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

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:org.jcvi.ometa.engine.LoadingEngine.java

public void batchLoad() throws Exception {
    String userName = usage.getUsername();
    String passWord = usage.getPassword();
    String serverUrl = usage.getServerUrl();

    String eventFileName = usage.getInputFilename();
    String eventName = usage.getEventName();
    String projectName = usage.getProjectName();
    String outputPath = usage.getOutputLocation();

    int batchSizeInt = 1;
    String batchSize = usage.getBatchSize();
    if (batchSize != null && !batchSize.isEmpty()) {
        batchSizeInt = Integer.parseInt(batchSize);
    }//w ww .j a v  a2 s . c  o m

    File eventFile = new File(eventFileName);

    Long timeStamp = new Date().getTime();
    File logFile = new File(outputPath + File.separator + "ometa.log");
    FileWriter logWriter = new FileWriter(logFile, false);

    int successCount = 0;
    File processedFile = new File(outputPath + File.separator + "ometa_processed.csv");
    FileWriter processedWriter = new FileWriter(processedFile, false);
    int failedCount = 0;
    File failedFile = new File(outputPath + File.separator + "ometa_failed.csv");
    FileWriter failedWriter = new FileWriter(failedFile, false);

    // Must break this file up, and deposit it into a temporary output directory.
    String userBase = System.getProperty("user.home");
    ScratchUtils.setScratchBaseLocation(userBase + "/" + Constants.SCRATCH_BASE_LOCATION);
    File scratchLoc = ScratchUtils.getScratchLocation(timeStamp, "LoadingEngine__" + eventFile.getName());

    int processedLineCount = 0;
    try {
        BeanWriter writer = new BeanWriter(serverUrl, userName, passWord);

        LineIterator lineIterator = FileUtils.lineIterator(eventFile);
        int lineCount = 0;

        String headerLine = null;
        while (lineIterator.hasNext()) {
            ++lineCount;
            String currLine = lineIterator.nextLine();

            if (lineCount == 1) {
                headerLine = currLine;
                processedWriter.write(currLine + "\n");
                failedWriter.write(currLine + "\n");
                continue;
            } else if (lineCount == 2 && (currLine.startsWith("#") || currLine.startsWith("\"#"))) { //skip comment line
                continue;
            } else {
                File singleEventFile = new File(scratchLoc.getAbsoluteFile() + File.separator + "temp.csv");
                List<String> lines = new ArrayList<String>(2);
                lines.add(headerLine);
                lines.add(currLine);
                FileUtils.writeLines(singleEventFile, lines);

                try {
                    String eventTarget = writer.writeEvent(singleEventFile, eventName, projectName, true);
                    logWriter.write(String.format("[%d] loaded event for %s\n", lineCount, eventTarget));
                    processedWriter.write(currLine + "\n");
                    successCount++;
                } catch (Exception ex) {
                    failedWriter.write(currLine + "\n");
                    logWriter.write(String.format("[%d] failed :\n", lineCount));
                    logWriter.write(ex.getMessage() + "\n");
                    failedCount++;
                }
                processedLineCount++;
            }
        }
    } catch (IOException ioe) {
        System.err.println("IOException: " + ioe.getMessage());
    } catch (Exception ex) {
        String exceptionString = ex.getCause() == null ? ex.getMessage() : ex.getCause().getMessage();
        logWriter.write(exceptionString);
        throw ex;
    } finally {
        if (scratchLoc != null && scratchLoc.exists()) {
            File cleanupDir = scratchLoc;
            String parentDirName = cleanupDir.getParentFile().getName();
            try {
                Long.parseLong(parentDirName);
                cleanupDir = cleanupDir.getParentFile();
            } catch (NumberFormatException nf) {
            }
            FileUtils.forceDelete(cleanupDir);
        }

        logWriter.close();
        processedWriter.close();
        failedWriter.close();
        System.out.printf("total: %d, processed: %d, failed: %d\n", processedLineCount, successCount,
                failedCount);
        System.out.println("log file: " + logFile.getAbsolutePath());
    }
}

---

From source file:org.jdev.emg.sonar.cci.CCIXmlMetricsDecorator.java

@Override
public void decorate(Resource resource, DecoratorContext context) {
    if (!Qualifiers.isFile(resource)) {
        return;/*from w w w  .j  a  va  2s  .c om*/
    }
    ProjectFileSystem fileSystem = context.getProject().getFileSystem();
    File file = lookup(resource, fileSystem);

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

    int numCommentLines;
    CCICountCommentParser commentCounter = new CCICountCommentParser();
    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.jenkinsci.plugins.autozoil.AutozoilSource.java

private void copyLineWithHighlightedContext(final StringBuilder output, final LineIterator lineIterator,
        String color, List<AutozoilFile> autozoilFiles) {
    String line = lineIterator.nextLine();

    for (AutozoilFile autozoilFile : autozoilFiles) {
        String substringToSearch = autozoilFile.getContext();
        if (substringToSearch == null)
            continue;

        // It should escape all HTML-specific characters
        substringToSearch = substringToSearch.replaceAll(" ", "&nbsp;");

        //FIXME: substring is not found if it contains Polish diacritical signs
        int pos = line.indexOf(substringToSearch);
        if (pos == -1)
            continue;

        line = line.substring(0, pos) + "<span style=\"color:#fff; padding:3px 3px 4px; background-color:"
                + color + "\">" + line.substring(pos, pos + substringToSearch.length()) + "</span>"
                + line.substring(pos + substringToSearch.length());
    }//from   www .  j av  a 2  s . c  om

    output.append(line);
    output.append("\n");
}

---

From source file:org.jibenakka.sample.mapreduce.wordcount.worker.Mapper.java

/**
 *
 * @param work//from   ww  w  .java 2  s . c  o m
 */
protected void extractFileMapResult(InitialMapWork work) {
    LinkedList<Future<Map<String, Integer>>> futureResults = new LinkedList<Future<Map<String, Integer>>>();
    LineIterator lineIterator = null;
    try {
        File fileToCount = work.getFileToCount();
        lineIterator = FileUtils.lineIterator(fileToCount);

        while (lineIterator.hasNext()) {
            // All work including special character handling done at worker
            // level
            String line = lineIterator.nextLine();
            // key is just the file name - initial mapping is easy
            // hard part comes with partitioning and reduction
            // we assume that we have unique file names in the dir
            MapWork newWork = new MapWork(fileToCount.getName(), line);

            Future<Map<String, Integer>> future = this.workRouter.sendRequestReplyFuture(newWork, 30000,
                    getContext());
            future.await();
            futureResults.add(future);
        }

        // FinalMapResult result = new FinalMapResult(
        // (LinkedList<Future<Map<String, Integer>>>) futureResults);
        getContext().channel().sendOneWay(futureResults);
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        if (lineIterator != null) {
            lineIterator.close();
        }
    }
}

---

From source file:org.kalypso.model.wspm.tuhh.schema.simulation.LengthSectionParser.java

private IStatus processLSFile(final String header, final String footer, final LogHelper log)
        throws FileNotFoundException, IOException {
    final Collection<IStatus> result = new ArrayList<>();
    final WspmWaterBody waterBody = m_calculation.getReach().getWaterBody();
    final TuhhStationComparator stationComparator = new TuhhStationComparator(waterBody.isDirectionUpstreams());

    LineIterator lineIterator = null;

    ResultLengthSection lsProc = null;/*  w w w . j av a 2 s. co  m*/
    try {
        lineIterator = IOUtils.lineIterator(new FileInputStream(m_lsFile),
                IWspmTuhhConstants.WSPMTUHH_CODEPAGE);

        BigDecimal firstStation = null; // station of previous line
        while (lineIterator.hasNext()) {
            if (log.checkCanceled())
                return Status.CANCEL_STATUS;

            final String nextLine = lineIterator.nextLine();

            /* Introduce space around 'NaN' and '***' values to make it parseable */

            if (nextLine.contains("NaN")) //$NON-NLS-1$
                log.log(false, Messages.getString("LengthSectionParser.0")); //$NON-NLS-1$

            // TODO: handle NaN-values to keep information alive (unfortunally BigDecimal throws a NumberFormatException)
            final String cleanLine1 = nextLine.replaceAll("-NaN", " null "); //$NON-NLS-1$ //$NON-NLS-2$
            final String cleanLine2 = cleanLine1.replaceAll("NaN", " null "); //$NON-NLS-1$ //$NON-NLS-2$
            final String cleanLine3 = cleanLine2.replaceAll("-999.999", " null "); //$NON-NLS-1$ //$NON-NLS-2$

            final BigDecimal station = NumberUtils.parseQuietDecimal(cleanLine3, 0, 11,
                    IWspmTuhhConstants.STATION_SCALE);
            final BigDecimal runoff = NumberUtils.parseQuietDecimal(cleanLine3, 17, 27, 3);

            /* Any lines where station or runoff cannot be parsed are filtered out */
            if (Objects.isNull(station, runoff))
                continue;

            /* A new section begins, if the new station is lower than the next station */
            final boolean sectionEnd = firstStation == null
                    || stationComparator.compare(firstStation, station) == 0;

            if (sectionEnd) {
                if (lsProc != null) {
                    final IStatus processorResult = closeProcessor(lsProc, footer);
                    if (!processorResult.isOK())
                        result.add(processorResult);
                }

                log.log(false, Messages.getString(
                        "org.kalypso.model.wspm.tuhh.schema.simulation.LengthSectionParser.2"), runoff); //$NON-NLS-1$
                lsProc = new ResultLengthSection(runoff, m_outputDir, m_calculation, m_epsThinning,
                        m_ovwMapURL);
                lsProc.addLine(header);

                lsProc.setTitlePattern(m_titlePattern);
                lsProc.setLsFilePattern(m_lsFilePattern);
            }

            /* clean line */
            lsProc.addLine(cleanLine3);

            if (firstStation == null)
                firstStation = station;
        }

        if (lsProc != null) {
            final IStatus processorResult = closeProcessor(lsProc, footer);
            if (!processorResult.isOK())
                result.add(processorResult);
        }
    } finally {
        LineIterator.closeQuietly(lineIterator);
    }

    if (result.isEmpty())
        return Status.OK_STATUS;

    final IStatus[] children = result.toArray(new IStatus[result.size()]);
    final String msg = String.format(Messages.getString("LengthSectionParser.1")); //$NON-NLS-1$
    return new MultiStatus(KalypsoModelWspmTuhhSchemaPlugin.getID(), 0, children, msg, null);
}

---

From source file:org.kalypso.wspwin.core.CalculationBean.java

public static CalculationBean[] readBerFile(final File berFile) throws ParseException, IOException {
    // if a zustand has no calculations, no .ber file is present.
    if (!berFile.exists())
        return new CalculationBean[0];

    final List<CalculationBean> beans = new ArrayList<>(10);

    LineIterator lineIt = null;
    try {/*from w w  w .j a va  2 s  .c om*/
        int count = 0;
        lineIt = FileUtils.lineIterator(berFile, "CP850"); //$NON-NLS-1$

        // ignore first line, we just read all lines
        lineIt.nextLine();
        count++;

        while (lineIt.hasNext()) {
            final String line = lineIt.nextLine();
            count++;

            if (line.length() < 60)
                throw new ParseException(Messages.getString("org.kalypso.wspwin.core.CalculationBean.0") + line, //$NON-NLS-1$
                        count);

            final String name = line.substring(0, 60).trim();

            final StringTokenizer tokenizer = new StringTokenizer(line.substring(60));

            if (tokenizer.countTokens() != 3)
                throw new ParseException(Messages.getString("org.kalypso.wspwin.core.CalculationBean.1") + line, //$NON-NLS-1$
                        count);

            final BigDecimal fromStation = new BigDecimal(tokenizer.nextToken());
            final BigDecimal toStation = new BigDecimal(tokenizer.nextToken());
            final String fileName = tokenizer.nextToken();

            beans.add(new CalculationBean(name, fileName, fromStation, toStation));
        }

        return beans.toArray(new CalculationBean[beans.size()]);
    } finally {
        LineIterator.closeQuietly(lineIt);
    }
}

---

From source file:org.kalypso.wspwin.core.LocalEnergyLossBean.java

/**
 * Reads a psi file (Energieverluste/Verlustbeiwerte/local energy losses)
 *///from w w  w. ja va  2 s . c o m
public static LocalEnergyLossBean[] read(final File lelFile) throws ParseException, IOException {
    final List<LocalEnergyLossBean> beans = new ArrayList<>(0);

    LineIterator lineIt = null;
    try {
        if (lelFile.exists()) {
            int count = 0;
            for (lineIt = FileUtils.lineIterator(lelFile, null); lineIt.hasNext();) {
                final String nextLine = lineIt.nextLine();
                count++;

                final StringTokenizer tokenizer = new StringTokenizer(nextLine);
                if (tokenizer.countTokens() % 2 != 0)
                    throw new ParseException(
                            Messages.getString("org.kalypso.wspwin.core.LocalEnergyLossBean.1") + nextLine, //$NON-NLS-1$
                            count);

                final int countKinds = tokenizer.countTokens() / 2 - 1;

                final String key = tokenizer.nextToken();

                if (!STATION.equalsIgnoreCase(key))
                    throw new ParseException(Messages.getString("org.kalypso.wspwin.core.LocalEnergyLossBean.2") //$NON-NLS-1$
                            + STATION + "': " + nextLine, count); //$NON-NLS-1$

                final BigDecimal station = new BigDecimal(tokenizer.nextToken());

                // read pairs: kind -> value
                final Collection<Pair<String, BigDecimal>> entries = new ArrayList<>();
                for (int i = 0; i < countKinds; i++) {
                    final String kind = tokenizer.nextToken();
                    final BigDecimal value = new BigDecimal(tokenizer.nextToken());
                    entries.add(Pair.of(kind, value));
                }

                final LocalEnergyLossBean lossBean = new LocalEnergyLossBean(station,
                        entries.toArray(new Pair[entries.size()]));
                beans.add(lossBean);
            }
        }
        return beans.toArray(new LocalEnergyLossBean[beans.size()]);
    } finally {
        LineIterator.closeQuietly(lineIt);
    }
}

---

From source file:org.kalypso.wspwin.core.RunOffEventBean.java

/** Reads a qwt or wsf file */
public static RunOffEventBean[] read(final File qwtFile) throws ParseException, IOException {
    // the qwt and wsf files may not exist; return empty list of beans
    if (!qwtFile.exists())
        return new RunOffEventBean[] {};

    final List<RunOffEventBean> beans = new ArrayList<>(10);

    LineIterator lineIt = null;
    try {/*from w ww.  j  av  a2s .c o m*/
        int count = 0;
        for (lineIt = FileUtils.lineIterator(qwtFile, null); lineIt.hasNext();) {
            final String nextLine = lineIt.nextLine().trim();
            count++;

            if (nextLine.isEmpty())
                continue;

            final StringTokenizer tokenizer = new StringTokenizer(nextLine);
            if (tokenizer.countTokens() != 2)
                throw new ParseException(
                        Messages.getString("org.kalypso.wspwin.core.RunOffEventBean.0") + nextLine, count); //$NON-NLS-1$

            final String eventName = tokenizer.nextToken();

            final RunOffEventBean bean = new RunOffEventBean(eventName);

            final int eventLength = Integer.parseInt(tokenizer.nextToken());

            // read block: station -> value
            for (int i = 0; i < eventLength; i++) {
                if (!lineIt.hasNext())
                    throw new ParseException(
                            Messages.getString("org.kalypso.wspwin.core.RunOffEventBean.1") + eventName, count); //$NON-NLS-1$

                final String line = lineIt.nextLine();
                count++;
                final StringTokenizer tz = new StringTokenizer(line);
                if (tz.countTokens() != 2)
                    throw new ParseException(
                            Messages.getString("org.kalypso.wspwin.core.RunOffEventBean.2") + nextLine, count); //$NON-NLS-1$

                final double station = Double.parseDouble(tz.nextToken());
                final double value = Double.parseDouble(tz.nextToken());
                bean.addEntry(BigDecimal.valueOf(station), BigDecimal.valueOf(value));
            }

            beans.add(bean);
        }

        return beans.toArray(new RunOffEventBean[beans.size()]);
    } finally {
        LineIterator.closeQuietly(lineIt);
    }
}

---

From source file:org.klab.com.etl.Movies.java

public void readFile(String file, BufferedWriter bw) {
    int _n_ = 0;/*from w  ww.j  a  v  a 2  s .  co  m*/
    int _r_ = 0;
    LineIterator it = null;
    String FILE_DATE = movieFileDate(file);
    try {
        it = FileUtils.lineIterator(new File(file), "UTF-8");
        while (it.hasNext()) {
            String line = it.nextLine();

            int amountOfTabsLine = StringUtils.countMatches(line, SEPARATOR);
            //This will decide the structure
            String fixedLine = fixLine(line);
            // do something with line
            // System.out.println("N:\t"+amountOfTabsLine+ "\t"+line);
            if (!fixedLine.isEmpty() && _n_ > 0) {
                String output = _n_ + "\t" + FILE_DATE + "\t" + amountOfTabsLine + "\t" + fixedLine;
                bw.write(output);
                bw.newLine();
                _r_++;
            }

            _n_++;
        }

    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();

    } finally {
        System.out.println("io > [" + _n_ + "][" + _r_ + "] > out");
        LineIterator.closeQuietly(it);
    }
}

---

From source file:org.klab.com.etl.Movies.java

public void readinHeader(File file) {
    LineIterator it = null;
    try {//from  www . j av a  2s.  c o  m
        it = FileUtils.lineIterator(file, "UTF-8");
        if (it.hasNext()) {
            String line = it.nextLine();
            getHeaderStructure(line);
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();

    } finally {
        LineIterator.closeQuietly(it);
    }
}

---

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