Example usage for org.apache.commons.io FilenameUtils getFullPath

List of usage examples for org.apache.commons.io FilenameUtils getFullPath

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Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils getFullPath.

Prototype

public static String getFullPath(String filename)

Source Link

Document

Gets the full path from a full filename, which is the prefix + path.

Usage

From source file:edu.cornell.med.icb.goby.modes.SplitTranscriptsMode.java

/**
 * Perform the split transcripts mode./*from w  w w  .  j  a va  2  s .  c  om*/
 *
 * @throws IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    // Load the gene to transcripts file
    if (!config.validate()) {
        throw new IOException("Invalid SplitTranscripts configuration");
    }
    final GeneTranscriptRelationships gtr = new GeneTranscriptRelationships();
    final IndexedIdentifier transcriptIdents = new IndexedIdentifier();
    final Int2ObjectMap<MutableString> transcriptIndexToIdMap = new Int2ObjectOpenHashMap<MutableString>();
    final List<FastXEntry> fastxEntries = new LinkedList<FastXEntry>();
    //
    // Pass through the file once to collect the transcript - gene relationships
    //
    int entryCount = 0;
    try {
        for (final FastXEntry entry : new FastXReader(config.getInputFile())) {
            entryCount++;
            parseHeader(entry.getEntryHeader());
            final MutableString transcriptId = transcriptHeader.get("transcriptId");
            final MutableString geneId = transcriptHeader.get("geneId");

            final int transcriptIndex = transcriptIdents.registerIdentifier(transcriptId);
            gtr.addRelationship(geneId, transcriptIndex);

            transcriptIndexToIdMap.put(transcriptIndex, transcriptId);

            fastxEntries.add(entry.clone());
        }
    } catch (CloneNotSupportedException e) {
        LOG.error("Couldn't clone for some reason", e);
        throw new GobyRuntimeException("Couldn't clone for some reason", e);
    }

    LOG.info("Loading map of genes-transcripts complete.");

    //
    // Scan through the transcript-gene relationships to determine which
    // transcript id goes into which file
    //
    final Int2IntMap transcriptIndex2FileIndex = new Int2IntOpenHashMap();
    final String configOutputFilename = config.getOutputBase() + ".config";
    final String configOutputPath = FilenameUtils.getFullPath(configOutputFilename);
    if (StringUtils.isNotBlank(configOutputPath)) {
        LOG.info("Creating output directory: " + configOutputPath);
        FileUtils.forceMkdir(new File(configOutputPath));
    }

    PrintWriter configOutput = null;
    try {
        configOutput = new PrintWriter(configOutputFilename);
        configOutput.println("Ensembl Gene ID\tEnsembl Transcript ID");

        final Int2IntMap fileIndex2NumberOfEntries = new Int2IntOpenHashMap();
        fileIndex2NumberOfEntries.defaultReturnValue(0);
        transcriptIndex2FileIndex.defaultReturnValue(-1);

        final int initialNumberOfFiles = getNumberOfFiles(gtr, transcriptIndex2FileIndex);

        for (int geneIndex = 0; geneIndex < gtr.getNumberOfGenes(); geneIndex++) {
            final MutableString geneId = gtr.getGeneId(geneIndex);
            final IntSet transcriptIndices = gtr.getTranscriptSet(geneIndex);
            int fileNum = 0;

            for (final int transcriptIndex : transcriptIndices) {
                if (transcriptIndex2FileIndex.get(transcriptIndex) != -1) {
                    LOG.warn("Skipping repeated transcriptIndex: " + transcriptIndex);
                    continue;
                }
                final int maxEntriesPerFile = config.getMaxEntriesPerFile();
                final int numberOfEntriesInOriginalBucket = fileIndex2NumberOfEntries.get(fileNum);
                final int adjustedFileIndex = fileNum
                        + initialNumberOfFiles * (numberOfEntriesInOriginalBucket / maxEntriesPerFile);

                transcriptIndex2FileIndex.put(transcriptIndex, adjustedFileIndex);
                fileIndex2NumberOfEntries.put(fileNum, fileIndex2NumberOfEntries.get(fileNum) + 1);
                final MutableString transcriptId = transcriptIndexToIdMap.get(transcriptIndex);
                configOutput.printf("%s\t%s%n", geneId, transcriptId);

                fileNum++;
            }
        }
    } finally {
        IOUtils.closeQuietly(configOutput);
    }

    final int numFiles = getFileIndices(transcriptIndex2FileIndex).size();
    if (LOG.isInfoEnabled()) {
        LOG.info(NumberFormat.getInstance().format(entryCount) + " entries will be written to " + numFiles
                + " files");
        final int maxEntriesPerFile = config.getMaxEntriesPerFile();
        if (maxEntriesPerFile < Integer.MAX_VALUE) {
            LOG.info("Each file will contain at most " + maxEntriesPerFile + " entries");
        }
    }

    // formatter for uniquely numbering files each with the same number of digits
    final NumberFormat fileNumberFormatter = getNumberFormatter(numFiles - 1);

    final ProgressLogger progressLogger = new ProgressLogger();
    progressLogger.expectedUpdates = entryCount;
    progressLogger.itemsName = "entries";
    progressLogger.start();

    // Write each file one at a time rather than in the order they appear in the input file
    // to avoid the issue of having too many streams open at the same or continually opening
    // and closing streams which is quite costly.  We could store the gene/transcripts in
    // memory and then just write the files at the end but that could be worse.
    for (final int fileIndex : getFileIndices(transcriptIndex2FileIndex)) {
        final String filename = config.getOutputBase() + "." + fileNumberFormatter.format(fileIndex) + ".fa.gz";
        PrintStream printStream = null;
        try {
            // each file is compressed
            printStream = new PrintStream(new GZIPOutputStream(new FileOutputStream(filename)));

            //
            // Read through the input file get the actual sequence information
            //
            final Iterator<FastXEntry> entries = fastxEntries.iterator();
            while (entries.hasNext()) {
                final FastXEntry entry = entries.next();
                parseHeader(entry.getEntryHeader());
                final MutableString transcriptId = transcriptHeader.get("transcriptId");
                final MutableString geneId = transcriptHeader.get("geneId");
                final int transcriptIndex = transcriptIdents.getInt(transcriptId);
                final int transcriptFileIndex = transcriptIndex2FileIndex.get(transcriptIndex);
                if (transcriptFileIndex == fileIndex) {
                    printStream.print(entry.getHeaderSymbol());
                    printStream.print(transcriptId);
                    printStream.print(" gene:");
                    printStream.println(geneId);
                    printStream.println(entry.getEntrySansHeader());
                    entries.remove();
                    progressLogger.lightUpdate();
                }
            }
        } finally {
            IOUtils.closeQuietly(printStream);
        }
    }

    assert progressLogger.count == entryCount : "Some entries were not processed!";
    progressLogger.done();
}

From source file:MSUmpire.PSMDataStructure.LCMSID.java

private static LCMSID FS_Read(String filepath, String tag) throws Exception {
    if (!tag.equals("")) {
        tag = "_" + tag;
    }//  w  w w.j a v a  2s  .  c  om
    if (!new File(
            FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS")
                    .exists()) {
        return null;
    }
    try {
        Logger.getRootLogger().info("Reading ID results from file:" + FilenameUtils.getFullPath(filepath)
                + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS...");

        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(filepath)
                + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        LCMSID lcmsid = (LCMSID) in.readObject(LCMSID.class);
        in.close();
        fileIn.close();
        return lcmsid;

    } catch (Exception ex) {
        Logger.getRootLogger().info("Reading LCMSID FS results failed.");
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return null;
    }
}

From source file:MSUmpire.PSMDataStructure.LCMSID.java

private boolean FSWrite(String filepath, String tag) {
    try {//from   w  w w  . j  a v a2s .  c  o  m
        if (!tag.equals("")) {
            tag = "_" + tag;
        }
        Logger.getRootLogger().info("Writing ID results to file:" + FilenameUtils.getFullPath(filepath)
                + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS...");
        FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(filepath)
                + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS", false);
        FSTObjectOutput out = new FSTObjectOutput(fout);
        ReduceMemoryUsage();
        out.writeObject(this, LCMSID.class);
        out.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}

From source file:au.com.redboxresearchdata.fascinator.harvester.MintJsonHarvester.java

private void appendToFullPathOfHarvestKeyValue(JsonObject harvest, String key, String appendage)
        throws HarvesterException {
    String currentValue = getHarvestKeyValue(harvest, key);
    // current rules config path may have been updated - ensure only the current path is used
    updateHarvestFileKeyValue(harvest, key, FilenameUtils.getFullPath(currentValue), appendage);
}

From source file:eu.mrbussy.pdfsplitter.Application.java

/**
 * Split the given PDF file into multiple files using pages.
 * //from   w  ww  .  ja va 2  s . c  o  m
 * @param filename
 *            - Name of the PDF to split
 * @param useSubFolder
 *            - Use a separate folder to place the files in.
 */
public static void SplitFile(File file, boolean useSubFolder) {
    PdfReader reader = null;
    String format = null;

    if (useSubFolder)
        format = "%1$s%2$s%4$s%2$s_%%03d.%3$s";
    else
        format = "%1$s%2$s_%%03d.%3$s";

    String splitFile = String.format(format, FilenameUtils.getFullPath(file.getAbsolutePath()),
            FilenameUtils.getBaseName(file.getAbsolutePath()),
            FilenameUtils.getExtension(file.getAbsolutePath()), IOUtils.DIR_SEPARATOR);

    try {
        reader = new PdfReader(new FileInputStream(file));

        if (reader.getNumberOfPages() > 0) {
            for (int pageNum = 1; pageNum <= reader.getNumberOfPages(); pageNum++) {
                System.out.println(String.format(splitFile, pageNum));
                String filename = String.format(splitFile, pageNum);
                Document document = new Document(reader.getPageSizeWithRotation(1));
                PdfCopy writer = new PdfCopy(document, new FileOutputStream(filename));
                document.open();
                // Copy the page from the original
                PdfImportedPage page = writer.getImportedPage(reader, pageNum);
                writer.addPage(page);
                document.close();
                writer.close();
            }
        }
    } catch (Exception ex) {
        // TODO Implement exception handling
        ex.printStackTrace(System.err);
    } finally {
        if (reader != null)
            // Always close the stream
            reader.close();
    }
}

From source file:com.egreen.tesla.server.api.component.Component.java

/**
 *
 * Copy Components .html,.css,.js files to Folder
 *
 * @param inputStream// ww w .  j a va2s .  co  m
 * @param fileName
 * @throws IOException
 */
private void saveEntry(final InputStream inputStream, String fileName) throws IOException {
    // InputStream inputStream = null;
    OutputStream outputStream = null;

    try {
        final String FileName = component_base + "/" + fileName;
        if (FilenameUtils.getExtension(FileName) != null && !FilenameUtils.getExtension(FileName).isEmpty()) {

            File fileDir = new File(FilenameUtils.getFullPath(FileName));
            fileDir.mkdirs();
            final File file1 = new File(FileName);
            file1.createNewFile();
            // write the inputStream to a FileOutputStream
            outputStream = new FileOutputStream(file1);

            int read = 0;
            byte[] bytes = new byte[1024];

            while ((read = inputStream.read(bytes)) != -1) {
                outputStream.write(bytes, 0, read);
            }

        }
    } catch (IOException e) {
        throw e;
    } finally {
        if (inputStream != null) {
            try {
                inputStream.close();
            } catch (IOException e) {
                throw e;
            }
        }
        if (outputStream != null) {
            try {
                // outputStream.flush();
                outputStream.close();
            } catch (IOException e) {
                throw e;
            }

        }
    }

}

From source file:it.drwolf.ridire.session.async.Mapper.java

private void createArchivedResource(File f, CrawledResource cr, EntityManager entityManager) {
    // System.out.println(System.getProperty("java.io.tmpdir"));
    String posEnabled = this.em.find(Parameter.class, Parameter.POS_ENABLED.getKey()).getValue();
    File resourceDir;/*from   ww w . ja  v a2s . c o  m*/
    int status = Parameter.FINISHED;
    try {
        resourceDir = new File(FilenameUtils.getFullPath(f.getCanonicalPath().replaceAll("__\\d+", ""))
                + JobMapperMonitor.RESOURCESDIR);
        if (!resourceDir.exists()) {
            FileUtils.forceMkdir(resourceDir);
        }
        ArchiveReader reader = ArchiveReaderFactory.get(f);
        ARCRecord record = (ARCRecord) reader.get(cr.getOffset());
        record.skipHttpHeader();
        byte[] buf = new byte[Mapper.BUFLENGTH];
        int count = 0;
        String resourceFile = cr.getDigest() + ".gz";
        GZIPOutputStream baos = new GZIPOutputStream(new FileOutputStream(new File(resourceDir, resourceFile)));
        while ((count = record.read(buf)) != -1) {
            baos.write(buf, 0, count);
        }
        baos.finish();
        baos.close();
        reader.close();
        // long t1 = System.currentTimeMillis();
        StringWithEncoding cleanText = this.createPlainTextResource(f, cr, entityManager);
        this.removeGZippedResource(resourceDir, resourceFile);
        // long t2 = System.currentTimeMillis();
        // System.out.println("Creazione plain text: " + (t2 - t1));
        String plainTextFileName = cr.getDigest() + ".txt";
        if (cleanText != null && cleanText.getString() != null && cleanText.getString().trim().length() > 0
                && cleanText.getCleaner() != null && (cleanText.getCleaner().equals(Mapper.ALCHEMY)
                        || cleanText.getCleaner().equals(Mapper.READABILITY))) {
            cr.setCleaner(cleanText.getCleaner());
            File plainTextFile = new File(resourceDir, plainTextFileName);
            FileUtils.writeStringToFile(plainTextFile, cleanText.getString(), cleanText.getEncoding());
            cr.setExtractedTextHash(MD5DigestCreator.getMD5Digest(plainTextFile));
            // language detection
            // t1 = System.currentTimeMillis();
            String language = this.detectLanguage(cleanText.getString());
            // t2 = System.currentTimeMillis();
            // System.out.println("Language detection: " + (t2 - t1));
            cr.setLanguage(language);
            if (language != null && language.equalsIgnoreCase(Mapper.ITALIAN) && posEnabled != null
                    && posEnabled.equalsIgnoreCase("true")) {
                // PoS tag if it's an italian text
                // t1 = System.currentTimeMillis();
                String posTagResourceFileName = this.createPoSTagResource(plainTextFile, entityManager,
                        cleanText.getEncoding());
                // t2 = System.currentTimeMillis();
                // System.out.println("PoS tagging: " + (t2 - t1));
                if (posTagResourceFileName != null) {
                    Integer wordsNumber = Mapper.countWordsFromPoSTagResource(posTagResourceFileName);
                    cr.setWordsNumber(wordsNumber);
                }
            }
        }
    } catch (Exception e) {
        status = Parameter.PROCESSING_ERROR;
        e.printStackTrace();
    }
    cr.setProcessed(status);
}

From source file:MSUmpire.DIA.TargetMatchScoring.java

private void ExportAlignmentResult() throws IOException {
    try {//from   w  ww.j  a v  a 2s . c om
        FileWriter writer = new FileWriter(FilenameUtils.getFullPath(Filename) + "/"
                + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_TargetReExtraction.xls");
        writer.write(
                "Modseq\tPredictRT\tPrecursorMz\tType\tClusterRT\tMS level\tApexDeltaScore\tCorrScore\tSpecDotProduct\tSpecCorrelation\tSpecConstrastAngle\tPPMScore\tRTOverlap\tIntScore\tMS1Corr\tNoB\tNoY\tRTdiff\tPrcursorPPM\tSumCorrScore\tSumCorrPPMScore\tPrecursorIsoPattern\tPrecursorCentralRank\tRank\tU-Score\tProbability\n");
        for (UmpireSpecLibMatch match : libTargetMatches) {
            int Rank = 1;
            for (PeakGroupScore target : match.TargetHits) {
                writer.write(match.pepIonID.ModSequence + "\t" + match.pepIonID.PredictRTString() + "\t"
                        + match.pepIonID.NeutralPrecursorMz() + "\tTarget\t" + target.PrecursorRT + "\t"
                        + target.MSlevel + "\t" + target.ApexDeltaScore + "\t" + target.AveCorrScore + "\t"
                        + target.SpecDotProduct + "\t" + target.SpecCorrelation + "\t" + target.ContrastAngle
                        + "\t" + target.PPMScore + "\t" + target.RTOverlapScore + "\t" + target.FragIntAvgScore
                        + "\t" + target.PrecursorCorr + "\t" + target.NoMatchB + "\t" + target.NoMatchY + "\t"
                        + target.RTDiff + "\t" + target.PrecursorPPM + "\t" + target.SumCorrScore + "\t"
                        + target.SumCorrPPMScore + "\t" + target.PrecursorIsoPattern + "\t"
                        + target.PrecursorCentralRank + "\t" + (Rank++) + "\t" + target.UmpireScore + "\t"
                        + target.MixtureModelLocalProb + "\n");
            }
            Rank = 1;
            for (PeakGroupScore target : match.DecoyHits) {
                writer.write(match.pepIonID.ModSequence + "\t" + match.pepIonID.PredictRTString() + "\t"
                        + match.pepIonID.NeutralPrecursorMz() + "\tTarget_Decoy\t" + target.PrecursorRT + "\t"
                        + target.MSlevel + "\t" + target.ApexDeltaScore + "\t" + target.AveCorrScore + "\t"
                        + target.SpecDotProduct + "\t" + target.SpecCorrelation + "\t" + target.ContrastAngle
                        + "\t" + target.PPMScore + "\t" + target.RTOverlapScore + "\t" + target.FragIntAvgScore
                        + "\t" + target.PrecursorCorr + "\t" + target.NoMatchB + "\t" + target.NoMatchY + "\t"
                        + target.RTDiff + "\t" + target.PrecursorPPM + "\t" + target.SumCorrScore + "\t"
                        + target.SumCorrPPMScore + "\t" + target.PrecursorIsoPattern + "\t"
                        + target.PrecursorCentralRank + "\t" + (Rank++) + "\t" + target.UmpireScore + "\t"
                        + target.MixtureModelLocalProb + "\n");
            }
        }
        for (UmpireSpecLibMatch match : libIDMatches) {
            int Rank = 1;
            for (PeakGroupScore target : match.TargetHits) {
                writer.write(match.pepIonID.ModSequence + "\t" + match.pepIonID.PredictRTString() + "\t"
                        + match.pepIonID.NeutralPrecursorMz() + "\tID\t" + target.PrecursorRT + "\t"
                        + target.MSlevel + "\t" + target.ApexDeltaScore + "\t" + target.AveCorrScore + "\t"
                        + target.SpecDotProduct + "\t" + target.SpecCorrelation + "\t" + target.ContrastAngle
                        + "\t" + target.PPMScore + "\t" + target.RTOverlapScore + "\t" + target.FragIntAvgScore
                        + "\t" + target.PrecursorCorr + "\t" + target.NoMatchB + "\t" + target.NoMatchY + "\t"
                        + target.RTDiff + "\t" + target.PrecursorPPM + "\t" + target.SumCorrScore + "\t"
                        + target.SumCorrPPMScore + "\t" + target.PrecursorIsoPattern + "\t"
                        + target.PrecursorCentralRank + "\t" + (Rank++) + "\t" + target.UmpireScore + "\t"
                        + target.MixtureModelLocalProb + "\n");
            }
            for (PeakGroupScore target : match.DecoyHits) {
                writer.write(match.pepIonID.ModSequence + "\t" + match.pepIonID.PredictRTString() + "\t"
                        + match.pepIonID.NeutralPrecursorMz() + "\tID_Decoy\t" + target.PrecursorRT + "\t"
                        + target.MSlevel + "\t" + target.ApexDeltaScore + "\t" + target.AveCorrScore + "\t"
                        + target.SpecDotProduct + "\t" + target.SpecCorrelation + "\t" + target.ContrastAngle
                        + "\t" + target.PPMScore + "\t" + target.RTOverlapScore + "\t" + target.FragIntAvgScore
                        + "\t" + target.PrecursorCorr + "\t" + target.NoMatchB + "\t" + target.NoMatchY + "\t"
                        + target.RTDiff + "\t" + target.PrecursorPPM + "\t" + target.SumCorrScore + "\t"
                        + target.SumCorrPPMScore + "\t" + target.PrecursorIsoPattern + "\t"
                        + target.PrecursorCentralRank + "\t" + (Rank++) + "\t" + target.UmpireScore + "\t"
                        + target.MixtureModelLocalProb + "\n");
            }
        }
        writer.close();
    } catch (Exception e) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e));
    }
}

From source file:net.bpelunit.framework.control.deploy.ode.ODEDeployer.java

private String getArchiveLocation(String pathToTest) {
    String pathToArchive = FilenameUtils.concat(pathToTest, FilenameUtils.getFullPath(fArchive));
    String archiveName = FilenameUtils.getName(fArchive);
    return FilenameUtils.concat(pathToArchive, archiveName);
}

From source file:gov.ca.cwds.rest.util.jni.CmsPKCompressor.java

private File createFile(String file) {
    return new File(FilenameUtils.getFullPath(file), FilenameUtils.getName(file)); // NOSONAR
}