Example usage for java.nio.file Files newBufferedReader

List of usage examples for java.nio.file Files newBufferedReader

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Introduction

In this page you can find the example usage for java.nio.file Files newBufferedReader.

Prototype

public static BufferedReader newBufferedReader(Path path, Charset cs) throws IOException

Source Link

Document

Opens a file for reading, returning a BufferedReader that may be used to read text from the file in an efficient manner.

Usage

From source file:org.jboss.as.test.integration.logging.perdeploy.Log4jPropertiesTestCase.java

@Test
public void logsTest() throws IOException {
    final String msg = "logTest: log4j.properties message";
    final int statusCode = getResponse(msg, Collections.singletonMap("includeLevel", "true"));
    assertTrue("Invalid response statusCode: " + statusCode, statusCode == HttpStatus.SC_OK);
    boolean trace = false;
    boolean fatal = false;
    String traceLine = msg + " - trace";
    String fatalLine = msg + " - fatal";
    try (final BufferedReader reader = Files.newBufferedReader(logFile, StandardCharsets.UTF_8)) {
        String line;//from  ww w .  j a  v a  2 s . c  o m
        while ((line = reader.readLine()) != null) {
            if (line.contains(traceLine)) {
                trace = true;
            }
            if (line.contains(fatalLine)) {
                fatal = true;
            }
        }
    }
    Assert.assertTrue("Log file should contain line: " + traceLine, trace);
    Assert.assertTrue("Log file should contain line: " + fatalLine, fatal);
}

From source file:org.mda.bcb.tcgagsdata.create.ReadPlatform.java

public void readPlatform(String thePlatform) throws IOException, Exception {
    TcgaGSData.printWithFlag("readPlatform for " + thePlatform + " beginning");
    TcgaGSData.printWithFlag("readPlatform can consume excessive amounts of time and memory");
    mNumberOfGenes = 0;//ww  w.  j a  v a  2 s  . c  om
    TreeMap<String, Integer> geneMap = null;
    {
        ReadPlatform_GeneEq lg = new ReadPlatform_GeneEq(mReadPath);
        lg.getNamesGenes(thePlatform);
        mGenes = lg.mGenes;
        geneMap = TcgaGSData.buildIndexMap(lg.mGenes);
        mNumberOfGenes = lg.mSize;
    }
    mNumberOfSamples = 0;
    boolean found = false;
    long start = System.currentTimeMillis();
    TreeSet<File> dataFileList = new TreeSet<>();
    dataFileList.addAll(FileUtils.listFiles(new File(mReadPath, thePlatform),
            new WildcardFileFilter("matrix_data_*.tsv"), TrueFileFilter.INSTANCE));
    for (File input : dataFileList) {
        try (BufferedReader br = Files.newBufferedReader(Paths.get(input.getAbsolutePath()),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            found = true;
            TcgaGSData.printWithFlag("readPlatform file=" + input.getAbsolutePath());
            // first line samples
            String line = br.readLine();
            TreeMap<String, Integer> sampleMap = TcgaGSData
                    .buildIndexMap(GSStringUtils.afterTab(line).split("\t", -1));
            if (0 == mNumberOfSamples) {
                mSamples = GSStringUtils.afterTab(line).split("\t", -1);
                mNumberOfSamples = mSamples.length;
                mGenesBySamplesValues = new double[mNumberOfGenes][mNumberOfSamples];
            } else {
                if (mNumberOfSamples != GSStringUtils.afterTab(line).split("\t", -1).length) {
                    throw new Exception("Expected sample count of " + mNumberOfSamples + " but found different "
                            + input.getAbsolutePath());
                }
            }
            line = br.readLine();
            while (null != line) {
                String gene = GSStringUtils.beforeTab(line);
                Integer intIndex = geneMap.get(gene);
                if (null != intIndex) {
                    int geneIndex = intIndex;
                    double[] valueList = convertToDouble(GSStringUtils.afterTab(line).split("\t", -1));
                    for (int x = 0; x < valueList.length; x++) {
                        int sampleIndex = sampleMap.get(mSamples[x]);
                        mGenesBySamplesValues[geneIndex][sampleIndex] = valueList[x];
                    }
                } else {
                    throw new Exception(
                            "readPlatform for " + thePlatform + " found unexpected 'gene' = " + gene);
                }
                line = br.readLine();
            }
        }
    }
    long finish = System.currentTimeMillis();
    TcgaGSData.printWithFlag(
            "readPlatform for " + thePlatform + " retrieved in " + ((finish - start) / 1000.0) + " seconds");
    if (false == found) {
        throw new Exception("readPlatform for " + thePlatform + " not found");
    } else {
        TcgaGSData.printWithFlag("write " + thePlatform + " to " + mWriteFile);
        writeFile();
    }
}

From source file:org.dbpedia.spotlight.lucene.index.external.utils.SSEIndexUtils.java

public static void decodeURI(Properties config, String toDecode, String decoded) {

    LOG.info("Start to decode URIs...");

    final BufferedReader reader;
    final BufferedWriter writer;
    final Path src = Paths.get(config.getProperty("org.dbpedia.spotlight.data." + toDecode, "").trim());
    final Path dst = Paths.get(config.getProperty("org.dbpedia.spotlight.data." + decoded, "").trim());
    String line;/* w  w  w .  j  a  v  a  2 s  . c o  m*/

    try {
        reader = Files.newBufferedReader(src, StandardCharsets.UTF_8);
        writer = Files.newBufferedWriter(dst, StandardCharsets.UTF_8);

        while ((line = reader.readLine()) != null) {
            line = line.replaceAll("%(?![0-9a-fA-F]{2})", "%25");
            line = line.replaceAll("\\+", "%2B");
            writer.write(URLDecoder.decode(line, "UTF-8"));
            writer.newLine();
        }
        writer.close();

        LOG.info("Done");

    } catch (Exception e) {
        e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
    }
}

From source file:org.opencb.biodata.formats.variant.annotation.io.VepFormatReader.java

@Override
public boolean open() {

    try {//from  w w w .j ava  2s.c o m
        this.path = Paths.get(this.filename);
        Files.exists(this.path);

        if (path.toFile().getName().endsWith(".gz")) {
            this.reader = new BufferedReader(
                    new InputStreamReader(new GZIPInputStream(new FileInputStream(path.toFile()))));
        } else {
            this.reader = Files.newBufferedReader(path, Charset.defaultCharset());
        }

    } catch (IOException ex) {
        Logger.getLogger(VariantVcfReader.class.getName()).log(Level.SEVERE, null, ex);
        return false;
    }

    return true;
}

From source file:filtercdnafile.CreateCdnaProteinFiles.java

/**
 * reads the protein file and writes the lines with the same id as in the proteinList in to
 * a new file.//from   ww w.  j av  a2  s. c  om
 * @throws ParseException
 * @throws IOException 
 */
private void readProteinFasta() throws ParseException, IOException {
    Pattern re = Pattern.compile("(?<=>)ENSRNOP\\d+");
    FileWriter writer = new FileWriter();
    Charset charset = Charset.forName("US-ASCII");
    try (BufferedReader reader = Files.newBufferedReader(proteinFile, charset)) {
        String line;
        writer.OpenFile(newFile);
        while ((line = reader.readLine()) != null) {
            if (line.contains(">")) {
                if (ID.isEmpty() == false & sequence.isEmpty() == false) {
                    //Skips the line if it is a  mitochondiral protein. 
                    if (!ID.contains("RGSC3.4:MT")) {
                        writer.writeLine(ID + "\t" + sequence);
                    }
                }
                ID = line;
                sequence = "";

            } else {
                sequence += line.trim();
            }
        }
        writer.writeLine(ID + "\t" + sequence);
        writer.CloseFile();
    } catch (IOException x) {
        System.err.format("IOException: %s%n", x);
    }
}

From source file:com.shekhargulati.reactivex.rxokhttp.SslCertificates.java

private SslCertificates(final Builder builder) throws SslCertificateException {
    if ((builder.caCertPath == null) || (builder.clientCertPath == null) || (builder.clientKeyPath == null)) {
        throw new SslCertificateException(
                "caCertPath, clientCertPath, and clientKeyPath must all be specified");
    }/*from   w w  w . j a v a2  s . com*/

    try {
        final CertificateFactory cf = CertificateFactory.getInstance("X.509");
        final Certificate caCert = cf.generateCertificate(Files.newInputStream(builder.caCertPath));
        final Certificate clientCert = cf.generateCertificate(Files.newInputStream(builder.clientCertPath));

        final PEMKeyPair clientKeyPair = (PEMKeyPair) new PEMParser(
                Files.newBufferedReader(builder.clientKeyPath, Charset.defaultCharset())).readObject();

        final PKCS8EncodedKeySpec spec = new PKCS8EncodedKeySpec(
                clientKeyPair.getPrivateKeyInfo().getEncoded());
        final KeyFactory kf = KeyFactory.getInstance("RSA");
        final PrivateKey clientKey = kf.generatePrivate(spec);

        final KeyStore trustStore = KeyStore.getInstance(KeyStore.getDefaultType());
        trustStore.load(null, null);
        trustStore.setEntry("ca", new KeyStore.TrustedCertificateEntry(caCert), null);

        final KeyStore keyStore = KeyStore.getInstance(KeyStore.getDefaultType());
        keyStore.load(null, KEY_STORE_PASSWORD);
        keyStore.setCertificateEntry("client", clientCert);
        keyStore.setKeyEntry("key", clientKey, KEY_STORE_PASSWORD, new Certificate[] { clientCert });

        this.sslContext = SSLContexts.custom().loadTrustMaterial(trustStore)
                .loadKeyMaterial(keyStore, KEY_STORE_PASSWORD).useTLS().build();
    } catch (java.security.cert.CertificateException | IOException | NoSuchAlgorithmException
            | InvalidKeySpecException | KeyStoreException | UnrecoverableKeyException
            | KeyManagementException e) {
        throw new SslCertificateException(e);
    }
}

From source file:com.pivotal.gfxd.demo.loader.LoadRunner.java

public void run(final String CSV_FILE) {

    List<String[]> lines = new LinkedList<>();
    String timestamp = null;//w w  w.ja v  a 2s  .  c o m

    try (BufferedReader br = Files.newBufferedReader(Paths.get(CSV_FILE), StandardCharsets.UTF_8)) {

        // Lines are in this form:
        // id, timestamp, value, property, plug_id, household_id, house_id

        for (String line = null; (line = br.readLine()) != null;) {
            String[] split = line.split(",");

            int houseId = Integer.parseInt(split[6]);
            if (houseId >= maxHouseId) {
                continue;
            }

            // We only care about 'load' values at the moment
            int property = Integer.parseInt(split[3]);
            if (property != 1) {
                continue;
            }

            // first iteration
            if (timestamp == null) {
                timestamp = split[1];
                lines.add(split);
                startTime = Long.parseLong(timestamp);
                // The stream of events need to appear as though they started
                // 'boostTime' seconds ago.
                deltaAdjust = (System.currentTimeMillis() / 1000) - startTime - boostTime;

            } else {
                // batch same timestamp objects
                if (timestamp.equals(split[1])) {
                    lines.add(split);

                } else {

                    // send batched records and create a new batch
                    this.asyncInsertBatch(lines, Long.parseLong(timestamp) + deltaAdjust);
                    lines = new LinkedList<>();
                    lines.add(split);
                    timestamp = split[1];
                }
            }
        }
        // insert last pending batch
        this.asyncInsertBatch(lines, Long.parseLong(timestamp) + deltaAdjust);

    } catch (IOException ioex) {
        logger.error("An error occurred during batch insertion or the file was not accessible. Message: "
                + ioex.getMessage());
    }

}

From source file:com.shekhargulati.reactivex.docker.client.ssl.DockerCertificates.java

private DockerCertificates(final Builder builder) throws DockerCertificateException {
    if ((builder.caCertPath == null) || (builder.clientCertPath == null) || (builder.clientKeyPath == null)) {
        throw new DockerCertificateException(
                "caCertPath, clientCertPath, and clientKeyPath must all be specified");
    }//w  ww . j  a  va 2 s.c om

    try {
        final CertificateFactory cf = CertificateFactory.getInstance("X.509");
        final Certificate caCert = cf.generateCertificate(Files.newInputStream(builder.caCertPath));
        final Certificate clientCert = cf.generateCertificate(Files.newInputStream(builder.clientCertPath));

        final PEMKeyPair clientKeyPair = (PEMKeyPair) new PEMParser(
                Files.newBufferedReader(builder.clientKeyPath, Charset.defaultCharset())).readObject();

        final PKCS8EncodedKeySpec spec = new PKCS8EncodedKeySpec(
                clientKeyPair.getPrivateKeyInfo().getEncoded());
        final KeyFactory kf = KeyFactory.getInstance("RSA");
        final PrivateKey clientKey = kf.generatePrivate(spec);

        final KeyStore trustStore = KeyStore.getInstance(KeyStore.getDefaultType());
        trustStore.load(null, null);
        trustStore.setEntry("ca", new KeyStore.TrustedCertificateEntry(caCert), null);

        final KeyStore keyStore = KeyStore.getInstance(KeyStore.getDefaultType());
        keyStore.load(null, KEY_STORE_PASSWORD);
        keyStore.setCertificateEntry("client", clientCert);
        keyStore.setKeyEntry("key", clientKey, KEY_STORE_PASSWORD, new Certificate[] { clientCert });

        this.sslContext = SSLContexts.custom().loadTrustMaterial(trustStore)
                .loadKeyMaterial(keyStore, KEY_STORE_PASSWORD).useTLS().build();
    } catch (CertificateException | IOException | NoSuchAlgorithmException | InvalidKeySpecException
            | KeyStoreException | UnrecoverableKeyException | KeyManagementException e) {
        throw new DockerCertificateException(e);
    }
}

From source file:com.digitalpebble.storm.crawler.spout.FileSpout.java

@SuppressWarnings("rawtypes")
@Override/*from w w w.  ja  va2  s.c  o  m*/
public void open(Map conf, TopologyContext context, SpoutOutputCollector collector) {
    _collector = collector;

    for (String inputFile : _inputFiles) {
        Path inputPath = Paths.get(inputFile);
        try (BufferedReader reader = Files.newBufferedReader(inputPath, StandardCharsets.UTF_8)) {
            String line = null;
            while ((line = reader.readLine()) != null) {
                if (StringUtils.isBlank(line))
                    continue;
                toPut.add(line.getBytes(StandardCharsets.UTF_8));
            }
        } catch (IOException x) {
            System.err.format("IOException: %s%n", x);
        }
    }
}

From source file:com.relicum.ipsum.io.PropertyIO.java

/**
 * Return a {@link java.util.Properties} read from the specified string file path.
 *
 * @param file the {@link java.nio.file.Path } name of the file to read the properties from.
 * @return the {@link java.util.Properties} instance.
 * @throws IOException the {@link java.io.IOException} if the file was not found or there were problems reading from it.
 *//*from   w w w. j  a v a  2  s.  c om*/
default Properties readFromFile(File file) throws IOException {

    Validate.notNull(file);

    if (Files.exists(file.toPath()))
        throw new FileNotFoundException("File at " + file.getPath() + " was not found");

    Properties properties = new Properties();
    try {

        properties.load(Files.newBufferedReader(file.toPath(), Charset.defaultCharset()));
    } catch (IOException e) {
        Logger.getGlobal().log(Level.SEVERE, e.getMessage(), e.getCause());
        throw e;
    }

    return properties;
}