.setAssignmentAcceptTime(
                                        DATE_FORMAT.parse(record.get("assignmentaccepttime")));
                                assignment.setAssignmentSubmitTime(
                                        DATE_FORMAT.parse(record.get("assignmentsubmittime")));
                                assignment.setHitComment(record.get("Answer.feedback"));
                                assignment.setHitID(hitID);
                                assignment.setTurkID(workerID);
                                assignment.setAssignmentId(assignmentId);

                                // and answer specific fields
                                String valueRaw = record.get(key);

                                // so far the label has had format aXXX_aYYY_a1, aXXX_aYYY_a2, or aXXX_aYYY_equal
                                // strip now only true label
                                String label = valueRaw.split("_")[2];

                                assignment.setValue(label);
                                String reason = record.get(key + "_reason");

                                // missing reason
                                if (reason == null) {
                                    assignmentsWithEmptyReason.add(assignmentId);
                                } else {
                                    assignment.setReason(reason);

                                    // get worker's stance
                                    String stanceRaw = record.get(key + "_stance");
                                    if (stanceRaw != null) {
                                        // parse stance
                                        String stance = stanceRaw.split("_stance_")[1];
                                        assignment.setWorkerStance(stance);
                                    }

                                    // we take maximal 5 assignments
                                    Collections.sort(annotatedArgumentPair.mTurkAssignments,
                                            new Comparator<AnnotatedArgumentPair.MTurkAssignment>() {
                                                @Override
                                                public int compare(AnnotatedArgumentPair.MTurkAssignment o1,
                                                        AnnotatedArgumentPair.MTurkAssignment o2) {
                                                    return o1.getAssignmentAcceptTime()
                                                            .compareTo(o2.getAssignmentAcceptTime());
                                                }
                                            });

                                    if (annotatedArgumentPair.mTurkAssignments
                                            .size() < MAXIMUM_ASSIGNMENTS_PER_HIT) {
                                        annotatedArgumentPair.mTurkAssignments.add(assignment);
                                    }
                                }
                            } catch (IllegalArgumentException | NullPointerException ex) {
                                System.err.println("Malformed annotations for HIT " + hitID + ", worker "
                                        + workerID + ", assignment " + assignmentId + "; " + ex.getMessage()
                                        + ", full record: " + record);
                            }
                        }
                    }
                }
            }

            // and if there are some annotations, add it to the result set
            if (!annotatedArgumentPair.mTurkAssignments.isEmpty()) {
                annotatedArgumentPairs.add(annotatedArgumentPair);
            }
        }

        if (!annotatedArgumentPairs.isEmpty()) {
            File outputFile = new File(outputDir, file.getName());
            XStreamTools.toXML(annotatedArgumentPairs, outputFile);

            System.out.println("Saved " + annotatedArgumentPairs.size() + " annotated pairs to " + outputFile);
            totalSavedPairs += annotatedArgumentPairs.size();
        }
    }

    System.out.println("Total saved " + totalSavedPairs + " pairs");

    // print assignments with empty reasons
    if (!assignmentsWithEmptyReason.isEmpty()) {
        System.out.println(
                "== Assignments with empty reason:\nassignmentIdToReject\tassignmentIdToRejectComment");
        for (String assignmentId : assignmentsWithEmptyReason) {
            System.out.println(
                    assignmentId + "\t\"Dear worker, you did not fill the required field with a reason.\"");
        }
    }

}

From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step7aLearningDataProducer.java

@SuppressWarnings("unchecked")
public static void main(String[] args) throws IOException {
    String inputDir = args[0];/*from  www .j a  v  a  2  s. c om*/
    File outputDir = new File(args[1]);

    if (!outputDir.exists()) {
        outputDir.mkdirs();
    }

    Collection<File> files = IOHelper.listXmlFiles(new File(inputDir));

    // for generating ConvArgStrict use this
    String prefix = "no-eq_DescendingScoreArgumentPairListSorter";

    // for oversampling using graph transitivity properties use this
    //        String prefix = "generated_no-eq_AscendingScoreArgumentPairListSorter";

    Iterator<File> iterator = files.iterator();
    while (iterator.hasNext()) {
        File file = iterator.next();

        if (!file.getName().startsWith(prefix)) {
            iterator.remove();
        }
    }

    int totalGoldPairsCounter = 0;

    Map<String, Integer> goldDataDistribution = new HashMap<>();

    DescriptiveStatistics statsPerTopic = new DescriptiveStatistics();

    int totalPairsWithReasonSameAsGold = 0;

    DescriptiveStatistics ds = new DescriptiveStatistics();

    for (File file : files) {
        List<AnnotatedArgumentPair> argumentPairs = (List<AnnotatedArgumentPair>) XStreamTools.getXStream()
                .fromXML(file);

        int pairsPerTopicCounter = 0;

        String name = file.getName().replaceAll(prefix, "").replaceAll("\\.xml", "");

        PrintWriter pw = new PrintWriter(new File(outputDir, name + ".csv"), "utf-8");

        pw.println("#id\tlabel\ta1\ta2");

        for (AnnotatedArgumentPair argumentPair : argumentPairs) {
            String goldLabel = argumentPair.getGoldLabel();

            if (!goldDataDistribution.containsKey(goldLabel)) {
                goldDataDistribution.put(goldLabel, 0);
            }

            goldDataDistribution.put(goldLabel, goldDataDistribution.get(goldLabel) + 1);

            pw.printf(Locale.ENGLISH, "%s\t%s\t%s\t%s%n", argumentPair.getId(), goldLabel,
                    multipleParagraphsToSingleLine(argumentPair.getArg1().getText()),
                    multipleParagraphsToSingleLine(argumentPair.getArg2().getText()));

            pairsPerTopicCounter++;

            int sameInOnePair = 0;

            // get gold reason statistics
            for (AnnotatedArgumentPair.MTurkAssignment assignment : argumentPair.mTurkAssignments) {
                String label = assignment.getValue();

                if (goldLabel.equals(label)) {
                    sameInOnePair++;
                }
            }

            ds.addValue(sameInOnePair);
            totalPairsWithReasonSameAsGold += sameInOnePair;
        }

        totalGoldPairsCounter += pairsPerTopicCounter;
        statsPerTopic.addValue(pairsPerTopicCounter);

        pw.close();
    }

    System.out.println("Total reasons matching gold " + totalPairsWithReasonSameAsGold);
    System.out.println(ds);

    System.out.println("Total gold pairs: " + totalGoldPairsCounter);
    System.out.println(statsPerTopic);

    int totalPairs = 0;
    for (Integer pairs : goldDataDistribution.values()) {
        totalPairs += pairs;
    }
    System.out.println("Total pairs: " + totalPairs);
    System.out.println(goldDataDistribution);

}

From source file:com.act.biointerpretation.ProductExtractor.java

public static void main(String[] args) throws Exception {
    CLIUtil cliUtil = new CLIUtil(ProductExtractor.class, HELP_MESSAGE, OPTION_BUILDERS);
    CommandLine cl = cliUtil.parseCommandLine(args);

    String orgPrefix = cl.getOptionValue(OPTION_ORGANISM_PREFIX);
    LOGGER.info("Using organism prefix %s", orgPrefix);

    MongoDB db = new MongoDB(DEFAULT_DB_HOST, DEFAULT_DB_PORT, cl.getOptionValue(OPTION_DB_NAME));

    Map<Long, String> validOrganisms = new TreeMap<>();
    DBIterator orgIter = db.getDbIteratorOverOrgs();
    Organism o = null;/*from  ww w.j av a  2  s .  c om*/
    while ((o = db.getNextOrganism(orgIter)) != null) {
        if (!o.getName().isEmpty() && o.getName().startsWith(orgPrefix)) {
            validOrganisms.put(o.getUUID(), o.getName());
        }
    }

    LOGGER.info("Found %d valid organisms", validOrganisms.size());

    Set<Long> productIds = new TreeSet<>(); // Use something with implicit ordering we can traverse in order.
    DBIterator reactionIterator = db.getIteratorOverReactions();
    Reaction r;
    while ((r = db.getNextReaction(reactionIterator)) != null) {
        Set<JSONObject> proteins = r.getProteinData();
        boolean valid = false;
        for (JSONObject j : proteins) {
            if (j.has("organism") && validOrganisms.containsKey(j.getLong("organism"))) {
                valid = true;
                break;
            } else if (j.has("organisms")) {
                JSONArray organisms = j.getJSONArray("organisms");
                for (int i = 0; i < organisms.length(); i++) {
                    if (validOrganisms.containsKey(organisms.getLong(i))) {
                        valid = true;
                        break;
                    }
                }
            }
        }

        if (valid) {
            for (Long id : r.getProducts()) {
                productIds.add(id);
            }
            for (Long id : r.getProductCofactors()) {
                productIds.add(id);
            }
        }
    }

    LOGGER.info("Found %d valid product ids for '%s'", productIds.size(), orgPrefix);
    PrintWriter writer = cl.hasOption(OPTION_OUTPUT_FILE)
            ? new PrintWriter(new FileWriter(cl.getOptionValue(OPTION_OUTPUT_FILE)))
            : new PrintWriter(System.out);

    for (Long id : productIds) {
        Chemical c = db.getChemicalFromChemicalUUID(id);
        String inchi = c.getInChI();
        if (inchi.startsWith("InChI=") && !inchi.startsWith("InChI=/FAKE")) {
            writer.println(inchi);
        }
    }

    if (cl.hasOption(OPTION_OUTPUT_FILE)) {
        writer.close();
    }
    LOGGER.info("Done.");
}