Example usage for java.nio.file Path toString

List of usage examples for java.nio.file Path toString

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Introduction

In this page you can find the example usage for java.nio.file Path toString.

Prototype

String toString();

Source Link

Document

Returns the string representation of this path.

Usage

From source file:ch.bender.evacuate.Runner.java

/**
 * visit//from w  w  w . jav a2 s.  c  o m
 * <p>
 * @param aPath
 * @return
 */
private FileVisitResult visit(Path aPath) {
    if (isExcluded(aPath)) {
        myLog.debug("Skip because on exclude list: " + aPath.toString());

        if (Files.isDirectory(aPath)) {
            myExclusionDirCount++;
        } else {
            myExclusionFileCount++;
        }

        return FileVisitResult.SKIP_SUBTREE;
    }

    Path subDirToBackupRoot = myBackupDir.relativize(aPath);
    Path origPendant = myOrigDir.resolve(subDirToBackupRoot);

    if (Files.notExists(origPendant)) {
        evacuate(aPath);

        if (Files.isDirectory(aPath)) {
            myEvacuationDirCount++;
            return FileVisitResult.SKIP_SUBTREE;
        }

        // else is file:
        myEvacuationFileCount++;
        return FileVisitResult.CONTINUE;
    }

    return FileVisitResult.CONTINUE;
}

From source file:com.splicemachine.storage.HNIOFileSystem.java

@Override
public void touchFile(Path path) throws IOException {
    if (!fs.createNewFile(toHPath(path))) {
        throw new FileAlreadyExistsException(path.toString());
    }//from  ww w.j  a  v a  2 s. c  o  m
}

From source file:ffx.potential.utils.PotentialsFileOpener.java

/**
 * At present, parses the PDB, XYZ, INT, or ARC file from the constructor
 * and creates MolecularAssembly and properties objects.
 *//*from   ww  w  .  j  a v  a 2  s .co m*/
@Override
public void run() {
    int numFiles = allFiles.length;
    for (int i = 0; i < numFiles; i++) {
        File fileI = allFiles[i];
        Path pathI = allPaths[i];
        MolecularAssembly assembly = new MolecularAssembly(pathI.toString());
        assembly.setFile(fileI);
        CompositeConfiguration properties = Keyword.loadProperties(fileI);
        ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
        ForceField forceField = forceFieldFilter.parse();
        String patches[] = properties.getStringArray("patch");
        for (String patch : patches) {
            logger.info(" Attempting to read force field patch from " + patch + ".");
            CompositeConfiguration patchConfiguration = new CompositeConfiguration();
            try {
                patchConfiguration.addProperty("propertyFile", fileI.getCanonicalPath());
            } catch (IOException e) {
                logger.log(Level.INFO, " Error loading {0}.", patch);
            }
            patchConfiguration.addProperty("parameters", patch);
            forceFieldFilter = new ForceFieldFilter(patchConfiguration);
            ForceField patchForceField = forceFieldFilter.parse();
            forceField.append(patchForceField);
            if (RotamerLibrary.addRotPatch(patch)) {
                logger.info(String.format(" Loaded rotamer definitions from patch %s.", patch));
            }
        }
        assembly.setForceField(forceField);
        if (new PDBFileFilter().acceptDeep(fileI)) {
            filter = new PDBFilter(fileI, assembly, forceField, properties);
        } else if (new XYZFileFilter().acceptDeep(fileI)) {
            filter = new XYZFilter(fileI, assembly, forceField, properties);
        } else if (new INTFileFilter().acceptDeep(fileI) || new ARCFileFilter().accept(fileI)) {
            filter = new INTFilter(fileI, assembly, forceField, properties);
        } else {
            throw new IllegalArgumentException(
                    String.format(" File %s could not be recognized as a valid PDB, XYZ, INT, or ARC file.",
                            pathI.toString()));
        }
        if (filter.readFile()) {
            if (!(filter instanceof PDBFilter)) {
                Utilities.biochemistry(assembly, filter.getAtomList());
            }
            filter.applyAtomProperties();
            assembly.finalize(true, forceField);
            //ForceFieldEnergy energy = new ForceFieldEnergy(assembly, filter.getCoordRestraints());
            ForceFieldEnergy energy;
            if (nThreads > 0) {
                energy = new ForceFieldEnergy(assembly, filter.getCoordRestraints(), nThreads);
            } else {
                energy = new ForceFieldEnergy(assembly, filter.getCoordRestraints());
            }
            assembly.setPotential(energy);
            assemblies.add(assembly);
            propertyList.add(properties);

            if (filter instanceof PDBFilter) {
                PDBFilter pdbFilter = (PDBFilter) filter;
                List<Character> altLocs = pdbFilter.getAltLocs();
                if (altLocs.size() > 1 || altLocs.get(0) != ' ') {
                    StringBuilder altLocString = new StringBuilder("\n Alternate locations found [ ");
                    for (Character c : altLocs) {
                        // Do not report the root conformer.
                        if (c == ' ') {
                            continue;
                        }
                        altLocString.append(format("(%s) ", c));
                    }
                    altLocString.append("]\n");
                    logger.info(altLocString.toString());
                }

                /**
                 * Alternate conformers may have different chemistry, so
                 * they each need to be their own MolecularAssembly.
                 */
                for (Character c : altLocs) {
                    if (c.equals(' ') || c.equals('A')) {
                        continue;
                    }
                    MolecularAssembly newAssembly = new MolecularAssembly(pathI.toString());
                    newAssembly.setForceField(assembly.getForceField());
                    pdbFilter.setAltID(newAssembly, c);
                    pdbFilter.clearSegIDs();
                    if (pdbFilter.readFile()) {
                        String fileName = assembly.getFile().getAbsolutePath();
                        newAssembly.setName(FilenameUtils.getBaseName(fileName) + " " + c);
                        filter.applyAtomProperties();
                        newAssembly.finalize(true, assembly.getForceField());
                        //energy = new ForceFieldEnergy(newAssembly, filter.getCoordRestraints());
                        if (nThreads > 0) {
                            energy = new ForceFieldEnergy(assembly, filter.getCoordRestraints(), nThreads);
                        } else {
                            energy = new ForceFieldEnergy(assembly, filter.getCoordRestraints());
                        }
                        newAssembly.setPotential(energy);
                        assemblies.add(newAssembly);
                    }
                }
            }
        } else {
            logger.warning(String.format(" Failed to read file %s", fileI.toString()));
        }
    }
    activeAssembly = assemblies.get(0);
    activeProperties = propertyList.get(0);
}

From source file:net.es.nsi.topology.translator.Options.java

/**
 * Processes the "configfile" command line and system property option.
 *
 * @param cmd Commands entered by the user.
 * @param configdir The application configuration directory.
 * @return The configuration file path.//  w ww .  j  a v a 2  s. c  o  m
 * @throws IOException
 */
private String getConfigFile(CommandLine cmd) throws IOException {
    String file = System.getProperty(Properties.SYSTEM_PROPERTY_CONFIGFILE);
    file = cmd.getOptionValue(ARGNAME_CONFIGFILE, file);

    Path path;
    if (Strings.isNullOrEmpty(file)) {
        path = Paths.get(basedir, DEFAULT_CONFIGFILE);
    } else {
        path = Paths.get(file);
        if (!path.isAbsolute()) {
            path = Paths.get(basedir, path.toString());
        }
    }

    try {
        file = path.toRealPath().toString();
    } catch (IOException ex) {
        System.err.println("Error: Configuration file not found " + path.toString() + "\n");
        throw ex;
    }

    return file;
}

From source file:com.evolveum.midpoint.tools.schemadist.SchemaDistMojo.java

private void serializeXml(Document dom, Path filePath, File workDir, File outDir)
        throws MojoFailureException, MojoExecutionException {
    Path fileRelPath = workDir.toPath().relativize(filePath);
    File outFile = new File(outDir, fileRelPath.toString());
    initializeOutDir(outFile.getParentFile());
    try {/*from w  ww  .  ja  v a 2s .  c  o  m*/
        DOMUtil.serializeDOMToFile(dom, outFile);
    } catch (TransformerFactoryConfigurationError | TransformerException e) {
        throw new MojoExecutionException(
                "Error serializing modified file " + fileRelPath + " to XML: " + e.getMessage(), e);
    }
}

From source file:com.google.cloud.tools.managedcloudsdk.install.ZipExtractorProvider.java

@Override
public void extract(Path archive, Path destination, ProgressListener progressListener) throws IOException {

    progressListener.start("Extracting archive: " + archive.getFileName(), ProgressListener.UNKNOWN);

    String canonicalDestination = destination.toFile().getCanonicalPath();

    // Use ZipFile instead of ZipArchiveInputStream so that we can obtain file permissions
    // on unix-like systems via getUnixMode(). ZipArchiveInputStream doesn't have access to
    // all the zip file data and will return "0" for any call to getUnixMode().
    try (ZipFile zipFile = new ZipFile(archive.toFile())) {
        // TextProgressBar progressBar = textBarFactory.newProgressBar(messageListener, count);
        Enumeration<ZipArchiveEntry> zipEntries = zipFile.getEntries();
        while (zipEntries.hasMoreElements()) {
            ZipArchiveEntry entry = zipEntries.nextElement();
            Path entryTarget = destination.resolve(entry.getName());

            String canonicalTarget = entryTarget.toFile().getCanonicalPath();
            if (!canonicalTarget.startsWith(canonicalDestination + File.separator)) {
                throw new IOException("Blocked unzipping files outside destination: " + entry.getName());
            }//from   w  w  w. j a v a 2 s. c  om

            progressListener.update(1);
            logger.fine(entryTarget.toString());

            if (entry.isDirectory()) {
                if (!Files.exists(entryTarget)) {
                    Files.createDirectories(entryTarget);
                }
            } else {
                if (!Files.exists(entryTarget.getParent())) {
                    Files.createDirectories(entryTarget.getParent());
                }
                try (OutputStream out = new BufferedOutputStream(Files.newOutputStream(entryTarget))) {
                    try (InputStream in = zipFile.getInputStream(entry)) {
                        IOUtils.copy(in, out);
                        PosixFileAttributeView attributeView = Files.getFileAttributeView(entryTarget,
                                PosixFileAttributeView.class);
                        if (attributeView != null) {
                            attributeView
                                    .setPermissions(PosixUtil.getPosixFilePermissions(entry.getUnixMode()));
                        }
                    }
                }
            }
        }
    }
    progressListener.done();
}

From source file:com.highcharts.export.controller.ExportController.java

public String createRandomFileName(String extension) {
    Path path = Paths.get(TempDir.outputDir.toString(),
            RandomStringUtils.randomAlphanumeric(8) + "." + extension);
    return path.toString();
}

From source file:com.bekwam.resignator.commands.UnsignCommand.java

private Path copyJAR(File sourceJarFile) throws CommandExecutionException {
    Path workingJarFile = Paths.get(tempDir.toString(), sourceJarFile.getName());

    try {/*from w w  w .  j av  a2 s.com*/
        Files.copy(Paths.get(sourceJarFile.getAbsolutePath()), workingJarFile);
    } catch (IOException exc) {
        String msg = String.format("can't copy %s to %s", sourceJarFile.getAbsolutePath(),
                workingJarFile.toString());
        logger.error(msg, exc);
        throw new CommandExecutionException(msg);
    }
    return workingJarFile;
}

From source file:dk.dma.msiproxy.common.repo.ThumbnailService.java

/**
 * Creates a thumbnail for the image file using libvips
 *
 * @param file      the image file/*from   w w w  .j a  v a2 s.  c  om*/
 * @param thumbFile the resulting thumbnail file
 * @param size      the size of the thumbnail
 */
private void createThumbnailUsingVips(Path file, Path thumbFile, IconSize size) throws IOException {

    try {

        // Example command: vipsthumbnail -s 64 -p bilinear -o thumb.png image2.jpg
        final Process proc = new ProcessBuilder(vipsCmd, "-s", String.valueOf(size.getSize()), "-p", "bilinear",
                "-o", thumbFile.toString(), file.toString()).directory(new File(System.getProperty("user.dir")))
                        .inheritIO().start();

        BufferedReader br = new BufferedReader(new InputStreamReader(proc.getInputStream()));
        String line;
        while ((line = br.readLine()) != null) {
            log.debug(line);
        }

        //Wait to get exit value
        int exitValue = proc.waitFor();
        log.debug("Exit Value is " + exitValue);

        // Update the timestamp of the thumbnail file to match the change date of the image file
        Files.setLastModifiedTime(thumbFile, Files.getLastModifiedTime(file));

    } catch (IOException | InterruptedException e) {
        log.error("Error creating thumbnail for image " + file, e);
        throw new IOException(e);
    }
}

From source file:info.pancancer.arch3.worker.WorkerRunnable.java

/**
 * Write the content of the job object to an INI file which will be used by the workflow.
 *
 * @param job//  w ww .ja va  2  s  .  c o m
 *            - the job object which must contain a HashMap, which will be used to write an INI file.
 * @return A Path object pointing to the new file will be returned.
 * @throws IOException
 */
private Path writeINIFile(Job job) throws IOException {
    log.info("INI is: " + job.getIniStr());
    EnumSet<PosixFilePermission> perms = EnumSet.of(PosixFilePermission.OWNER_READ,
            PosixFilePermission.OWNER_WRITE, PosixFilePermission.OWNER_EXECUTE, PosixFilePermission.GROUP_READ,
            PosixFilePermission.GROUP_WRITE, PosixFilePermission.OTHERS_READ, PosixFilePermission.OTHERS_WRITE);
    FileAttribute<?> attrs = PosixFilePermissions.asFileAttribute(perms);
    Path pathToINI = Files.createTempFile("seqware_", ".ini", attrs);
    log.info("INI file: " + pathToINI.toString());
    try (BufferedWriter bw = new BufferedWriter(
            new OutputStreamWriter(new FileOutputStream(pathToINI.toFile()), StandardCharsets.UTF_8))) {
        bw.write(job.getIniStr());
        bw.flush();
    }
    return pathToINI;
}