@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);
}
}
public FileTree visit(FileVisitor visitor) {
if (!tarFile.exists()) {
return this;
}
if (!tarFile.isFile()) {
throw new InvalidUserDataException(
String.format("Cannot expand %s as it is not a file.", this));
}
AtomicBoolean stopFlag = new AtomicBoolean();
try {
FileInputStream inputStream = new FileInputStream(tarFile);
try {
NoCloseTarInputStream tar = new NoCloseTarInputStream(inputStream);
TarArchiveEntry entry;
while (!stopFlag.get() && (entry = tar.getNextTarEntry()) != null) {
if (entry.isDirectory()) {
visitor.visitDir(new DetailsImpl(entry, tar, stopFlag));
} else {
visitor.visitFile(new DetailsImpl(entry, tar, stopFlag));
}
}
} finally {
inputStream.close();
}
} catch (Exception e) {
throw new GradleException(String.format("Could not expand %s.", this), e);
}
return this;
}
/**
* 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 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;
}
/**
* 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);
}
}
}
}
/**
* 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);
}
/**
* 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 boolean isDirectory() {
return entry.isDirectory();
}
/**
* 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();
}
