Example usage for org.apache.commons.io.filefilter TrueFileFilter INSTANCE

Introduction

In this page you can find the example usage for org.apache.commons.io.filefilter TrueFileFilter INSTANCE.

Prototype

IOFileFilter INSTANCE

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Document

Singleton instance of true filter.

Usage

From source file:org.jts.protocolvalidator.DefinitionFinder.java

/**
 * Returns a List of Files under the specified path whose name ends with the extension '.xml' or '.jsidl'.
 * If path refers to a single file, returns a list containing one element-the file referred to by path itself,
 * if that file's name ends with extension '.xml' or '.jsidl'.
 *//*from   w w  w.jav  a2s.  co m*/
private static List<File> getFileList(File mainFilePath, File path, File schema) {

    List<File> fileList = new ArrayList<File>();
    List<File> tmpFileList = new ArrayList<File>(FileUtils.listFiles(path,
            new SuffixFileFilter(new String[] { ".xml", ".jsidl" }), TrueFileFilter.INSTANCE));
    if (mainFilePath.isDirectory() || path.isFile()) {
        // input error
        return null;
    }

    fileList.add(mainFilePath);
    fileList.addAll(getDependencies(mainFilePath, path, schema, tmpFileList));

    return fileList;
}

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From source file:org.jvnet.hudson.plugins.thinbackup.backup.HudsonBackup.java

private List<File> findAllConfigurations(File dir) {
    Collection<File> listFiles = FileUtils.listFiles(dir, FileFilterUtils.nameFileFilter(CONFIG_XML),
            TrueFileFilter.INSTANCE);

    List<File> confs = new ArrayList<File>();
    for (File file : listFiles) {
        confs.add(file.getParentFile());
    }/*from   w  w w.  j  a v  a  2 s  . c  o m*/

    return confs;
}

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From source file:org.jvnet.hudson.plugins.thinbackup.backup.HudsonBackup.java

private void backupRootFolder(String folderName) throws IOException {
    backupRootFolder(folderName, TrueFileFilter.INSTANCE);
}

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From source file:org.jvnet.hudson.plugins.thinbackup.restore.HudsonRestore.java

private void restore(final File toRestore) throws IOException {
    final IOFileFilter nextBuildNumberFileFilter = FileFilterUtils.nameFileFilter("nextBuildNumber");
    IOFileFilter restoreNextBuildNumberFilter;

    if (restoreNextBuildNumber) {
        restoreNextBuildNumberFilter = FileFilterUtils.trueFileFilter();

        final Collection<File> restore = FileUtils.listFiles(toRestore, nextBuildNumberFileFilter,
                TrueFileFilter.INSTANCE);
        final Map<String, Integer> nextBuildNumbers = new HashMap<String, Integer>();
        for (final File file : restore) {
            BufferedReader reader = null;
            try {
                reader = new BufferedReader(new FileReader(file));
                nextBuildNumbers.put(file.getParentFile().getName(), Integer.parseInt(reader.readLine()));
            } finally {
                if (reader != null) {
                    reader.close();/*from   www. j ava 2 s. c  om*/
                }
            }
        }

        final Collection<File> current = FileUtils.listFiles(hudsonHome, nextBuildNumberFileFilter,
                TrueFileFilter.INSTANCE);
        for (final File file : current) {
            BufferedReader reader = null;
            try {
                reader = new BufferedReader(new FileReader(file));
                final int currentBuildNumber = Integer.parseInt(reader.readLine());
                final Integer toRestoreNextBuildNumber = nextBuildNumbers.get(file.getParentFile().getName());
                if (currentBuildNumber < toRestoreNextBuildNumber) {
                    restoreNextBuildNumber(file, toRestoreNextBuildNumber);
                }
            } finally {
                if (reader != null) {
                    reader.close();
                }
            }
        }
    } else {
        restoreNextBuildNumberFilter = FileFilterUtils.notFileFilter(nextBuildNumberFileFilter);
    }

    FileUtils.copyDirectory(toRestore, this.hudsonHome, restoreNextBuildNumberFilter, true);

    if (restorePlugins)
        restorePlugins(toRestore);
}

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From source file:org.kalypso.kalypsomodel1d2d.conv.results.ResultMeta1d2dHelper.java

private static void removeResourceFolder(final IResource resource, final boolean removeOriginalRawRes)
        throws CoreException {
    final File[] children = resource.getLocation().toFile().listFiles();
    if (children != null) {
        if (children.length == 0 || removeOriginalRawRes) {
            try {
                resource.delete(true, new NullProgressMonitor());
            } catch (final Exception e) {
                // FIXME: why?! the problem is elsewhere!!
                e.printStackTrace();/*from   w  w w  . jav  a2s .  c  om*/

                // FIXME:

                final IOFileFilter lNoDirFilter = FalseFileFilter.INSTANCE;

                final WildcardFileFilter lFilter = new WildcardFileFilter(new String[] { "*" }); //$NON-NLS-1$
                final Collection<File> files = FileUtils.listFiles(resource.getLocation().toFile(), lFilter,
                        lNoDirFilter);
                for (final File lFile : files)
                    deleteFileOrDirectory(lFile);

                final IOFileFilter lDirFilter = TrueFileFilter.INSTANCE;
                final Collection<File> dirs = FileUtils.listFiles(resource.getLocation().toFile(), lFilter,
                        lDirFilter);
                for (final File lDir : dirs)
                    deleteFileOrDirectory(lDir);
            }
        } else {
            for (int i = 0; i < children.length; i++) {
                if (!children[i].getName().toLowerCase().contains(ORIGINAL_2D_FILE_NAME)) {
                    try {
                        final IResource resourceChild = ResourceUtilities
                                .findFileFromURL(children[i].toURI().toURL());
                        if (resourceChild instanceof IFolder) {
                            removeResourceFolder(resourceChild, removeOriginalRawRes);
                        } else {
                            if (resourceChild != null)
                                resourceChild.delete(true, new NullProgressMonitor());
                            children[i].delete();
                        }
                    } catch (final MalformedURLException e) {
                        e.printStackTrace();
                    }
                }
            }
        }
    } else {
        resource.delete(true, new NullProgressMonitor());
    }
}

---

From source file:org.limy.eclipse.qalab.action.part.CalcCoberturaAction.java

/**
 * instrument?SNXt@Cdest/classesRs?[?B/*from   w  w w . j  ava2s.  c o  m*/
 * @throws IOException 
 * @throws CoreException 
 */
private void copyAllClassFiles() throws CoreException, IOException {

    for (IPath path : getEnv().getBinPaths(true)) {
        String dir = LimyQalabUtils.createFullPath(getJavaProject(), path);
        FileUtils.copyDirectory(new File(dir), getDestFile("classes"));
    }
    Collection<Object> files = FileUtils.listFiles(getDestFile("classes"), new SuffixFileFilter("Test.class"),
            TrueFileFilter.INSTANCE);
    for (Object file : files) {
        ((File) file).delete();
    }

}

---

From source file:org.m2latex.mojo.TexFileUtilsImpl.java

public List getLatexMainDocuments(File directory) throws MojoExecutionException {
    ArrayList mainFiles = new ArrayList();

    Collection texFiles = FileUtils.listFiles(directory, FileFilterUtils.suffixFileFilter(".tex"),
            TrueFileFilter.INSTANCE);
    for (Iterator iterator = texFiles.iterator(); iterator.hasNext();) {
        File file = (File) iterator.next();
        if (isTexMainFile(file)) {
            mainFiles.add(file);/*from ww  w .j a  v a  2  s . c om*/
        }
    }
    return mainFiles;
}

---

From source file:org.mda.bcb.tcgagsdata.create.Compilation.java

public void process() throws IOException, Exception {
    TcgaGSData.printWithFlag("Compilation::process - mClinicalDir=" + mClinicalDir);
    TcgaGSData.printWithFlag("Compilation::process - mInputFiles=" + mInputFiles);
    TcgaGSData.printWithFlag("Compilation::process - mOutputFile=" + mOutputFile);
    Collection<File> results = FileUtils.listFiles(new File(mClinicalDir),
            FileFilterUtils.nameFileFilter(mInputFiles), TrueFileFilter.INSTANCE);
    ArrayList<String> headers = getHeaders(results);
    TreeSet<String> patients = new TreeSet<>();
    TreeSet<String> lines = new TreeSet<>();
    String headerLine = null;// w  ww  .  jav  a 2 s  . com
    for (String header : headers) {
        if (null == headerLine) {
            headerLine = header;
        } else {
            headerLine = headerLine + "\t" + header;
        }
    }
    boolean headersNeeded = true;
    for (File clinFile : results) {
        TcgaGSData.printWithFlag("Compilation::process - clinFile=" + clinFile.getAbsolutePath());
        try (BufferedReader br = Files.newBufferedReader(Paths.get(clinFile.getAbsolutePath()),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            String line = br.readLine();
            ArrayList<String> currentHeaders = new ArrayList<>();
            currentHeaders.addAll(Arrays.asList(line.split("\t", -1)));
            for (line = br.readLine(); null != line; line = br.readLine()) {
                String newLine = null;
                String[] splitted = line.split("\t", -1);
                for (String header : headers) {
                    String token = "NA";
                    int index = currentHeaders.indexOf(header);
                    if (index > -1) {
                        token = splitted[index];
                    }
                    if (null == newLine) {
                        newLine = token;
                    } else {
                        newLine = newLine + "\t" + token;
                    }
                }
                lines.add(newLine);
                String patient = GSStringUtils.beforeTab(newLine);
                if (false == patients.add(patient)) {
                    throw new Exception("ERROR - patient duplicated " + patient);
                }
            }
        }
    }
    try (BufferedWriter bw = Files.newBufferedWriter(Paths.get(mOutputFile),
            Charset.availableCharsets().get("ISO-8859-1"))) {
        bw.write(headerLine);
        bw.newLine();
        for (String line : lines) {
            bw.write(line);
            bw.newLine();
        }
    }
}

---

From source file:org.mda.bcb.tcgagsdata.create.Metadata.java

static public String findMetadataFile(File theDir) {
    File metadataFile = FileUtils
            .listFiles(theDir, new WildcardFileFilter("metadata*.tsv"), TrueFileFilter.INSTANCE).iterator()
            .next();//  w w w. jav a2 s .c o m
    return metadataFile.getAbsolutePath();
}

---

From source file:org.mda.bcb.tcgagsdata.create.ReadPlatform.java

public void readPlatform(String thePlatform) throws IOException, Exception {
    TcgaGSData.printWithFlag("readPlatform for " + thePlatform + " beginning");
    TcgaGSData.printWithFlag("readPlatform can consume excessive amounts of time and memory");
    mNumberOfGenes = 0;/*from   ww w .  j  av a 2 s  .c  om*/
    TreeMap<String, Integer> geneMap = null;
    {
        ReadPlatform_GeneEq lg = new ReadPlatform_GeneEq(mReadPath);
        lg.getNamesGenes(thePlatform);
        mGenes = lg.mGenes;
        geneMap = TcgaGSData.buildIndexMap(lg.mGenes);
        mNumberOfGenes = lg.mSize;
    }
    mNumberOfSamples = 0;
    boolean found = false;
    long start = System.currentTimeMillis();
    TreeSet<File> dataFileList = new TreeSet<>();
    dataFileList.addAll(FileUtils.listFiles(new File(mReadPath, thePlatform),
            new WildcardFileFilter("matrix_data_*.tsv"), TrueFileFilter.INSTANCE));
    for (File input : dataFileList) {
        try (BufferedReader br = Files.newBufferedReader(Paths.get(input.getAbsolutePath()),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            found = true;
            TcgaGSData.printWithFlag("readPlatform file=" + input.getAbsolutePath());
            // first line samples
            String line = br.readLine();
            TreeMap<String, Integer> sampleMap = TcgaGSData
                    .buildIndexMap(GSStringUtils.afterTab(line).split("\t", -1));
            if (0 == mNumberOfSamples) {
                mSamples = GSStringUtils.afterTab(line).split("\t", -1);
                mNumberOfSamples = mSamples.length;
                mGenesBySamplesValues = new double[mNumberOfGenes][mNumberOfSamples];
            } else {
                if (mNumberOfSamples != GSStringUtils.afterTab(line).split("\t", -1).length) {
                    throw new Exception("Expected sample count of " + mNumberOfSamples + " but found different "
                            + input.getAbsolutePath());
                }
            }
            line = br.readLine();
            while (null != line) {
                String gene = GSStringUtils.beforeTab(line);
                Integer intIndex = geneMap.get(gene);
                if (null != intIndex) {
                    int geneIndex = intIndex;
                    double[] valueList = convertToDouble(GSStringUtils.afterTab(line).split("\t", -1));
                    for (int x = 0; x < valueList.length; x++) {
                        int sampleIndex = sampleMap.get(mSamples[x]);
                        mGenesBySamplesValues[geneIndex][sampleIndex] = valueList[x];
                    }
                } else {
                    throw new Exception(
                            "readPlatform for " + thePlatform + " found unexpected 'gene' = " + gene);
                }
                line = br.readLine();
            }
        }
    }
    long finish = System.currentTimeMillis();
    TcgaGSData.printWithFlag(
            "readPlatform for " + thePlatform + " retrieved in " + ((finish - start) / 1000.0) + " seconds");
    if (false == found) {
        throw new Exception("readPlatform for " + thePlatform + " not found");
    } else {
        TcgaGSData.printWithFlag("write " + thePlatform + " to " + mWriteFile);
        writeFile();
    }
}

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