Example usage for org.apache.commons.io LineIterator nextLine

List of usage examples for org.apache.commons.io LineIterator nextLine

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Introduction

In this page you can find the example usage for org.apache.commons.io LineIterator nextLine.

Prototype

public String nextLine()

Source Link

Document

Returns the next line in the wrapped Reader.

Usage

From source file:nl.knaw.huygens.timbuctoo.tools.importer.neww.WomenWritersImporter.java

private Set<String> collectCollaborators() throws Exception {
    Set<String> ids = Sets.newHashSet();
    LineIterator iterator = getLineIterator("relations.json");
    String line = "";
    try {/*ww  w . j  a v a  2 s  .  c om*/
        while (iterator.hasNext()) {
            line = preprocessJson(iterator.nextLine());
            if (!line.isEmpty()) {
                XRelation object = objectMapper.readValue(line, XRelation.class);
                String relationType = filterField(object.relation_type);
                if ("collaborated_with".equals(relationType)) {
                    String leftObject = verifyNonEmptyField(line, "leftObject", filterField(object.leftObject));
                    String leftId = verifyNonEmptyField(line, "leftId", filterField(object.leftId));
                    if ("Person".equals(leftObject)) {
                        ids.add(leftId);
                    }
                }
            }
        }
    } catch (Exception e) {
        throw e;
    } finally {
        LineIterator.closeQuietly(iterator);
    }
    return ids;
}

From source file:nl.knaw.huygens.timbuctoo.tools.importer.neww.WomenWritersImporter.java

private void importRelations() throws Exception {
    relationTypeConcordance = getRelationTypeConcordance();
    LineIterator iterator = getLineIterator("relations.json");
    String line = "";
    try {//from   w  ww.  j av a 2s .c  o m
        while (iterator.hasNext()) {
            line = preprocessJson(iterator.nextLine());
            if (!line.isEmpty()) {
                handleRelation(line);
            }
        }
    } catch (Exception e) {
        System.out.println(line);
        throw e;
    } finally {
        LineIterator.closeQuietly(iterator);
        relationTypeConcordance = null;
    }
}

From source file:nl.opengeogroep.safetymaps.server.admin.stripes.LayerActionBean.java

@Before(stages = LifecycleStage.BindingAndValidation)
private void findMapfiles() {
    try {/*from  www.  j  a va 2  s. c  o  m*/
        JSONArray a = new JSONArray();
        File search = Cfg.getPath("static_mapserver_searchdirs");

        if (search != null) {
            for (File f : FileUtils.listFiles(search, new String[] { "map" }, true)) {
                JSONObject m = new JSONObject();
                m.put("path", f.getPath().substring(search.getPath().length() + 1));
                a.put(m);

                // Naive mapfile parser. Perhaps replace by JavaScript client-side
                // GetCap parsing
                JSONArray l = new JSONArray();
                m.put("layers", l);
                LineIterator it = FileUtils.lineIterator(f, "US-ASCII");
                try {
                    while (it.hasNext()) {
                        String line = it.nextLine().trim();
                        if (line.equals("LAYER")) {
                            String n = it.nextLine().trim();
                            n = n.substring(6, n.length() - 1);
                            l.put(n);
                        }
                    }
                } finally {
                    it.close();
                }
            }
        }
        mapFilesJson = a.toString(4);
    } catch (Exception e) {
    }
}

From source file:nl.ru.cmbi.vase.tools.util.ToolBox.java

public static StringBuilder getStringBuilderFromFile(final String fileName) throws IOException {
    // int STRINGBUILDER_SIZE = 403228383; // big!
    File file = new File(fileName);
    LineIterator it = FileUtils.lineIterator(file);
    StringBuilder sb = new StringBuilder(); // STRINGBUILDER_SIZE
    while (it.hasNext()) {
        sb.append(it.nextLine());
        sb.append("\n");
    }/*from  w ww. ja v a  2 s . c  o m*/
    it.close();
    return sb;
}

From source file:org.adf.emg.sonar.ojaudit.JavaMetricsDecorator.java

@Override
public void decorate(Resource resource, DecoratorContext context) {
    if (!(Qualifiers.isFile(resource) && resource.getName().endsWith(".java"))) {
        // only process .java files
        return;//from   w w w.  j  av  a2 s.c  o  m
    }
    ProjectFileSystem fileSystem = context.getProject().getFileSystem();
    File file = lookup(resource, fileSystem);

    LineIterator iterator = null;
    int numLines = 0;
    int numBlankLines = 0;
    int numCommentLines = 0;
    try {
        Charset charset = fileSystem.getSourceCharset();
        iterator = charset == null ? FileUtils.lineIterator(file)
                : FileUtils.lineIterator(file, charset.name());
        boolean inComment = false;
        while (iterator.hasNext()) {
            String trimmedLine = iterator.nextLine().trim();
            numLines++;
            boolean lineHasCode = false;
            boolean lineHasComment = false;
            while (!trimmedLine.isEmpty()) {
                if (inComment) { // in a comment. try to find end marker
                    int endIndex = trimmedLine.indexOf(END_COMMENT);
                    if (endIndex == -1) { // (rest of) line is comment
                        lineHasComment = true;
                        trimmedLine = ""; // remove comment
                    } else { // remove comment to see if there is code after it
                        lineHasComment = true;
                        trimmedLine = trimmedLine.substring(endIndex + END_COMMENT.length());
                        inComment = false;
                    }
                } else { // not in a comment
                    if (trimmedLine.startsWith("//")) {
                        trimmedLine = "";
                        continue;
                    }
                    // try to find begin comment marker
                    int startIndex = trimmedLine.indexOf(START_COMMENT);
                    if (startIndex == -1) { // (rest of) line is non-comment
                        lineHasCode = true;
                        trimmedLine = ""; // remove non-comment
                    } else if (startIndex == 0) { // line starts with start marker
                        inComment = true;
                        trimmedLine = trimmedLine.substring(startIndex + START_COMMENT.length());
                    } else { // line contains start marker
                        lineHasCode = true;
                        inComment = true;
                        trimmedLine = trimmedLine.substring(startIndex + START_COMMENT.length());
                    }
                }
                trimmedLine = trimmedLine.trim();
            }
            if (!lineHasCode) {
                if (lineHasComment) {
                    numCommentLines++;
                } else {
                    numBlankLines++;
                }
            }
        }
    } catch (IOException e) {
        LOG.warn("error reading " + file + " to collect metrics", e);
    } finally {
        LineIterator.closeQuietly(iterator);
    }

    context.saveMeasure(CoreMetrics.LINES, (double) numLines); // Lines
    context.saveMeasure(CoreMetrics.COMMENT_LINES, (double) numCommentLines); // Non Commenting Lines of Code
    context.saveMeasure(CoreMetrics.NCLOC, (double) numLines - numBlankLines - numCommentLines); // Comment Lines
}

From source file:org.adf.emg.sonar.ojaudit.XmlMetricsDecorator.java

@Override
public void decorate(Resource resource, DecoratorContext context) {
    if (!Qualifiers.isFile(resource)) {
        return;//from  www  .  j a v a 2s .  co  m
    }
    ProjectFileSystem fileSystem = context.getProject().getFileSystem();
    File file = lookup(resource, fileSystem);

    try {
        if (readFirstByte(file) != '<') {
            return;
        }
    } catch (IOException e) {
        throw new SonarException(e);
    }

    int numCommentLines;
    CountCommentParser commentCounter = new CountCommentParser();
    try {
        numCommentLines = commentCounter.countLinesOfComment(FileUtils.openInputStream(file));
        if (numCommentLines == -1) {
            return;
        }
    } catch (IOException e) {
        throw new SonarException(e);
    }

    LineIterator iterator = null;
    int numLines = 0;
    int numBlankLines = 0;
    try {
        Charset charset = fileSystem.getSourceCharset();
        iterator = charset == null ? FileUtils.lineIterator(file)
                : FileUtils.lineIterator(file, charset.name());
        while (iterator.hasNext()) {
            String line = iterator.nextLine();
            numLines++;
            if (line.trim().isEmpty()) {
                numBlankLines++;
            }
        }
    } catch (IOException e) {
        LOG.warn("error reading " + file + " to collect metrics", e);
    } finally {
        LineIterator.closeQuietly(iterator);
    }

    context.saveMeasure(CoreMetrics.LINES, (double) numLines); // Lines
    context.saveMeasure(CoreMetrics.COMMENT_LINES, (double) numCommentLines); // Non Commenting Lines of Code
    context.saveMeasure(CoreMetrics.NCLOC, (double) numLines - numBlankLines - numCommentLines); // Comment Lines
}

From source file:org.apache.accumulo.test.AuditMessageIT.java

/**
 * Returns a List of Audit messages that have been grep'd out of the MiniAccumuloCluster output.
 *
 * @param stepName/*w w w .  j  a  v a 2  s  .co m*/
 *          A unique name for the test being executed, to identify the System.out messages.
 * @return A List of the Audit messages, sorted (so in chronological order).
 */
private ArrayList<String> getAuditMessages(String stepName) throws IOException {
    // ACCUMULO-3144 Make sure we give the processes enough time to flush the write buffer
    try {
        Thread.sleep(2000);
    } catch (InterruptedException e) {
        Thread.currentThread().interrupt();
        throw new IOException("Interrupted waiting for data to be flushed to output streams");
    }

    for (MiniAccumuloClusterImpl.LogWriter lw : getCluster().getLogWriters()) {
        lw.flush();
    }

    // Grab the audit messages
    System.out.println("Start of captured audit messages for step " + stepName);

    ArrayList<String> result = new ArrayList<String>();
    File[] files = getCluster().getConfig().getLogDir().listFiles();
    assertNotNull(files);
    for (File file : files) {
        // We want to grab the files called .out
        if (file.getName().contains(".out") && file.isFile() && file.canRead()) {
            LineIterator it = FileUtils.lineIterator(file, UTF_8.name());
            try {
                while (it.hasNext()) {
                    String line = it.nextLine();
                    if (line.matches(".* \\[" + AuditedSecurityOperation.AUDITLOG + "\\s*\\].*")) {
                        // Only include the message if startTimestamp is null. or the message occurred after the startTimestamp value
                        if ((lastAuditTimestamp == null)
                                || (line.substring(0, 23).compareTo(lastAuditTimestamp) > 0))
                            result.add(line);
                    }
                }
            } finally {
                LineIterator.closeQuietly(it);
            }
        }
    }
    Collections.sort(result);

    for (String s : result) {
        System.out.println(s);
    }
    System.out.println("End of captured audit messages for step " + stepName);
    if (result.size() > 0)
        lastAuditTimestamp = (result.get(result.size() - 1)).substring(0, 23);

    return result;
}

From source file:org.apache.accumulo.test.AuditMessageIT.java

@Test
public void testImportExportOperationsAudits() throws AccumuloSecurityException, AccumuloException,
        TableExistsException, TableNotFoundException, IOException, InterruptedException {

    conn.securityOperations().createLocalUser(AUDIT_USER_1, new PasswordToken(PASSWORD));
    conn.securityOperations().grantSystemPermission(AUDIT_USER_1, SystemPermission.SYSTEM);
    conn.securityOperations().changeUserAuthorizations(AUDIT_USER_1, auths);
    grantEverySystemPriv(conn, AUDIT_USER_1);

    // Connect as Audit User and do a bunch of stuff.
    // Start testing activities here
    auditConnector = getCluster().getConnector(AUDIT_USER_1, new PasswordToken(PASSWORD));
    auditConnector.tableOperations().create(OLD_TEST_TABLE_NAME);

    // Insert some play data
    BatchWriter bw = auditConnector.createBatchWriter(OLD_TEST_TABLE_NAME, new BatchWriterConfig());
    Mutation m = new Mutation("myRow");
    m.put("cf1", "cq1", "v1");
    m.put("cf1", "cq2", "v3");
    bw.addMutation(m);/* ww  w .j  a va  2s  . c o m*/
    bw.close();

    // Prepare to export the table
    File exportDir = new File(getCluster().getConfig().getDir().toString() + "/export");

    auditConnector.tableOperations().offline(OLD_TEST_TABLE_NAME);
    auditConnector.tableOperations().exportTable(OLD_TEST_TABLE_NAME, exportDir.toString());

    // We've exported the table metadata to the MiniAccumuloCluster root dir. Grab the .rf file path to re-import it
    File distCpTxt = new File(exportDir.toString() + "/distcp.txt");
    File importFile = null;
    LineIterator it = FileUtils.lineIterator(distCpTxt, UTF_8.name());

    // Just grab the first rf file, it will do for now.
    String filePrefix = "file:";
    try {
        while (it.hasNext() && importFile == null) {
            String line = it.nextLine();
            if (line.matches(".*\\.rf")) {
                importFile = new File(line.replaceFirst(filePrefix, ""));
            }
        }
    } finally {
        LineIterator.closeQuietly(it);
    }
    FileUtils.copyFileToDirectory(importFile, exportDir);
    auditConnector.tableOperations().importTable(NEW_TEST_TABLE_NAME, exportDir.toString());

    // Now do a Directory (bulk) import of the same data.
    auditConnector.tableOperations().create(THIRD_TEST_TABLE_NAME);
    File failDir = new File(exportDir + "/tmp");
    assertTrue(failDir.mkdirs() || failDir.isDirectory());
    auditConnector.tableOperations().importDirectory(THIRD_TEST_TABLE_NAME, exportDir.toString(),
            failDir.toString(), false);
    auditConnector.tableOperations().online(OLD_TEST_TABLE_NAME);

    // Stop testing activities here

    ArrayList<String> auditMessages = getAuditMessages("testImportExportOperationsAudits");

    assertEquals(1,
            findAuditMessage(auditMessages, String
                    .format(AuditedSecurityOperation.CAN_CREATE_TABLE_AUDIT_TEMPLATE, OLD_TEST_TABLE_NAME))
                            .size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_ONLINE_OFFLINE_TABLE_AUDIT_TEMPLATE,
                            "offlineTable", OLD_TEST_TABLE_NAME)).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String.format(AuditedSecurityOperation.CAN_EXPORT_AUDIT_TEMPLATE,
                    OLD_TEST_TABLE_NAME, exportDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String.format(AuditedSecurityOperation.CAN_IMPORT_AUDIT_TEMPLATE,
                    NEW_TEST_TABLE_NAME, filePrefix + exportDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String
                    .format(AuditedSecurityOperation.CAN_CREATE_TABLE_AUDIT_TEMPLATE, THIRD_TEST_TABLE_NAME))
                            .size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_BULK_IMPORT_AUDIT_TEMPLATE,
                            THIRD_TEST_TABLE_NAME, filePrefix + exportDir.toString(),
                            filePrefix + failDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_ONLINE_OFFLINE_TABLE_AUDIT_TEMPLATE,
                            "onlineTable", OLD_TEST_TABLE_NAME)).size());

}

From source file:org.apache.accumulo.test.AuditMessageTest.java

/**
 * Returns a List of Audit messages that have been grep'd out of the MiniAccumuloCluster output.
 * /*from  www  .j a va 2s .  c o m*/
 * @param stepName
 *          A unique name for the test being executed, to identify the System.out messages.
 * @return A List of the Audit messages, sorted (so in chronological order).
 */
private ArrayList<String> getAuditMessages(String stepName) throws IOException {

    for (MiniAccumuloCluster.LogWriter lw : logWriters) {
        lw.flush();
    }

    // Grab the audit messages
    System.out.println("Start of captured audit messages for step " + stepName);

    ArrayList<String> result = new ArrayList<String>();
    for (File file : logDir.listFiles()) {
        // We want to grab the files called .out
        if (file.getName().contains(".out") && file.isFile() && file.canRead()) {
            LineIterator it = FileUtils.lineIterator(file, Constants.UTF8.name());
            try {
                while (it.hasNext()) {
                    String line = it.nextLine();
                    if (line.matches(".* \\[" + AuditedSecurityOperation.AUDITLOG + "\\s*\\].*")) {
                        // Only include the message if startTimestamp is null. or the message occurred after the startTimestamp value
                        if ((lastAuditTimestamp == null)
                                || (line.substring(0, 23).compareTo(lastAuditTimestamp) > 0))
                            result.add(line);
                    }
                }
            } finally {
                LineIterator.closeQuietly(it);
            }
        }
    }
    Collections.sort(result);

    for (String s : result) {
        System.out.println(s);
    }
    System.out.println("End of captured audit messages for step " + stepName);
    if (result.size() > 0)
        lastAuditTimestamp = (result.get(result.size() - 1)).substring(0, 23);

    return result;
}

From source file:org.apache.accumulo.test.AuditMessageTest.java

@Test(timeout = 60 * 1000)
public void testImportExportOperationsAudits() throws AccumuloSecurityException, AccumuloException,
        TableExistsException, TableNotFoundException, IOException, InterruptedException {

    conn.securityOperations().createLocalUser(AUDIT_USER_1, new PasswordToken(PASSWORD));
    conn.securityOperations().grantSystemPermission(AUDIT_USER_1, SystemPermission.SYSTEM);
    conn.securityOperations().changeUserAuthorizations(AUDIT_USER_1, auths);
    grantEverySystemPriv(conn, AUDIT_USER_1);

    // Connect as Audit User and do a bunch of stuff.
    // Start testing activities here
    auditConnector = accumulo.getConnector(AUDIT_USER_1, PASSWORD);
    auditConnector.tableOperations().create(OLD_TEST_TABLE_NAME);

    // Insert some play data
    BatchWriter bw = auditConnector.createBatchWriter(OLD_TEST_TABLE_NAME, new BatchWriterConfig());
    Mutation m = new Mutation("myRow");
    m.put("cf1", "cq1", "v1");
    m.put("cf1", "cq2", "v3");
    bw.addMutation(m);/*w w  w  . j a v a 2s.co  m*/
    bw.close();

    // Prepare to export the table
    File exportDir = new File(accumulo.getConfig().getDir().toString() + "/export");

    auditConnector.tableOperations().offline(OLD_TEST_TABLE_NAME);
    auditConnector.tableOperations().exportTable(OLD_TEST_TABLE_NAME, exportDir.toString());

    // We've exported the table metadata to the MiniAccumuloCluster root dir. Grab the .rf file path to re-import it
    File distCpTxt = new File(exportDir.toString() + "/distcp.txt");
    File importFile = null;
    LineIterator it = FileUtils.lineIterator(distCpTxt, Constants.UTF8.name());

    // Just grab the first rf file, it will do for now.
    String filePrefix = "file:";
    try {
        while (it.hasNext() && importFile == null) {
            String line = it.nextLine();
            if (line.matches(".*\\.rf")) {
                importFile = new File(line.replaceFirst(filePrefix, ""));
            }
        }
    } finally {
        LineIterator.closeQuietly(it);
    }
    FileUtils.copyFileToDirectory(importFile, exportDir);
    auditConnector.tableOperations().importTable(NEW_TEST_TABLE_NAME, exportDir.toString());

    // Now do a Directory (bulk) import of the same data.
    auditConnector.tableOperations().create(THIRD_TEST_TABLE_NAME);
    File failDir = new File(exportDir + "/tmp");
    failDir.mkdirs();
    auditConnector.tableOperations().importDirectory(THIRD_TEST_TABLE_NAME, exportDir.toString(),
            failDir.toString(), false);
    auditConnector.tableOperations().online(OLD_TEST_TABLE_NAME);

    // Stop testing activities here

    ArrayList<String> auditMessages = getAuditMessages("testImportExportOperationsAudits");

    assertEquals(1,
            findAuditMessage(auditMessages, String
                    .format(AuditedSecurityOperation.CAN_CREATE_TABLE_AUDIT_TEMPLATE, OLD_TEST_TABLE_NAME))
                            .size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_ONLINE_OFFLINE_TABLE_AUDIT_TEMPLATE,
                            "offlineTable", OLD_TEST_TABLE_NAME)).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String.format(AuditedSecurityOperation.CAN_EXPORT_AUDIT_TEMPLATE,
                    OLD_TEST_TABLE_NAME, exportDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String.format(AuditedSecurityOperation.CAN_IMPORT_AUDIT_TEMPLATE,
                    NEW_TEST_TABLE_NAME, exportDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages, String
                    .format(AuditedSecurityOperation.CAN_CREATE_TABLE_AUDIT_TEMPLATE, THIRD_TEST_TABLE_NAME))
                            .size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_BULK_IMPORT_AUDIT_TEMPLATE,
                            THIRD_TEST_TABLE_NAME, filePrefix + exportDir.toString(),
                            filePrefix + failDir.toString())).size());
    assertEquals(1,
            findAuditMessage(auditMessages,
                    String.format(AuditedSecurityOperation.CAN_ONLINE_OFFLINE_TABLE_AUDIT_TEMPLATE,
                            "onlineTable", OLD_TEST_TABLE_NAME)).size());

}