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

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

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Introduction

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

Prototype

public static boolean isExtension(String filename, Collection<String> extensions)

Source Link

Document

Checks whether the extension of the filename is one of those specified.

Usage

From source file:it.isislab.dmason.util.SystemManagement.Master.thrower.DMasonMaster.java

/**Used for setting the name of last worker version
 * //  w w  w . j  av a  2  s . c om
 * @return 0 if no file
 *          1 if more then 2 file
 *          2 if number of file is correct
 */
private int getCurWorkerJarName() {
    File file = new File(FTP_HOME + dirSeparator + UPDATE_DIR);
    File[] files = file.listFiles();

    if (files.length == 0)
        return 0;
    if (files.length > 2)
        return 1;
    if (files.length == 2) {
        for (File curfile : files) {
            if (curfile.isFile() && FilenameUtils.isExtension(curfile.getName(), "jar")) {
                workerJarName = curfile.getName();
                return 2;
            }
        }
        return 1;
    }
    return -1;
}

From source file:nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression.ReadGenoAndAsFromIndividual.java

public static void readGenoAndAsFromIndividual(String loc_of_bam1, String genotype_loc,
        String coupling_location, String outputLocation, String snpLocation) throws IOException, Exception {

    if (GlobalVariables.verbosity >= 1) {
        //Print ASREADS header
        System.out.println("---- Starting ASREADS for the following settings: ----");
        System.out.println("\t input bam:         " + loc_of_bam1);
        System.out.println("\t genotype location: " + genotype_loc);
        System.out.println("\t coupling file:     " + coupling_location);
        System.out.println("\t output location:   " + outputLocation);
        if (!snpLocation.equals("")) {
            System.out.println("\t snp Location:      " + snpLocation);
        } else {/*from w w w  . j  a v a 2 s  .c  o  m*/
            System.out.println("\t snp Location:      " + "NONE");
        }

        System.out.println("------------------------------------------------------");
    }

    //parse command line arguments
    String loc_of_bam;
    loc_of_bam = loc_of_bam1;
    System.out.println("Location of bam file: ");
    System.out.println(loc_of_bam);

    if (!new File(loc_of_bam).exists()) {
        throw new IllegalArgumentException("ERROR! Location of bam file is not an existing file. Exitting.");
    } else {
        if (GlobalVariables.verbosity >= 10) {
            System.out.println("Location of bam file is an existing file, will continue.");
        }
    }

    RandomAccessGenotypeData TTdataSet;
    VcfGenotypeData VCFdataSet;
    HashMap<String, GeneticVariant> variantIdMap;
    String[] individual_names;

    String tabixLoc = genotype_loc + ".tbi";

    //open vcf dataset
    //based on extention and existance of both files. 
    if (FilenameUtils.isExtension(genotype_loc, "gz") && new File(tabixLoc).exists()
            && new File(genotype_loc).exists()) {
        try {
            VCFdataSet = new VcfGenotypeData(new File(genotype_loc), new File(tabixLoc), 0.99);
            variantIdMap = VCFdataSet.getVariantIdMap();
            individual_names = VCFdataSet.getSampleNames();
        } catch (IOException ex) {
            System.err.println("Error reading vcf dataset: " + genotype_loc);
            throw new IllegalArgumentException();
        }

    } else if (new File(genotype_loc + "/GenotypeMatrix.dat").exists()) {
        //assuming trityper dataset based on the genotype matrix
        try {
            TTdataSet = new TriTyperGenotypeData(new File(genotype_loc));
            variantIdMap = TTdataSet.getVariantIdMap();
            individual_names = TTdataSet.getSampleNames();
        } catch (IOException ex) {
            System.err.println("Error reading trityper dataset: " + genotype_loc);
            throw new IllegalArgumentException();
        }

    } else {
        throw new IllegalDataException("could not find a Trityper or vcf file in the genotype location");
    }

    //get the variants in the variantIdMAP

    Set<String> snpNames = variantIdMap.keySet();

    ArrayList<String> SNPsToAnalyze;
    SNPsToAnalyze = new ArrayList<String>();

    //If available, read the file with rs numbers.
    if (!snpLocation.equals("")) {

        ArrayList<String> includeSNPs = UtilityMethods.readFileIntoStringArrayList(snpLocation);

        int snpsNotFound = 0;

        for (String snp_to_include : includeSNPs) {
            if (snpNames.contains(snp_to_include)) {
                SNPsToAnalyze.add(snp_to_include);
            } else {
                snpsNotFound++;
            }
        }

        if (GlobalVariables.verbosity >= 1) {
            System.out.println("WARNING: Did not find " + Integer.toString(snpsNotFound) + " out of "
                    + Integer.toString(includeSNPs.size()) + " SNPs in the include file.");
        }
    } else {
        for (String snp_to_include : snpNames) {
            SNPsToAnalyze.add(snp_to_include);
        }
    }

    //String path = "/gcc/groups/lld/tmp01/projects/bamFiles/";
    //sample_map contains all the individuals that are in the sample file.
    HashMap sample_map = convert_individual_names(individual_names, coupling_location);

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("Sample names were loaded.");
    }
    if (GlobalVariables.verbosity >= 100) {
        System.out.println(sample_map.toString());
    }

    //Twice because my files have the .MERGED.sorted.bam suffix attached to them.
    String sample_name = FilenameUtils
            .getBaseName(FilenameUtils.getBaseName(FilenameUtils.getBaseName(loc_of_bam)));

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("sample_name: " + sample_name);
        System.out.println("sample_map:  " + sample_map.toString());
    }

    Object sample_idx = sample_map.get(sample_name);

    if (sample_idx == null) {
        throw new IllegalArgumentException("Couldn't find the filename in the sample names. Quitting.");
    }

    int sample_index = Integer.parseInt(sample_idx.toString());

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("sample_index: " + sample_index);
    }

    //bam file path and filename
    String path_and_filename = loc_of_bam;
    File sample_file = new File(path_and_filename);

    SamReader bam_file = SamReaderFactory.makeDefault().open(sample_file);

    if (GlobalVariables.verbosity >= 10) {
        System.out.println("Initialized for reading bam file");
    }

    PrintWriter writer = new PrintWriter(outputLocation, "UTF-8");

    int i = 0;
    for (String i_snp : SNPsToAnalyze) {

        //System.out.println(i_snp);

        GeneticVariant this_variant = variantIdMap.get(i_snp);

        String chromosome = this_variant.getSequenceName();
        String position = String.valueOf(this_variant.getStartPos());

        // We only do analyses if we find a SNP and it is biallelic
        // However this is trityper data, so if we use
        // the allele count is used for the check of something. 

        //DO NOT ENTER A SEPARATED GENOMIC DATASET OTHERWISE THIS WILL BREAK.
        if (this_variant.isSnp() & this_variant.isBiallelic()) {

            String row_of_table = get_allele_specific_overlap_at_snp(this_variant, sample_index, chromosome,
                    position, bam_file);

            //commented out the phasing part.

            writer.println(chromosome + "\t" + position + "\t" + i_snp + "\t"
                    + this_variant.getVariantAlleles().getAllelesAsChars()[0] + "\t"
                    + this_variant.getVariantAlleles().getAllelesAsChars()[1] + "\t" + row_of_table + "\t"
                    + Arrays.toString(this_variant.getSampleVariants().get(sample_index).getAllelesAsChars()) //+ "\t" +
            //Boolean.toString(this_variant.getSamplePhasing().get(sample_index))
            );
        }

        i++;

        if ((i % 10000 == 0) && (GlobalVariables.verbosity >= 10)) {

            System.out.println("Finished " + Integer.toString(i) + " SNPs");

        }

    }
    writer.close();
}

From source file:org.apache.gobblin.compaction.mapreduce.MRCompactorJobRunner.java

@Override
public void run() {
    Configuration conf = HadoopUtils.getConfFromState(this.dataset.jobProps());

    // Turn on mapreduce output compression by default
    if (conf.get("mapreduce.output.fileoutputformat.compress") == null
            && conf.get("mapred.output.compress") == null) {
        conf.setBoolean("mapreduce.output.fileoutputformat.compress", true);
    }/* ww w  . j av a2  s  .  co m*/

    // Disable delegation token cancellation by default
    if (conf.get("mapreduce.job.complete.cancel.delegation.tokens") == null) {
        conf.setBoolean("mapreduce.job.complete.cancel.delegation.tokens", false);
    }

    try {
        DateTime compactionTimestamp = getCompactionTimestamp();
        LOG.info("MR Compaction Job Timestamp " + compactionTimestamp.getMillis());
        if (this.dataset.jobProps().getPropAsBoolean(MRCompactor.COMPACTION_JOB_LATE_DATA_MOVEMENT_TASK,
                false)) {
            List<Path> newLateFilePaths = Lists.newArrayList();
            for (String filePathString : this.dataset.jobProps()
                    .getPropAsList(MRCompactor.COMPACTION_JOB_LATE_DATA_FILES)) {
                if (FilenameUtils.isExtension(filePathString, getApplicableFileExtensions())) {
                    newLateFilePaths.add(new Path(filePathString));
                }
            }

            Path lateDataOutputPath = this.outputDeduplicated ? this.dataset.outputLatePath()
                    : this.dataset.outputPath();
            LOG.info(String.format("Copying %d late data files to %s", newLateFilePaths.size(),
                    lateDataOutputPath));
            if (this.outputDeduplicated) {
                if (!this.fs.exists(lateDataOutputPath)) {
                    if (!this.fs.mkdirs(lateDataOutputPath)) {
                        throw new RuntimeException(
                                String.format("Failed to create late data output directory: %s.",
                                        lateDataOutputPath.toString()));
                    }
                }
            }
            this.copyDataFiles(lateDataOutputPath, newLateFilePaths);
            if (this.outputDeduplicated) {
                dataset.checkIfNeedToRecompact(datasetHelper);
            }
            this.status = Status.COMMITTED;
        } else {
            if (this.fs.exists(this.dataset.outputPath()) && !canOverwriteOutputDir()) {
                LOG.warn(String.format("Output paths %s exists. Will not compact %s.",
                        this.dataset.outputPath(), this.dataset.inputPaths()));
                this.status = Status.COMMITTED;
                return;
            }
            addJars(conf);
            Job job = Job.getInstance(conf);
            this.configureJob(job);
            this.submitAndWait(job);
            if (shouldPublishData(compactionTimestamp)) {
                // remove all invalid empty files due to speculative task execution
                List<Path> goodPaths = CompactionAvroJobConfigurator.getGoodFiles(job,
                        this.dataset.outputTmpPath(), this.tmpFs);

                if (!this.recompactAllData && this.recompactFromDestPaths) {
                    // append new files without deleting output directory
                    addGoodFilesToOutputPath(goodPaths);
                    // clean up late data from outputLateDirectory, which has been set to inputPath
                    deleteFilesByPaths(this.dataset.inputPaths());
                } else {
                    moveTmpPathToOutputPath();
                    if (this.recompactFromDestPaths) {
                        deleteFilesByPaths(this.dataset.additionalInputPaths());
                    }
                }
                submitSlaEvent(job);
                LOG.info("Successfully published data for input folder " + this.dataset.inputPaths());
                this.status = Status.COMMITTED;
            } else {
                LOG.info("Data not published for input folder " + this.dataset.inputPaths()
                        + " due to incompleteness");
                this.status = Status.ABORTED;
                return;
            }
        }
        if (renameSourceDir) {
            MRCompactor.renameSourceDirAsCompactionComplete(this.fs, this.dataset);
        } else {
            this.markOutputDirAsCompleted(compactionTimestamp);
        }
        this.submitRecordsCountsEvent();
    } catch (Throwable t) {
        throw Throwables.propagate(t);
    }
}

From source file:org.apache.jena.atlas.io.IO.java

/** The filename without any compression extension, or the original filename.
 *  It tests for compression types handled by {@link #openFileEx}.
 *//* ww w  .j a v a  2  s  .  co  m*/
static public String filenameNoCompression(String filename) {
    if (FilenameUtils.isExtension(filename, extensions)) {
        return FilenameUtils.removeExtension(filename);
    }
    return filename;
}

From source file:org.apache.maven.plugin.cxx.CMakeMojo.java

protected String baseNameAsStaticLibrary(String sName, boolean bMavenDependency) {
    if (FilenameUtils.isExtension(sName, FilenameUtils.getExtension(staticLibrarySuffix))) {
        sName = FilenameUtils.removeExtension(sName) + (bMavenDependency ? "${STATIC_LIBRARY_SUFFIX}" : "");
        if (!StringUtils.isEmpty(staticLibraryPrefix)) {
            if (0 == sName.indexOf(staticLibraryPrefix)) {
                sName = sName.replaceFirst(Pattern.quote(staticLibraryPrefix), "");
                sName = (bMavenDependency ? "${STATIC_LIBRARY_PREFIX}" : "") + sName;
            } else {
                sName = "";
            }/*from  w w w .  j av a  2s .com*/
        } else {
            sName = (bMavenDependency ? "${STATIC_LIBRARY_PREFIX}" : "") + sName;
        }
    }
    return sName;
}

From source file:org.apache.maven.plugin.cxx.CMakeMojo.java

protected String baseNameAsSharedModule(String sName, boolean bMavenDependency) {
    if (FilenameUtils.isExtension(sName, FilenameUtils.getExtension(sharedModuleSuffix))) {
        sName = FilenameUtils.removeExtension(sName) + (bMavenDependency ? "${SHARED_MODULE_SUFFIX}" : "");
        if (!StringUtils.isEmpty(sharedModulePrefix)) {
            if (0 == sName.indexOf(sharedModulePrefix)) {
                sName = sName.replaceFirst(Pattern.quote(sharedModulePrefix), "");
                sName = (bMavenDependency ? "${SHARED_MODULE_PREFIX}" : "") + sName;
            } else {
                sName = "";
            }/*from   w w  w . j a  v a  2s . c  om*/
        } else {
            sName = (bMavenDependency ? "${SHARED_MODULE_PREFIX}" : "") + sName;
        }
    }
    return sName;
}

From source file:org.apache.maven.plugin.cxx.CMakeMojo.java

protected String baseNameAsSharedLibrary(String sName, boolean bMavenDependency) {
    if (FilenameUtils.isExtension(sName, FilenameUtils.getExtension(sharedLibrarySuffix))) {
        sName = FilenameUtils.removeExtension(sName) + (bMavenDependency ? "${SHARED_LIBRARY_SUFFIX}" : "");
        if (!StringUtils.isEmpty(sharedLibraryPrefix)) {
            if (0 == sName.indexOf(sharedLibraryPrefix)) {
                sName = sName.replaceFirst(Pattern.quote(sharedLibraryPrefix), "");
                sName = (bMavenDependency ? "${SHARED_LIBRARY_PREFIX}" : "") + sName;
            } else {
                sName = "";
            }/*  w w w .ja va2  s  . co m*/
        } else {
            sName = (bMavenDependency ? "${SHARED_LIBRARY_PREFIX}" : "") + sName;
        }
    }
    return sName;
}

From source file:org.apache.maven.plugins.scmpublish.AbstractScmPublishMojo.java

protected boolean requireNormalizeNewlines(File f) throws IOException {
    if (normalizeExtensions == null) {
        normalizeExtensions = new HashSet<String>(Arrays.asList(NORMALIZE_EXTENSIONS));
        if (extraNormalizeExtensions != null) {
            normalizeExtensions.addAll(Arrays.asList(extraNormalizeExtensions));
        }//from   ww w.jav  a 2s  .  c  o m
    }

    return FilenameUtils.isExtension(f.getName(), normalizeExtensions);
}

From source file:org.batoo.jpa.parser.impl.acl.ClassloaderAnnotatedClassLocator.java

private Set<Class<?>> findClasses(ClassLoader cl, Set<Class<?>> classes, String root, String path) {
    final File file = new File(path);

    if (file.isDirectory()) {
        ClassloaderAnnotatedClassLocator.LOG.debug("Processing directory {0}", path);

        for (final String child : file.list()) {
            this.findClasses(cl, classes, root, path + "/" + child);
        }/*from w ww . j  a  v  a2 s  .  co m*/
    } else {
        if (FilenameUtils.isExtension(path, "class")) {
            final String normalizedPath = FilenameUtils.separatorsToUnix(FilenameUtils.normalize(path));

            final int rootLength = FilenameUtils.normalizeNoEndSeparator(root).length();
            String className = normalizedPath.substring(rootLength + 1).replaceAll("/", ".");
            className = StringUtils.left(className, className.length() - 6);

            final Class<?> clazz = this.isPersistentClass(cl, className);
            if (clazz != null) {
                ClassloaderAnnotatedClassLocator.LOG.debug("Found persistent class {0}", className);
                classes.add(clazz);
            }
        }
    }

    return classes;
}

From source file:org.codice.ddf.commands.catalog.ImportCommand.java

private File initImportFile(String importFile) {
    File file = new File(importFile);

    if (!file.exists()) {
        throw new CatalogCommandRuntimeException("File does not exist: " + importFile);
    }//from  w  w w.  j  a  v a  2 s.  com

    if (!FilenameUtils.isExtension(importFile, "zip")) {
        throw new CatalogCommandRuntimeException("File must be a zip file: " + importFile);
    }

    return file;
}