Example usage for java.io LineNumberReader readLine

Introduction

In this page you can find the example usage for java.io LineNumberReader readLine.

Prototype

public String readLine() throws IOException

Source Link

Document

Read a line of text.

Usage

From source file:edu.stanford.muse.util.Util.java

/**
 * returns collection of lines from given file (UTF-8).
 * trims spaces from the lines,//  w  w  w  . ja  v  a 2 s  .c o m
 * ignores lines starting with # if ignoreCommentLines is true
 */
public static List<String> getLinesFromReader(Reader reader, boolean ignoreCommentLines) throws IOException {
    LineNumberReader lnr = new LineNumberReader(reader);
    List<String> result = new ArrayList<String>();
    while (true) {
        String line = lnr.readLine();
        if (line == null)
            break;
        line = line.trim();

        if (ignoreCommentLines && (line.length() == 0 || line.charAt(0) == '#'))
            continue;

        result.add(line);
    }
    return result;
}

From source file:com.netscape.cms.logging.LogFile.java

/**
 * This method actually does the logging, and is not overridden
 * by subclasses, so you can call it and know that it will do exactly
 * what you see below.//w w  w .j  av  a  2s  .c om
 */
private synchronized void doLog(ILogEvent event, boolean noFlush) throws ELogException {

    String entry = logEvt2String(event);

    if (mLogWriter == null) {
        String[] params = { mFileName, entry };

        if (mLogSigning) {
            ConsoleError.send(new SystemEvent(CMS.getUserMessage("CMS_LOG_LOGFILE_CLOSED", params)));
            // Failed to write to audit log, shut down CMS
            shutdownCMS();
        }
        throw new ELogException(CMS.getUserMessage("CMS_LOG_LOGFILE_CLOSED", params));
    } else {
        try {
            mLogWriter.write(entry, 0/*offset*/, entry.length());

            if (mLogSigning == true) {
                if (mSignature != null) {
                    // include newline for calculating MAC
                    mSignature.update(entry.getBytes("UTF-8"));
                } else {
                    CMS.debug("LogFile: mSignature is not yet ready... null in log()");
                }
            }
            if (mTrace) {
                CharArrayWriter cw = new CharArrayWriter(200);
                PrintWriter pw = new PrintWriter(cw);
                Exception e = new Exception();
                e.printStackTrace(pw);
                char[] c = cw.toCharArray();
                cw.close();
                pw.close();

                CharArrayReader cr = new CharArrayReader(c);
                LineNumberReader lr = new LineNumberReader(cr);

                String text = null;
                String method = null;
                String fileAndLine = null;
                if (lr.ready()) {
                    text = lr.readLine();
                    do {
                        text = lr.readLine();
                    } while (text.indexOf("logging") != -1);
                    int p = text.indexOf("(");
                    fileAndLine = text.substring(p);

                    String classandmethod = text.substring(0, p);
                    int q = classandmethod.lastIndexOf(".");
                    method = classandmethod.substring(q + 1);
                    mLogWriter.write(fileAndLine, 0/*offset*/, fileAndLine.length());
                    mLogWriter.write(" ", 0/*offset*/, " ".length());
                    mLogWriter.write(method, 0/*offset*/, method.length());
                }
            }
            mLogWriter.newLine();

            if (mLogSigning == true) {
                if (mSignature != null) {
                    mSignature.update(LINE_SEP_BYTE);
                } else {
                    CMS.debug("LogFile: mSignature is null in log() 2");
                }
            }
        } catch (IOException e) {
            ConsoleError.send(new SystemEvent(
                    CMS.getUserMessage("CMS_LOG_WRITE_FAILED", mFileName, entry, e.toString())));
            if (mLogSigning) {
                // Failed to write to audit log, shut down CMS
                e.printStackTrace();
                shutdownCMS();
            }
        } catch (IllegalStateException e) {
            CMS.debug("LogFile: exception thrown in log(): " + e.toString());
            ConsoleError
                    .send(new SignedAuditEvent(CMS.getLogMessage(LOG_SIGNED_AUDIT_EXCEPTION, e.toString())));
        } catch (GeneralSecurityException gse) {
            // DJN: handle error
            CMS.debug("LogFile: exception thrown in log(): " + gse.toString());
            gse.printStackTrace();
            ConsoleError
                    .send(new SignedAuditEvent(CMS.getLogMessage(LOG_SIGNED_AUDIT_EXCEPTION, gse.toString())));
        } catch (Exception ee) { // Make darn sure we got everything
            ConsoleError
                    .send(new SignedAuditEvent(CMS.getLogMessage(LOG_SIGNED_AUDIT_EXCEPTION, ee.toString())));
            if (mLogSigning) {
                // Failed to write to audit log, shut down CMS
                ee.printStackTrace();
                shutdownCMS();
            }

        }

        // XXX
        // Although length will be in Unicode dual-bytes, the PrintWriter
        // will only print out 1 byte per character.  I suppose this could
        // be dependent on the encoding of your log file, but it ain't that
        // smart yet.  Also, add one for the newline. (hmm, on NT, CR+LF)
        int nBytes = entry.length() + 1;

        mBytesWritten += nBytes;
        mBytesUnflushed += nBytes;

        if (mBufferSize > 0 && mBytesUnflushed > mBufferSize && !noFlush) {
            flush();
        }
    }
}

From source file:massbank.BatchJobWorker.java

/**
 * Ytt@C???iHTML`?j//from w w w.j av a 2s .  c o m
 * @param time NGXg 
 * @param resultFile t@C
 * @param htmlFile YtpHTMLt@C
 */
private void createHtmlFile(String time, File resultFile, File htmlFile) {
    NumberFormat nf = NumberFormat.getNumberInstance();
    LineNumberReader in = null;
    PrintWriter out = null;
    try {
        in = new LineNumberReader(new FileReader(resultFile));
        out = new PrintWriter(new BufferedWriter(new FileWriter(htmlFile)));

        // wb_?[?o
        String reqIonStr = "Both";
        try {
            if (Integer.parseInt(this.ion) > 0) {
                reqIonStr = "Positive";
            } else if (Integer.parseInt(this.ion) < 0) {
                reqIonStr = "Negative";
            }
        } catch (NumberFormatException nfe) {
            nfe.printStackTrace();
        }
        out.println("<html>");
        out.println("<head><title>MassBank Batch Service Results</title></head>");
        out.println("<body>");
        out.println(
                "<h1><a href=\"http://www.massbank.jp/\" target=\"_blank\">MassBank</a> Batch Service Results</h1>");
        out.println("<hr>");
        out.println("<h2>Request Date : " + time + "<h2>");
        out.println("Instrument Type : " + this.inst + "<br>");
        out.println("Ion Mode : " + reqIonStr + "<br>");
        out.println("<br><hr>");

        // ?o
        String line;
        long queryCnt = 0;
        boolean readName = false;
        boolean readHit = false;
        boolean readNum = false;
        while ((line = in.readLine()) != null) {
            if (in.getLineNumber() < 4) {
                continue;
            }
            if (!readName) {
                queryCnt++;
                out.println("<h2>Query " + nf.format(queryCnt) + "</h2><br>");
                out.println("Name: " + line.trim() + "<br>");
                readName = true;
            } else if (!readHit) {
                out.println("Hit: " + nf.format(Integer.parseInt(line.trim())) + "<br>");
                readHit = true;
            } else if (!readNum) {
                out.println("<table border=\"1\">");
                out.println("<tr><td colspan=\"6\">Top " + line.trim() + " List</td></tr>");
                out.println(
                        "<tr><th>Accession</th><th>Title</th><th>Formula</th><th>Ion</th><th>Score</th><th>Hit</th></tr>");
                readNum = true;
            } else {
                if (!line.trim().equals("")) {
                    String[] data = formatLine(line);
                    String acc = data[0];
                    String title = data[1];
                    String formula = data[2];
                    String ion = data[3];
                    String score = data[4];
                    String hit = data[5];

                    out.println("<tr>");
                    out.println("<td><a href=\"http://www.massbank.jp/jsp/FwdRecord.jsp?id=" + acc
                            + "\" target=\"_blank\">" + acc + "</td>");
                    out.println("<td>" + title + "</td>");
                    out.println("<td>" + formula + "</td>");
                    out.println("<td>" + ion + "</td>");
                    out.println("<td>" + score + "</td>");
                    out.println("<td align=\"right\">" + hit + "</td>");
                    out.println("</tr>");
                } else {
                    out.println("</table>");
                    out.println("<hr>");
                    readName = false;
                    readHit = false;
                    readNum = false;
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        try {
            if (in != null) {
                in.close();
            }
        } catch (IOException e) {
        }
        if (out != null) {
            out.flush();
            out.close();
        }
    }
}

From source file:edu.stanford.muse.util.Util.java

public static Collection<String> breakIntoParas(String input) throws IOException {
    List<String> paras = new ArrayList<String>();
    LineNumberReader lnr = new LineNumberReader(new StringReader(input));

    StringBuilder currentPara = new StringBuilder();

    while (true) {
        String line = lnr.readLine();
        if (line == null)
            break;
        line = line.trim();/*w ww  .  j a v  a2 s . c  o m*/

        if (line.length() == 0) {
            // end para
            if (currentPara.length() > 0)
                paras.add(currentPara.toString());
            currentPara = new StringBuilder();
        } else {
            currentPara.append(line);
            currentPara.append("\n");
        }
    }

    // add any residue
    if (currentPara.length() > 0)
        paras.add(currentPara.toString());
    return paras;
}

From source file:net.rptools.maptool.launcher.MapToolLauncher.java

/**
 * Read the given XML file and look for specially formatted lines so that a
 * description of the files purpose and text to display in a tooltip are
 * retrieved. The current process involves looking for XML comments that
 * match the regex <code><b>^&lt;!--\s+(\w+):\s*(.*)\s+--&gt;$</b></code>
 * and pull out the two fields; the first field is the key and the second is
 * the value for storing the information in the returned object.
 * //from w w  w .  ja  va 2  s.c o  m
 * @param xml
 *            <code>File</code> object representing the file to read
 * @return a {@link LoggingConfig} object which stores information about the
 *         XML file
 */
private LoggingConfig readDescFromXmlFile(File xml) {
    final LoggingConfig config = new LoggingConfig(xml, new JCheckBox());
    LineNumberReader lnbr = null;
    final String REGEX = "^<!--\\s+(\\w+):\\s*(.*)\\s+-->$"; //$NON-NLS-1$
    final Pattern pattern = Pattern.compile(REGEX);
    try {
        int count = 0;
        lnbr = new LineNumberReader(new BufferedReader(new FileReader(xml)));
        String line = lnbr.readLine();
        config.addProperty("desc", xml.getName()); //$NON-NLS-1$
        config.addProperty("ttip", xml.getName()); //$NON-NLS-1$
        while (count < 2 && line != null) {
            line = line.trim();
            final Matcher m = pattern.matcher(line);
            if (m.matches()) {
                final String key = m.group(1);
                final String value = m.group(2);
                config.addProperty(key, value);
                count++;
            }
            line = lnbr.readLine();
        }
        if (count < 2) {
            JOptionPane.showMessageDialog(null,
                    CopiedFromOtherJars.getText("msg.error.loggingBadFormat", xml.getName()), //$NON-NLS-1$
                    CopiedFromOtherJars.getText("msg.title.loggingBadFormat", xml), //$NON-NLS-1$
                    ERROR_MESSAGE);
        }
    } catch (final FileNotFoundException e) {
    } catch (final IOException e) {
    } finally {
        CopiedFromOtherJars.closeQuietly(lnbr);
    }
    return config;
}

From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java

/**
 * Verify boot fails with a bad MetricsProvider
 *//*from  ww w.  jav a 2 s  . c o m*/
@Test
public void testInvalidMetricsProvider() throws Exception {
    ClientBase.setupTestEnv();

    // setup the logger to capture all logs
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    WriterAppender appender = getConsoleAppender(os, Level.WARN);
    Logger qlogger = Logger.getLogger("org.apache.zookeeper.server.quorum");
    qlogger.addAppender(appender);

    try {
        final int CLIENT_PORT_QP1 = PortAssignment.unique();

        String quorumCfgSection = "server.1=127.0.0.1:" + PortAssignment.unique() + ":"
                + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n" + "server.2=127.0.0.1:"
                + PortAssignment.unique() + ":" + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n"
                + "metricsProvider.className=BadClass\n";

        MainThread q1 = new MainThread(1, CLIENT_PORT_QP1, quorumCfgSection);
        q1.start();

        boolean isup = ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP1, 5000);

        Assert.assertFalse("Server never came up", isup);

        q1.shutdown();

        Assert.assertTrue("waiting for server 1 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP1, ClientBase.CONNECTION_TIMEOUT));

    } finally {
        qlogger.removeAppender(appender);
    }

    LineNumberReader r = new LineNumberReader(new StringReader(os.toString()));
    String line;
    boolean found = false;
    Pattern p = Pattern.compile(".*BadClass.*");
    while ((line = r.readLine()) != null) {
        found = p.matcher(line).matches();
        if (found) {
            break;
        }
    }
    Assert.assertTrue("complains about metrics provider", found);
}

From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java

/**
 * Verify handling of quorum defaults/*from  w  ww .ja  v a  2 s.  c  o m*/
 * * default electionAlg is fast leader election
 */
@Test
public void testQuorumDefaults() throws Exception {
    ClientBase.setupTestEnv();

    // setup the logger to capture all logs
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    WriterAppender appender = getConsoleAppender(os, Level.INFO);
    appender.setImmediateFlush(true);
    Logger zlogger = Logger.getLogger("org.apache.zookeeper");
    zlogger.addAppender(appender);

    try {
        final int CLIENT_PORT_QP1 = PortAssignment.unique();
        final int CLIENT_PORT_QP2 = PortAssignment.unique();

        String quorumCfgSection = "server.1=127.0.0.1:" + PortAssignment.unique() + ":"
                + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\nserver.2=127.0.0.1:"
                + PortAssignment.unique() + ":" + PortAssignment.unique() + ";" + CLIENT_PORT_QP2;

        MainThread q1 = new MainThread(1, CLIENT_PORT_QP1, quorumCfgSection);
        MainThread q2 = new MainThread(2, CLIENT_PORT_QP2, quorumCfgSection);
        q1.start();
        q2.start();

        Assert.assertTrue("waiting for server 1 being up",
                ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP1, CONNECTION_TIMEOUT));
        Assert.assertTrue("waiting for server 2 being up",
                ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP2, CONNECTION_TIMEOUT));

        q1.shutdown();
        q2.shutdown();

        Assert.assertTrue("waiting for server 1 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP1, ClientBase.CONNECTION_TIMEOUT));
        Assert.assertTrue("waiting for server 2 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP2, ClientBase.CONNECTION_TIMEOUT));

    } finally {
        zlogger.removeAppender(appender);
    }
    os.close();
    LineNumberReader r = new LineNumberReader(new StringReader(os.toString()));
    String line;
    boolean found = false;
    Pattern p = Pattern.compile(".*FastLeaderElection.*");
    while ((line = r.readLine()) != null) {
        found = p.matcher(line).matches();
        if (found) {
            break;
        }
    }
    Assert.assertTrue("fastleaderelection used", found);
}

From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java

/**
 * Verify boot fails with a MetricsProvider with fails to start
 *//*  www  .  j  a  v  a  2  s.  co  m*/
@Test
public void testFaultyMetricsProviderOnStart() throws Exception {
    ClientBase.setupTestEnv();

    // setup the logger to capture all logs
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    WriterAppender appender = getConsoleAppender(os, Level.WARN);
    Logger qlogger = Logger.getLogger("org.apache.zookeeper.server.quorum");
    qlogger.addAppender(appender);

    try {
        final int CLIENT_PORT_QP1 = PortAssignment.unique();

        String quorumCfgSection = "server.1=127.0.0.1:" + PortAssignment.unique() + ":"
                + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n" + "server.2=127.0.0.1:"
                + PortAssignment.unique() + ":" + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n"
                + "metricsProvider.className="
                + BaseTestMetricsProvider.MetricsProviderWithErrorInStart.class.getName() + "\n";

        MainThread q1 = new MainThread(1, CLIENT_PORT_QP1, quorumCfgSection);
        q1.start();

        boolean isup = ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP1, 5000);

        Assert.assertFalse("Server never came up", isup);

        q1.shutdown();

        Assert.assertTrue("waiting for server 1 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP1, ClientBase.CONNECTION_TIMEOUT));

    } finally {
        qlogger.removeAppender(appender);
    }

    LineNumberReader r = new LineNumberReader(new StringReader(os.toString()));
    String line;
    boolean found = false;
    Pattern p = Pattern.compile(".*MetricsProviderLifeCycleException.*");
    while ((line = r.readLine()) != null) {
        found = p.matcher(line).matches();
        if (found) {
            break;
        }
    }
    Assert.assertTrue("complains about metrics provider MetricsProviderLifeCycleException", found);
}

From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java

/**
 * Verify boot fails with a MetricsProvider with fails to start
 */// ww w. j  a  v a 2s.c  o  m
@Test
public void testFaultyMetricsProviderOnConfigure() throws Exception {
    ClientBase.setupTestEnv();

    // setup the logger to capture all logs
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    WriterAppender appender = getConsoleAppender(os, Level.WARN);
    Logger qlogger = Logger.getLogger("org.apache.zookeeper.server.quorum");
    qlogger.addAppender(appender);

    try {
        final int CLIENT_PORT_QP1 = PortAssignment.unique();

        String quorumCfgSection = "server.1=127.0.0.1:" + PortAssignment.unique() + ":"
                + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n" + "server.2=127.0.0.1:"
                + PortAssignment.unique() + ":" + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n"
                + "metricsProvider.className="
                + BaseTestMetricsProvider.MetricsProviderWithErrorInConfigure.class.getName() + "\n";

        MainThread q1 = new MainThread(1, CLIENT_PORT_QP1, quorumCfgSection);
        q1.start();

        boolean isup = ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP1, 5000);

        Assert.assertFalse("Server never came up", isup);

        q1.shutdown();

        Assert.assertTrue("waiting for server 1 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP1, ClientBase.CONNECTION_TIMEOUT));

    } finally {
        qlogger.removeAppender(appender);
    }

    LineNumberReader r = new LineNumberReader(new StringReader(os.toString()));
    String line;
    boolean found = false;
    Pattern p = Pattern.compile(".*MetricsProviderLifeCycleException.*");
    while ((line = r.readLine()) != null) {
        found = p.matcher(line).matches();
        if (found) {
            break;
        }
    }
    Assert.assertTrue("complains about metrics provider MetricsProviderLifeCycleException", found);
}

From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java

/**
 * Test verifies that the server shouldn't be affected but runtime errors on stop()
 *//*from www .j a  v  a 2  s .  c o  m*/
@Test
public void testFaultyMetricsProviderOnStop() throws Exception {
    ClientBase.setupTestEnv();
    BaseTestMetricsProvider.MetricsProviderCapturingLifecycle.reset();

    // setup the logger to capture all logs
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    WriterAppender appender = getConsoleAppender(os, Level.WARN);
    Logger qlogger = Logger.getLogger("org.apache.zookeeper.server.quorum");
    qlogger.addAppender(appender);

    try {
        final int CLIENT_PORT_QP1 = PortAssignment.unique();
        final int CLIENT_PORT_QP2 = PortAssignment.unique();

        String quorumCfgSectionServer = "server.1=127.0.0.1:" + PortAssignment.unique() + ":"
                + PortAssignment.unique() + ";" + CLIENT_PORT_QP1 + "\n" + "server.2=127.0.0.1:"
                + PortAssignment.unique() + ":" + PortAssignment.unique() + ";" + CLIENT_PORT_QP2 + "\n";

        // server 1 boots with a MetricsProvider
        String quorumCfgSectionServer1 = quorumCfgSectionServer + "metricsProvider.className="
                + BaseTestMetricsProvider.MetricsProviderWithErrorInStop.class.getName() + "\n";

        MainThread q1 = new MainThread(1, CLIENT_PORT_QP1, quorumCfgSectionServer1);
        MainThread q2 = new MainThread(2, CLIENT_PORT_QP2, quorumCfgSectionServer);
        q1.start();
        q2.start();

        boolean isup1 = ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP1, 30000);
        boolean isup2 = ClientBase.waitForServerUp("127.0.0.1:" + CLIENT_PORT_QP2, 30000);
        Assert.assertTrue("Server 1 never came up", isup1);
        Assert.assertTrue("Server 2 never came up", isup2);

        q1.shutdown();
        q2.shutdown();

        Assert.assertTrue("waiting for server 1 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP1, ClientBase.CONNECTION_TIMEOUT));

        Assert.assertTrue("waiting for server 2 down",
                ClientBase.waitForServerDown("127.0.0.1:" + CLIENT_PORT_QP2, ClientBase.CONNECTION_TIMEOUT));
    } finally {
        qlogger.removeAppender(appender);
    }

    Assert.assertTrue("metrics provider lifecycle error",
            BaseTestMetricsProvider.MetricsProviderWithErrorInStop.stopCalled.get());

    LineNumberReader r = new LineNumberReader(new StringReader(os.toString()));
    String line;
    boolean found = false;
    Pattern p = Pattern.compile(".*Error while stopping metrics.*");
    while ((line = r.readLine()) != null) {
        found = p.matcher(line).matches();
        if (found) {
            break;
        }
    }
    Assert.assertTrue("complains about metrics provider", found);
}