Example usage for org.apache.commons.io FileUtils moveFile

List of usage examples for org.apache.commons.io FileUtils moveFile

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Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils moveFile.

Prototype

public static void moveFile(File srcFile, File destFile) throws IOException

Source Link

Document

Moves a file.

Usage

From source file:nl.mpi.lamus.workspace.exporting.implementation.LamusVersioningHandler.java

/**
 * @see VersioningHandler#moveOrCopyFileToOrphansFolder(nl.mpi.lamus.workspace.model.Workspace, nl.mpi.lamus.workspace.model.WorkspaceNode)
 *//*from w w w.  ja v a2 s  .  co m*/
@Override
public URL moveOrCopyFileToOrphansFolder(Workspace workspace, WorkspaceNode nodeToMove, boolean copy) {

    File orphanOldLocation = null;

    File archiveLocation = null;

    //if file was not in the archive already, then it will be moved from its workspace location
    //if file is in the archive and is a resource, then it will be moved from its archive location
    //if file is metadata, then it will be moved from its workspace location; if it is also in the archive, then it has to be removed from there

    if (nodeToMove.getArchiveURI() != null) {
        CorpusNode archiveNode = corpusStructureProvider.getNode(nodeToMove.getArchiveURI());
        archiveLocation = nodeResolver.getLocalFile(archiveNode);
    }

    if (nodeToMove.getArchiveURI() == null || nodeUtil.isNodeMetadata(nodeToMove)) {
        URL orphanOldLocationUrl = nodeToMove.getWorkspaceURL();
        orphanOldLocation = new File(orphanOldLocationUrl.getPath());
        if (archiveFileLocationProvider.isFileInOrphansDirectory(orphanOldLocation)) {
            logger.info("File already in orphans directory: " + orphanOldLocation.getAbsolutePath());
            return orphanOldLocationUrl;
        }
    }

    if (orphanOldLocation == null) {
        orphanOldLocation = archiveLocation;
    }

    String filename;
    if (orphanOldLocation != null) {
        filename = orphanOldLocation.getName();
    } else {
        throw new IllegalStateException("No valid file location was found.");
    }

    File orphanNewLocation;
    try {
        File orphansDirectory = archiveFileLocationProvider
                .getOrphansDirectory(workspace.getTopNodeArchiveURL().toURI());
        if (!archiveFileHelper.canWriteTargetDirectory(orphansDirectory)) {
            logger.error("Problem with write permissions in target directory " + orphansDirectory);
            return null;
        }
        orphanNewLocation = archiveFileHelper.getFinalFile(orphansDirectory, filename);
    } catch (URISyntaxException ex) {
        String errorMessage = "Error retrieving archive location of node " + workspace.getTopNodeArchiveURI();
        logger.error(errorMessage, ex);
        return null;
    }

    try {
        if (!copy) {
            FileUtils.moveFile(orphanOldLocation, orphanNewLocation);
            if (archiveLocation != null) {
                Files.deleteIfExists(archiveLocation.toPath());
            }
        } else {
            FileUtils.copyFile(orphanOldLocation, orphanNewLocation);
        }

    } catch (IOException ex) {
        logger.error("File couldn't be " + (copy ? "copied" : "moved") + " from [" + orphanOldLocation
                + "] to [" + orphanNewLocation + "]", ex);
        return null;
    }

    URL newFileUrl = null;
    try {
        newFileUrl = orphanNewLocation.toURI().toURL();
    } catch (MalformedURLException ex) {
        logger.warn((copy ? "Copied" : "Moved") + " file location is not a URL", ex);
    }

    return newFileUrl;
}

From source file:nl.mpi.lamus.workspace.exporting.implementation.LamusVersioningHandler.java

private URL moveFileTo(WorkspaceNode nodeToMove, boolean toDelete) {

    CorpusNode archiveNode = corpusStructureProvider.getNode(nodeToMove.getArchiveURI());
    File currentFile = nodeResolver.getLocalFile(archiveNode);

    File targetDirectory;/*from  w  w  w  .j a v a  2  s  .  co  m*/
    if (toDelete) {
        targetDirectory = archiveFileHelper.getDirectoryForDeletedNode(nodeToMove.getWorkspaceID());
    } else { // node is replaced
        targetDirectory = archiveFileHelper.getDirectoryForReplacedNode(nodeToMove.getWorkspaceID());
    }

    if (!archiveFileHelper.canWriteTargetDirectory(targetDirectory)) {
        logger.error("Problem with write permissions in target directory " + targetDirectory);
        return null;
    }

    File targetFile = archiveFileHelper.getTargetFileForReplacedOrDeletedNode(targetDirectory,
            handleParser.stripAndValidateHandleIfPrefixIsKnown(nodeToMove.getArchiveURI()), currentFile);

    try {
        FileUtils.moveFile(currentFile, targetFile);
    } catch (IOException ex) {
        logger.error("File couldn't be moved from [" + currentFile + "] to [" + targetFile + "]", ex);
        return null;
    }

    URL movedFileURL = null;
    try {
        movedFileURL = targetFile.toURI().toURL();
    } catch (MalformedURLException ex) {
        logger.warn("Moved file location is not a URL", ex);
    }

    return movedFileURL;
}

From source file:nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis.java

public void run() throws IOException {
    initialize();//from   ww  w  . ja  va  2 s  .  co  m
    loadProbeAnnotation();

    String outdir = settings.getOutput();
    if (usetmp) {
        outdir = tempDir;
    }

    System.out.println("Placing output here: " + outdir);
    outdir = Gpio.formatAsDirectory(outdir);
    Gpio.createDir(outdir);

    System.out.println(
            "Permutations: " + settings.getStartPermutations() + " until " + settings.getNrPermutations());

    String zscoretableheader = null;
    if (settings.isMakezscoretable()) {
        StringBuilder builder = new StringBuilder();
        builder.append("SNP\tAlleles\tAlleleAssessed");
        for (int t = 0; t < traitList.length; t++) {
            builder.append("\t").append(traitList[t].getMetaTraitName()).append("_")
                    .append(traitList[t].getAnnotation());
        }
        zscoretableheader = builder.toString();
    }

    int availableProcessors = Runtime.getRuntime().availableProcessors();
    int cores = settings.getNrThreads();
    if (cores < 1) {
        cores = 1;
    } else if (cores > availableProcessors) {
        cores = availableProcessors;
    }

    System.out.println("Will try to make use of " + cores + " CPU cores");
    System.out.println();

    HashSet<QTLPair> prevSet = null;
    for (int permutation = settings.getStartPermutations(); permutation <= settings
            .getNrPermutations(); permutation++) {
        // load probe annotation and index
        // this particular probe annotation can take multiple probes for a single location into account.

        HashSet<QTLPair> set = new HashSet<>();

        Descriptives.initializeZScoreToPValue();

        // re-intialize for each permutation, just to be sure
        if (permutation > settings.getStartPermutations()) {
            initialize();
            System.out.println("Loading probe annotation from: " + settings.getProbetranslationfile());
            loadProbeAnnotation();
            if (traitList.length == 0) {
                System.err.println("Error: no annotation loaded.");
                System.exit(-1);
            }
        }
        //         clearResultsBuffer();

        // create dataset objects
        System.out.println("Running permutation " + permutation);
        datasets = new BinaryMetaAnalysisDataset[settings.getDatasetlocations().size()];

        System.out.println("Loading datasets");
        for (int d = 0; d < datasets.length; d++) {
            datasets[d] = new BinaryMetaAnalysisDataset(settings.getDatasetlocations().get(d),
                    settings.getDatasetnames().get(d), settings.getDatasetPrefix().get(d), permutation,
                    settings.getDatasetannotations().get(d), probeAnnotation,
                    settings.getFeatureOccuranceScaleMaps().get(d));
        }

        System.out.println("Loaded " + datasets.length + " datasets");

        // create meta-analysis SNP index. have to recreate this every permutation,
        // since the order of SNPs is generated at random.
        System.out.println("Creating SNP index");
        createSNPIndex(outdir);
        System.out.println("Total of " + snpIndex.length + " SNPs");

        System.out.println("Creating probe index");
        createProbeIndex(outdir);
        System.out.println("Total of " + probeIndex.length + " probes");

        // make index of snp/probe combinations, if any specified
        createSNPProbeCombos(outdir);

        // load SNP annotation for SNPs present in dataset
        //         if (snpChr == null) {
        System.out.println("Loading SNP annotation from " + settings.getSNPAnnotationFile());
        loadSNPAnnotation();
        //         }

        // run analysis
        System.out.println("Type of analysis: " + settings.getAnalysisType());
        System.out.println("Cis-window: " + settings.getCisdistance());
        System.out.println("Trans-window: " + settings.getTransdistance());

        TextFile zscoreTableTf = null;
        TextFile zscoreTableTfNrSamples = null;

        if (settings.isMakezscoretable()) {

            String tableoutfile = outdir + "ZScoreMatrix-Permutation" + permutation + ".txt.gz";
            String tableoutfileNrSamples = outdir + "ZScoreMatrixNrSamples-Permutation" + permutation
                    + ".txt.gz";
            if (permutation == 0) {
                tableoutfile = outdir + "ZScoreMatrix.txt.gz";
                tableoutfileNrSamples = outdir + "ZScoreMatrixNrSamples.txt.gz";
            }
            System.out.println("Writing z-score table: " + tableoutfile);
            zscoreTableTf = new TextFile(tableoutfile, TextFile.W, 10 * 1048576);
            zscoreTableTfNrSamples = new TextFile(tableoutfileNrSamples, TextFile.W, 10 * 1048576);

            // write header
            zscoreTableTf.writeln(zscoretableheader);
            zscoreTableTfNrSamples.writeln(zscoretableheader);
        }

        ExecutorService threadPool = Executors.newFixedThreadPool(cores);
        CompletionService<Triple<ArrayList<QTL>, String, String>> pool = new ExecutorCompletionService<Triple<ArrayList<QTL>, String, String>>(
                threadPool);

        maxSavedPvalue = -Double.MAX_VALUE;
        locationToStoreResult = 0;
        bufferHasOverFlown = false;
        System.out.println("Max P: " + maxSavedPvalue + "\tLocationToStoreResult: " + locationToStoreResult);

        System.out.println("Starting meta-analysis");
        ProgressBar pb = new ProgressBar(snpList.length);
        int returned = 0;
        ArrayList<Future> futures = new ArrayList<>();
        for (int snp = 0; snp < snpList.length; snp++) {
            // this can go in different threads..
            boolean outputallzscores = true;
            if (permutation > 0) {
                outputallzscores = fullpermutationoutput;
            }
            BinaryMetaAnalysisTask t = new BinaryMetaAnalysisTask(settings, probeAnnotation, datasets, snpIndex,
                    snpList, snpChr, snpPositions, probeIndex, snpprobeCombos, traitMap, traitList, snp, DEBUG,
                    outputallzscores);
            futures.add(pool.submit(t));
        }

        // give the threadpool the signal to shutdown
        threadPool.shutdown();

        int addcalled = 0;
        while (returned < snpList.length) {
            try {
                Future<Triple<ArrayList<QTL>, String, String>> threadfuture = pool.take();
                if (threadfuture != null) {
                    Triple<ArrayList<QTL>, String, String> result = threadfuture.get();

                    for (QTL q : result.getLeft()) {
                        if (!DEBUG) {
                            addEQTL(q);
                        } else {

                            //                        int snpid = q.getSNPId();
                            //                        MetaQTL4MetaTrait trait = q.getMetaTrait();

                            //                        QTLPair combo = new QTLPair();
                            //                        combo.snpid = snpid;
                            //                        combo.trait = trait;
                            //                        set.add(combo);

                        }

                        addcalled++;
                    }
                    if (settings.isMakezscoretable()) {
                        zscoreTableTf.writeln(result.getMiddle());

                        zscoreTableTfNrSamples.writeln(result.getRight());
                    }
                    result = null;
                    returned++;
                    pb.iterate();
                }
                threadfuture = null;
            } catch (InterruptedException e) {
                e.printStackTrace();
            } catch (ExecutionException e) {
                e.printStackTrace();
            }
        }
        pb.close();

        if (DEBUG) {
            if (prevSet != null) {
                // compare sets
                TextFile tf = new TextFile(outdir + "debug-p" + permutation + ".txt", TextFile.W);
                for (QTLPair p : prevSet) {
                    if (!set.contains(p)) {
                        tf.writeln(snpList[p.snpid] + "\t" + p.trait.getMetaTraitName());
                    }
                }
                tf.close();
            }
            prevSet = set;
        }

        System.out.println("Snps returned: " + returned + "\tNr of snps submitted: " + snpList.length
                + "\tNr of eQTLs evaluated: " + addcalled);
        System.out.println("Max P: " + maxSavedPvalue + "\tLocationToStoreResult: " + locationToStoreResult);

        if (settings.isMakezscoretable()) {
            zscoreTableTf.close();
            zscoreTableTfNrSamples.close();

            if (usetmp) {

                String filename = "ZScoreMatrix-Permutation" + permutation + ".txt.gz";
                if (permutation == 0) {
                    filename = "ZScoreMatrix.txt.gz";
                }
                File source = new File(tempDir + filename);
                File dest = new File(settings.getOutput() + filename);
                if (dest.exists()) {
                    System.out.println(
                            "Destination file: " + dest.getAbsolutePath() + " exists already.. Deleting!");
                    dest.delete();
                }
                System.out.println(
                        "Moving file: " + tempDir + filename + " --> " + settings.getOutput() + filename);
                FileUtils.moveFile(source, dest);

                filename = "ZScoreMatrixNrSamples-Permutation" + permutation + ".txt.gz";
                if (permutation == 0) {
                    filename = "ZScoreMatrixNrSamples.txt.gz";
                }
                source = new File(tempDir + filename);
                dest = new File(settings.getOutput() + filename);
                if (dest.exists()) {
                    System.out.println(
                            "Destination file: " + dest.getAbsolutePath() + " exists already.. Deleting!");
                    dest.delete();
                }
                System.out.println(
                        "Moving file: " + tempDir + filename + " --> " + settings.getOutput() + filename);
                FileUtils.moveFile(source, dest);
            }
        }

        for (BinaryMetaAnalysisDataset dataset : datasets) {
            dataset.close();
        }

        if (!DEBUG) {
            writeBuffer(outdir, permutation);

        }
    }
    if (usetmp) {
        // move remaining contents of tmp dir to final directory
        File source = new File(tempDir);
        File dest = new File(settings.getOutput());
        FileUtils.copyDirectory(source, dest);
        FileUtils.cleanDirectory(source);
    }
}

From source file:nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis.java

private void writeBuffer(String outdir, int permutation) throws IOException {

    // sort the finalbuffer for a last time
    if (locationToStoreResult != 0) {
        Arrays.parallelSort(finalEQTLs, 0, locationToStoreResult);
    }/*from w w  w . j a va2 s  .c o m*/

    String outfilename = outdir + "eQTLs.txt.gz";
    FileFormat outformat = FileFormat.LARGE;
    if (permutation > 0) {
        outfilename = outdir + "PermutedEQTLsPermutationRound" + permutation + ".txt.gz";
        if (!fullpermutationoutput) {
            outformat = FileFormat.REDUCED;
        }
    }

    String tab = "\t";
    String newline = "\n";

    TextFile output = new TextFile(outfilename, TextFile.W, 10 * 1048576);

    String header = "PValue\t" + "SNPName\t" + "SNPChr\t" + "SNPChrPos\t" + "ProbeName\t" + "ProbeChr\t"
            + "ProbeCenterChrPos\t" + "CisTrans\t" + "SNPType\t" + "AlleleAssessed\t" + "OverallZScore\t"
            + "DatasetsWhereSNPProbePairIsAvailableAndPassesQC\t" + "DatasetsZScores\t" + "DatasetsNrSamples\t"
            + "IncludedDatasetsMeanProbeExpression\t" + "IncludedDatasetsProbeExpressionVariance\t"
            + "HGNCName\t" + "IncludedDatasetsCorrelationCoefficient\t" + "Meta-Beta (SE)\t" + "Beta (SE)\t"
            + "FoldChange";
    if (outformat.equals(FileFormat.REDUCED)) {
        header = "PValue\tSNP\tProbe\tGene\tAlleles\tAlleleAssessed\tZScore";
    }
    output.writeln(header);
    // PValue   SNPName   SNPChr   SNPChrPos   ProbeName   ProbeChr   ProbeCenterChrPos   CisTrans   SNPType   AlleleAssessed   OverallZScore   DatasetsWhereSNPProbePairIsAvailableAndPassesQC   DatasetsZScores   DatasetsNrSamples   IncludedDatasetsMeanProbeExpression   IncludedDatasetsProbeExpressionVariance   HGNCName   IncludedDatasetsCorrelationCoefficient   Meta-Beta (SE)   Beta (SE)   FoldChange   FDR

    DecimalFormat dformat = new DecimalFormat("###.####", new DecimalFormatSymbols(Locale.US));
    DecimalFormat pformat = new DecimalFormat("###.########", new DecimalFormatSymbols(Locale.US));
    DecimalFormat smallpFormat = new DecimalFormat("0.####E0", new DecimalFormatSymbols(Locale.US));

    int ctr = 0;
    for (int i = 0; i < settings.getFinalEQTLBufferMaxLength(); i++) {
        if (finalEQTLs[i] != null) {
            ctr++;
        }
    }
    int totalctr = 0;
    for (int i = 0; i < finalEQTLs.length; i++) {
        if (finalEQTLs[i] != null) {
            totalctr++;
        }
    }
    System.out.println("There are " + ctr + " results in the buffer to write. " + totalctr
            + " QTLs are in memory at the moment.");
    ProgressBar pb = new ProgressBar(ctr, "Writing: " + outfilename);

    String cistr = "Cis";
    String transtr = "Trans";
    String greyz = "Greyzone";

    for (int i = 0; i < settings.getFinalEQTLBufferMaxLength(); i++) {
        QTL q = finalEQTLs[i];
        if (q != null) {
            //            StringBuilder sb = new StringBuilder(4096);
            if (outformat.equals(FileFormat.LARGE)) {
                if (q.getPvalue() < 1E-4) {
                    output.append(smallpFormat.format(q.getPvalue()));
                } else {
                    output.append(pformat.format(q.getPvalue()));
                }
                output.append(tab);
                int snpId = q.getSNPId();
                output.append(snpList[snpId]);
                output.append(tab);
                output.append(snpChr[snpId]);
                output.append(tab);
                output.append("" + snpPositions[snpId]);
                output.append(tab);
                MetaQTL4MetaTrait t = q.getMetaTrait();
                output.append(t.getMetaTraitName());
                output.append(tab);
                output.append(t.getChr());
                output.append(tab);
                output.append("" + t.getChrMidpoint());
                output.append(tab);
                int dist = Math.abs(t.getChrMidpoint() - snpPositions[snpId]);
                boolean sameChr = t.getChr().equals(snpChr[snpId]);
                if (sameChr && dist < settings.getCisdistance()) {
                    output.append(cistr);
                } else if (sameChr && dist < settings.getTransdistance()) {
                    output.append(greyz);
                } else {
                    output.append(transtr);
                }

                output.append(tab);
                output.append(q.getAlleles());
                output.append(tab);
                output.append(q.getAlleleAssessed());
                output.append(tab);
                output.append(dformat.format(q.getZscore()));

                float[] datasetZScores = q.getDatasetZScores();
                String[] dsBuilder = new String[datasets.length];
                String[] dsNBuilder = new String[datasets.length];
                String[] dsZBuilder = new String[datasets.length];

                for (int d = 0; d < datasetZScores.length; d++) {

                    if (!Float.isNaN(datasetZScores[d])) {
                        String str = dformat.format(datasetZScores[d]);

                        dsBuilder[d] = settings.getDatasetnames().get(d);
                        dsNBuilder[d] = "" + q.getDatasetSampleSizes()[d];
                        dsZBuilder[d] = str;
                    } else {
                        dsBuilder[d] = "-";
                        dsNBuilder[d] = "-";
                        dsZBuilder[d] = "-";
                    }
                }

                output.append(tab);
                output.append(Strings.concat(dsBuilder, Strings.semicolon));

                output.append(tab);
                output.append(Strings.concat(dsZBuilder, Strings.semicolon));

                output.append(tab);
                output.append(Strings.concat(dsNBuilder, Strings.semicolon));
                output.append("\t-\t-\t");

                output.append(t.getAnnotation());
                output.append("\t-\t-\t-\t-");
                output.append(newline);

            } else {
                //               header = "PValue\tSNP\tProbe\tGene\tAlleles\tAlleleAssessed\tZScore";

                int snpId = q.getSNPId();
                MetaQTL4MetaTrait t = q.getMetaTrait();

                if (q.getPvalue() < 1E-4) {
                    output.append(smallpFormat.format(q.getPvalue()));
                } else {
                    output.append(pformat.format(q.getPvalue()));
                }
                output.append(tab);
                output.append(snpList[snpId]);
                output.append(tab);
                output.append(t.getMetaTraitName());
                output.append(tab);
                output.append(t.getAnnotation());
                output.append(tab);
                output.append(q.getAlleles());
                output.append(tab);
                output.append(q.getAlleleAssessed());
                output.append(tab);
                output.append(dformat.format(q.getZscore()));
                output.append(newline);
            }

            pb.iterate();
        }
        finalEQTLs[i] = null; // trash it immediately
    }

    pb.close();
    output.close();
    finalEQTLs = null; // ditch the whole resultset

    if (usetmp) {

        String filename = "eQTLs.txt.gz";
        if (permutation > 0) {
            filename = "PermutedEQTLsPermutationRound" + permutation + ".txt.gz";
        }
        File source = new File(tempDir + filename);
        File dest = new File(settings.getOutput() + filename);
        if (dest.exists()) {
            System.out.println("Destination file: " + dest.getAbsolutePath() + " exists already.. Deleting!");
            dest.delete();
        }
        System.out.println("Moving file: " + tempDir + filename + " --> " + settings.getOutput() + filename);
        FileUtils.moveFile(source, dest);

    }

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

From source file:no.dusken.aranea.admin.control.UploadFileController.java

@Override
protected ModelAndView onSubmit(HttpServletRequest request, HttpServletResponse response, Object object,
        BindException bindException) throws Exception {

    String url = ServletRequestUtils.getRequiredStringParameter(request, "imageUrl");

    // get the uploaded file
    MultipartHttpServletRequest multipartRequest = (MultipartHttpServletRequest) request;
    MultipartFile file = multipartRequest.getFile("file");
    if (file == null) {
        // There is no file. Exit
        log.error("Could not extract file from request");
        return new ModelAndView(new EmptyView());
    }/* w  ww .ja  va2  s  . c  om*/
    // transfer the file to a temporary location
    String originalName = file.getOriginalFilename();
    log.debug("Got file: {}", originalName);
    File tmpFile = new File(resourceDir + "/images/tmp/" + originalName);
    tmpFile.getParentFile().mkdirs();
    file.transferTo(tmpFile);

    // move the file to the final destination
    File newFile = new File(resourceDir + "/images/" + url);
    newFile.getParentFile().mkdirs();
    FileUtils.moveFile(tmpFile, newFile);
    // SUCCESS!
    response.setStatus(200);

    return new ModelAndView(new EmptyView());
}

From source file:ome.io.bioformats.BfPyramidPixelBuffer.java

/**
 * This method should never exit without releasing the lock.
 *///from  www .  j  a v a2  s  .  co m
private void closeWriter() throws IOException {
    try {
        if (writer != null) {
            writer.close();
            writer = null;
        }
    } finally {
        try {
            if (writerFile != null) {
                try {
                    FileUtils.moveFile(writerFile, readerFile);
                } finally {
                    writerFile = null;
                }
            }
        } finally {
            releaseLock();
        }
    }
}

From source file:omero.util.TempFileManager.java

/**
 * Command-line interface to the global {@link TempFileManager} instance (
 * {@link #manger}). Valid arguments: "--debug", "clean", "dir", and for
 * testing, "lock"/*from  w ww .  j  a v a 2  s.c  om*/
 */
public static void main(String[] _args) throws IOException {
    List<String> args = Arrays.asList(_args);

    if (args.size() > 0) {

        // Debug may already be activated. See static block above.
        if (args.contains("--debug") && !System.getenv().containsKey("DEBUG")) {
            ConsoleAppender console = new ConsoleAppender();
            console.setName("System.err");
            console.setTarget(ConsoleAppender.SYSTEM_ERR);
            console.setLayout(new SimpleLayout());
            console.activateOptions();
            Logger logger = Logger.getLogger("omero");
            logger.addAppender(console);
            logger.setLevel(Level.DEBUG);
            logger.addAppender(console);
        }

        if (args.contains("clean")) {
            manager.cleanUserDir();
            System.exit(0);
        } else if (args.contains("dir")) {
            System.out.println(manager.getTempDir().getAbsolutePath());
            System.exit(0);
        } else if (args.contains("test")) {
            File test = new File("/tmp/test");
            if (test.exists()) {
                test.delete();
                System.out.println("Deleted test");
            }
            File f = create_path();
            System.out.println(f.getAbsolutePath());
            f.deleteOnExit();
            FileUtils.writeStringToFile(f, "test");
            FileUtils.moveFile(f, test);
            System.exit(0);
        } else if (args.contains("lock")) {
            System.out.println("Locking " + manager.getTempDir().getAbsolutePath());
            System.out.println("Waiting on user input...");
            System.in.read();
            System.exit(0);
        }
    }
    System.err.println("Usage: TempFileManager clean");
    System.err.println("   or: TempFileManager dir");
    System.exit(2);

}

From source file:org.ado.biblio.desktop.db.DatabaseConnectionTest.java

public void setUp() throws Exception {
    FileUtils.deleteQuietly(DATABASE_FILE_TMP);
    if (DATABASE_FILE.exists()) {
        FileUtils.moveFile(DATABASE_FILE, DATABASE_FILE_TMP);
    }/*from   ww w . jav a  2 s .c  o m*/
    Locale.setDefault(Locale.ENGLISH);
}

From source file:org.ado.biblio.desktop.db.DatabaseConnectionTest.java

@After
public void tearDown() throws Exception {
    FileUtils.deleteQuietly(DATABASE_FILE);
    if (DATABASE_FILE_TMP.exists()) {
        FileUtils.moveFile(DATABASE_FILE_TMP, DATABASE_FILE);
    }//  ww w .  j a  v a 2s  .  c o m
}

From source file:org.ado.picasa.Main.java

private static void downloadAlbum(FirefoxDriver driver, String album, File outputDir) {
    try {//from w  ww . ja v  a 2  s  .  c  om
        final String albumName = getAlbumName(album);
        System.out.println(String.format("> album name: %s  url: %s", albumName, album));
        driver.navigate().to(album);

        final List<String> photoHrefLinks = driver.findElements(By.xpath("//div[@class='goog-icon-list']//a"))
                .stream().filter(a -> MediaType.PHOTO.equals(getMediaType(a))).map(a -> a.getAttribute("href"))
                .collect(Collectors.toList());

        for (String href : photoHrefLinks) {
            downloadPhoto(driver, href);
        }

        driver.navigate().to(album);

        final List<String> videoHrefLinks = driver.findElements(By.xpath("//div[@class='goog-icon-list']//a"))
                .stream().filter(a -> MediaType.VIDEO.equals(getMediaType(a))).map(a -> a.getAttribute("href"))
                .collect(Collectors.toList());

        int index = 1;
        final FileDownloader fileDownloader = new FileDownloader(driver, outputDir.getAbsolutePath());
        for (String videoUrl : getVideoUrls(driver, videoHrefLinks, album)) {
            try {
                new FileHandler(fileDownloader.downloader(videoUrl, albumName + index++ + ".m4v"));
            } catch (Exception e) {
                System.err.println(String.format("Cannot download video '%s'.", videoUrl));
                e.printStackTrace();
            }
        }

        TimeUnit.SECONDS.sleep(10);
        System.out.println(String.format("moving photos to directory: %s", albumName));
        final File albumDirectory = new File(outputDir, albumName);
        for (File file : FileUtils.listFiles(outputDir, null, false)) {
            try {
                FileUtils.moveFileToDirectory(file, albumDirectory, true);
            } catch (IOException e) {
                FileUtils.moveFile(file,
                        new File(albumDirectory, file.getName() + "-" + System.currentTimeMillis()));
            }
        }
    } catch (Exception e) {
        System.err.println(String.format("Cannot download album '%s'", album));
        e.printStackTrace();
    }
}