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:org.seqdoop.hadoop_bam.TestVCFOutputFormat.java

@Test
public void testSimple() throws Exception {
    VariantContextBuilder vctx_builder = new VariantContextBuilder();

    ArrayList<Allele> alleles = new ArrayList<Allele>();
    alleles.add(Allele.create("A", false));
    alleles.add(Allele.create("C", true));
    vctx_builder.alleles(alleles);/*from   w  ww .j  a  v a 2s. co  m*/

    GenotypesContext genotypes = GenotypesContext.NO_GENOTYPES;
    vctx_builder.genotypes(genotypes);

    HashSet<String> filters = new HashSet<String>();
    vctx_builder.filters(filters);

    HashMap<String, Object> attributes = new HashMap<String, Object>();
    attributes.put("NS", new Integer(4));
    vctx_builder.attributes(attributes);

    vctx_builder.loc("20", 2, 2);
    vctx_builder.log10PError(-8.0);

    String[] expected = new String[] { "20", "2", ".", "C", "A", "80", "PASS", "NS=4" };

    VariantContext ctx = vctx_builder.make();
    writable.set(ctx);
    writer.write(1L, writable);
    writer.close(taskAttemptContext);

    LineNumberReader reader = new LineNumberReader(new FileReader(test_vcf_output));
    skipHeader(reader);
    String[] fields = Arrays.copyOf(reader.readLine().split("\t"), expected.length);
    Assert.assertArrayEquals("comparing VCF single line", expected, fields);
}

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From source file:ch.cyberduck.core.i18n.RegexLocale.java

private void load(final String table, final File file) throws IOException {
    final LineNumberReader reader = new LineNumberReader(
            new InputStreamReader(new FileInputStream(file), Charset.forName("UTF-16")));
    try {/* www .j a  v a2  s .  c  om*/
        String line;
        while ((line = reader.readLine()) != null) {
            final Matcher matcher = pattern.matcher(line);
            if (matcher.matches()) {
                cache.put(new Key(table, matcher.group(1)), matcher.group(2));
            }
        }
    } finally {
        IOUtils.closeQuietly(reader);
    }
}

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From source file:org.apache.qpid.amqp_1_0.client.Send.java

public void run() {

    final String queue = getArgs()[0];

    String message = "";

    try {//from ww  w.  jav  a2 s  .  c o  m
        Connection conn = newConnection();

        Session session = conn.createSession();

        Sender s = session.createSender(queue, getWindowSize(), getMode(), getLinkName());

        Transaction txn = null;

        if (useTran()) {
            txn = session.createSessionLocalTransaction();
        }

        if (!useStdIn()) {
            if (getArgs().length <= 2) {
                if (getArgs().length == 2) {
                    message = getArgs()[1];
                }
                for (int i = 0; i < getCount(); i++) {

                    Properties properties = new Properties();
                    properties.setMessageId(UnsignedLong.valueOf(i));
                    if (getSubject() != null) {
                        properties.setSubject(getSubject());
                    }
                    Section bodySection;
                    byte[] bytes = (message + "  " + i).getBytes();
                    if (bytes.length < getMessageSize()) {
                        byte[] origBytes = bytes;
                        bytes = new byte[getMessageSize()];
                        System.arraycopy(origBytes, 0, bytes, 0, origBytes.length);
                        for (int x = origBytes.length; x < bytes.length; x++) {
                            bytes[x] = (byte) '.';
                        }
                        bodySection = new Data(new Binary(bytes));
                    } else {
                        bodySection = new AmqpValue(message + " " + i);
                    }

                    Section[] sections = { properties, bodySection };
                    final Message message1 = new Message(Arrays.asList(sections));

                    s.send(message1, txn);
                }
            } else {
                for (int i = 1; i < getArgs().length; i++) {
                    s.send(new Message(getArgs()[i]), txn);
                }

            }
        } else {
            LineNumberReader buf = new LineNumberReader(new InputStreamReader(System.in));

            try {
                while ((message = buf.readLine()) != null) {
                    s.send(new Message(message), txn);
                }
            } catch (IOException e) {
                // TODO
                e.printStackTrace();
            }
        }

        if (txn != null) {
            txn.commit();
        }

        s.close();

        session.close();
        conn.close();
    } catch (Sender.SenderClosingException e) {
        e.printStackTrace(); //TODO.
    } catch (Connection.ConnectionException e) {
        e.printStackTrace(); //TODO.
    } catch (Sender.SenderCreationException e) {
        e.printStackTrace(); //TODO.
    }

}

---

From source file:net.sf.ginp.tags.GetFolderInfo.java

/**
 *  Called when a Start tag is processed.
 *
 *@return                   Description of the Return Value
 *@exception  JspException  Description of the Exception
 *///from w w  w .j  av a  2 s. co  m
public final int doStartTag() throws JspException {
    String title = "";
    String description = "";
    String date = "";
    String time = "";

    try {
        model = ModelUtil.getModel((HttpServletRequest) pageContext.getRequest());
    } catch (Exception e) {
        throw new JspException(e);
    }

    try {
        File fl = new File(
                model.getCollection().getRoot() + model.getCollection().getPath() + "ginpfolder.xml");

        if (fl.exists()) {
            FileReader fr = new FileReader(fl);
            LineNumberReader lr = new LineNumberReader(fr);
            StringBuffer sb = new StringBuffer();
            String temp;

            while ((temp = lr.readLine()) != null) {
                sb.append(temp + "\n");
            }

            // Date
            date = StringTool.getXMLTagContent("date", sb.toString());

            if (date != null) {
                pageContext.setAttribute("date", date);
            } else {
                pageContext.setAttribute("date", "");
            }

            // Time
            time = StringTool.getXMLTagContent("time", sb.toString());

            if (time != null) {
                pageContext.setAttribute("time", time);
            } else {
                pageContext.setAttribute("time", "");
            }

            // Title
            temp = StringTool.getXMLTagContent("title", sb.toString());
            title = StringTool.getXMLTagContent(model.getLocale().getLanguage(), temp);

            if (title != null) {
                pageContext.setAttribute("title", title);
            } else {
                pageContext.setAttribute("title", "");
            }

            // description
            temp = StringTool.getXMLTagContent("description", sb.toString());
            description = StringTool.getXMLTagContent(model.getLocale().getLanguage(), temp);

            if (description != null) {
                pageContext.setAttribute("description", description);
            } else {
                pageContext.setAttribute("description", "");
            }

            pageContext.setAttribute("path", model.getCollection().getPath());
            pageContext.setAttribute("colid", "" + model.getCurrCollectionId());
            pageContext.setAttribute("langcode", "" + model.getLocale().getLanguage());

            return EVAL_BODY_AGAIN;
        } else {
            return SKIP_BODY;
        }
    } catch (Exception ex) {
        return SKIP_BODY;
    }
}

---

From source file:com.thoughtworks.go.server.database.MigrateHsqldbToH2.java

private void replayScript(File scriptFile) throws SQLException, IOException {
    if (!scriptFile.exists()) {
        return;/*from  ww w .  j av a 2  s  .  com*/
    }

    System.out.println("Migrating hsql file: " + scriptFile.getName());
    Connection con = source.getConnection();
    Statement stmt = con.createStatement();
    stmt.executeUpdate("SET REFERENTIAL_INTEGRITY FALSE");
    LineNumberReader reader = new LineNumberReader(new FileReader(scriptFile));
    String line;
    while ((line = reader.readLine()) != null) {
        try {
            String table = null;
            Matcher matcher = createTable.matcher(line);
            if (matcher.find()) {
                table = matcher.group(2).trim();
            }

            if (line.equals("CREATE SCHEMA PUBLIC AUTHORIZATION DBA")) {
                continue;
            }
            if (line.equals("CREATE SCHEMA CRUISE AUTHORIZATION DBA")) {
                continue;
            }
            if (line.startsWith("CREATE USER SA PASSWORD")) {
                continue;
            }
            if (line.contains("BUILDEVENT VARCHAR(255)")) {
                line = line.replace("BUILDEVENT VARCHAR(255)", "BUILDEVENT LONGVARCHAR");
            }
            if (line.contains("COMMENT VARCHAR(4000)")) {
                line = line.replace("COMMENT VARCHAR(4000)", "COMMENT LONGVARCHAR");
            }
            if (line.contains("CREATE MEMORY TABLE")) {
                line = line.replace("CREATE MEMORY TABLE", "CREATE CACHED TABLE");
            }
            if (table != null && table.equals("MATERIALPROPERTIES") && line.contains("VALUE VARCHAR(255),")) {
                line = line.replace("VALUE VARCHAR(255),", "VALUE LONGVARCHAR,");
            }
            if (line.startsWith("GRANT DBA TO SA")) {
                continue;
            }
            if (line.startsWith("CONNECT USER")) {
                continue;
            }
            if (line.contains("DISCONNECT")) {
                continue;
            }
            if (line.contains("AUTOCOMMIT")) {
                continue;
            }
            stmt.executeUpdate(line);
            if (reader.getLineNumber() % LINES_PER_DOT == 0) {
                System.out.print(".");
                System.out.flush();
            }
            if (reader.getLineNumber() % (80 * LINES_PER_DOT) == 0) {
                System.out.println();
            }

        } catch (SQLException e) {
            bomb("Error executing : " + line, e);
        }
    }
    stmt.executeUpdate("SET REFERENTIAL_INTEGRITY TRUE");
    stmt.executeUpdate("CHECKPOINT SYNC");
    System.out.println("\nDone.");
    reader.close();
    stmt.close();
    con.close();
}

---

From source file:org.openanzo.jdbc.opgen.ant.DDLTask.java

private void writeFile(Writer writer, String filename, String file, String outputFormat)
        throws FileNotFoundException, IOException {
    Reader in = new InputStreamReader(new FileInputStream(file), "UTF-8");
    LineNumberReader lnr = new LineNumberReader(in);
    StringBuilder content = new StringBuilder();
    String line;//w  ww. j av a 2s  .co m
    while ((line = lnr.readLine()) != null) {
        line = StringUtils.trim(line);
        if (line.length() == 0 || line.startsWith("#"))
            continue;
        line = Pattern.compile("[\\s+]", Pattern.MULTILINE).matcher(line).replaceAll(" ");
        line = Pattern.compile(";+", Pattern.MULTILINE).matcher(line).replaceAll(";;");
        line = Pattern.compile("&sc", Pattern.MULTILINE).matcher(line).replaceAll(";");
        line = Pattern.compile("&plus", Pattern.MULTILINE).matcher(line).replaceAll("+");
        content.append(line);
        content.append(" ");
    }
    writer.write(content.toString());
    in.close();
    lnr.close();
}

---

From source file:com.sg2net.utilities.ListaCAP.ListaComuniCapFromInternet.java

public Collection<Comune> donwloadAndParse() {
    try {/*from   w ww .  java  2 s.c  o  m*/
        List<Comune> comuni = new ArrayList<>();
        HttpClient httpclient = new DefaultHttpClient();
        HttpGet httpget = new HttpGet(ZIP_URL);
        HttpResponse response = httpclient.execute(httpget);
        HttpEntity entity = response.getEntity();
        if (entity != null) {
            try (InputStream instream = entity.getContent();) {
                ZipInputStream zipInputStream = new ZipInputStream(instream);
                ZipEntry entry = zipInputStream.getNextEntry();

                if (entry != null) {
                    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
                    byte data[] = new byte[BUFFER];
                    int count = 0;
                    while ((count = zipInputStream.read(data, 0, BUFFER)) != -1) {
                        outputStream.write(data, 0, count);
                    }
                    StringReader reader = new StringReader(
                            new String(outputStream.toByteArray(), HTML_ENCODING));
                    LineNumberReader lineReader = new LineNumberReader(reader);
                    String line;
                    int lineNumber = 0;
                    while ((line = lineReader.readLine()) != null) {
                        logger.trace("line " + (lineNumber + 1) + " from zip file=" + line);
                        if (lineNumber > 0) {
                            String[] values = line.split(";");
                            if (values.length >= 9) {
                                Comune comune = new Comune(values[CODICE_ISTAT_POS],
                                        values[CODICE_CATASTALE_POS], values[NOME_POS], values[PROVINCIA_POS]);
                                comuni.add(comune);
                                String capStr = values[CAP_POS];
                                Collection<String> capList;
                                if (capStr.endsWith("x")) {
                                    capList = getListaCAPFromHTMLPage(values[URL_COMUNE_POS]);
                                } else {
                                    capList = new HashSet<>();
                                    capList.add(capStr);
                                }
                                comune.setCodiciCap(capList);
                            }
                        }
                        lineNumber++;
                    }
                }
            }
        }
        return comuni;
    } catch (IOException e) {
        logger.error(e.getMessage(), e);
        throw new RuntimeException(e.getMessage(), e);
    }
}

---

From source file:nl.b3p.viewer.util.databaseupdate.ScriptRunner.java

/**
 * Runs an SQL script (read in using the Reader parameter) using the
 * connection passed in//from ww w . j av a2 s . com
 *
 * @param conn - the connection to use for the script
 * @param reader - the source of the script
 * @throws SQLException if any SQL errors occur
 * @throws IOException if there is an error reading from the Reader
 */
private void runScript(Connection conn, Reader reader) throws IOException, SQLException {
    StringBuffer command = null;
    try {
        LineNumberReader lineReader = new LineNumberReader(reader);
        String line = null;
        while ((line = lineReader.readLine()) != null) {
            if (command == null) {
                command = new StringBuffer();
            }
            String trimmedLine = line.trim();
            if (trimmedLine.startsWith("--")) {
                log.debug(trimmedLine);
            } else if (trimmedLine.length() < 1 || trimmedLine.startsWith("//")) {
                // Do nothing
            } else if (trimmedLine.length() < 1 || trimmedLine.startsWith("--")) {
                // Do nothing
            } else if (!fullLineDelimiter && trimmedLine.endsWith(getDelimiter())
                    || fullLineDelimiter && trimmedLine.equals(getDelimiter())) {
                command.append(line.substring(0, line.lastIndexOf(getDelimiter())));
                command.append(" ");
                Statement statement = conn.createStatement();

                log.debug(command);

                boolean hasResults = false;
                if (stopOnError) {
                    hasResults = statement.execute(command.toString());
                } else {
                    try {
                        statement.execute(command.toString());
                    } catch (SQLException e) {
                        e.fillInStackTrace();
                        log.error("Error executing: " + command, e);
                    }
                }

                if (autoCommit && !conn.getAutoCommit()) {
                    conn.commit();
                }

                ResultSet rs = statement.getResultSet();
                if (hasResults && rs != null) {
                    ResultSetMetaData md = rs.getMetaData();
                    int cols = md.getColumnCount();
                    for (int i = 0; i < cols; i++) {
                        String name = md.getColumnLabel(i);
                        log.debug(name + "\t");
                    }
                    while (rs.next()) {
                        for (int i = 0; i < cols; i++) {
                            String value = rs.getString(i);
                            log.debug(value + "\t");
                        }
                    }
                }

                command = null;
                try {
                    statement.close();
                } catch (Exception e) {
                    // Ignore to workaround a bug in Jakarta DBCP
                }
                Thread.yield();
            } else {
                command.append(line);
                command.append(" ");
            }
        }
        if (!autoCommit) {
            conn.commit();
        }
    } catch (SQLException e) {
        e.fillInStackTrace();
        log.error("Error executing: " + command, e);
        throw e;
    } catch (IOException e) {
        e.fillInStackTrace();
        log.error("Error executing: " + command, e);
        throw e;
    } finally {
        if (!this.autoCommit) {
            conn.rollback();
        }
    }
}

---

From source file:com.liferay.portal.scripting.ScriptingImpl.java

protected String getErrorMessage(String script, Exception e) {
    StringBundler sb = new StringBundler();

    sb.append(getErrorMessage(e));/*from   ww w.  jav a  2s .com*/
    sb.append(StringPool.NEW_LINE);

    try {
        LineNumberReader lineNumberReader = new LineNumberReader(new UnsyncStringReader(script));

        while (true) {
            String line = lineNumberReader.readLine();

            if (line == null) {
                break;
            }

            sb.append("Line ");
            sb.append(lineNumberReader.getLineNumber());
            sb.append(": ");
            sb.append(line);
            sb.append(StringPool.NEW_LINE);
        }
    } catch (IOException ioe) {
        sb.setIndex(0);

        sb.append(getErrorMessage(e));
        sb.append(StringPool.NEW_LINE);
        sb.append(script);
    }

    return sb.toString();
}

---

From source file:mitm.common.security.ca.handlers.comodo.AutoAuthorize.java

private void handleResponse(int statusCode, HttpMethod httpMethod) throws IOException {
    if (statusCode != HttpStatus.SC_OK) {
        throw new IOException("Error Authorize. Message: " + httpMethod.getStatusLine());
    }//from   ww  w .j a  va 2s .co m

    InputStream input = httpMethod.getResponseBodyAsStream();

    if (input == null) {
        throw new IOException("Response body is null.");
    }

    /*
     * we want to set a max on the number of bytes to download. We do not want a rogue server to return 1GB.
     */
    InputStream limitInput = new SizeLimitedInputStream(input, MAX_HTTP_RESPONSE_SIZE);

    String response = IOUtils.toString(limitInput, CharEncoding.US_ASCII);

    if (logger.isDebugEnabled()) {
        logger.debug("Response:\r\n" + response);
    }

    LineNumberReader lineReader = new LineNumberReader(new StringReader(response));

    String statusParameter = lineReader.readLine();

    errorCode = CustomClientStatusCode.fromCode(statusParameter);

    if (errorCode.getID() < CustomClientStatusCode.SUCCESSFUL.getID()) {
        error = true;

        errorMessage = lineReader.readLine();
    } else {
        error = false;
    }
}

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