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.profiles.NonExistingProfileTestCase.java

@Test
public void defaultLoggingTest() throws IOException {
    final String msg = "defaultLoggingTest: This is a test message";
    final int statusCode = getResponse(msg);
    assertTrue("Invalid response statusCode: " + statusCode, statusCode == HttpStatus.SC_OK);
    // check logs
    boolean logFound = false;
    try (final BufferedReader br = Files.newBufferedReader(loggingTestLog, StandardCharsets.UTF_8)) {
        String line;//from  ww  w.  j  a v  a  2  s .  co m
        while ((line = br.readLine()) != null) {
            if (line.contains(msg)) {
                logFound = true;
                break;
            }
        }
    }
    Assert.assertTrue(logFound);
}

From source file:com.ignorelist.kassandra.steam.scraper.Configuration.java

public static Configuration fromPropertiesFile(Path propertiesFile) throws IOException {
    Reader propertiesReader = Files.newBufferedReader(propertiesFile, Charsets.UTF_8);
    try {//from w  ww  . jav a 2s.  co  m
        Properties properties = new Properties();
        properties.load(propertiesReader);
        return fromProperties(properties);
    } finally {
        IOUtils.closeQuietly(propertiesReader);
    }
}

From source file:net.sourceforge.pmd.lang.java.rule.errorprone.AvoidDuplicateLiteralsRule.java

private LineNumberReader getLineReader() throws IOException {
    return new LineNumberReader(
            Files.newBufferedReader(getProperty(EXCEPTION_FILE_DESCRIPTOR).toPath(), StandardCharsets.UTF_8));
}

From source file:nextflow.fs.dx.DxFileSystemProvider.java

/**
 * Find out the default DnaNexus project id in the specified configuration file
 *
 * @return The string value/* w  w  w . j a  v a  2 s. c o m*/
 */
static String getContextIdByConfig(File config) {

    StringBuilder buffer = new StringBuilder();
    try {
        BufferedReader reader = Files.newBufferedReader(config.toPath(), Charset.defaultCharset());
        String line;
        while ((line = reader.readLine()) != null) {
            buffer.append(line).append('\n');
        }

        JsonNode object = DxJson.parseJson(buffer.toString());
        return object.get("DX_PROJECT_CONTEXT_ID").textValue();
    } catch (FileNotFoundException e) {
        throw new IllegalStateException(String.format(
                "Unable to load DnaNexus configuration file: %s -- cannot configure file system", config), e);
    } catch (IOException e) {
        throw new IllegalStateException("Unable to configure DnaNexus file system", e);
    }
}

From source file:org.apache.kylin.monitor.QueryParser.java

public void parseQueryLog(String filePath, String dPath) throws ParseException, IOException {

    logger.info("Start parsing file " + filePath + " !");

    //        writer config init
    FileSystem fs = this.getHdfsFileSystem();
    org.apache.hadoop.fs.Path resultStorePath = new org.apache.hadoop.fs.Path(dPath);
    OutputStreamWriter writer = new OutputStreamWriter(fs.append(resultStorePath));
    CSVWriter cwriter = new CSVWriter(writer, '|', CSVWriter.NO_QUOTE_CHARACTER);

    SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss,SSS");
    Pattern p_query_start = Pattern.compile("^\\[.*\\]:\\[(.*),.*\\]\\[.*\\]\\[.*QueryService.logQuery.*\\].*");
    Pattern p_query_end = Pattern.compile("^Message:(.*)$");
    Pattern p_query_body = Pattern.compile(
            "^\\[.*\\]:\\[((\\d{4}-\\d{2}-\\d{2}).*)\\]\\[.*\\]\\[.*\\].*\n^=+\\[QUERY\\]=+\n^SQL:(.*)\n^User:(.*)\n^Success:(.*)\n^Duration:(.*)\n^Project:(.*)\n^(Realization Names|Cube Names): \\[(.*)\\]\n^Cuboid Ids: \\[(.*)\\]\n^Total scan count:(.*)\n^Result row count:(.*)\n^Accept Partial:(.*)\n(^Is Partial Result:(.*)\n)?^Hit Cache:(.*)\n^Message:(.*)",
            Pattern.MULTILINE);//from   w  ww.  j av  a 2 s  .  c  om
    Matcher m_query_start = p_query_start.matcher("");
    Matcher m_query_end = p_query_end.matcher("");
    Matcher m_query_body = p_query_body.matcher("");

    boolean query_start = false;
    StringBuffer query_body = new StringBuffer("");
    Path path = Paths.get(filePath);
    try {
        BufferedReader reader = Files.newBufferedReader(path, ENCODING);
        String line = null;
        while ((line = reader.readLine()) != null) {
            m_query_start.reset(line); //reset the input
            m_query_end.reset(line);

            // set start flag ,clear StringBuffer
            if (m_query_start.find()) {
                query_start = true;
                query_body = new StringBuffer("");
            }
            if (query_start) {
                query_body.append(line + "\n");
            }
            if (m_query_end.find()) {
                query_start = false;
                m_query_body.reset(query_body);
                logger.info("parsing query...");
                logger.info(query_body);
                //                    skip group(8) and group(14)
                if (m_query_body.find()) {
                    ArrayList<String> groups = new ArrayList<String>();
                    int grp_count = m_query_body.groupCount();
                    for (int i = 1; i <= grp_count; i++) {
                        if (i != 8 && i != 14) {
                            String grp_item = m_query_body.group(i);
                            grp_item = grp_item == null ? "" : grp_item.trim();
                            groups.add(grp_item);
                        }
                    }

                    long start_time = format.parse(groups.get(0)).getTime()
                            - (int) (Double.parseDouble(groups.get(5)) * 1000);
                    groups.set(0, format.format(new Date(start_time)));
                    groups.add(DEPLOY_ENV);
                    String[] recordArray = groups.toArray(new String[groups.size()]);
                    //                        write to hdfs
                    cwriter.writeNext(recordArray);

                }

            }

        }
    } catch (IOException ex) {
        logger.info("Failed to write to hdfs:", ex);
    } finally {
        if (writer != null) {
            writer.close();
        }
        if (cwriter != null) {
            cwriter.close();
        }
        if (fs != null) {
            fs.close();
        }
    }

    logger.info("Finish parsing file " + filePath + " !");

}

From source file:org.apache.tika.cli.TikaCLIBatchIntegrationTest.java

@Test
public void testDigester() throws Exception {
    /*//w ww  .  ja va 2  s  . co m
            try {
    String[] params = {"-i", escape(testDataFile.getAbsolutePath()),
            "-o", escape(tempOutputDir.getAbsolutePath()),
            "-numConsumers", "10",
            "-J", //recursive Json
            "-t" //plain text in content
    };
    TikaCLI.main(params);
    reader = new InputStreamReader(
            new FileInputStream(new File(tempOutputDir, "test_recursive_embedded.docx.json")), UTF_8);
    List<Metadata> metadataList = JsonMetadataList.fromJson(reader);
    assertEquals(12, metadataList.size());
    assertEquals("59f626e09a8c16ab6dbc2800c685f772", metadataList.get(0).get("X-TIKA:digest:MD5"));
    assertEquals("22e6e91f408d018417cd452d6de3dede", metadataList.get(5).get("X-TIKA:digest:MD5"));
            } finally {
    IOUtils.closeQuietly(reader);
            }
    */
    String[] params = { "-i", testInputDirForCommandLine, "-o", tempOutputDirForCommandLine, "-numConsumers",
            "10", "-J", //recursive Json
            "-t", //plain text in content
            "-digest", "sha512" };
    TikaCLI.main(params);
    Path jsonFile = tempOutputDir.resolve("test_recursive_embedded.docx.json");
    try (Reader reader = Files.newBufferedReader(jsonFile, UTF_8)) {

        List<Metadata> metadataList = JsonMetadataList.fromJson(reader);
        assertEquals(12, metadataList.size());
        assertNotNull(metadataList.get(0).get("X-TIKA:digest:SHA512"));
        assertTrue(metadataList.get(0).get("X-TIKA:digest:SHA512").startsWith("ee46d973ee1852c01858"));
    }
}

From source file:popgenutils.dfcp.PrepareVCF4DFCP.java

/**
 * //w ww  .  j  ava  2  s  . c  o  m
 */
private void filterpop() {
    Set<Integer> indices_to_keep = new HashSet<Integer>();
    Map<String, String> sample_to_pop = new HashMap<String, String>();
    Map<String, String> sample_to_superpop = new HashMap<String, String>();
    Set<String> pops_to_keep = new HashSet<String>();

    for (int i = 0; i < 9; i++) {
        indices_to_keep.add(i);
    }

    String[] popsparts = popstokeep.split(",");
    for (String pop : popsparts) {
        pops_to_keep.add(pop);
    }

    try (BufferedReader in = Files.newBufferedReader(Paths.get(popmappingfile), Charset.forName("UTF-8"))) {
        String line = null;
        while ((line = in.readLine()) != null) {
            String[] parts = line.split("\t");
            sample_to_pop.put(parts[0], parts[1]);
            sample_to_superpop.put(parts[0], parts[2]);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }

    StringBuilder header = new StringBuilder();
    try (BufferedReader in = Files.newBufferedReader(Paths.get(filename), Charset.forName("UTF-8"))) {
        BufferedWriter out = null;

        String line = null;
        while ((line = in.readLine()) != null) {

            if (line.startsWith("#CHROM")) {
                //samples begin at 9
                out = Files.newBufferedWriter(
                        Paths.get(output_dir + "/" + "popfilter_" + Paths.get(filename).getFileName()),
                        Charset.forName("UTF-8"));
                out.write(header.toString());
                String[] parts = line.split("\t");
                for (int i = 9; i < parts.length; i++) {
                    if (pops_to_keep.contains(sample_to_superpop.get(parts[i])))
                        indices_to_keep.add(i);
                }
                out.write(parts[0]);
                for (int i = 1; i < parts.length; i++) {
                    if (indices_to_keep.contains(i))
                        out.write("\t" + parts[i]);
                }
                out.write(System.getProperty("line.separator"));
            } else if (line.startsWith("#")) {
                header.append(line + System.getProperty("line.separator"));
            } else {
                // format at 8
                String[] parts = line.split("\t");
                out.write(parts[0]);
                for (int i = 1; i < parts.length; i++) {
                    if (indices_to_keep.contains(i))
                        out.write("\t" + parts[i]);
                }
                out.write(System.getProperty("line.separator"));

            }
        }
        out.close();
    } catch (IOException e) {
        System.err.println("could not read from file " + filename);
        e.printStackTrace();
    }
}

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

public TreeSet<String> getDiseaseSampleData(File theFile, boolean theBarcodeFlag) throws IOException {
    TreeSet<String> results = new TreeSet<>();
    try (BufferedReader br = Files.newBufferedReader(Paths.get(theFile.getAbsolutePath()),
            Charset.availableCharsets().get("ISO-8859-1"))) {
        for (String line = br.readLine(); null != line; line = br.readLine()) {
            String[] splitted = line.split("\t", -1);
            for (int index = 1; index < splitted.length; index++) {
                if (true == theBarcodeFlag) {
                    results.add(splitted[index]);
                } else {
                    results.add(trimToPatientId(splitted[index]));
                }//from  ww w.ja  v  a  2s.  co m
            }
        }
    }
    return results;
}

From source file:de.bps.onyx.plugin.OnyxModule.java

public static ResourceEvaluation isOnyxTest(File file, String filename) {
    ResourceEvaluation eval = new ResourceEvaluation();
    BufferedReader reader = null;
    try {/*from w  w  w. ja  va 2  s. c  om*/
        ImsManifestFileFilter visitor = new ImsManifestFileFilter();
        Path fPath = PathUtils.visit(file, filename, visitor);
        if (visitor.isValid()) {
            Path qtiPath = fPath.resolve("imsmanifest.xml");
            reader = Files.newBufferedReader(qtiPath, StandardCharsets.UTF_8);
            while (reader.ready()) {
                String l = reader.readLine();
                if (l.indexOf("imsqti_xmlv2p1") != -1 || l.indexOf("imsqti_test_xmlv2p1") != -1
                        || l.indexOf("imsqti_assessment_xmlv2p1") != -1) {
                    eval.setValid(true);
                    break;
                }
            }
        } else {
            eval.setValid(false);
        }
    } catch (NoSuchFileException nsfe) {
        eval.setValid(false);
    } catch (IOException | IllegalArgumentException e) {
        log.error("", e);
        eval.setValid(false);
    } finally {
        IOUtils.closeQuietly(reader);
    }
    return eval;
}

From source file:org.jboss.as.test.integration.logging.operations.CustomFormattersTestCase.java

@Test
public void testUsage() throws Exception {

    // Create the custom formatter
    CompositeOperationBuilder builder = CompositeOperationBuilder.create();
    ModelNode op = Operations.createAddOperation(CUSTOM_FORMATTER_ADDRESS);
    op.get("class").set("java.util.logging.XMLFormatter");
    // the module doesn't really matter since it's a JDK, so we'll just use the jboss-logmanager.
    op.get("module").set("org.jboss.logmanager");
    builder.addStep(op);/*from   w ww  .  ja v  a  2s .  c  o  m*/

    // Create the handler
    op = Operations.createAddOperation(HANDLER_ADDRESS);
    final ModelNode file = op.get("file");
    file.get("relative-to").set("jboss.server.log.dir");
    file.get("path").set(FILE_NAME);
    op.get("append").set(false);
    op.get("autoflush").set(true);
    op.get("named-formatter").set(CUSTOM_FORMATTER_NAME);
    builder.addStep(op);

    // Add the handler to the root logger
    op = Operations.createOperation("add-handler", ROOT_LOGGER_ADDRESS);
    op.get(ModelDescriptionConstants.NAME).set(HANDLER_NAME);
    builder.addStep(op);

    executeOperation(builder.build());

    // Get the log file
    op = Operations.createOperation("resolve-path", HANDLER_ADDRESS);
    ModelNode result = executeOperation(op);
    final Path logFile = Paths.get(Operations.readResult(result).asString());

    // The file should exist
    Assert.assertTrue("The log file was not created.", Files.exists(logFile));

    // Log 5 records
    doLog("Test message: ", 5);

    // Read the log file
    try (BufferedReader reader = Files.newBufferedReader(logFile, StandardCharsets.UTF_8)) {
        final Pattern pattern = Pattern.compile("^(<message>)+(Test message: \\d)+(</message>)$");
        final List<String> messages = new ArrayList<>(5);
        String line;
        while ((line = reader.readLine()) != null) {
            final String trimmedLine = line.trim();
            final Matcher m = pattern.matcher(trimmedLine);
            // Very simple xml parsing
            if (m.matches()) {
                messages.add(m.group(2));
            }
        }

        // Should be 5 messages
        Assert.assertEquals(5, messages.size());
        // Check each message
        int count = 0;
        for (String msg : messages) {
            Assert.assertEquals("Test message: " + count++, msg);
        }
    }

    builder = CompositeOperationBuilder.create();
    // Remove the handler from the root-logger
    op = Operations.createOperation("remove-handler", ROOT_LOGGER_ADDRESS);
    op.get(ModelDescriptionConstants.NAME).set(HANDLER_NAME);
    builder.addStep(op);

    // Remove the custom formatter
    op = Operations.createRemoveOperation(CUSTOM_FORMATTER_ADDRESS);
    builder.addStep(op);

    // Remove the handler
    op = Operations.createRemoveOperation(HANDLER_ADDRESS);
    builder.addStep(op);

    executeOperation(builder.build());

    // So we don't pollute other, verify the formatter and handler have been removed
    op = Operations.createReadAttributeOperation(ROOT_LOGGER_ADDRESS, "handlers");
    result = executeOperation(op);
    // Should be a list type
    final List<ModelNode> handlers = Operations.readResult(result).asList();
    for (ModelNode handler : handlers) {
        Assert.assertNotEquals(CUSTOM_FORMATTER_NAME, handler.asString());
    }
    verifyRemoved(CUSTOM_FORMATTER_ADDRESS);
    verifyRemoved(HANDLER_ADDRESS);

    // Delete the log file
    Files.delete(logFile);
    // Ensure it's been deleted
    Assert.assertFalse(Files.exists(logFile));
}