Examples with Files java.nio.file.Files used on opensource projects

Example 11 with Files

use of java.nio.file.Files in project nifi by apache.

the class FlowConfigurationArchiveManager method archive.

/**
 * Archive current flow configuration file by copying the original file to the archive directory.
 * Before creating new archive file, this method removes old archives to satisfy following conditions:
 * <ul>
 * <li>Number of archive files less than or equal to maxCount</li>
 * <li>Keep archive files which has last modified timestamp no older than current system timestamp - maxTimeMillis</li>
 * <li>Total size of archive files less than or equal to maxStorageBytes</li>
 * </ul>
 * This method keeps other files intact, so that users can keep particular archive by copying it with different name.
 * Whether a given file is archive file or not is determined by the filename.
 * Since archive file name consists of timestamp up to seconds, if archive is called multiple times within a second,
 * it will overwrite existing archive file with the same name.
 * @return Newly created archive file, archive filename is computed by adding ISO8601
 * timestamp prefix to the original filename, ex) 20160706T160719+0900_flow.xml.gz
 * @throws IOException If it fails to create new archive file.
 * Although, other IOExceptions like the ones thrown during removing expired archive files will not be thrown.
 */
public File archive() throws IOException {
    final String originalFlowConfigFileName = flowConfigFile.getFileName().toString();
    final File archiveFile = setupArchiveFile();
    // Collect archive files by its name
    final long now = System.currentTimeMillis();
    final AtomicLong totalArchiveSize = new AtomicLong(0);
    final List<Path> archives = Files.walk(archiveDir, 1).filter(p -> {
        final String filename = p.getFileName().toString();
        if (Files.isRegularFile(p) && filename.endsWith("_" + originalFlowConfigFileName)) {
            final Matcher matcher = archiveFilenamePattern.matcher(filename);
            if (matcher.matches() && filename.equals(matcher.group(1) + "_" + originalFlowConfigFileName)) {
                try {
                    totalArchiveSize.getAndAdd(Files.size(p));
                } catch (IOException e) {
                    logger.warn("Failed to get file size of {} due to {}", p, e);
                }
                return true;
            }
        }
        return false;
    }).collect(Collectors.toList());
    // Sort by timestamp.
    archives.sort(Comparator.comparingLong(path -> path.toFile().lastModified()));
    logger.debug("archives={}", archives);
    final int archiveCount = archives.size();
    final long flowConfigFileSize = Files.size(flowConfigFile);
    IntStream.range(0, archiveCount).filter(i -> {
        // If maxCount is specified, remove old archives
        boolean old = maxCount != null && maxCount > 0 && (archiveCount - i) > maxCount - 1;
        // If maxTime is specified, remove expired archives
        final File archive = archives.get(i).toFile();
        old = old || (maxTimeMillis != null && maxTimeMillis > 0 && (now - archive.lastModified()) > maxTimeMillis);
        // If maxStorage is specified, remove old archives
        old = old || (maxStorageBytes != null && maxStorageBytes > 0 && (totalArchiveSize.get() + flowConfigFileSize > maxStorageBytes));
        if (old) {
            totalArchiveSize.getAndAdd(archive.length() * -1);
            logger.info("Removing old archive file {} to reduce storage usage. currentSize={}", archive, totalArchiveSize);
        }
        return old;
    }).forEach(i -> {
        try {
            Files.delete(archives.get(i));
        } catch (IOException e) {
            logger.warn("Failed to delete {} to reduce storage usage, due to {}", archives.get(i), e);
        }
    });
    // Create new archive file.
    Files.copy(flowConfigFile, archiveFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
    if (maxStorageBytes != null && maxStorageBytes > 0 && flowConfigFileSize > maxStorageBytes) {
        logger.warn("Size of {} ({}) exceeds configured maxStorage size ({}). Archive won't be able to keep old files.", flowConfigFile, flowConfigFileSize, maxStorageBytes);
    }
    return archiveFile;
}

Example 12 with Files

use of java.nio.file.Files in project jabref by JabRef.

the class WriteXMPEntryEditorAction method actionPerformed.

@Override
public void actionPerformed(ActionEvent actionEvent) {
    setEnabled(false);
    panel.output(Localization.lang("Writing XMP-metadata..."));
    panel.frame().setProgressBarIndeterminate(true);
    panel.frame().setProgressBarVisible(true);
    BibEntry entry = editor.getEntry();
    // Make a list of all PDFs linked from this entry:
    List<Path> files = entry.getFiles().stream().filter(file -> file.getFileType().equalsIgnoreCase("pdf")).map(file -> file.findIn(panel.getBibDatabaseContext(), Globals.prefs.getFileDirectoryPreferences())).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toList());
    // We want to offload the actual work to a background thread, so we have a worker
    // thread:
    AbstractWorker worker = new WriteXMPWorker(files, entry);
    // Using Spin, we get a thread that gets synchronously offloaded to a new thread,
    // blocking the execution of this method:
    worker.getWorker().run();
    // After the worker thread finishes, we are unblocked and ready to print the
    // status message:
    panel.output(message);
    panel.frame().setProgressBarVisible(false);
    setEnabled(true);
}

Example 13 with Files

use of java.nio.file.Files in project gatk by broadinstitute.

the class ReadsSparkSinkUnitTest method readsSinkShardedTest.

@Test(dataProvider = "loadReadsBAM", groups = "spark")
public void readsSinkShardedTest(String inputBam, String outputFileName, String referenceFile, String outputFileExtension) throws IOException {
    final File outputFile = createTempFile(outputFileName, outputFileExtension);
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    ReadsSparkSource readSource = new ReadsSparkSource(ctx);
    JavaRDD<GATKRead> rddParallelReads = readSource.getParallelReads(inputBam, referenceFile);
    // ensure that the output is in two shards
    rddParallelReads = rddParallelReads.repartition(2);
    SAMFileHeader header = readSource.getHeader(inputBam, referenceFile);
    ReadsSparkSink.writeReads(ctx, outputFile.getAbsolutePath(), referenceFile, rddParallelReads, header, ReadsWriteFormat.SHARDED);
    int shards = outputFile.listFiles((dir, name) -> !name.startsWith(".") && !name.startsWith("_")).length;
    Assert.assertEquals(shards, 2);
    // check that no local .crc files are created
    int crcs = outputFile.listFiles((dir, name) -> name.startsWith(".") && name.endsWith(".crc")).length;
    Assert.assertEquals(crcs, 0);
    JavaRDD<GATKRead> rddParallelReads2 = readSource.getParallelReads(outputFile.getAbsolutePath(), referenceFile);
    // reads are not globally sorted, so don't test that
    Assert.assertEquals(rddParallelReads.count(), rddParallelReads2.count());
}

Example 14 with Files

use of java.nio.file.Files in project jabref by JabRef.

the class CiteKeyBasedFileFinder method findFilesByExtension.

/**
     * Returns a list of all files in the given directories which have one of the given extension.
     */
public Set<Path> findFilesByExtension(List<Path> directories, List<String> extensions) {
    Objects.requireNonNull(extensions, "Extensions must not be null!");
    BiPredicate<Path, BasicFileAttributes> isFileWithCorrectExtension = (path, attributes) -> !Files.isDirectory(path) && extensions.contains(FileHelper.getFileExtension(path).orElse(""));
    Set<Path> result = new HashSet<>();
    for (Path directory : directories) {
        try (Stream<Path> files = Files.find(directory, Integer.MAX_VALUE, isFileWithCorrectExtension)) {
            result.addAll(files.collect(Collectors.toSet()));
        } catch (IOException e) {
            LOGGER.error("Problem in finding files", e);
        }
    }
    return result;
}

Example 15 with Files

use of java.nio.file.Files in project winery by eclipse.

the class WriterUtils method storeTypes.

public static void storeTypes(Path path, String namespace, String id) {
    LOGGER.debug("Store type: {}", id);
    try {
        MediaType mediaType = MediaTypes.MEDIATYPE_XSD;
        TImport.Builder builder = new TImport.Builder(Namespaces.XML_NS);
        builder.setNamespace(namespace);
        builder.setLocation(id + ".xsd");
        GenericImportId rid = new XSDImportId(namespace, id, false);
        TDefinitions definitions = BackendUtils.createWrapperDefinitions(rid);
        definitions.getImport().add(builder.build());
        CsarImporter.storeDefinitions(rid, definitions);
        RepositoryFileReference ref = BackendUtils.getRefOfDefinitions(rid);
        List<File> files = Files.list(path).filter(Files::isRegularFile).map(Path::toFile).collect(Collectors.toList());
        for (File file : files) {
            BufferedInputStream stream = new BufferedInputStream(new FileInputStream(file));
            RepositoryFileReference fileRef = new RepositoryFileReference(ref.getParent(), file.getName());
            RepositoryFactory.getRepository().putContentToFile(fileRef, stream, mediaType);
        }
    } catch (IllegalArgumentException | IOException e) {
        throw new IllegalStateException(e);
    }
}