Examples with SeekableByteChannel java.nio.channels.SeekableByteChannel used on opensource projects

Example 6 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project helios by spotify.

the class X509CertificateFactory method saveToCache.

private static void saveToCache(final Path cacheDirectory, final Path cacheCertPath, final Path cacheKeyPath, final CertificateAndPrivateKey certificateAndPrivateKey) {
    try {
        Files.createDirectories(cacheDirectory);
        final String certPem = asPemString(certificateAndPrivateKey.getCertificate());
        final String keyPem = asPemString(certificateAndPrivateKey.getPrivateKey());
        // overwrite any existing file, and make sure it's only readable by the current user
        final Set<StandardOpenOption> options = ImmutableSet.of(CREATE, WRITE);
        final Set<PosixFilePermission> perms = ImmutableSet.of(PosixFilePermission.OWNER_READ, PosixFilePermission.OWNER_WRITE);
        final FileAttribute<Set<PosixFilePermission>> attrs = PosixFilePermissions.asFileAttribute(perms);
        try (final SeekableByteChannel sbc = Files.newByteChannel(cacheCertPath, options, attrs)) {
            sbc.write(ByteBuffer.wrap(certPem.getBytes()));
        }
        try (final SeekableByteChannel sbc = Files.newByteChannel(cacheKeyPath, options, attrs)) {
            sbc.write(ByteBuffer.wrap(keyPem.getBytes()));
        }
        log.debug("cached generated certificate to {}", cacheCertPath);
    } catch (IOException e) {
        // couldn't save to the cache, oh well
        log.warn("error caching generated certificate", e);
    }
}

Example 7 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project bazel by bazelbuild.

the class ZipFiles method unixExternalFileAttributes.

/**
   * Returns the external file attributes of each entry as a mapping from the entry name to the
   * 32-bit value. As long as the attributes are generated by a Unix host, this includes the POSIX
   * file permissions in the upper two bytes. Entries not generated by a Unix host are not included
   * in the result.
   */
public static Map<String, Integer> unixExternalFileAttributes(Path zipFile) throws IOException {
    // Field descriptions in comments were taken from this document:
    // http://pkware.cachefly.net/webdocs/casestudies/APPNOTE.TXT
    ImmutableMap.Builder<String, Integer> attributes = new ImmutableMap.Builder<>();
    try (SeekableByteChannel input = Files.newByteChannel(zipFile)) {
        // The data we care about is toward the end of the file, after the compressed data for each
        // file. We begin by looking for the start of the end of central directory record, which is
        // marked by the signature 0x06054b50
        //
        // This contains the centralDirectoryStartOffset value, which tells us where to seek to find
        // the first central directory entry. Each such entry is marked by the signature 0x02014b50
        // and appear in sequence, one entry for each file in the .zip.
        //
        // The central directory entry contains many values, including the file name, the external
        // file attributes, and the version made by value. If the version made by indicates a Unix
        // host (0x03??), we include the external file attributes in the returned map.
        long offset = input.size() - 4;
        while (offset >= 0) {
            input.position(offset);
            int signature = readBytes(4, input);
            if (signature == 0x06054b50) {
                break;
            } else if (signature == 0x06064b50) {
                throw new IOException("Zip64 format not supported: " + zipFile);
            }
            offset--;
        }
        if (offset < 0) {
            throw new IOException();
        }
        // Read end of central directory structure
        input.position(input.position() + // number of this disk
        2 + // number of the disk with the start of the central directory
        2);
        int entryCount = readBytes(2, input);
        input.position(input.position() + // total number of entries in the central directory
        2);
        input.position(input.position() + // size of the central directory
        4);
        int centralDirectoryStartOffset = readBytes(4, input);
        if (0xffffffff == centralDirectoryStartOffset) {
            throw new IOException("Zip64 format not supported.");
        }
        input.position(centralDirectoryStartOffset);
        int entriesFound = 0;
        // Read each central directory entry
        while ((entriesFound < entryCount) && (readBytes(4, input) == 0x02014b50)) {
            int versionMadeBy = readBytes(2, input);
            input.position(input.position() + // version needed to extract
            2 + // general purpose bit flag
            2 + // compression method
            2 + // last mod file time
            2 + // last mod file date
            2 + // crc-32
            4 + // compressed size
            4 + // uncompressed size
            4);
            int filenameLength = readBytes(2, input);
            int extraFieldLength = readBytes(2, input);
            int fileCommentLength = readBytes(2, input);
            input.position(input.position() + // disk number start
            2 + // internal file attributes
            2);
            int externalFileAttributes = readBytes(4, input);
            input.position(input.position() + // relative offset of local header
            4);
            ByteBuffer filenameBuffer = ByteBuffer.allocate(filenameLength);
            if (filenameLength != input.read(filenameBuffer)) {
                throw new IOException(String.format("Could not read file name (length %d) in central directory record", filenameLength));
            }
            input.position(input.position() + extraFieldLength + fileCommentLength);
            entriesFound++;
            if ((versionMadeBy >> 8) == 3) {
                // Zip made by a Unix host - the external file attributes are POSIX permissions.
                String filename = new String(filenameBuffer.array(), StandardCharsets.UTF_8);
                attributes.put(filename, externalFileAttributes);
            }
        }
        if (entriesFound != entryCount) {
            System.err.printf("WARNING: Expected %d entries in central directory record in '%s', but found %d\n", entryCount, zipFile, entriesFound);
        }
    }
    return attributes.build();
}

Example 8 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project ratpack by ratpack.

the class IoUtils method read.

public static ByteBuf read(ByteBufAllocator allocator, Path path) throws IOException {
    try (SeekableByteChannel sbc = Files.newByteChannel(path);
        InputStream in = Channels.newInputStream(sbc)) {
        int size = Ints.checkedCast(sbc.size());
        ByteBuf byteBuf = allocator.directBuffer(size, size);
        byteBuf.writeBytes(in, size);
        return byteBuf;
    }
}

Example 9 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class ReadsDataSourceUnitTest method testManuallySpecifiedIndicesWithCustomReaderFactoryAndNullWrappers.

@Test(dataProvider = "manuallySpecifiedIndexTestData")
public void testManuallySpecifiedIndicesWithCustomReaderFactoryAndNullWrappers(final List<Path> bams, final List<Path> indices) {
    final SamReaderFactory customFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.STRICT);
    // ReadsDataSource should not be using the wrapper since the files are not on the Google cloud.
    // So we pass this invalid wrapper: if the code tries to use it, it'll blow up.
    Function<SeekableByteChannel, SeekableByteChannel> nullWrapper = (SeekableByteChannel) -> null;
    try (final ReadsDataSource readsSource = new ReadsDataSource(bams, indices, customFactory, nullWrapper, nullWrapper)) {
        Assert.assertTrue(readsSource.indicesAvailable(), "Explicitly-provided indices not detected for bams: " + bams);
        final Iterator<GATKRead> queryReads = readsSource.query(new SimpleInterval("1", 1, 300));
        int queryCount = 0;
        while (queryReads.hasNext()) {
            ++queryCount;
            queryReads.next();
        }
        Assert.assertEquals(queryCount, 5, "Wrong number of reads returned in query");
    }
}

Example 10 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project DataflowJavaSDK-examples by GoogleCloudPlatform.

the class MinimalWordCountJava8Test method buildMockGcsUtil.

private GcsUtil buildMockGcsUtil() throws IOException {
    GcsUtil mockGcsUtil = Mockito.mock(GcsUtil.class);
    // Any request to open gets a new bogus channel
    Mockito.when(mockGcsUtil.open(Mockito.any(GcsPath.class))).then(new Answer<SeekableByteChannel>() {

        @Override
        public SeekableByteChannel answer(InvocationOnMock invocation) throws Throwable {
            return FileChannel.open(Files.createTempFile("channel-", ".tmp"), StandardOpenOption.CREATE, StandardOpenOption.DELETE_ON_CLOSE);
        }
    });
    // Any request for expansion returns a list containing the original GcsPath
    // This is required to pass validation that occurs in TextIO during apply()
    Mockito.when(mockGcsUtil.expand(Mockito.any(GcsPath.class))).then(new Answer<List<GcsPath>>() {

        @Override
        public List<GcsPath> answer(InvocationOnMock invocation) throws Throwable {
            return ImmutableList.of((GcsPath) invocation.getArguments()[0]);
        }
    });
    return mockGcsUtil;
}