Example usage for org.apache.commons.io FileUtils readLines

List of usage examples for org.apache.commons.io FileUtils readLines

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Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils readLines.

Prototype

public static List readLines(File file) throws IOException

Source Link

Document

Reads the contents of a file line by line to a List of Strings using the default encoding for the VM.

Usage

From source file:hu.bme.mit.trainbenchmark.generator.sql.SqlSerializer.java

@Override
public void persistModel() throws IOException, InterruptedException {
    final String footerFilePath = gc.getConfigBase().getWorkspaceDir() + SQL_METAMODEL_DIR
            + "railway-footer.sql";
    final File footerFile = new File(footerFilePath);

    final List<String> lines = FileUtils.readLines(footerFile);
    for (final String line : lines) {
        write(line);//from  w ww  . ja  v  a  2s .  co  m
    }

    writer.close();

    compact();
}

From source file:de.tudarmstadt.ukp.dkpro.tc.mallet.report.MalletBatchCrossValidationReport.java

@Override
public void execute() throws Exception {
    StorageService store = getContext().getStorageService();

    FlexTable<String> table = FlexTable.forClass(String.class);

    Map<String, List<Double>> key2resultValues = new HashMap<String, List<Double>>();

    for (TaskContextMetadata subcontext : getSubtasks()) {
        String name = BatchTask.class.getSimpleName() + "CrossValidation";
        // one CV batch (which internally ran numFolds times)
        if (subcontext.getLabel().startsWith(name)) {
            Map<String, String> discriminatorsMap = store
                    .retrieveBinary(subcontext.getId(), Task.DISCRIMINATORS_KEY, new PropertiesAdapter())
                    .getMap();// w w  w .j ava2  s  .  co m

            File eval = store.getStorageFolder(subcontext.getId(), EVAL_FILE_NAME + SUFFIX_CSV);

            Map<String, String> resultMap = new HashMap<String, String>();

            String[][] evalMatrix = null;

            int i = 0;
            for (String line : FileUtils.readLines(eval)) {
                String[] tokenizedLine = StrTokenizer.getCSVInstance(line).getTokenArray();
                if (evalMatrix == null) {
                    evalMatrix = new String[FileUtils.readLines(eval).size()][tokenizedLine.length];
                }
                evalMatrix[i] = tokenizedLine;
                i++;
            }

            // columns
            for (int j = 0; j < evalMatrix[0].length; j++) {
                String header = evalMatrix[0][j];
                String[] vals = new String[evalMatrix.length - 1];
                // rows
                for (int k = 1; k < evalMatrix.length; k++) {
                    if (evalMatrix[k][j].equals("null")) {
                        vals[k - 1] = String.valueOf(0.);
                    } else {
                        vals[k - 1] = evalMatrix[k][j];
                    }
                }
                Mean mean = new Mean();
                Sum sum = new Sum();
                StandardDeviation std = new StandardDeviation();

                double[] dVals = new double[vals.length];
                Set<String> sVals = new HashSet<String>();
                for (int k = 0; k < vals.length; k++) {
                    try {
                        dVals[k] = Double.parseDouble(vals[k]);
                        sVals = null;
                    } catch (NumberFormatException e) {
                        dVals = null;
                        sVals.add(vals[k]);
                    }
                }

                if (dVals != null) {
                    if (nonAveragedResultsMeasures.contains(header)) {
                        resultMap.put(header, String.valueOf(sum.evaluate(dVals)));
                    } else {
                        resultMap.put(header, String.valueOf(mean.evaluate(dVals)) + "\u00B1"
                                + String.valueOf(std.evaluate(dVals)));
                    }
                } else {
                    if (sVals.size() > 1) {
                        resultMap.put(header, "---");
                    } else {
                        resultMap.put(header, vals[0]);
                    }
                }
            }

            String key = getKey(discriminatorsMap);

            List<Double> results;
            if (key2resultValues.get(key) == null) {
                results = new ArrayList<Double>();
            } else {
                results = key2resultValues.get(key);

            }
            key2resultValues.put(key, results);

            Map<String, String> values = new HashMap<String, String>();
            Map<String, String> cleanedDiscriminatorsMap = new HashMap<String, String>();

            for (String disc : discriminatorsMap.keySet()) {
                if (!ReportUtils.containsExcludePattern(disc, discriminatorsToExclude)) {
                    cleanedDiscriminatorsMap.put(disc, discriminatorsMap.get(disc));
                }
            }
            values.putAll(cleanedDiscriminatorsMap);
            values.putAll(resultMap);

            table.addRow(subcontext.getLabel(), values);
        }
    }

    getContext().getLoggingService().message(getContextLabel(), ReportUtils.getPerformanceOverview(table));

    // Excel cannot cope with more than 255 columns
    if (table.getColumnIds().length <= 255) {
        getContext().storeBinary(EVAL_FILE_NAME + "_compact" + SUFFIX_EXCEL, table.getExcelWriter());
    }
    getContext().storeBinary(EVAL_FILE_NAME + "_compact" + SUFFIX_CSV, table.getCsvWriter());

    table.setCompact(false);
    // Excel cannot cope with more than 255 columns
    if (table.getColumnIds().length <= 255) {
        getContext().storeBinary(EVAL_FILE_NAME + SUFFIX_EXCEL, table.getExcelWriter());
    }
    getContext().storeBinary(EVAL_FILE_NAME + SUFFIX_CSV, table.getCsvWriter());

    // output the location of the batch evaluation folder
    // otherwise it might be hard for novice users to locate this
    File dummyFolder = store.getStorageFolder(getContext().getId(), "dummy");
    // TODO can we also do this without creating and deleting the dummy folder?
    getContext().getLoggingService().message(getContextLabel(),
            "Storing detailed results in:\n" + dummyFolder.getParent() + "\n");
    dummyFolder.delete();
}

From source file:de.tudarmstadt.ukp.dkpro.tc.ml.uima.TcAnnotatorDocument.java

private List<String> initFeatureExtractors() throws Exception {
    List<String> featureExtractors = new ArrayList<>();
    List<String> featureConfiguration = FileUtils
            .readLines(new File(tcModelLocation, MODEL_FEATURE_EXTRACTORS));
    for (String featureExtractor : featureConfiguration) {
        featureExtractors.add(featureExtractor);
    }/*from  w  w  w .  j  a  v  a 2  s.c om*/
    return featureExtractors;
}

From source file:edu.isistan.carcha.lsa.TraceabilityComparator.java

/**
 * Run./*  w  ww .  ja  v  a2  s  .c  o  m*/
 *
 * @param args the args
 * @throws IOException Signals that an I/O exception has occurred.
 */
private void run(String[] args) throws IOException {
    //read the requirement concerns and the architectural concerns
    List<String> reqConcerns = FileUtils.readLines(new File(args[2]));
    List<String> archConcerns = FileUtils.readLines(new File(args[3]));

    //where we will put the results
    String outputDirectory = args[4];

    double[] thresholds = { 0.70, 0.75, 0.80, 0.90 };

    //check if the space is a file o a directory
    //directory: run the traceability for each file in the directory
    //file: run the traceability
    File sspaceInput = new File(args[1]);
    List<File> filesToAnalyze = new ArrayList<File>();

    if (sspaceInput.isDirectory()) {
        for (File sspaceFile : sspaceInput.listFiles()) {
            if (sspaceFile.isFile()) {
                filesToAnalyze.add(sspaceFile);
            }
        }
    } else {
        filesToAnalyze.add(sspaceInput);
    }

    for (File sspaceFile : filesToAnalyze) {
        //build the document vector to compare sentences
        StaticSemanticSpace sspace = new StaticSemanticSpace(sspaceFile);
        DocumentVectorBuilder builder = new DocumentVectorBuilder(sspace);
        this.setOutputDirectory(new File(outputDirectory + File.separator + sspaceFile.getName()));
        for (Double threshold : thresholds) {
            this.setSspaceFileName(sspaceFile.getName());
            this.setThreshold(threshold);
            this.run(builder, reqConcerns, archConcerns);
        }
    }
}

From source file:de.tudarmstadt.ukp.dkpro.tc.crfsuite.CRFSuiteBatchCrossValidationReport.java

@Override
public void execute() throws Exception {
    StorageService store = getContext().getStorageService();

    FlexTable<String> table = FlexTable.forClass(String.class);

    Map<String, List<Double>> key2resultValues = new HashMap<String, List<Double>>();

    for (TaskContextMetadata subcontext : getSubtasks()) {
        String name = ExperimentCrossValidation.class.getSimpleName();
        // one CV batch (which internally ran numFolds times)
        if (subcontext.getLabel().startsWith(name)) {
            Map<String, String> discriminatorsMap = store
                    .retrieveBinary(subcontext.getId(), Task.DISCRIMINATORS_KEY, new PropertiesAdapter())
                    .getMap();//from   w w  w  .  java2s. c  o  m

            File eval = store.getStorageFolder(subcontext.getId(), EVAL_FILE_NAME + SUFFIX_CSV);

            Map<String, String> resultMap = new HashMap<String, String>();

            String[][] evalMatrix = null;

            int i = 0;
            for (String line : FileUtils.readLines(eval)) {
                String[] tokenizedLine = StrTokenizer.getCSVInstance(line).getTokenArray();
                if (evalMatrix == null) {
                    evalMatrix = new String[FileUtils.readLines(eval).size()][tokenizedLine.length];
                }
                evalMatrix[i] = tokenizedLine;
                i++;
            }

            // columns
            for (int j = 0; j < evalMatrix[0].length; j++) {
                String header = evalMatrix[0][j];
                String[] vals = new String[evalMatrix.length - 1];
                // rows
                for (int k = 1; k < evalMatrix.length; k++) {
                    if (evalMatrix[k][j].equals("null")) {
                        vals[k - 1] = String.valueOf(0.);
                    } else {
                        vals[k - 1] = evalMatrix[k][j];
                    }

                }
                Mean mean = new Mean();
                Sum sum = new Sum();
                StandardDeviation std = new StandardDeviation();

                double[] dVals = new double[vals.length];
                Set<String> sVals = new HashSet<String>();
                for (int k = 0; k < vals.length; k++) {
                    try {
                        dVals[k] = Double.parseDouble(vals[k]);
                        sVals = null;
                    } catch (NumberFormatException e) {
                        dVals = null;
                        sVals.add(vals[k]);
                    }
                }

                if (dVals != null) {
                    if (nonAveragedResultsMeasures.contains(header)) {
                        resultMap.put(header + foldSum, String.valueOf(sum.evaluate(dVals)));
                    } else {
                        resultMap.put(header + foldAveraged, String.valueOf(
                                mean.evaluate(dVals) + "\u00B1" + String.valueOf(std.evaluate(dVals))));
                    }
                } else {
                    if (sVals.size() > 1) {
                        resultMap.put(header, "---");
                    } else {
                        resultMap.put(header, vals[0]);
                    }
                }
            }

            String key = getKey(discriminatorsMap);

            List<Double> results;
            if (key2resultValues.get(key) == null) {
                results = new ArrayList<Double>();
            } else {
                results = key2resultValues.get(key);

            }
            key2resultValues.put(key, results);

            Map<String, String> values = new HashMap<String, String>();
            Map<String, String> cleanedDiscriminatorsMap = new HashMap<String, String>();

            for (String disc : discriminatorsMap.keySet()) {
                if (!ReportUtils.containsExcludePattern(disc, discriminatorsToExclude)) {
                    cleanedDiscriminatorsMap.put(disc, discriminatorsMap.get(disc));
                }
            }
            values.putAll(cleanedDiscriminatorsMap);
            values.putAll(resultMap);

            table.addRow(subcontext.getLabel(), values);
        }
    }

    getContext().getLoggingService().message(getContextLabel(), ReportUtils.getPerformanceOverview(table));
    // Excel cannot cope with more than 255 columns
    if (table.getColumnIds().length <= 255) {
        getContext().storeBinary(EVAL_FILE_NAME + "_compact" + SUFFIX_EXCEL, table.getExcelWriter());
    }
    getContext().storeBinary(EVAL_FILE_NAME + "_compact" + SUFFIX_CSV, table.getCsvWriter());

    table.setCompact(false);
    // Excel cannot cope with more than 255 columns
    if (table.getColumnIds().length <= 255) {
        getContext().storeBinary(EVAL_FILE_NAME + SUFFIX_EXCEL, table.getExcelWriter());
    }
    getContext().storeBinary(EVAL_FILE_NAME + SUFFIX_CSV, table.getCsvWriter());

    // output the location of the batch evaluation folder
    // otherwise it might be hard for novice users to locate this
    File dummyFolder = store.getStorageFolder(getContext().getId(), "dummy");
    // TODO can we also do this without creating and deleting the dummy folder?
    getContext().getLoggingService().message(getContextLabel(),
            "Storing detailed results in:\n" + dummyFolder.getParent() + "\n");
    dummyFolder.delete();
}

From source file:dk.nsi.haiba.lprimporter.testdata.SQLStatementsFromCSVFiles.java

private void generateProceduresData() throws IOException {
    File file = FileUtils.toFile(getClass().getClassLoader().getResource("data/T_PROCEDURER.csv"));
    boolean first = true;
    List<String> lines = FileUtils.readLines(file);
    for (String line : lines) {
        if (first) {
            // first row is column metadata
            first = false;/*from  w  w w .ja  v  a  2  s.com*/
            continue;
        }

        String[] splits = line.split(",");
        String recnum = splits[0];
        String code = splits[1];
        String odate = splits[2];
        String otime = splits[3];
        if (otime.length() == 0) {
            otime = "0";
        }
        String tillaeg = splits[4];
        String sygehus = splits[5];
        String afdeling = splits[6];
        String type = "A";

        StringBuffer sql = new StringBuffer();
        sql.append(
                "INSERT INTO T_PROCEDURER (V_RECNUM, C_OPR, C_TILOPR, C_OPRART, D_ODTO, V_OTIME, C_OSGH, C_OAFD) VALUES (");
        sql.append(recnum);
        sql.append(", '");
        sql.append(code);
        sql.append("', '");
        sql.append(tillaeg);
        sql.append("', '");
        sql.append(type);
        sql.append("', '");
        sql.append(odate);
        sql.append("', ");
        sql.append(otime);
        sql.append(", '");
        sql.append(sygehus);
        sql.append("', '");
        sql.append(afdeling);
        sql.append("');");

        System.out.println(sql.toString());
    }
}

From source file:de.unisb.cs.st.javalanche.mutation.runtime.testDriver.junit.Junit4MutationTestDriver.java

private void removeExludedTests() {
    String excludes = ConfigurationLocator.getJavalancheConfiguration().getExcludedTests();
    if (excludes != null) {
        List<String> excludeList = new ArrayList<String>();
        if (excludes.startsWith("file://")) {
            String fileName = excludes.substring(7);
            try {
                excludeList = FileUtils.readLines(new File(fileName));
            } catch (IOException e) {
                e.printStackTrace();//from  w w  w  .j a  v a2 s .  c o m
            }

        } else {
            String[] split = excludes.split(":");
            excludeList = Arrays.asList(split);
        }
        for (String string : excludeList) {
            if (allTests.containsKey(string)) {
                allTests.remove(string);
            }
        }
    }

}

From source file:biz.gabrys.lesscss.extended.compiler.storage.DataStorageImpl.java

/**
 * {@inheritDoc}//w ww. jav  a 2s  .  c  o  m
 * @throws DataStorageException if an I/O error occurred.
 * @since 1.0
 */
public List<String> getLines(final String fileName) {
    synchronized (mutex) {
        final File cache = getFile(fileName);
        if (cache == null) {
            return null;
        }
        try {
            return FileUtils.readLines(cache);
        } catch (final IOException e) {
            throw new DataStorageException(e);
        }
    }
}

From source file:de.tudarmstadt.ukp.similarity.experiments.coling2012.util.ColingUtils.java

@SuppressWarnings("unchecked")
public static List<String> readGoldstandard(Dataset dataset) throws IOException {
    List<String> gold = new ArrayList<String>();

    if (dataset.equals(Dataset.MeterCorpus)) {
        List<String> originalLines = FileUtils.readLines(getGoldstandard(dataset));
        originalLines.remove(0); // remove header

        List<String> order = FileUtils
                .readLines(new File(UTILS_DIR + "/doc-order/" + dataset.toString() + ".txt"));

        // Process documents in the correct order
        for (String line : order) {
            String[] linesplit = line.split("\t");
            String docID = linesplit[0].substring(linesplit[0].indexOf("/newspapers/") + 1) + ".txt";

            // Look up document in the original gold standard file
            for (String origLine : originalLines) {
                String[] origLineSplit = origLine.split("\t");
                if (origLineSplit[0].equals(docID)) {
                    gold.add(origLineSplit[4]);
                    break;
                }/*from w w w. j  a v  a  2  s. co m*/
            }
        }
    } else if (dataset.equals(Dataset.WikipediaRewriteCorpus)) {
        List<String> originalLines = FileUtils.readLines(getGoldstandard(dataset));
        originalLines.remove(0); // remove header

        List<String> order = FileUtils
                .readLines(new File(UTILS_DIR + "/doc-order/" + dataset.toString() + ".txt"));

        // Process documents in the correct order
        for (String line : order) {
            String[] linesplit = line.split("\t");
            String docID = linesplit[0] + ".txt";

            // Look up document in the original gold standard file
            for (String origLine : originalLines) {
                String[] origLineSplit = origLine.split("\t");
                if (origLineSplit[0].equals(docID)) {
                    gold.add(origLineSplit[4]);
                    break;
                }
            }
        }
    } else if (dataset.equals(Dataset.WebisCrowdParaphraseCorpus)) {
        gold = FileUtils.readLines(getGoldstandard(dataset));
    }

    return gold;
}

From source file:edu.cmu.cs.lti.discoursedb.io.bazaar.converter.BazaarConverter.java

private void convert(String messageFileDir, String roomFileDir, String agentname)
        throws ParseException, IOException {

    Map<String, String> roomIdNameMap = new HashMap<>();
    List<String> messages = new ArrayList<>();

    //Read input file and preprocess
    String lineFragment = null;//from ww w. j  a va2  s.  co  m
    for (String line : FileUtils.readLines(new File(messageFileDir))) {
        //line fragments occur in case we have line feeds in a column
        if (lineFragment != null) {
            line = lineFragment + line;
            lineFragment = null;
        }
        if (line.endsWith("\\") || line.endsWith("\\\r\f")) {
            line = line.replaceAll("\\\r\f", "");
            lineFragment = line;
        } else {
            if (line.contains("\\\"We're Ready\\\"")) {
                line = line.replaceAll("\"We're Ready\\\\\"", "We're Ready\\\\");
            }
            if (line.contains("\\\"ready\\\"")) {
                line = line.replaceAll("\\\\\"ready\\\\\"", "\\\\ready\\\\");
            }
            if (line.contains("\\\"" + agentname + "\\\"")) {
                line = line.replaceAll("\\\\\"" + agentname + "\\\\\"", "\\\\" + agentname + "\\\\");
            }
            messages.add(line);
        }
    }

    // Phase 1: read through input room file once and map all entities
    try (InputStream in = new FileInputStream(roomFileDir)) {
        CsvMapper mapper = new CsvMapper();
        CsvSchema schema = mapper.schemaFor(Room.class).withColumnSeparator(',');
        MappingIterator<Room> rIter = mapper.readerFor(Room.class).with(schema).readValues(in);
        while (rIter.hasNextValue()) {
            Room r = rIter.next();
            if (!roomIdNameMap.containsKey(r.getId()))
                roomIdNameMap.put(r.getId(), r.getName());
            converterService.mapRoom(r, dataSetName, discourseName);
        }
    } catch (IOException e) {
        log.error("Error reading room file", e);
    }

    // Phase 2: read through input message file and map relationships between room and message
    CsvMapper mapper = new CsvMapper();
    CsvSchema schema = mapper.schemaFor(Message.class).withColumnSeparator(',');
    for (String message : messages) {
        Message m = mapper.readerFor(Message.class).with(schema).readValue(message);
        if (m.getType().equals("text") || m.getType().equals("image") || m.getType().equals("private")) {
            converterService.mapMessage(m, dataSetName, discourseName, roomIdNameMap);
        } else {
            converterService.mapInteraction(m, dataSetName, discourseName, roomIdNameMap);
        }
    }
}