Examples with ZipInputStream java.util.zip.ZipInputStream used on opensource projects

Example 86 with ZipInputStream

use of java.util.zip.ZipInputStream in project nifi by apache.

the class TestMergeContent method testZip.

@Test
public void testZip() throws IOException {
    final TestRunner runner = TestRunners.newTestRunner(new MergeContent());
    runner.setProperty(MergeContent.MAX_BIN_AGE, "1 sec");
    runner.setProperty(MergeContent.MERGE_FORMAT, MergeContent.MERGE_FORMAT_ZIP);
    createFlowFiles(runner);
    runner.run();
    runner.assertQueueEmpty();
    runner.assertTransferCount(MergeContent.REL_MERGED, 1);
    runner.assertTransferCount(MergeContent.REL_FAILURE, 0);
    runner.assertTransferCount(MergeContent.REL_ORIGINAL, 3);
    final MockFlowFile bundle = runner.getFlowFilesForRelationship(MergeContent.REL_MERGED).get(0);
    try (final InputStream rawIn = new ByteArrayInputStream(runner.getContentAsByteArray(bundle));
        final ZipInputStream in = new ZipInputStream(rawIn)) {
        Assert.assertNotNull(in.getNextEntry());
        final byte[] part1 = IOUtils.toByteArray(in);
        Assert.assertTrue(Arrays.equals("Hello".getBytes("UTF-8"), part1));
        in.getNextEntry();
        final byte[] part2 = IOUtils.toByteArray(in);
        Assert.assertTrue(Arrays.equals(", ".getBytes("UTF-8"), part2));
        in.getNextEntry();
        final byte[] part3 = IOUtils.toByteArray(in);
        Assert.assertTrue(Arrays.equals("World!".getBytes("UTF-8"), part3));
    }
    bundle.assertAttributeEquals(CoreAttributes.MIME_TYPE.key(), "application/zip");
}

Example 87 with ZipInputStream

use of java.util.zip.ZipInputStream in project nifi by apache.

the class ZipUnpackerSequenceFileWriter method processInputStream.

@Override
protected void processInputStream(InputStream stream, final FlowFile flowFile, final Writer writer) throws IOException {
    try (final ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(stream))) {
        ZipEntry zipEntry;
        while ((zipEntry = zipIn.getNextEntry()) != null) {
            if (zipEntry.isDirectory()) {
                continue;
            }
            final File file = new File(zipEntry.getName());
            final String key = file.getName();
            long fileSize = zipEntry.getSize();
            final InputStreamWritable inStreamWritable = new InputStreamWritable(zipIn, (int) fileSize);
            writer.append(new Text(key), inStreamWritable);
            logger.debug("Appending FlowFile {} to Sequence File", new Object[] { key });
        }
    }
}

Example 88 with ZipInputStream

use of java.util.zip.ZipInputStream in project ice by JBEI.

the class TraceSequences method addTraceSequence.

public boolean addTraceSequence(File file, String uploadFileName) {
    entryAuthorization.expectRead(userId, entry);
    FileInputStream inputStream;
    try {
        inputStream = new FileInputStream(file);
    } catch (FileNotFoundException e) {
        Logger.error(e);
        return false;
    }
    if (uploadFileName.toLowerCase().endsWith(".zip")) {
        try (ZipInputStream zis = new ZipInputStream(inputStream)) {
            ZipEntry zipEntry;
            while (true) {
                zipEntry = zis.getNextEntry();
                if (zipEntry != null) {
                    if (!zipEntry.isDirectory() && !zipEntry.getName().startsWith("__MACOSX")) {
                        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
                        int c;
                        while ((c = zis.read()) != -1) {
                            byteArrayOutputStream.write(c);
                        }
                        String zipFilename = Paths.get(zipEntry.getName()).getFileName().toString();
                        boolean parsed = parseTraceSequence(zipFilename, byteArrayOutputStream.toByteArray());
                        if (!parsed) {
                            String errMsg = ("Could not parse \"" + zipEntry.getName() + "\". Only Fasta, GenBank & ABI files are supported.");
                            Logger.error(errMsg);
                            return false;
                        }
                    }
                } else {
                    break;
                }
            }
        } catch (IOException e) {
            String errMsg = ("Could not parse zip file.");
            Logger.error(errMsg);
            return false;
        }
    } else {
        try {
            boolean parsed = parseTraceSequence(uploadFileName, IOUtils.toByteArray(inputStream));
            if (!parsed) {
                String errMsg = ("Could not parse \"" + uploadFileName + "\". Only Fasta, GenBank & ABI files are supported.");
                Logger.error(errMsg);
                return false;
            }
        } catch (IOException e) {
            Logger.error(e);
            return false;
        }
    }
    return true;
}

Example 89 with ZipInputStream

use of java.util.zip.ZipInputStream in project processdash by dtuma.

the class FileBackupManager method createExternalizedBackupFile.

private File createExternalizedBackupFile(URL backup) throws IOException {
    // open the existing backup file as a ZIP stream
    ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(backup.openStream()));
    // create a temporary file for externalizing purposes
    File result = TempFileFactory.get().createTempFile("pdash-backup", ".zip");
    result.deleteOnExit();
    ZipOutputStream zipOut = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(result)));
    zipOut.setLevel(9);
    ExternalResourceManager extMgr = ExternalResourceManager.getInstance();
    // copy all the files from the existing backup into the externalized
    // backup (but skip any files that appear to be externalized)
    ZipEntry e;
    while ((e = zipIn.getNextEntry()) != null) {
        String filename = e.getName();
        if (extMgr.isArchivedItem(filename))
            continue;
        ZipEntry eOut = new ZipEntry(filename);
        eOut.setTime(e.getTime());
        zipOut.putNextEntry(eOut);
        FileUtils.copyFile(zipIn, zipOut);
        zipOut.closeEntry();
    }
    zipIn.close();
    // now, ask the external resource manager to augment the ZIP.
    extMgr.addExternalResourcesToBackup(zipOut);
    zipOut.finish();
    zipOut.close();
    return result;
}

Example 90 with ZipInputStream

use of java.util.zip.ZipInputStream in project processdash by dtuma.

the class WBSSynchronizer method getUserDumpData.

private Element getUserDumpData(File f) {
    FileInputStream fileInputStream = null;
    Element result = null;
    String datasetID = null;
    try {
        fileInputStream = new FileInputStream(f);
        ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(fileInputStream));
        NonclosingInputStream nis = new NonclosingInputStream(zipIn);
        ZipEntry e;
        while ((e = zipIn.getNextEntry()) != null) {
            if (e.getName().equals(USER_DUMP_ENTRY_NAME)) {
                result = XMLUtils.parse(nis).getDocumentElement();
                if (result.hasAttribute(DATASET_ID_ATTR))
                    break;
            } else if (e.getName().equals(MANIFEST_ENTRY_NAME)) {
                datasetID = getDatasetIdFromManifest(nis);
            }
        }
    } catch (Exception e) {
        logger.severe("Unable to read user dump data from file " + f);
        e.printStackTrace();
    }
    FileUtils.safelyClose(fileInputStream);
    if (result == null) {
        // the user's exported pdash file did not contain a dump file.
        logger.fine("No " + USER_DUMP_ENTRY_NAME + " file found in " + f);
    } else if (XMLUtils.hasValue(datasetID)) {
        result.setAttribute(DATASET_ID_ATTR, datasetID);
    }
    return result;
}