public void testFormat() throws Exception {
localFs = FileSystem.getLocal(defaultConf);
localFs.delete(workDir, true);
Job job = new Job(new Configuration(defaultConf));
Path file = new Path(workDir, "test.txt");
int seed = new Random().nextInt();
Random random = new Random(seed);
// for a variety of lengths
for (int length = 0; length < MAX_LENGTH; length += random.nextInt(MAX_LENGTH / 10) + 1) {
// create a file with length entries
Writer writer = new OutputStreamWriter(localFs.create(file));
try {
MyClass mc = new MyClass();
for (int i = 0; i < length; i++) {
mc.s = Integer.toString(i);
mc.v = i;
byte[] raw = MessagePack.pack(mc);
byte[] b64e = base64_.encodeBase64(raw);
byte[] b64d = base64_.decode(b64e);
MyClass mc2 = MessagePack.unpack(b64d, mc.getClass());
assertEquals(mc.s, mc2.s);
assertEquals(mc.v, mc2.v);
writer.write(base64_.encodeToString(raw));
}
} finally {
writer.close();
}
checkFormat(job);
}
}
public void inject(Path crawlDb, Path urlDir) throws IOException {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
long start = System.currentTimeMillis();
if (LOG.isInfoEnabled()) {
LOG.info("Injector: starting at " + sdf.format(start));
LOG.info("Injector: crawlDb: " + crawlDb);
LOG.info("Injector: urlDir: " + urlDir);
}
Path tempDir =
new Path(
getConf().get("mapred.temp.dir", ".")
+ "/inject-temp-"
+ Integer.toString(new Random().nextInt(Integer.MAX_VALUE)));
// map text input file to a <url,CrawlDatum> file
if (LOG.isInfoEnabled()) {
LOG.info("Injector: Converting injected urls to crawl db entries.");
}
JobConf sortJob = new NutchJob(getConf());
sortJob.setJobName("inject " + urlDir);
FileInputFormat.addInputPath(sortJob, urlDir);
sortJob.setMapperClass(InjectMapper.class);
FileOutputFormat.setOutputPath(sortJob, tempDir);
sortJob.setOutputFormat(SequenceFileOutputFormat.class);
sortJob.setOutputKeyClass(Text.class);
sortJob.setOutputValueClass(CrawlDatum.class);
sortJob.setLong("injector.current.time", System.currentTimeMillis());
RunningJob mapJob = JobClient.runJob(sortJob);
long urlsInjected = mapJob.getCounters().findCounter("injector", "urls_injected").getValue();
long urlsFiltered = mapJob.getCounters().findCounter("injector", "urls_filtered").getValue();
LOG.info("Injector: total number of urls rejected by filters: " + urlsFiltered);
LOG.info(
"Injector: total number of urls injected after normalization and filtering: "
+ urlsInjected);
// merge with existing crawl db
if (LOG.isInfoEnabled()) {
LOG.info("Injector: Merging injected urls into crawl db.");
}
JobConf mergeJob = CrawlDb.createJob(getConf(), crawlDb);
FileInputFormat.addInputPath(mergeJob, tempDir);
mergeJob.setReducerClass(InjectReducer.class);
JobClient.runJob(mergeJob);
CrawlDb.install(mergeJob, crawlDb);
// clean up
FileSystem fs = FileSystem.get(getConf());
fs.delete(tempDir, true);
long end = System.currentTimeMillis();
LOG.info(
"Injector: finished at "
+ sdf.format(end)
+ ", elapsed: "
+ TimingUtil.elapsedTime(start, end));
}
// the method which actually copies the caches locally and unjars/unzips them
// and does chmod for the files
private static Path localizeCache(
Configuration conf, URI cache, long confFileStamp, CacheStatus cacheStatus, boolean isArchive)
throws IOException {
FileSystem fs = getFileSystem(cache, conf);
FileSystem localFs = FileSystem.getLocal(conf);
Path parchive = null;
if (isArchive) {
parchive =
new Path(
cacheStatus.localizedLoadPath, new Path(cacheStatus.localizedLoadPath.getName()));
} else {
parchive = cacheStatus.localizedLoadPath;
}
if (!localFs.mkdirs(parchive.getParent())) {
throw new IOException(
"Mkdirs failed to create directory " + cacheStatus.localizedLoadPath.toString());
}
String cacheId = cache.getPath();
fs.copyToLocalFile(new Path(cacheId), parchive);
if (isArchive) {
String tmpArchive = parchive.toString().toLowerCase();
File srcFile = new File(parchive.toString());
File destDir = new File(parchive.getParent().toString());
if (tmpArchive.endsWith(".jar")) {
RunJar.unJar(srcFile, destDir);
} else if (tmpArchive.endsWith(".zip")) {
FileUtil.unZip(srcFile, destDir);
} else if (isTarFile(tmpArchive)) {
FileUtil.unTar(srcFile, destDir);
}
// else will not do anyhting
// and copy the file into the dir as it is
}
long cacheSize = FileUtil.getDU(new File(parchive.getParent().toString()));
cacheStatus.size = cacheSize;
addCacheInfoUpdate(cacheStatus);
// do chmod here
try {
// Setting recursive permission to grant everyone read and execute
Path localDir = new Path(cacheStatus.localizedBaseDir, cacheStatus.uniqueParentDir);
LOG.info("Doing chmod on localdir :" + localDir);
FileUtil.chmod(localDir.toString(), "ugo+rx", true);
} catch (InterruptedException e) {
LOG.warn("Exception in chmod" + e.toString());
}
// update cacheStatus to reflect the newly cached file
cacheStatus.mtime = getTimestamp(conf, cache);
return cacheStatus.localizedLoadPath;
}
@Override
public void close() throws IOException {
super.close();
if (fs != null) {
try {
fs.close();
} catch (IOException ie) {
// this might already be closed
// ignore
}
}
}
private void dirCleanup() {
Configuration conf = new Configuration();
try {
FileSystem fs = FileSystem.get(conf);
Path dirPath = new Path(testPath);
if (fs.exists(dirPath)) {
fs.delete(dirPath, true);
}
} catch (IOException ex) {
LOG.warn("IO Error in test cleanup", ex);
}
}
protected void setup(Context context) throws IOException, InterruptedException {
super.setup(context);
Path pt = new Path("/user/yao/query/query");
FileSystem fs = FileSystem.get(new Configuration());
BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(pt)));
String line = br.readLine();
String[] keywords = line.split(",");
k0 = keywords[0];
k1 = keywords[1];
k2 = keywords[2];
br.close();
}
/**
* Combine the status stored in the index and the underlying status.
*
* @param h status stored in the index
* @param cache caching the underlying file statuses
* @return the combined file status
* @throws IOException
*/
private FileStatus toFileStatus(HarStatus h, Map<String, FileStatus> cache) throws IOException {
FileStatus underlying = null;
if (cache != null) {
underlying = cache.get(h.partName);
}
if (underlying == null) {
final Path p = h.isDir ? archivePath : new Path(archivePath, h.partName);
underlying = fs.getFileStatus(p);
if (cache != null) {
cache.put(h.partName, underlying);
}
}
long modTime = 0;
int version = metadata.getVersion();
if (version < 3) {
modTime = underlying.getModificationTime();
} else if (version == 3) {
modTime = h.getModificationTime();
}
return new FileStatus(
h.isDir() ? 0L : h.getLength(),
h.isDir(),
underlying.getReplication(),
underlying.getBlockSize(),
modTime,
underlying.getAccessTime(),
underlying.getPermission(),
underlying.getOwner(),
underlying.getGroup(),
makeRelative(this.uri.getPath(), new Path(h.name)));
}
private String copyFromLocal(FileSystem fs, Path basePath, String[] files) throws IOException {
StringBuilder csv = new StringBuilder(files.length * (basePath.toString().length() + 16));
for (String localFile : files) {
Path src = new Path(localFile);
String filename = src.getName();
Path dst = new Path(basePath, filename);
URI localFileURI = null;
try {
localFileURI = new URI(localFile);
} catch (URISyntaxException e) {
throw new IOException(e);
}
if (localFileURI.getScheme() == null || localFileURI.getScheme().startsWith("file")) {
LOG.info("Copy {} from local filesystem to {}", localFile, dst);
fs.copyFromLocalFile(false, true, src, dst);
} else {
LOG.info("Copy {} from DFS to {}", localFile, dst);
FileUtil.copy(fs, src, fs, dst, false, true, conf);
}
if (csv.length() > 0) {
csv.append(LIB_JARS_SEP);
}
csv.append(dst.toString());
}
return csv.toString();
}
public void configure(JobConf conf) {
numberOfCenters = Integer.valueOf(conf.get("numberOfCenters"));
centersDirectory = conf.get("centersReadDirectory");
try {
Configuration c = new Configuration();
FileSystem fs = FileSystem.get(c);
for (int index = 0; index < numberOfCenters; ++index) {
SequenceFile.Reader reader =
new SequenceFile.Reader(fs, new Path(centersDirectory + "/centers/" + index), c);
LongWritable key = new LongWritable();
Point value = new Point();
reader.next(key, value);
Point center = (Point) value;
centers.add(center);
reader.close();
}
} catch (IOException e) {
// do nothing
// I hope this doesn't happen
System.out.println("well, damn.");
e.printStackTrace();
}
}
private static boolean hasFile(
dbutil db_util, FileSystem fs, String db_name, String file_id, String file_path)
throws Exception {
Get file_id_get = new Get(file_id.getBytes());
Result file_result = db_util.doGet(db_name, file_id_get);
KeyValue file_names = file_result.getColumnLatest("d".getBytes(), "filenames".getBytes());
if (file_names == null) {
return false;
}
String all_files = new String(file_names.getValue());
String[] files = all_files.split("\n");
for (String line : files) {
if (line.equals(file_path)) {
if (fs.globStatus(new Path(line + "*")).length == 0) {
Put new_put = new Put(file_id.getBytes());
new_put.add(
"d".getBytes(),
"filenames".getBytes(),
all_files.replace(file_path + "\n", "").getBytes());
db_util.doPut(db_name, new_put);
return false;
}
return true;
}
}
return false;
}
private void verifyOutputTextFiles(
FileSystem fs, Configuration conf, String dir, String prefix, List<String> bodies)
throws IOException {
int found = 0;
int expected = bodies.size();
for (String outputFile : getAllFiles(dir)) {
String name = (new File(outputFile)).getName();
if (name.startsWith(prefix)) {
FSDataInputStream input = fs.open(new Path(outputFile));
BufferedReader reader = new BufferedReader(new InputStreamReader(input));
String body = null;
while ((body = reader.readLine()) != null) {
bodies.remove(body);
found++;
}
reader.close();
}
}
Assert.assertTrue(
"Found = "
+ found
+ ", Expected = "
+ expected
+ ", Left = "
+ bodies.size()
+ " "
+ bodies,
bodies.size() == 0);
}
/**
* Initialize a Har filesystem per har archive. The archive home directory is the top level
* directory in the filesystem that contains the HAR archive. Be careful with this method, you do
* not want to go on creating new Filesystem instances per call to path.getFileSystem(). the uri
* of Har is har://underlyingfsscheme-host:port/archivepath. or har:///archivepath. This assumes
* the underlying filesystem to be used in case not specified.
*/
@Override
public void initialize(URI name, Configuration conf) throws IOException {
// initialize the metadata cache, if needed
initializeMetadataCache(conf);
// decode the name
URI underLyingURI = decodeHarURI(name, conf);
// we got the right har Path- now check if this is
// truly a har filesystem
Path harPath = archivePath(new Path(name.getScheme(), name.getAuthority(), name.getPath()));
if (harPath == null) {
throw new IOException("Invalid path for the Har Filesystem. " + name.toString());
}
if (fs == null) {
fs = FileSystem.get(underLyingURI, conf);
}
uri = harPath.toUri();
archivePath = new Path(uri.getPath());
harAuth = getHarAuth(underLyingURI);
// check for the underlying fs containing
// the index file
Path masterIndexPath = new Path(archivePath, "_masterindex");
Path archiveIndexPath = new Path(archivePath, "_index");
if (!fs.exists(masterIndexPath) || !fs.exists(archiveIndexPath)) {
throw new IOException(
"Invalid path for the Har Filesystem. " + "No index file in " + harPath);
}
metadata = harMetaCache.get(uri);
if (metadata != null) {
FileStatus mStat = fs.getFileStatus(masterIndexPath);
FileStatus aStat = fs.getFileStatus(archiveIndexPath);
if (mStat.getModificationTime() != metadata.getMasterIndexTimestamp()
|| aStat.getModificationTime() != metadata.getArchiveIndexTimestamp()) {
// the archive has been overwritten since we last read it
// remove the entry from the meta data cache
metadata = null;
harMetaCache.remove(uri);
}
}
if (metadata == null) {
metadata = new HarMetaData(fs, masterIndexPath, archiveIndexPath);
metadata.parseMetaData();
harMetaCache.put(uri, metadata);
}
}
private void insertFile(
Path apkPath, Map<String, String> zip_properties, File insert, String method, Path location)
throws AndrolibException, IOException {
// ZipFileSystem only writes at .close()
// http://mail.openjdk.java.net/pipermail/nio-dev/2012-July/001764.html
try (FileSystem fs = FileSystems.newFileSystem(apkPath, null)) {
Path root = fs.getPath("/");
// in order to get the path relative to the zip, we strip off the absolute path, minus what we
// already have in the zip. thus /var/files/apktool/apk/unknown/folder/file => /folder/file
Path dest =
fs.getPath(root.toString(), insert.getAbsolutePath().replace(location.toString(), ""));
Path newFile = Paths.get(insert.getAbsolutePath());
Files.copy(newFile, dest, StandardCopyOption.REPLACE_EXISTING);
fs.close();
}
}
/** Start the JobTracker process, listen on the indicated port */
JobTracker(Configuration conf) throws IOException {
//
// Grab some static constants
//
maxCurrentTasks = conf.getInt("mapred.tasktracker.tasks.maximum", 2);
RETIRE_JOB_INTERVAL = conf.getLong("mapred.jobtracker.retirejob.interval", 24 * 60 * 60 * 1000);
RETIRE_JOB_CHECK_INTERVAL = conf.getLong("mapred.jobtracker.retirejob.check", 60 * 1000);
TASK_ALLOC_EPSILON = conf.getFloat("mapred.jobtracker.taskalloc.loadbalance.epsilon", 0.2f);
PAD_FRACTION = conf.getFloat("mapred.jobtracker.taskalloc.capacitypad", 0.1f);
MIN_SLOTS_FOR_PADDING = 3 * maxCurrentTasks;
// This is a directory of temporary submission files. We delete it
// on startup, and can delete any files that we're done with
this.conf = conf;
JobConf jobConf = new JobConf(conf);
this.systemDir = jobConf.getSystemDir();
this.fs = FileSystem.get(conf);
FileUtil.fullyDelete(fs, systemDir);
fs.mkdirs(systemDir);
// Same with 'localDir' except it's always on the local disk.
jobConf.deleteLocalFiles(SUBDIR);
// Set ports, start RPC servers, etc.
InetSocketAddress addr = getAddress(conf);
this.localMachine = addr.getHostName();
this.port = addr.getPort();
this.interTrackerServer = RPC.getServer(this, addr.getPort(), 10, false, conf);
this.interTrackerServer.start();
Properties p = System.getProperties();
for (Iterator it = p.keySet().iterator(); it.hasNext(); ) {
String key = (String) it.next();
String val = (String) p.getProperty(key);
LOG.info("Property '" + key + "' is " + val);
}
this.infoPort = conf.getInt("mapred.job.tracker.info.port", 50030);
this.infoServer = new JobTrackerInfoServer(this, infoPort);
this.infoServer.start();
this.startTime = System.currentTimeMillis();
new Thread(this.expireTrackers).start();
new Thread(this.retireJobs).start();
new Thread(this.initJobs).start();
}
public void copyInitialState(Path origAppDir) throws IOException {
// locate previous snapshot
String newAppDir = this.dag.assertAppPath();
FSRecoveryHandler recoveryHandler = new FSRecoveryHandler(origAppDir.toString(), conf);
// read snapshot against new dependencies
Object snapshot = recoveryHandler.restore();
if (snapshot == null) {
throw new IllegalArgumentException("No previous application state found in " + origAppDir);
}
InputStream logIs = recoveryHandler.getLog();
// modify snapshot state to switch app id
((StreamingContainerManager.CheckpointState) snapshot).setApplicationId(this.dag, conf);
Path checkpointPath = new Path(newAppDir, LogicalPlan.SUBDIR_CHECKPOINTS);
FileSystem fs = FileSystem.newInstance(origAppDir.toUri(), conf);
// remove the path that was created by the storage agent during deserialization and replacement
fs.delete(checkpointPath, true);
// write snapshot to new location
recoveryHandler = new FSRecoveryHandler(newAppDir, conf);
recoveryHandler.save(snapshot);
OutputStream logOs = recoveryHandler.rotateLog();
IOUtils.copy(logIs, logOs);
logOs.flush();
logOs.close();
logIs.close();
// copy sub directories that are not present in target
FileStatus[] lFiles = fs.listStatus(origAppDir);
for (FileStatus f : lFiles) {
if (f.isDirectory()) {
String targetPath = f.getPath().toString().replace(origAppDir.toString(), newAppDir);
if (!fs.exists(new Path(targetPath))) {
LOG.debug("Copying {} to {}", f.getPath(), targetPath);
FileUtil.copy(fs, f.getPath(), fs, new Path(targetPath), false, conf);
// FSUtil.copy(fs, f, fs, new Path(targetPath), false, false, conf);
} else {
LOG.debug("Ignoring {} as it already exists under {}", f.getPath(), targetPath);
// FSUtil.setPermission(fs, new Path(targetPath), new FsPermission((short)0777));
}
}
}
}
public FileStatus getPartFileStatus(Path partPath) throws IOException {
FileStatus status;
status = partFileStatuses.get(partPath);
if (status == null) {
status = fs.getFileStatus(partPath);
partFileStatuses.put(partPath, status);
}
return status;
}
private void insertFolder(
Path apkPath, Map<String, String> zip_properties, File insert, String method, Path location)
throws AndrolibException, IOException {
try (FileSystem fs = FileSystems.newFileSystem(apkPath, null)) {
Path root = fs.getPath("/");
Path dest =
fs.getPath(root.toString(), insert.getAbsolutePath().replace(location.toString(), ""));
Path parent = dest.normalize();
// check for folder existing in apkFileSystem
if (parent != null && Files.notExists(parent)) {
if (!Files.isDirectory(parent, LinkOption.NOFOLLOW_LINKS)) {
Files.createDirectories(parent);
}
}
fs.close();
}
}
/**
* Returns a List of FsContent objects from TSK based on sql query.
*
* @param image is a Image object that denotes which image to get the files from
* @param query is a sql string query that is to be run
* @return FFSqlitedb is a List of FsContent objects
*/
@SuppressWarnings("deprecation")
public List<FsContent> extractFiles(Image image, String query) {
Collection<FileSystem> imageFS = tskCase.getFileSystems(image);
List<String> fsIds = new LinkedList<String>();
for (FileSystem img : imageFS) {
Long tempID = img.getId();
fsIds.add(tempID.toString());
}
String allFS = new String();
for (int i = 0; i < fsIds.size(); i++) {
if (i == 0) {
allFS += " AND (0";
}
allFS += " OR fs_obj_id = '" + fsIds.get(i) + "'";
if (i == fsIds.size() - 1) {
allFS += ")";
}
}
List<FsContent> FFSqlitedb = null;
ResultSet rs = null;
try {
rs = tskCase.runQuery(query + allFS);
FFSqlitedb = tskCase.resultSetToFsContents(rs);
} catch (SQLException ex) {
logger.log(
Level.SEVERE, "Error while trying to extract files for:" + this.getClass().getName(), ex);
this.addErrorMessage(this.getName() + ": Error while trying to extract files to analyze.");
} finally {
if (rs != null) {
try {
tskCase.closeRunQuery(rs);
} catch (SQLException ex) {
logger.log(
Level.SEVERE,
"Error while trying to close result set after extract files for:"
+ this.getClass().getName(),
ex);
}
}
}
return FFSqlitedb;
}
/**
* Clear the entire contents of the cache and delete the backing files. This should only be used
* when the server is reinitializing, because the users are going to lose their files.
*/
public static void purgeCache(Configuration conf, MRAsyncDiskService service) throws IOException {
synchronized (cachedArchives) {
LocalFileSystem localFs = FileSystem.getLocal(conf);
for (Map.Entry<String, CacheStatus> f : cachedArchives.entrySet()) {
try {
deleteLocalPath(service, localFs, f.getValue().localizedLoadPath);
} catch (IOException ie) {
LOG.debug("Error cleaning up cache", ie);
}
}
cachedArchives.clear();
}
}
/**
* Get block locations from the underlying fs and fix their offsets and lengths.
*
* @param file the input file status to get block locations
* @param start the start of the desired range in the contained file
* @param len the length of the desired range
* @return block locations for this segment of file
* @throws IOException
*/
@Override
public BlockLocation[] getFileBlockLocations(FileStatus file, long start, long len)
throws IOException {
HarStatus hstatus = getFileHarStatus(file.getPath());
Path partPath = new Path(archivePath, hstatus.getPartName());
FileStatus partStatus = metadata.getPartFileStatus(partPath);
// get all part blocks that overlap with the desired file blocks
BlockLocation[] locations =
fs.getFileBlockLocations(partStatus, hstatus.getStartIndex() + start, len);
return fixBlockLocations(locations, start, len, hstatus.getStartIndex());
}
/**
* decode the raw URI to get the underlying URI
*
* @param rawURI raw Har URI
* @return filtered URI of the underlying fileSystem
*/
private URI decodeHarURI(URI rawURI, Configuration conf) throws IOException {
String tmpAuth = rawURI.getAuthority();
// we are using the default file
// system in the config
// so create a underlying uri and
// return it
if (tmpAuth == null) {
// create a path
return FileSystem.getDefaultUri(conf);
}
String authority = rawURI.getAuthority();
if (authority == null) {
throw new IOException(
"URI: "
+ rawURI
+ " is an invalid Har URI since authority==null."
+ " Expecting har://<scheme>-<host>/<path>.");
}
int i = authority.indexOf('-');
if (i < 0) {
throw new IOException(
"URI: "
+ rawURI
+ " is an invalid Har URI since '-' not found."
+ " Expecting har://<scheme>-<host>/<path>.");
}
if (rawURI.getQuery() != null) {
// query component not allowed
throw new IOException("query component in Path not supported " + rawURI);
}
URI tmp;
try {
// convert <scheme>-<host> to <scheme>://<host>
URI baseUri = new URI(authority.replaceFirst("-", "://"));
tmp =
new URI(
baseUri.getScheme(),
baseUri.getAuthority(),
rawURI.getPath(),
rawURI.getQuery(),
rawURI.getFragment());
} catch (URISyntaxException e) {
throw new IOException(
"URI: " + rawURI + " is an invalid Har URI. Expecting har://<scheme>-<host>/<path>.");
}
return tmp;
}
public static void recursePath(Configuration conf, Path path, Job job) {
try {
FileSystem fs = path.getFileSystem(conf);
FileStatus[] fstats = fs.listStatus(path);
if (fstats != null) {
for (FileStatus f : fstats) {
Path p = f.getPath();
;
if (fs.isFile(p)) {
// connection times out otherwise
System.err.println("file:" + p.toString());
FileInputFormat.addInputPath(job, p);
} else {
System.err.println("dir:" + p.toString());
recursePath(conf, p, job);
}
}
}
} catch (IOException e) {
// shouldn't be here
throw new RuntimeException(e);
}
}
HarFsInputStream(FileSystem fs, Path path, long start, long length, int bufferSize)
throws IOException {
if (length < 0) {
throw new IllegalArgumentException("Negative length [" + length + "]");
}
underLyingStream = fs.open(path, bufferSize);
underLyingStream.seek(start);
// the start of this file in the part file
this.start = start;
// the position pointer in the part file
this.position = start;
// the end pointer in the part file
this.end = start + length;
}
public static void extractQueryFeatures2HDFS(String filename, Job job) throws IOException {
// Read the local image.jpg as a Mat
Mat query_mat_float =
Highgui.imread(LOCAL_USER_DIR + ID + INPUT + "/" + filename, CvType.CV_32FC3);
// Convert RGB to GRAY
Mat query_gray = new Mat();
Imgproc.cvtColor(query_mat_float, query_gray, Imgproc.COLOR_RGB2GRAY);
// Convert the float type to unsigned integer(required by SIFT)
Mat query_mat_byte = new Mat();
query_gray.convertTo(query_mat_byte, CvType.CV_8UC3);
// // Resize the image to 1/FACTOR both width and height
// Mat query_mat_byte = FeatureExtraction.resize(query_mat_byte);
// Extract the feature from the (Mat)image
Mat query_features = FeatureExtraction.extractFeature(query_mat_byte);
System.out.println(PREFIX + "Extracting the query image feature...");
System.out.println("query_mat(float,color):" + query_mat_float);
System.out.println("query_mat(float,gray):" + query_gray);
System.out.println("query_mat(byte,gray):" + query_mat_byte);
System.out.println("query_mat_features:" + query_features);
System.out.println();
// Store the feature to the hdfs in order to use it later in different map tasks
System.out.println(PREFIX + "Generating the feature file for the query image in HDFS...");
FileSystem fs = FileSystem.get(job.getConfiguration());
String featureFileName = filename.substring(0, filename.lastIndexOf(".")) + ".json";
FSDataOutputStream fsDataOutputStream =
fs.create(new Path(HDFS_HOME + USER + ID + INPUT + "/" + featureFileName));
BufferedWriter bw =
new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
bw.write(FeatureExtraction.mat2json(query_features));
bw.close();
System.out.println(PREFIX + "Query feature extraction finished...");
System.out.println();
}
/*
* Returns the relative path of the dir this cache will be localized in
* relative path that this cache will be localized in. For
* hdfs://hostname:port/absolute_path -- the relative path is
* hostname/absolute path -- if it is just /absolute_path -- then the
* relative path is hostname of DFS this mapred cluster is running
* on/absolute_path
*/
public static String makeRelative(URI cache, Configuration conf) throws IOException {
String host = cache.getHost();
if (host == null) {
host = cache.getScheme();
}
if (host == null) {
URI defaultUri = FileSystem.get(conf).getUri();
host = defaultUri.getHost();
if (host == null) {
host = defaultUri.getScheme();
}
}
String path = host + cache.getPath();
path = path.replace(":/", "/"); // remove windows device colon
return path;
}
private static Path checkCacheStatusValidity(
Configuration conf,
URI cache,
long confFileStamp,
CacheStatus cacheStatus,
FileStatus fileStatus,
boolean isArchive)
throws IOException {
FileSystem fs = FileSystem.get(cache, conf);
// Has to be
if (!ifExistsAndFresh(conf, fs, cache, confFileStamp, cacheStatus, fileStatus)) {
throw new IOException(
"Stale cache file: " + cacheStatus.localizedLoadPath + " for cache-file: " + cache);
}
LOG.info(
String.format(
"Using existing cache of %s->%s", cache.toString(), cacheStatus.localizedLoadPath));
return cacheStatus.localizedLoadPath;
}
private static void deleteCache(Configuration conf, MRAsyncDiskService asyncDiskService)
throws IOException {
List<CacheStatus> deleteSet = new LinkedList<CacheStatus>();
// try deleting cache Status with refcount of zero
synchronized (cachedArchives) {
for (Iterator<String> it = cachedArchives.keySet().iterator(); it.hasNext(); ) {
String cacheId = (String) it.next();
CacheStatus lcacheStatus = cachedArchives.get(cacheId);
if (lcacheStatus.refcount == 0) {
// delete this cache entry from the global list
// and mark the localized file for deletion
deleteSet.add(lcacheStatus);
it.remove();
}
}
}
// do the deletion asynchronously, after releasing the global lock
Thread cacheFileCleaner =
new Thread(new CacheFileCleanTask(asyncDiskService, FileSystem.getLocal(conf), deleteSet));
cacheFileCleaner.start();
}
public void testFormat() throws Exception {
JobConf job = new JobConf(conf);
FileSystem fs = FileSystem.getLocal(conf);
Path dir = new Path(System.getProperty("test.build.data", ".") + "/mapred");
Path file = new Path(dir, "test.seq");
Reporter reporter = Reporter.NULL;
int seed = new Random().nextInt();
// LOG.info("seed = "+seed);
Random random = new Random(seed);
fs.delete(dir, true);
FileInputFormat.setInputPaths(job, dir);
// for a variety of lengths
for (int length = 0; length < MAX_LENGTH; length += random.nextInt(MAX_LENGTH / 10) + 1) {
// LOG.info("creating; entries = " + length);
// create a file with length entries
SequenceFile.Writer writer =
SequenceFile.createWriter(fs, conf, file, IntWritable.class, BytesWritable.class);
try {
for (int i = 0; i < length; i++) {
IntWritable key = new IntWritable(i);
byte[] data = new byte[random.nextInt(10)];
random.nextBytes(data);
BytesWritable value = new BytesWritable(data);
writer.append(key, value);
}
} finally {
writer.close();
}
// try splitting the file in a variety of sizes
InputFormat<IntWritable, BytesWritable> format =
new SequenceFileInputFormat<IntWritable, BytesWritable>();
IntWritable key = new IntWritable();
BytesWritable value = new BytesWritable();
for (int i = 0; i < 3; i++) {
int numSplits = random.nextInt(MAX_LENGTH / (SequenceFile.SYNC_INTERVAL / 20)) + 1;
// LOG.info("splitting: requesting = " + numSplits);
InputSplit[] splits = format.getSplits(job, numSplits);
// LOG.info("splitting: got = " + splits.length);
// check each split
BitSet bits = new BitSet(length);
for (int j = 0; j < splits.length; j++) {
RecordReader<IntWritable, BytesWritable> reader =
format.getRecordReader(splits[j], job, reporter);
try {
int count = 0;
while (reader.next(key, value)) {
// if (bits.get(key.get())) {
// LOG.info("splits["+j+"]="+splits[j]+" : " +
// key.get());
// LOG.info("@"+reader.getPos());
// }
assertFalse("Key in multiple partitions.", bits.get(key.get()));
bits.set(key.get());
count++;
}
// LOG.info("splits["+j+"]="+splits[j]+" count=" +
// count);
} finally {
reader.close();
}
}
assertEquals("Some keys in no partition.", length, bits.cardinality());
}
}
}
/**
* Launch application for the dag represented by this client.
*
* @throws YarnException
* @throws IOException
*/
public void startApplication() throws YarnException, IOException {
Class<?>[] defaultClasses;
if (applicationType.equals(YARN_APPLICATION_TYPE)) {
// TODO restrict the security check to only check if security is enabled for webservices.
if (UserGroupInformation.isSecurityEnabled()) {
defaultClasses = DATATORRENT_SECURITY_CLASSES;
} else {
defaultClasses = DATATORRENT_CLASSES;
}
} else {
throw new IllegalStateException(applicationType + " is not a valid application type.");
}
LinkedHashSet<String> localJarFiles = findJars(dag, defaultClasses);
if (resources != null) {
localJarFiles.addAll(resources);
}
YarnClusterMetrics clusterMetrics = yarnClient.getYarnClusterMetrics();
LOG.info(
"Got Cluster metric info from ASM"
+ ", numNodeManagers="
+ clusterMetrics.getNumNodeManagers());
// GetClusterNodesRequest clusterNodesReq = Records.newRecord(GetClusterNodesRequest.class);
// GetClusterNodesResponse clusterNodesResp =
// rmClient.clientRM.getClusterNodes(clusterNodesReq);
// LOG.info("Got Cluster node info from ASM");
// for (NodeReport node : clusterNodesResp.getNodeReports()) {
// LOG.info("Got node report from ASM for"
// + ", nodeId=" + node.getNodeId()
// + ", nodeAddress" + node.getHttpAddress()
// + ", nodeRackName" + node.getRackName()
// + ", nodeNumContainers" + node.getNumContainers()
// + ", nodeHealthStatus" + node.getHealthReport());
// }
List<QueueUserACLInfo> listAclInfo = yarnClient.getQueueAclsInfo();
for (QueueUserACLInfo aclInfo : listAclInfo) {
for (QueueACL userAcl : aclInfo.getUserAcls()) {
LOG.info(
"User ACL Info for Queue"
+ ", queueName="
+ aclInfo.getQueueName()
+ ", userAcl="
+ userAcl.name());
}
}
// Get a new application id
YarnClientApplication newApp = yarnClient.createApplication();
appId = newApp.getNewApplicationResponse().getApplicationId();
// Dump out information about cluster capability as seen by the resource manager
int maxMem = newApp.getNewApplicationResponse().getMaximumResourceCapability().getMemory();
LOG.info("Max mem capabililty of resources in this cluster " + maxMem);
int amMemory = dag.getMasterMemoryMB();
if (amMemory > maxMem) {
LOG.info(
"AM memory specified above max threshold of cluster. Using max value."
+ ", specified="
+ amMemory
+ ", max="
+ maxMem);
amMemory = maxMem;
}
if (dag.getAttributes().get(LogicalPlan.APPLICATION_ID) == null) {
dag.setAttribute(LogicalPlan.APPLICATION_ID, appId.toString());
}
// Create launch context for app master
LOG.info("Setting up application submission context for ASM");
ApplicationSubmissionContext appContext = Records.newRecord(ApplicationSubmissionContext.class);
// set the application id
appContext.setApplicationId(appId);
// set the application name
appContext.setApplicationName(dag.getValue(LogicalPlan.APPLICATION_NAME));
appContext.setApplicationType(this.applicationType);
if (YARN_APPLICATION_TYPE.equals(this.applicationType)) {
// appContext.setMaxAppAttempts(1); // no retries until Stram is HA
}
// Set up the container launch context for the application master
ContainerLaunchContext amContainer = Records.newRecord(ContainerLaunchContext.class);
// Setup security tokens
// If security is enabled get ResourceManager and NameNode delegation tokens.
// Set these tokens on the container so that they are sent as part of application submission.
// This also sets them up for renewal by ResourceManager. The NameNode delegation rmToken
// is also used by ResourceManager to fetch the jars from HDFS and set them up for the
// application master launch.
if (UserGroupInformation.isSecurityEnabled()) {
Credentials credentials = new Credentials();
String tokenRenewer = conf.get(YarnConfiguration.RM_PRINCIPAL);
if (tokenRenewer == null || tokenRenewer.length() == 0) {
throw new IOException("Can't get Master Kerberos principal for the RM to use as renewer");
}
// For now, only getting tokens for the default file-system.
FileSystem fs = StramClientUtils.newFileSystemInstance(conf);
try {
final Token<?> tokens[] = fs.addDelegationTokens(tokenRenewer, credentials);
if (tokens != null) {
for (Token<?> token : tokens) {
LOG.info("Got dt for " + fs.getUri() + "; " + token);
}
}
} finally {
fs.close();
}
addRMDelegationToken(tokenRenewer, credentials);
DataOutputBuffer dob = new DataOutputBuffer();
credentials.writeTokenStorageToStream(dob);
ByteBuffer fsTokens = ByteBuffer.wrap(dob.getData(), 0, dob.getLength());
amContainer.setTokens(fsTokens);
}
// set local resources for the application master
// local files or archives as needed
// In this scenario, the jar file for the application master is part of the local resources
Map<String, LocalResource> localResources = new HashMap<String, LocalResource>();
// copy required jar files to dfs, to be localized for containers
FileSystem fs = StramClientUtils.newFileSystemInstance(conf);
try {
Path appsBasePath =
new Path(StramClientUtils.getDTDFSRootDir(fs, conf), StramClientUtils.SUBDIR_APPS);
Path appPath = new Path(appsBasePath, appId.toString());
String libJarsCsv = copyFromLocal(fs, appPath, localJarFiles.toArray(new String[] {}));
LOG.info("libjars: {}", libJarsCsv);
dag.getAttributes().put(LogicalPlan.LIBRARY_JARS, libJarsCsv);
LaunchContainerRunnable.addFilesToLocalResources(
LocalResourceType.FILE, libJarsCsv, localResources, fs);
if (archives != null) {
String[] localFiles = archives.split(",");
String archivesCsv = copyFromLocal(fs, appPath, localFiles);
LOG.info("archives: {}", archivesCsv);
dag.getAttributes().put(LogicalPlan.ARCHIVES, archivesCsv);
LaunchContainerRunnable.addFilesToLocalResources(
LocalResourceType.ARCHIVE, archivesCsv, localResources, fs);
}
if (files != null) {
String[] localFiles = files.split(",");
String filesCsv = copyFromLocal(fs, appPath, localFiles);
LOG.info("files: {}", filesCsv);
dag.getAttributes().put(LogicalPlan.FILES, filesCsv);
LaunchContainerRunnable.addFilesToLocalResources(
LocalResourceType.FILE, filesCsv, localResources, fs);
}
dag.getAttributes().put(LogicalPlan.APPLICATION_PATH, appPath.toString());
if (dag.getAttributes().get(OperatorContext.STORAGE_AGENT) == null) {
/* which would be the most likely case */
Path checkpointPath = new Path(appPath, LogicalPlan.SUBDIR_CHECKPOINTS);
// use conf client side to pickup any proxy settings from dt-site.xml
dag.setAttribute(
OperatorContext.STORAGE_AGENT, new FSStorageAgent(checkpointPath.toString(), conf));
}
if (dag.getAttributes().get(LogicalPlan.CONTAINER_OPTS_CONFIGURATOR) == null) {
dag.setAttribute(
LogicalPlan.CONTAINER_OPTS_CONFIGURATOR, new BasicContainerOptConfigurator());
}
// Set the log4j properties if needed
if (!log4jPropFile.isEmpty()) {
Path log4jSrc = new Path(log4jPropFile);
Path log4jDst = new Path(appPath, "log4j.props");
fs.copyFromLocalFile(false, true, log4jSrc, log4jDst);
FileStatus log4jFileStatus = fs.getFileStatus(log4jDst);
LocalResource log4jRsrc = Records.newRecord(LocalResource.class);
log4jRsrc.setType(LocalResourceType.FILE);
log4jRsrc.setVisibility(LocalResourceVisibility.APPLICATION);
log4jRsrc.setResource(ConverterUtils.getYarnUrlFromURI(log4jDst.toUri()));
log4jRsrc.setTimestamp(log4jFileStatus.getModificationTime());
log4jRsrc.setSize(log4jFileStatus.getLen());
localResources.put("log4j.properties", log4jRsrc);
}
if (originalAppId != null) {
Path origAppPath = new Path(appsBasePath, this.originalAppId);
LOG.info("Restart from {}", origAppPath);
copyInitialState(origAppPath);
}
// push logical plan to DFS location
Path cfgDst = new Path(appPath, LogicalPlan.SER_FILE_NAME);
FSDataOutputStream outStream = fs.create(cfgDst, true);
LogicalPlan.write(this.dag, outStream);
outStream.close();
Path launchConfigDst = new Path(appPath, LogicalPlan.LAUNCH_CONFIG_FILE_NAME);
outStream = fs.create(launchConfigDst, true);
conf.writeXml(outStream);
outStream.close();
FileStatus topologyFileStatus = fs.getFileStatus(cfgDst);
LocalResource topologyRsrc = Records.newRecord(LocalResource.class);
topologyRsrc.setType(LocalResourceType.FILE);
topologyRsrc.setVisibility(LocalResourceVisibility.APPLICATION);
topologyRsrc.setResource(ConverterUtils.getYarnUrlFromURI(cfgDst.toUri()));
topologyRsrc.setTimestamp(topologyFileStatus.getModificationTime());
topologyRsrc.setSize(topologyFileStatus.getLen());
localResources.put(LogicalPlan.SER_FILE_NAME, topologyRsrc);
// Set local resource info into app master container launch context
amContainer.setLocalResources(localResources);
// Set the necessary security tokens as needed
// amContainer.setContainerTokens(containerToken);
// Set the env variables to be setup in the env where the application master will be run
LOG.info("Set the environment for the application master");
Map<String, String> env = new HashMap<String, String>();
// Add application jar(s) location to classpath
// At some point we should not be required to add
// the hadoop specific classpaths to the env.
// It should be provided out of the box.
// For now setting all required classpaths including
// the classpath to "." for the application jar(s)
// including ${CLASSPATH} will duplicate the class path in app master, removing it for now
// StringBuilder classPathEnv = new StringBuilder("${CLASSPATH}:./*");
StringBuilder classPathEnv = new StringBuilder("./*");
String classpath = conf.get(YarnConfiguration.YARN_APPLICATION_CLASSPATH);
for (String c :
StringUtils.isBlank(classpath)
? YarnConfiguration.DEFAULT_YARN_APPLICATION_CLASSPATH
: classpath.split(",")) {
if (c.equals("$HADOOP_CLIENT_CONF_DIR")) {
// SPOI-2501
continue;
}
classPathEnv.append(':');
classPathEnv.append(c.trim());
}
env.put("CLASSPATH", classPathEnv.toString());
// propagate to replace node managers user name (effective in non-secure mode)
env.put("HADOOP_USER_NAME", UserGroupInformation.getLoginUser().getUserName());
amContainer.setEnvironment(env);
// Set the necessary command to execute the application master
ArrayList<CharSequence> vargs = new ArrayList<CharSequence>(30);
// Set java executable command
LOG.info("Setting up app master command");
vargs.add(javaCmd);
if (dag.isDebug()) {
vargs.add("-agentlib:jdwp=transport=dt_socket,server=y,suspend=n");
}
// Set Xmx based on am memory size
// default heap size 75% of total memory
vargs.add("-Xmx" + (amMemory * 3 / 4) + "m");
vargs.add("-XX:+HeapDumpOnOutOfMemoryError");
vargs.add("-XX:HeapDumpPath=/tmp/dt-heap-" + appId.getId() + ".bin");
vargs.add("-Dhadoop.root.logger=" + (dag.isDebug() ? "DEBUG" : "INFO") + ",RFA");
vargs.add("-Dhadoop.log.dir=" + ApplicationConstants.LOG_DIR_EXPANSION_VAR);
vargs.add(String.format("-D%s=%s", StreamingContainer.PROP_APP_PATH, dag.assertAppPath()));
if (dag.isDebug()) {
vargs.add("-Dlog4j.debug=true");
}
String loggersLevel = conf.get(DTLoggerFactory.DT_LOGGERS_LEVEL);
if (loggersLevel != null) {
vargs.add(String.format("-D%s=%s", DTLoggerFactory.DT_LOGGERS_LEVEL, loggersLevel));
}
vargs.add(StreamingAppMaster.class.getName());
vargs.add("1>" + ApplicationConstants.LOG_DIR_EXPANSION_VAR + "/AppMaster.stdout");
vargs.add("2>" + ApplicationConstants.LOG_DIR_EXPANSION_VAR + "/AppMaster.stderr");
// Get final command
StringBuilder command = new StringBuilder(9 * vargs.size());
for (CharSequence str : vargs) {
command.append(str).append(" ");
}
LOG.info("Completed setting up app master command " + command.toString());
List<String> commands = new ArrayList<String>();
commands.add(command.toString());
amContainer.setCommands(commands);
// Set up resource type requirements
// For now, only memory is supported so we set memory requirements
Resource capability = Records.newRecord(Resource.class);
capability.setMemory(amMemory);
appContext.setResource(capability);
// Service data is a binary blob that can be passed to the application
// Not needed in this scenario
// amContainer.setServiceData(serviceData);
appContext.setAMContainerSpec(amContainer);
// Set the priority for the application master
Priority pri = Records.newRecord(Priority.class);
pri.setPriority(amPriority);
appContext.setPriority(pri);
// Set the queue to which this application is to be submitted in the RM
appContext.setQueue(queueName);
// Submit the application to the applications manager
// SubmitApplicationResponse submitResp = rmClient.submitApplication(appRequest);
// Ignore the response as either a valid response object is returned on success
// or an exception thrown to denote some form of a failure
String specStr =
Objects.toStringHelper("Submitting application: ")
.add("name", appContext.getApplicationName())
.add("queue", appContext.getQueue())
.add("user", UserGroupInformation.getLoginUser())
.add("resource", appContext.getResource())
.toString();
LOG.info(specStr);
if (dag.isDebug()) {
// LOG.info("Full submission context: " + appContext);
}
yarnClient.submitApplication(appContext);
} finally {
fs.close();
}
}
public int run(String[] args) throws IOException, ClassNotFoundException, InterruptedException {
if (args.length != 2) {
System.out.println("Usage: FeatureMatching ID <inputName.jpeg/inputName.jpg>");
System.exit(1);
}
SimpleDateFormat sdf = new SimpleDateFormat("", Locale.US);
sdf.applyPattern("yyyy-MM-dd_HH-mm-ss");
String time = sdf.format(new Date());
Job job = Job.getInstance();
ID = "/" + args[0];
String filename = args[1];
filename = filename.toLowerCase();
System.out.println("current filename:" + filename);
// Detect illegal username (if the username dir doesn't exist)
File userPath = new File(LOCAL_USER_DIR + ID);
if (!userPath.exists()) {
System.out.println("Unauthorized username!!!\nExiting......");
System.exit(1);
}
// Preprocess the input image.jpg from local dir: /local.../user/ID/input/image.jpg
// Save the features to local dir: hdfs://.../user/ID/input/image.jpg
extractQueryFeatures2HDFS(filename, job);
// Add the feature file to the hdfs cache
String featureFileName = filename.substring(0, filename.lastIndexOf(".")) + ".json";
// job.addCacheFile(new Path(HDFS_HOME + USER + ID + INPUT + "/" +
// featureFileName).toUri());
job.getConfiguration()
.set("featureFilePath", HDFS_HOME + USER + ID + INPUT + "/" + featureFileName);
// Check the file type. Only support jpeg/jpg type images
String type = filename.substring(args[1].lastIndexOf("."));
if (!(type.equals(".jpg") || type.equals(".jpeg"))) {
System.out.println("Image type not supported!!!\nExiting");
System.exit(1);
}
// Input: hdfs://.../features/
// The feature dir is a location of all features extracted from the database
String inputPathStr = HDFS_HOME + FEATURES;
// Output: hdfs://.../user/ID/output/
String outputPathStr = HDFS_HOME + USER + ID + OUTPUT + "/" + time;
job.setInputFormatClass(KeyValueTextInputFormat.class);
// job.setOutputFormatClass(TextOutputFormat.class);
// Get the lists of all feature files: /.../features/data/part-*
FileSystem fs = FileSystem.get(job.getConfiguration());
FileStatus[] statuses = fs.listStatus(new Path(inputPathStr));
StringBuffer sb = new StringBuffer();
for (FileStatus fileStatus : statuses) {
sb.append(fileStatus.getPath() + ",");
}
sb.deleteCharAt(sb.lastIndexOf(","));
job.setJarByClass(FeatureMatching.class);
job.setMapperClass(FeatureMatchMapper.class);
job.setReducerClass(FeatureMatchReducer.class);
// only need one reducer to collect the result
job.setNumReduceTasks(1);
job.setMapOutputKeyClass(IntWritable.class);
job.setMapOutputValueClass(Text.class);
job.setOutputKeyClass(Text.class);
job.setOutputValueClass(DoubleWritable.class);
// Input a directory, so need the recursive input
FileInputFormat.setInputDirRecursive(job, true);
// Set the PathFilter, to omit _SUCCESS files
// (This is not working correctly, as the PathFilter class is an interface rather than a class.
// But the 2nd arg asks me to extend the PathFilter)
// FileInputFormat.setInputPathFilter(job, MyPathFilter.class);
//
// FileInputFormat.setInputPaths(job, new Path(inputPathStr));
FileInputFormat.setInputPaths(job, sb.toString());
FileOutputFormat.setOutputPath(job, new Path(outputPathStr));
boolean success = job.waitForCompletion(true);
return success ? 0 : 1;
}