public File getFile() {
if (file == null) {
file = new File(tmpDir, entry.getName());
copyTo(file);
}
return file;
}
@Override
public void unarchive(InputStream source, File target) {
try (TarArchiveInputStream tIn = new TarArchiveInputStream(source)) {
TarArchiveEntry entry = tIn.getNextTarEntry();
while (entry != null) {
if (entry.isDirectory()) {
entry = tIn.getNextTarEntry();
continue;
}
File curfile = new File(target, entry.getName());
File parent = curfile.getParentFile();
if (!parent.exists()) {
parent.mkdirs();
}
try (OutputStream out = new FileOutputStream(curfile)) {
IOUtils.copy(tIn, out);
entry = tIn.getNextTarEntry();
}
}
} catch (IOException e) {
throw new IllegalStateException(e);
}
}
/**
* Move to the next tar entry.
*
* @param rootDir an entry path
* @return true if a next tar entry can be read, or if this entry name is a sub-folder of rootDir
*/
protected boolean hasNext(final String rootDir) {
try {
/*
* if reader.available() is not equal to 0, then it means that this entry
* has been loaded, but not read.
*/
while (reader.available() == 0
&& (tarEntry = reader.getNextTarEntry()) == null) { // Next tar entry
if (++inputPos >= input.length) {
reader.close();
return false;
}
// Next archive file
reader.close();
logger.info("Reading dump: {}", this.input[inputPos]);
reader = getTarInputStream(input[inputPos]);
}
} catch (IOException e) {
logger.error("Error while reading the input: {}\n{}", input[inputPos], e);
}
/*
* When returning from this method, the inputstream is positionned at a regular file,
* i.e., metadata, outgoing-triples.nt or incoming-triples.nt.
*/
if (tarEntry.isDirectory()) {
return hasNext(rootDir);
}
return rootDir == null || tarEntry.getName().startsWith(rootDir) ? true : false;
}
public static List<File> untar(final File inputtar, final File outputDir)
throws IOException, ArchiveException {
final List<File> unpackedFiles = new ArrayList<File>();
if (OMWPP.DEBUG) {
Log.i("OMWPPtar", String.format("Unzipping tar file %s.", inputtar.getAbsoluteFile()));
}
final InputStream is = new FileInputStream(inputtar);
final TarArchiveInputStream tarInputStream =
(TarArchiveInputStream) new TarArchiveInputStream(is);
TarArchiveEntry entry = null;
while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
if (OMWPP.DEBUG) Log.i("OMWPPtar", "Read entry: " + entry.getName());
String filename = entry.getName().substring(entry.getName().lastIndexOf("/") + 1);
if (filename.toLowerCase().endsWith(".png") || filename.toLowerCase().endsWith(".jpg")) {
if (OMWPP.DEBUG) Log.i("OMWPPtar", "Is background, extracting.");
final File outputFile = new File(outputDir, filename);
final OutputStream outputFileStream = new FileOutputStream(outputFile);
IOUtils.copy(tarInputStream, outputFileStream);
outputFileStream.close();
unpackedFiles.add(outputFile);
} else if (filename.toLowerCase().endsWith(".gz")) {
// RECURSIVE CALL
final File outputFile = new File(outputDir, filename);
final OutputStream outputFileStream = new FileOutputStream(outputFile);
IOUtils.copy(tarInputStream, outputFileStream);
outputFileStream.close();
gunzip(outputFile, SDROOT);
outputFile.delete();
} else if (filename.toLowerCase().endsWith(".tar")) {
// RECURSIVE CALL
final File outputFile = new File(outputDir, filename);
final OutputStream outputFileStream = new FileOutputStream(outputFile);
IOUtils.copy(tarInputStream, outputFileStream);
outputFileStream.close();
untar(outputFile, SDROOT);
outputFile.delete();
} else {
if (OMWPP.DEBUG) Log.i("OMWPPtar", "Is not background, skipping.");
}
}
tarInputStream.close();
return unpackedFiles;
}
@Test
public void downloadDroplet() {
this.applicationId
.then(this::uploadAndStartApplication)
.flatMap(
applicationId ->
this.cloudFoundryClient
.applicationsV2()
.downloadDroplet(
DownloadApplicationDropletRequest.builder()
.applicationId(applicationId)
.build()))
.as(Stream::from)
.reduceWith(ByteArrayOutputStream::new, ApplicationsTest::collectIntoByteArrayInputStream)
.map(
bytes -> {
boolean staticFile = false;
boolean indexFile = false;
try {
TarArchiveInputStream tis =
new TarArchiveInputStream(
new GZIPInputStream(new ByteArrayInputStream(bytes.toByteArray())));
for (TarArchiveEntry entry = tis.getNextTarEntry();
entry != null;
entry = tis.getNextTarEntry()) {
if (entry.getName().contains("Staticfile")) {
staticFile = true;
}
if (entry.getName().contains("index.html")) {
indexFile = true;
}
}
} catch (IOException e) {
throw new RuntimeException(e);
}
return staticFile && indexFile;
})
.subscribe(testSubscriber().assertEquals(true));
}
/**
* Unpacks a workflow into specified directory. To be more precise: workflow package should
* contain only a single directory with the workflow. This method will extract its contents into
* target directory.
*
* @param target new workflow root directory
*/
public void extract(File target) throws IOException {
BufferedInputStream in = new BufferedInputStream(new FileInputStream(file));
GzipCompressorInputStream gzIn = new GzipCompressorInputStream(in);
TarArchiveInputStream tarIn = new TarArchiveInputStream(gzIn);
TarArchiveEntry entry;
while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
// The archive should contain only a single directory: we want to unpack its content.
final File outputFile =
new File(target, entry.getName().substring(entry.getName().indexOf('/') + 1));
if (entry.isDirectory()) {
FileUtils.forceMkdir(outputFile);
} else {
OutputStream outputFileStream = null;
try {
outputFileStream = new FileOutputStream(outputFile);
IOUtils.copy(tarIn, outputFileStream);
} finally {
IOUtils.closeQuietly(outputFileStream);
}
}
}
}
public static String getVersionFromArtifact(ByteBuffer artifact) throws IOException {
String versionNumber = null;
try (CompressorInputStream uncompressedInput =
new GzipCompressorInputStream(new ByteArrayInputStream(artifact.array()))) {
ArchiveInputStream input = new TarArchiveInputStream(uncompressedInput);
TarArchiveEntry entry;
while ((entry = (TarArchiveEntry) input.getNextEntry()) != null) {
if (!entry.isDirectory() && entry.getName().endsWith(VERSION_FILE)) {
versionNumber = IOUtils.toString(input, Charsets.UTF_8).trim();
break;
}
}
}
return versionNumber;
}
public TarArchiveEntry map(final TarArchiveEntry entry) {
final String name = entry.getName();
final TarArchiveEntry newEntry =
new TarArchiveEntry(prefix + '/' + Utils.stripPath(strip, name), true);
// Set ownership
if (uid > -1) {
newEntry.setUserId(uid);
} else {
newEntry.setUserId(entry.getUserId());
}
if (gid > -1) {
newEntry.setGroupId(gid);
} else {
newEntry.setGroupId(entry.getGroupId());
}
if (user != null) {
newEntry.setUserName(user);
} else {
newEntry.setUserName(entry.getUserName());
}
if (group != null) {
newEntry.setGroupName(group);
} else {
newEntry.setGroupName(entry.getGroupName());
}
// Set permissions
if (newEntry.isDirectory()) {
if (dirMode > -1) {
newEntry.setMode(dirMode);
} else {
newEntry.setMode(entry.getMode());
}
} else {
if (fileMode > -1) {
newEntry.setMode(fileMode);
} else {
newEntry.setMode(entry.getMode());
}
}
newEntry.setSize(entry.getSize());
return newEntry;
}
/*
* Given a zip stream, unzips it and returns an input stream to the desired data file.
*
* @param importDataRecord ImportDataRecord
* @param is InputStream
* @return InputStream
*/
private InputStream readContent(ImportDataRecord importDataRecord, InputStream is)
throws Exception {
InputStream toReturn = null;
try {
// decompress .gz file
if (LOG.isInfoEnabled()) {
LOG.info("readContent(), decompressing: " + importDataRecord.getCanonicalPathToData());
}
InputStream unzippedContent = new GzipCompressorInputStream(is);
// if tarball, untar
if (importDataRecord.getCanonicalPathToData().toLowerCase().endsWith("tar.gz")) {
if (LOG.isInfoEnabled()) {
LOG.info("readContent(), gzip file is a tarball, untarring");
}
TarArchiveInputStream tis = new TarArchiveInputStream(unzippedContent);
TarArchiveEntry entry = null;
while ((entry = tis.getNextTarEntry()) != null) {
String entryName = entry.getName();
String dataFile = importDataRecord.getDataFilename();
if (dataFile.contains(DatatypeMetadata.TUMOR_TYPE_TAG)) {
dataFile =
dataFile.replaceAll(
DatatypeMetadata.TUMOR_TYPE_TAG, importDataRecord.getTumorType().toUpperCase());
}
if (entryName.contains(dataFile)) {
if (LOG.isInfoEnabled()) {
LOG.info("Processing tar-archive: " + importDataRecord.getDataFilename());
}
toReturn = tis;
break;
}
}
} else {
toReturn = unzippedContent;
}
} catch (Exception e) {
throw e;
}
// outta here
return toReturn;
}
/**
* Unpack the content read from <i>source</i> into <i>targetFolder</i>. If the
* <i>skipTopFolder</i> is set, then don't assume that the archive contains one single folder and
* unpack the content of that folder, not including the folder itself.
*
* @param source The input source. Must be in <i>TAR</i> format.
* @param targetFolder The destination folder for the unpack. Not used when a <tt>fileCatcher</tt>
* is provided
* @param skipTopFolder Set to <code>true</code> to unpack beneath the top folder of the archive.
* The archive must consist of one single folder and nothing else in order for this to work.
* @param fileCatcher Used when specific files should be picked from the archive without writing
* them to disk. Can be <tt>null</tt>.
* @throws IOException
*/
public static void unpack(
InputStream source, File targetFolder, boolean skipTopFolder, FileCatcher fileCatcher)
throws IOException {
String topFolderName = null;
Map<File, Map<Integer, List<String>>> chmodMap =
new HashMap<File, Map<Integer, List<String>>>();
TarArchiveInputStream in = new TarArchiveInputStream(source);
try {
TarArchiveEntry te = in.getNextTarEntry();
if (te == null) {
throw new IOException("No entry in the tar file");
}
do {
if (te.isGlobalPaxHeader()) continue;
String name = te.getName();
if (name.startsWith("./._"))
// MacOS specific extended attributes addition. Just skip it
continue;
if (skipTopFolder) {
int firstSlash = name.indexOf('/');
if (firstSlash < 0) throw new IOException("Archive doesn't contain one single folder");
String tfName = name.substring(0, firstSlash);
if (topFolderName == null) topFolderName = tfName;
else if (!tfName.equals(topFolderName))
throw new IOException("Archive doesn't contain one single folder");
name = name.substring(firstSlash + 1);
}
if (name.length() == 0) continue;
String linkName = te.getLinkName();
if (linkName != null) {
if (linkName.trim().equals("")) linkName = null;
}
if (fileCatcher != null) {
if (linkName == null && !te.isDirectory() && fileCatcher.accept(name)) {
if (fileCatcher.catchData(name, in))
// We're done here
return;
}
continue;
}
File outFile = new File(targetFolder, name);
if (linkName != null) {
if (!OsUtil.link(targetFolder, name, te.getLinkName()))
throw new IOException(
"Archive contains links but they are not supported on this platform");
} else {
if (te.isDirectory()) {
outFile.mkdirs();
} else {
outFile.getParentFile().mkdirs();
OutputStream target = new FileOutputStream(outFile);
StreamUtil.copy(in, target);
target.close();
outFile.setLastModified(te.getModTime().getTime());
}
registerChmodFile(chmodMap, targetFolder, Integer.valueOf(te.getMode()), name);
}
} while ((te = in.getNextTarEntry()) != null);
} finally {
StreamUtil.close(in);
}
chmod(chmodMap);
}
public void execute() {
if (repoDir == null) {
log("repoDir attribute is empty !", LogLevel.ERR.getLevel());
throw new RuntimeException("Bad attributes for apt-repo task");
}
log("repo dir: " + repoDir);
File repoFolder = new File(repoDir);
if (!repoFolder.exists()) {
repoFolder.mkdirs();
}
File[] files =
repoFolder.listFiles(
new FileFilter() {
public boolean accept(File pathname) {
if (pathname.getName().endsWith(FILE_DEB_EXT)) {
return true;
}
return false;
}
});
Packages packages = new Packages();
for (int i = 0; i < files.length; i++) {
File file = files[i];
PackageEntry packageEntry = new PackageEntry();
packageEntry.setSize(file.length());
packageEntry.setSha1(Utils.getDigest("SHA-1", file));
packageEntry.setSha256(Utils.getDigest("SHA-256", file));
packageEntry.setMd5sum(Utils.getDigest("MD5", file));
String fileName = file.getName();
packageEntry.setFilename(fileName);
log("found deb: " + fileName);
try {
ArchiveInputStream control_tgz;
ArArchiveEntry entry;
TarArchiveEntry control_entry;
ArchiveInputStream debStream =
new ArchiveStreamFactory().createArchiveInputStream("ar", new FileInputStream(file));
while ((entry = (ArArchiveEntry) debStream.getNextEntry()) != null) {
if (entry.getName().equals("control.tar.gz")) {
ControlHandler controlHandler = new ControlHandler();
GZIPInputStream gzipInputStream = new GZIPInputStream(debStream);
control_tgz =
new ArchiveStreamFactory().createArchiveInputStream("tar", gzipInputStream);
while ((control_entry = (TarArchiveEntry) control_tgz.getNextEntry()) != null) {
log("control entry: " + control_entry.getName(), LogLevel.DEBUG.getLevel());
if (control_entry.getName().trim().equals(CONTROL_FILE_NAME)) {
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
IOUtils.copy(control_tgz, outputStream);
String content_string = outputStream.toString("UTF-8");
outputStream.close();
controlHandler.setControlContent(content_string);
log("control cont: " + outputStream.toString("utf-8"), LogLevel.DEBUG.getLevel());
break;
}
}
control_tgz.close();
if (controlHandler.hasControlContent()) {
controlHandler.handle(packageEntry);
} else {
throw new RuntimeException("no control content found for: " + file.getName());
}
break;
}
}
debStream.close();
packages.addPackageEntry(packageEntry);
} catch (Exception e) {
String msg = FAILED_TO_CREATE_APT_REPO + " " + file.getName();
log(msg, e, LogLevel.ERR.getLevel());
throw new RuntimeException(msg, e);
}
}
try {
File packagesFile = new File(repoDir, PACKAGES_GZ);
packagesWriter =
new BufferedWriter(
new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(packagesFile))));
packagesWriter.write(packages.toString());
DefaultHashes hashes = Utils.getDefaultDigests(packagesFile);
ReleaseInfo pinfo = new ReleaseInfo(PACKAGES_GZ, packagesFile.length(), hashes);
Release release = new Release();
release.addInfo(pinfo);
final File releaseFile = new File(repoDir, RELEASE);
FileUtils.fileWrite(releaseFile, release.toString());
} catch (IOException e) {
throw new RuntimeException("writing files failed", e);
} finally {
if (packagesWriter != null) {
try {
packagesWriter.close();
} catch (IOException e) {
throw new RuntimeException("writing files failed", e);
}
}
}
}
/**
* Untar an input file into an output file.
*
* <p>The output file is created in the output folder, having the same name as the input file,
* minus the '.tar' extension.
*
* @param archiveFile input TAR file
* @param lastModified when collection has been last modified
* @throws FileNotFoundException
* @throws ArchiveException
*/
private static List<FileWithMeta> performUnTar(
File archiveFile,
IonConfig config,
Collection collection,
String lastModified,
Context context)
throws FileNotFoundException, IOException, ArchiveException {
File collectionFolder = FilePaths.getCollectionFolderPath(config, context);
File collectionFolderTemp = FilePaths.getTempFilePath(collectionFolder);
final List<FileWithMeta> untaredFiles = new LinkedList<>();
InputStream is = null;
TarArchiveInputStream debInputStream = null;
try {
IonLog.d(
TAG,
String.format(
"Untaring %s to dir %s.", archiveFile.getPath(), collectionFolder.getPath()));
is = new FileInputStream(archiveFile);
debInputStream =
(TarArchiveInputStream) new ArchiveStreamFactory().createArchiveInputStream("tar", is);
TarArchiveEntry entry;
List<ArchiveIndex> index = null;
boolean indexHasBeenRead = false;
while ((entry = (TarArchiveEntry) debInputStream.getNextEntry()) != null) {
if (!indexHasBeenRead) {
// get index.json
InputStreamReader inputStreamReader = new InputStreamReader(debInputStream, "UTF-8");
index =
Arrays.asList(
GsonHolder.getInstance().fromJson(inputStreamReader, ArchiveIndex[].class));
indexHasBeenRead = true;
continue;
}
// write the "content" files
if (!entry.isDirectory()) {
String archiveFileName = entry.getName();
ArchiveIndex fileInfo = ArchiveIndex.getByName(archiveFileName, index);
if (fileInfo == null) {
IonLog.w(
TAG, "Skipping " + entry.getName() + " because it was not found in index.json.");
continue;
}
IonLog.i(TAG, fileInfo.url);
FileWithMeta fileWithMeta = getFilePath(fileInfo, collectionFolderTemp, config, context);
File targetFile = fileWithMeta.file;
FileUtils.createDir(targetFile.getParentFile());
targetFile = FileUtils.writeToFile(debInputStream, targetFile);
if (targetFile != null) {
untaredFiles.add(fileWithMeta);
}
}
}
} finally {
// finished reading TAR archive
if (is != null) {
is.close();
}
if (debInputStream != null) {
debInputStream.close();
}
if (archiveFile != null && archiveFile.exists()) {
archiveFile.delete();
}
}
// if lastModified date was not passed, look if cache index entry exists for collection and
// retrieve it from there
if (collection != null && lastModified == null) {
CollectionCacheIndex collectionCacheIndex = CollectionCacheIndex.retrieve(config, context);
lastModified = collectionCacheIndex == null ? null : collectionCacheIndex.getLastModified();
IonLog.d(TAG, "Restoring last_modified from cache index: " + lastModified);
}
// delete old cache index entries of the collection in shared preferences and in memory cache
CacheIndexStore.clearCollection(config, context);
MemoryCache.clear();
// replace collection folder (containing json files) - deletes old file cache
boolean jsonWriteSuccess = FileUtils.move(collectionFolderTemp, collectionFolder, true);
if (!jsonWriteSuccess) {
throw new IOException("JSON files could not be moved to final path.");
}
// replace media files in collection
File mediaFolderTemp = FilePaths.getMediaFolderPath(config, context, true);
File mediaFolder = FilePaths.getMediaFolderPath(config, context, false);
if (mediaFolderTemp.exists()) {
boolean mediaWriteSuccess = FileUtils.move(mediaFolderTemp, mediaFolder, true);
if (!mediaWriteSuccess) {
throw new IOException("Media files could not be moved to final path.");
}
} else {
IonLog.w(TAG, "No media files were contained in archive.");
}
// add collection to file cache again
if (collection != null) {
MemoryCache.saveCollection(collection, config, context);
try {
saveCollectionToFileCache(config, collection, context);
CollectionCacheIndex.save(config, context, lastModified);
} catch (IOException e) {
IonLog.e("ION Archive", "Collection could not be saved.");
IonLog.ex(e);
}
}
// cache index entries are not written yet at this point
return untaredFiles;
}
public RelativePath getRelativePath() {
return new RelativePath(true, entry.getName().split("/"));
}
public String getDisplayName() {
return String.format("tar entry %s!%s", tarFile, entry.getName());
}
/**
* Extracts files to the specified destination
*
* @param file the file to extract to
* @param dest the destination directory
* @throws IOException
*/
public static void unzipFileTo(String file, String dest) throws IOException {
File target = new File(file);
if (!target.exists()) throw new IllegalArgumentException("Archive doesnt exist");
FileInputStream fin = new FileInputStream(target);
int BUFFER = 2048;
byte data[] = new byte[BUFFER];
if (file.endsWith(".zip")) {
// get the zip file content
ZipInputStream zis = new ZipInputStream(fin);
// get the zipped file list entry
ZipEntry ze = zis.getNextEntry();
while (ze != null) {
String fileName = ze.getName();
File newFile = new File(dest + File.separator + fileName);
log.info("file unzip : " + newFile.getAbsoluteFile());
// create all non exists folders
// else you will hit FileNotFoundException for compressed folder
new File(newFile.getParent()).mkdirs();
FileOutputStream fos = new FileOutputStream(newFile);
int len;
while ((len = zis.read(data)) > 0) {
fos.write(data, 0, len);
}
fos.close();
ze = zis.getNextEntry();
}
zis.closeEntry();
zis.close();
} else if (file.endsWith(".tar.gz") || file.endsWith(".tgz")) {
BufferedInputStream in = new BufferedInputStream(fin);
GzipCompressorInputStream gzIn = new GzipCompressorInputStream(in);
TarArchiveInputStream tarIn = new TarArchiveInputStream(gzIn);
TarArchiveEntry entry = null;
/** Read the tar entries using the getNextEntry method * */
while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
log.info("Extracting: " + entry.getName());
/** If the entry is a directory, create the directory. * */
if (entry.isDirectory()) {
File f = new File(dest + File.separator + entry.getName());
f.mkdirs();
}
/**
* If the entry is a file,write the decompressed file to the disk and close destination
* stream.
*/
else {
int count;
FileOutputStream fos = new FileOutputStream(dest + File.separator + entry.getName());
BufferedOutputStream destStream = new BufferedOutputStream(fos, BUFFER);
while ((count = tarIn.read(data, 0, BUFFER)) != -1) {
destStream.write(data, 0, count);
}
destStream.flush();
;
IOUtils.closeQuietly(destStream);
}
}
/** Close the input stream * */
tarIn.close();
} else if (file.endsWith(".gz")) {
GZIPInputStream is2 = new GZIPInputStream(fin);
File extracted = new File(target.getParent(), target.getName().replace(".gz", ""));
if (extracted.exists()) extracted.delete();
extracted.createNewFile();
OutputStream fos = FileUtils.openOutputStream(extracted);
IOUtils.copyLarge(is2, fos);
is2.close();
fos.flush();
fos.close();
}
target.delete();
}
