@Test
public void insert_rowkey_prefix_date() throws IOException {
System.out.println(errorTable);
errorTable.setAutoFlushTo(false);
List<Put> puts = new ArrayList<Put>();
long t1 = System.currentTimeMillis();
for (int i = 0; i < 10000000; i++) {
String uuid = UUID.randomUUID().toString().replaceAll("-", "").substring(0, 8);
Put put = new Put(Bytes.toBytes("20150705" + "_" + uuid));
put.add(
fBytes,
Bytes.toBytes("stacktrace"),
Bytes.toBytes("java.io.IOException:file not found" + UUID.randomUUID().toString()));
// puts.add(put);
errorTable.put(put);
if (i % 10000 == 0) {
errorTable.flushCommits();
}
}
errorTable.flushCommits();
long t2 = System.currentTimeMillis();
System.out.println("count=" + puts.size() + ",t2-t1=" + (t2 - t1));
// errorTable.close();
}
/** Sets up configuration based on params */
private static boolean setup(Hashtable<String, String> curConf, Configuration argConf) {
if (argConf.get("file") == null) {
logger.fatal("Missing file parameter");
System.exit(1);
}
if (argConf.get("hdfs_base_path") == null) {
logger.fatal("Missing HDFS base path, check gestore-conf.xml");
System.exit(1);
}
if (argConf.get("hdfs_temp_path") == null) {
logger.fatal("Missing HDFS temp path, check gestore-conf.xml");
System.exit(1);
}
if (argConf.get("local_temp_path") == null) {
logger.fatal("Missing local temp path, check gestore-conf.xml");
System.exit(1);
}
// Input paramaters
curConf.put("run_id", argConf.get("run", ""));
curConf.put("task_id", argConf.get("task", ""));
curConf.put("file_id", argConf.get("file"));
curConf.put("local_path", argConf.get("path", ""));
curConf.put("type", argConf.get("type", "l2r"));
curConf.put("timestamp_start", argConf.get("timestamp_start", "1"));
curConf.put(
"timestamp_stop", argConf.get("timestamp_stop", Integer.toString(Integer.MAX_VALUE)));
curConf.put("delimiter", argConf.get("regex", "ID=.*"));
curConf.put("taxon", argConf.get("taxon", "all"));
curConf.put("intermediate", argConf.get("full_run", "false"));
curConf.put("quick_add", argConf.get("quick_add", "false"));
Boolean full_run = curConf.get("intermediate").matches("(?i).*true.*");
curConf.put("format", argConf.get("format", "unknown"));
curConf.put("split", argConf.get("split", "1"));
curConf.put("copy", argConf.get("copy", "true"));
// Constants
curConf.put("base_path", argConf.get("hdfs_base_path"));
curConf.put("temp_path", argConf.get("hdfs_temp_path"));
curConf.put("local_temp_path", argConf.get("local_temp_path"));
curConf.put("db_name_files", argConf.get("hbase_file_table"));
curConf.put("db_name_runs", argConf.get("hbase_run_table"));
curConf.put("db_name_updates", argConf.get("hbase_db_update_table"));
// Timestamps
Date currentTime = new Date();
Date endDate = new Date(new Long(curConf.get("timestamp_stop")));
curConf.put("timestamp_real", Long.toString(currentTime.getTime()));
return true;
}
public void doScan() throws IOException {
Table tableRef = connection.getTable(TableName.valueOf(table));
Scan scan = new Scan();
ResultScanner scanner = tableRef.getScanner(scan);
long now = System.currentTimeMillis();
if (verbose) System.out.println("Starting scan");
for (Result res : scanner) {
if (verbose) System.out.println(res);
}
if (verbose) System.out.printf("Scan finished: %d ms\n\n", System.currentTimeMillis() - now);
tableRef.close();
}
private static void waitUntil(long until) {
long now = System.currentTimeMillis();
while (now <= until) {
try {
Thread.sleep(1L);
now = System.currentTimeMillis();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
}
}
@Override
public void mutateMany(Map<String, Map<ByteBuffer, KCVMutation>> mutations, StoreTransaction txh)
throws StorageException {
final long delTS = System.currentTimeMillis();
final long putTS = delTS + 1;
Map<ByteBuffer, Pair<Put, Delete>> commandsPerKey = convertToCommands(mutations, putTS, delTS);
List<Row> batch = new ArrayList<Row>(commandsPerKey.size()); // actual batch operation
// convert sorted commands into representation required for 'batch' operation
for (Pair<Put, Delete> commands : commandsPerKey.values()) {
if (commands.getFirst() != null) batch.add(commands.getFirst());
if (commands.getSecond() != null) batch.add(commands.getSecond());
}
try {
HTableInterface table = null;
try {
table = connectionPool.getTable(tableName);
table.batch(batch);
table.flushCommits();
} finally {
IOUtils.closeQuietly(table);
}
} catch (IOException e) {
throw new TemporaryStorageException(e);
} catch (InterruptedException e) {
throw new TemporaryStorageException(e);
}
waitUntil(putTS);
}
static {
try {
props.load(ClassLoader.getSystemResource(Constants.PROPERTIES).openStream());
} catch (IOException e) {
logger.error("Fail to locate properties file.");
System.exit(1);
}
}
@Override
public void tweet(User user, String tweetText) throws IOException {
final long epoch = System.currentTimeMillis();
final long tranposeEpoch = Long.MAX_VALUE - epoch;
final byte[] epochBytes = Bytes.toBytes(epoch);
final byte[] tweetBytes = Bytes.toBytes(tweetText);
byte[] nameBytes = Bytes.toBytes(user.getName());
/** put tweet into tweets */
Put tweetRowPut = new Put(generateTweetId(user));
tweetRowPut.add(_DEFAULT, _NAME, nameBytes);
tweetRowPut.add(_DEFAULT, _MAIL, Bytes.toBytes(user.getEmail()));
tweetRowPut.add(_DEFAULT, _TWEET, tweetBytes);
tweetRowPut.add(_DEFAULT, _TIME, epochBytes);
tweetsTable.put(tweetRowPut);
/** put tweets for followers */
Scan followerScan = new Scan();
followerScan.setStartRow(Bytes.toBytes(user.getUserId() + "-"));
followerScan.setStopRow(Bytes.toBytes((user.getUserId() + 1) + "-"));
ResultScanner followerRS = followersTable.getScanner(followerScan);
/** put users on tweet to her own tweetline */
Put put =
new Put(Bytes.toBytes(user.getUserId() + "-" + tranposeEpoch + "-" + user.getUserId()));
put.add(_DEFAULT, _NAME, nameBytes);
put.add(_DEFAULT, _TWEET, tweetBytes);
put.add(_DEFAULT, _TIME, epochBytes);
List<Row> puts = new ArrayList<Row>();
puts.add(put);
for (Result result : followerRS) {
Long followerid = Bytes.toLong(result.getColumnLatest(_DEFAULT, _USERID).getValue());
put = new Put(Bytes.toBytes(followerid + "-" + tranposeEpoch + "-" + user.getUserId()));
put.add(_DEFAULT, _NAME, nameBytes);
put.add(_DEFAULT, _TWEET, tweetBytes);
put.add(_DEFAULT, _TIME, epochBytes);
puts.add(put);
}
followerRS.close();
try {
tweetlineTable.batch(puts);
} catch (InterruptedException e) {
e.printStackTrace(); // @TODO log and handle properly.
}
}
@Test
public void scan_by_prefix_date() throws IOException {
FilterList fl = new FilterList();
Filter filter =
new RowFilter(CompareFilter.CompareOp.EQUAL, new SubstringComparator("20150903"));
fl.addFilter(filter);
Scan scan = new Scan();
scan.setFilter(fl);
long t1 = System.currentTimeMillis();
ResultScanner rs = errorTable.getScanner(scan);
Result result;
int count = 0;
while ((result = rs.next()) != null) {
System.out.println("rowkey=" + new String(result.getRow()));
System.out.println(
"value=" + new String(result.getValue(fBytes, Bytes.toBytes("stacktrace"))));
System.out.println();
count++;
}
long t2 = System.currentTimeMillis();
System.out.println("count=" + count + ",t2 - t1=" + ((t2 - t1) / 1000));
}
public static void main(String[] args) throws Exception {
if (args.length < 5) {
System.err.printf(
"Usage: %s <conf> <keytab> <user> <table> <reps> [-v]\n", ExampleJavaClient.class);
System.exit(-1);
}
ExampleJavaClient exampleJavaClient = new ExampleJavaClient(args[0], args[1], args[2], args[3]);
exampleJavaClient.initialise();
if (args.length == 6 && args[5].equals("-v")) {
exampleJavaClient.verbose(true);
}
int reps = Integer.parseInt(args[4]);
long start = System.currentTimeMillis();
System.out.println("Beginning " + reps + " scans");
for (int i = 0; i < reps; ++i) {
exampleJavaClient.doScan();
}
System.out.println("Runtime: " + (System.currentTimeMillis() - start) + "ms");
System.out.println("Ended scans for " + args[2]);
}
public HostRankHBaseTest() {
super(HostRankHBaseTest.class.getName());
// Let's set up the hbase root directory.
Configuration conf = HBaseConfiguration.create();
try {
FileSystem fs = FileSystem.get(conf);
String randomStr = UUID.randomUUID().toString();
String tmpdir = System.getProperty("java.io.tmpdir") + "/" + randomStr + "/";
hbaseRootdir = fs.makeQualified(new Path(tmpdir));
conf.set(HConstants.HBASE_DIR, hbaseRootdir.toString());
fs.mkdirs(hbaseRootdir);
} catch (IOException ioe) {
fail("Could not create hbase root directory.");
}
// Start the test utility.
testUtil = new HBaseTestingUtility(conf);
}
public static void main(String[] args) throws Exception {
Configuration conf = HBaseConfiguration.create();
IntegrationTestingUtility.setUseDistributedCluster(conf);
IntegrationTestDDLMasterFailover masterFailover = new IntegrationTestDDLMasterFailover();
Connection connection = null;
int ret = 1;
try {
// Initialize connection once, then pass to Actions
LOG.debug("Setting up connection ...");
connection = ConnectionFactory.createConnection(conf);
masterFailover.setConnection(connection);
ret = ToolRunner.run(conf, masterFailover, args);
} catch (IOException e) {
LOG.fatal("Failed to establish connection. Aborting test ...", e);
} finally {
connection = masterFailover.getConnection();
if (connection != null) {
connection.close();
}
System.exit(ret);
}
}
@Override
public QueryResult getVariantsHistogramByRegion(
Region region, String sourceId, boolean histogramLogarithm, int histogramMax) {
QueryResult<ObjectMap> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<ObjectMap> data = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
long startTime = System.currentTimeMillis();
long startDbTime = System.currentTimeMillis();
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("studies.studyId", sourceId);
DBCollection collection = db.getCollection("variants");
DBCursor queryResults = collection.find(query);
queryResult.setDbTime(System.currentTimeMillis() - startDbTime);
int resultSize = queryResults.size();
if (resultSize > histogramMax) { // Need to group results to fit maximum size of the histogram
int sumChunkSize = resultSize / histogramMax;
int i = 0, j = 0;
int featuresCount = 0;
ObjectMap item = null;
for (DBObject result : queryResults) {
// featuresCount += result.getInt("features_count");
// if (i == 0) {
// item = new ObjectMap("chromosome", result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// } else if (i == sumChunkSize - 1 || j == resultSize - 1) {
// if (histogramLogarithm) {
// item.put("featuresCount", (featuresCount > 0) ?
// Math.log(featuresCount) : 0);
// } else {
// item.put("featuresCount", featuresCount);
// }
// item.put("end", result.getInt("end"));
// data.add(item);
// i = -1;
// featuresCount = 0;
// }
// j++;
// i++;
}
} else {
for (DBObject result : queryResults) {
// ObjectMap item = new ObjectMap("chromosome",
// result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// if (histogramLogarithm) {
// int features_count = result.getInt("features_count");
// result.put("featuresCount", (features_count > 0) ?
// Math.log(features_count) : 0);
// } else {
// item.put("featuresCount", result.getInt("features_count"));
// }
// item.put("end", result.getInt("end"));
// data.add(item);
}
}
queryResult.setResult(data);
queryResult.setNumResults(data.size());
queryResult.setTime(System.currentTimeMillis() - startTime);
return queryResult;
}
@Test
public void testRun() throws Exception {
TableName tn = TableName.valueOf(tableName);
byte[] mobValueBytes = new byte[100];
// get the path where mob files lie in
Path mobFamilyPath = MobUtils.getMobFamilyPath(TEST_UTIL.getConfiguration(), tn, family);
Put put = new Put(Bytes.toBytes(row));
put.addColumn(Bytes.toBytes(family), Bytes.toBytes(qf), 1, mobValueBytes);
Put put2 = new Put(Bytes.toBytes(row + "ignore"));
put2.addColumn(Bytes.toBytes(family), Bytes.toBytes(qf), 1, mobValueBytes);
table.mutate(put);
table.mutate(put2);
table.flush();
admin.flush(tn);
FileStatus[] fileStatuses = TEST_UTIL.getTestFileSystem().listStatus(mobFamilyPath);
// check the generation of a mob file
assertEquals(1, fileStatuses.length);
String mobFile1 = fileStatuses[0].getPath().getName();
Configuration configuration = new Configuration(TEST_UTIL.getConfiguration());
configuration.setFloat(MobConstants.MOB_SWEEP_TOOL_COMPACTION_RATIO, 0.6f);
configuration.setStrings(TableInputFormat.INPUT_TABLE, tableName);
configuration.setStrings(TableInputFormat.SCAN_COLUMN_FAMILY, family);
configuration.setStrings(SweepJob.WORKING_VISITED_DIR_KEY, "jobWorkingNamesDir");
configuration.setStrings(SweepJob.WORKING_FILES_DIR_KEY, "compactionFileDir");
configuration.setStrings(
CommonConfigurationKeys.IO_SERIALIZATIONS_KEY, JavaSerialization.class.getName());
configuration.set(SweepJob.WORKING_VISITED_DIR_KEY, "compactionVisitedDir");
configuration.setLong(
MobConstants.MOB_SWEEP_TOOL_COMPACTION_START_DATE,
System.currentTimeMillis() + 24 * 3600 * 1000);
ZooKeeperWatcher zkw = new ZooKeeperWatcher(configuration, "1", new DummyMobAbortable());
TableName lockName = MobUtils.getTableLockName(tn);
String znode = ZKUtil.joinZNode(zkw.tableLockZNode, lockName.getNameAsString());
configuration.set(SweepJob.SWEEP_JOB_ID, "1");
configuration.set(SweepJob.SWEEP_JOB_TABLE_NODE, znode);
ServerName serverName = SweepJob.getCurrentServerName(configuration);
configuration.set(SweepJob.SWEEP_JOB_SERVERNAME, serverName.toString());
TableLockManager tableLockManager =
TableLockManager.createTableLockManager(configuration, zkw, serverName);
TableLock lock = tableLockManager.writeLock(lockName, "Run sweep tool");
lock.acquire();
try {
// use the same counter when mocking
Counter counter = new GenericCounter();
Reducer<Text, KeyValue, Writable, Writable>.Context ctx = mock(Reducer.Context.class);
when(ctx.getConfiguration()).thenReturn(configuration);
when(ctx.getCounter(Matchers.any(SweepCounter.class))).thenReturn(counter);
when(ctx.nextKey()).thenReturn(true).thenReturn(false);
when(ctx.getCurrentKey()).thenReturn(new Text(mobFile1));
byte[] refBytes = Bytes.toBytes(mobFile1);
long valueLength = refBytes.length;
byte[] newValue = Bytes.add(Bytes.toBytes(valueLength), refBytes);
KeyValue kv2 =
new KeyValue(
Bytes.toBytes(row),
Bytes.toBytes(family),
Bytes.toBytes(qf),
1,
KeyValue.Type.Put,
newValue);
List<KeyValue> list = new ArrayList<KeyValue>();
list.add(kv2);
when(ctx.getValues()).thenReturn(list);
SweepReducer reducer = new SweepReducer();
reducer.run(ctx);
} finally {
lock.release();
}
FileStatus[] filsStatuses2 = TEST_UTIL.getTestFileSystem().listStatus(mobFamilyPath);
String mobFile2 = filsStatuses2[0].getPath().getName();
// new mob file is generated, old one has been archived
assertEquals(1, filsStatuses2.length);
assertEquals(false, mobFile2.equalsIgnoreCase(mobFile1));
// test sequence file
String workingPath = configuration.get(SweepJob.WORKING_VISITED_DIR_KEY);
FileStatus[] statuses = TEST_UTIL.getTestFileSystem().listStatus(new Path(workingPath));
Set<String> files = new TreeSet<String>();
for (FileStatus st : statuses) {
files.addAll(
getKeyFromSequenceFile(TEST_UTIL.getTestFileSystem(), st.getPath(), configuration));
}
assertEquals(1, files.size());
assertEquals(true, files.contains(mobFile1));
}
public static void main(String[] args) throws Exception {
int result = ToolRunner.run(new Configuration(), new move(), args);
System.exit(result);
}
@Override
public QueryResult<Variant> getAllVariantsByRegionAndStudy(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new LinkedList<>();
boolean includeSamples;
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("samples")
&& !options.containsKey("stats")
&& !options.containsKey("effects")) {
includeSamples = true;
includeStats = true;
includeEffects = true;
} else {
includeSamples = options.containsKey("samples") && options.getBoolean("samples");
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
try {
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
HTable table = new HTable(admin.getConfiguration(), tableName);
dbstart = System.currentTimeMillis();
Scan regionScan = new Scan(startRow.getBytes(), stopRow.getBytes());
ResultScanner scanres = table.getScanner(regionScan);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
// Iterate over results and, optionally, their samples and statistics
for (Result result : scanres) {
String[] rowkeyParts = new String(result.getRow(), CHARSET_UTF_8).split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
// Get basic result fields from Protocol Buffers message
NavigableMap<byte[], byte[]> infoMap = result.getFamilyMap("i".getBytes());
byte[] byteInfo = infoMap.get((sourceId + "_data").getBytes());
VariantFieldsProtos.VariantInfo protoInfo =
VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
String reference = protoInfo.getReference();
String alternate = StringUtils.join(protoInfo.getAlternateList(), ",");
String format = StringUtils.join(protoInfo.getFormatList(), ":");
Variant variant = new Variant(chromosome, position, position, reference, alternate);
// Set samples if requested
if (includeSamples) {
NavigableMap<byte[], byte[]> sampleMap = result.getFamilyMap("d".getBytes());
Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
// Set samples
for (byte[] s : sampleMap.keySet()) {
String sampleName = (new String(s, CHARSET_UTF_8)).replaceAll(sourceId + "_", "");
VariantFieldsProtos.VariantSample sample =
VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
String sample1 = sample.getSample();
String[] values = sample1.split(":");
String[] fields = format.split(":");
Map<String, String> singleSampleMap = new HashMap<>();
for (int i = 0; i < fields.length; i++) {
singleSampleMap.put(fields[i], values[i]);
}
// TODO
// variant.addSampleData(sampleName, singleSampleMap);
}
}
// Set stats if requested
if (includeStats) {
byte[] byteStats = infoMap.get((sourceId + "_stats").getBytes());
VariantFieldsProtos.VariantStats protoStats =
VariantFieldsProtos.VariantStats.parseFrom(byteStats);
VariantStats variantStats =
new VariantStats(
chromosome,
position,
reference,
alternate,
protoStats.getMaf(),
protoStats.getMgf(),
protoStats.getMafAllele(),
protoStats.getMgfGenotype(),
protoStats.getMissingAlleles(),
protoStats.getMissingGenotypes(),
protoStats.getMendelianErrors(),
protoStats.getIsIndel(),
protoStats.getCasesPercentDominant(),
protoStats.getControlsPercentDominant(),
protoStats.getCasesPercentRecessive(),
protoStats.getControlsPercentRecessive());
variant.setStats(variantStats);
}
if (includeEffects) {
QueryResult<VariantEffect> queryEffects = getEffectsByVariant(variant, options);
variant.setEffect(queryEffects.getResult());
}
results.add(variant);
}
} catch (IOException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
return queryResult;
}
public int run(String[] args) throws Exception {
// printUsage();
/*
* SETUP
*/
Configuration argConf = getConf();
Hashtable<String, String> confArg = new Hashtable<String, String>();
setup(confArg, argConf);
Date currentTime = new Date();
Date endDate = new Date(new Long(confArg.get("timestamp_stop")));
Boolean full_run = confArg.get("intermediate").matches("(?i).*true.*");
Boolean quick_add = confArg.get("quick_add").matches("(?i).*true.*");
logger.info("Running GeStore");
// ZooKeeper setup
Configuration config = HBaseConfiguration.create();
zkWatcher = new ZooKeeperWatcher(config, "Testing", new HBaseAdmin(config));
zkInstance =
new ZooKeeper(
ZKConfig.getZKQuorumServersString(config),
config.getInt("zookeeper.session.timeout", -1),
zkWatcher);
if (!confArg.get("task_id").isEmpty()) {
confArg.put("temp_path", confArg.get("temp_path") + confArg.get("task_id"));
}
String lockRequest = confArg.get("file_id");
if (!confArg.get("run_id").isEmpty())
lockRequest = lockRequest + "_" + confArg.get("run_id") + "_";
if (!confArg.get("task_id").isEmpty())
lockRequest = lockRequest + "_" + confArg.get("task_id") + "_";
// Get type of movement
toFrom type_move = checkArgs(confArg);
if (type_move == toFrom.LOCAL2REMOTE && !confArg.get("format").equals("unknown")) {
List<String> arguments = new ArrayList<String>();
arguments.add("-Dinput=" + confArg.get("local_path"));
arguments.add("-Dtable=" + confArg.get("file_id"));
arguments.add("-Dtimestamp=" + confArg.get("timestamp_stop"));
arguments.add("-Dtype=" + confArg.get("format"));
arguments.add("-Dtarget_dir=" + confArg.get("base_path") + "_" + confArg.get("file_id"));
arguments.add("-Dtemp_hdfs_path=" + confArg.get("temp_path"));
arguments.add("-Drun_id=" + confArg.get("run_id"));
if (!confArg.get("run_id").isEmpty()) arguments.add("-Drun_id=" + confArg.get("run_id"));
if (!confArg.get("task_id").isEmpty()) arguments.add("-Dtask_id=" + confArg.get("task_id"));
if (quick_add) arguments.add("-Dquick_add=" + confArg.get("quick_add"));
String lockName = lock(lockRequest);
String[] argumentString = arguments.toArray(new String[arguments.size()]);
adddb.main(argumentString);
unlock(lockName);
System.exit(0);
}
// Database registration
dbutil db_util = new dbutil(config);
db_util.register_database(confArg.get("db_name_files"), true);
db_util.register_database(confArg.get("db_name_runs"), true);
db_util.register_database(confArg.get("db_name_updates"), true);
FileSystem hdfs = FileSystem.get(config);
FileSystem localFS = FileSystem.getLocal(config);
// Get source type
confArg.put("source", getSource(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
confArg.put(
"database", isDatabase(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
if (!confArg.get("source").equals("local")
&& type_move == toFrom.REMOTE2LOCAL
&& !confArg.get("timestamp_stop").equals(Integer.toString(Integer.MAX_VALUE))) {
confArg.put("timestamp_stop", Long.toString(latestVersion(confArg, db_util)));
}
/*
* Get previous timestamp
*/
Get run_id_get = new Get(confArg.get("run_id").getBytes());
Result run_get = db_util.doGet(confArg.get("db_name_runs"), run_id_get);
KeyValue run_file_prev =
run_get.getColumnLatest(
"d".getBytes(), (confArg.get("file_id") + "_db_timestamp").getBytes());
String last_timestamp = new String("0");
if (null != run_file_prev && !confArg.get("source").equals("local")) {
long last_timestamp_real = run_file_prev.getTimestamp();
Long current_timestamp = new Long(confArg.get("timestamp_real"));
if ((current_timestamp - last_timestamp_real) > 36000) {
last_timestamp = new String(run_file_prev.getValue());
Integer lastTimestamp = new Integer(last_timestamp);
lastTimestamp += 1;
last_timestamp = lastTimestamp.toString();
logger.info("Last timestamp: " + last_timestamp + " End data: " + endDate);
Date last_run = new Date(run_file_prev.getTimestamp());
if (last_run.before(endDate) && !full_run) {
confArg.put("timestamp_start", last_timestamp);
}
}
}
Integer tse = new Integer(confArg.get("timestamp_stop"));
Integer tss = new Integer(confArg.get("timestamp_start"));
if (tss > tse) {
logger.info("No new version of requested file.");
return 0;
}
/*
* Generate file
*/
String lockName = lock(lockRequest);
Get file_id_get = new Get(confArg.get("file_id").getBytes());
Result file_get = db_util.doGet(confArg.get("db_name_files"), file_id_get);
if (!file_get.isEmpty()) {
boolean found =
hasFile(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
getFullPath(confArg));
if (confArg.get("source").equals("fullfile")) {
found = false;
}
String filenames_put =
getFileNames(
db_util, confArg.get("db_name_files"), confArg.get("file_id"), getFullPath(confArg));
// Filename not found in file database
if (!found && type_move == toFrom.REMOTE2LOCAL) {
if (!confArg.get("source").equals("local")) {
// Generate intermediate file
if (getFile(hdfs, confArg, db_util) == null) {
unlock(lockName);
return 1;
}
// Put generated file into file database
if (!confArg.get("format").equals("fullfile")) {
putFileEntry(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
confArg.get("full_file_name"),
confArg.get("source"));
}
} else {
logger.warn("Remote file not found, and cannot be generated! File: " + confArg);
unlock(lockName);
return 1;
}
}
} else {
if (type_move == toFrom.REMOTE2LOCAL) {
logger.warn("Remote file not found, and cannot be generated.");
unlock(lockName);
return 1;
}
}
/*
* Copy file
* Update tables
*/
if (type_move == toFrom.LOCAL2REMOTE) {
if (!confArg.get("format").equals("fullfile")) {
putFileEntry(
db_util,
hdfs,
confArg.get("db_name_files"),
confArg.get("file_id"),
getFullPath(confArg),
confArg.get("source"));
}
putRunEntry(
db_util,
confArg.get("db_name_runs"),
confArg.get("run_id"),
confArg.get("file_id"),
confArg.get("type"),
confArg.get("timestamp_real"),
confArg.get("timestamp_stop"),
getFullPath(confArg),
confArg.get("delimiter"));
hdfs.copyFromLocalFile(new Path(confArg.get("local_path")), new Path(getFullPath(confArg)));
} else if (type_move == toFrom.REMOTE2LOCAL) {
FileStatus[] files = hdfs.globStatus(new Path(getFullPath(confArg) + "*"));
putRunEntry(
db_util,
confArg.get("db_name_runs"),
confArg.get("run_id"),
confArg.get("file_id"),
confArg.get("type"),
confArg.get("timestamp_real"),
confArg.get("timestamp_stop"),
getFullPath(confArg),
confArg.get("delimiter"));
unlock(lockName);
for (FileStatus file : files) {
Path cur_file = file.getPath();
Path cur_local_path =
new Path(new String(confArg.get("local_path") + confArg.get("file_id")));
String suffix = getSuffix(getFileName(confArg), cur_file.getName());
if (suffix.length() > 0) {
cur_local_path = cur_local_path.suffix(new String("." + suffix));
}
if (confArg.get("copy").equals("true")) {
String crc = hdfs.getFileChecksum(cur_file).toString();
if (checksumLocalTest(cur_local_path, crc)) {
continue;
} else {
hdfs.copyToLocalFile(cur_file, cur_local_path);
writeChecksum(cur_local_path, crc);
}
} else {
System.out.println(cur_local_path + "\t" + cur_file);
}
}
}
unlock(lockName);
return 0;
}
private byte[] generateTweetId(User user) {
return Bytes.toBytes(user.getUserId() + "-" + (Long.MAX_VALUE - System.currentTimeMillis()));
}
@Test
public void testHostRank() throws Exception {
if (System.getProperty("prop.mapred.job.tracker") != null) {
if (LOG.isInfoEnabled())
LOG.info("testHBaseInputOutput: Ignore this test if not local mode.");
return;
}
File jarTest = new File(System.getProperty("prop.jarLocation"));
if (!jarTest.exists()) {
fail(
"Could not find Giraph jar at "
+ "location specified by 'prop.jarLocation'. "
+ "Make sure you built the main Giraph artifact?.");
}
MiniHBaseCluster cluster = null;
MiniZooKeeperCluster zkCluster = null;
FileSystem fs = null;
try {
// using the restart method allows us to avoid having the hbase
// root directory overwritten by /home/$username
zkCluster = testUtil.startMiniZKCluster();
testUtil.restartHBaseCluster(2);
cluster = testUtil.getMiniHBaseCluster();
final byte[] OL_BYTES = Bytes.toBytes("ol");
final byte[] S_BYTES = Bytes.toBytes("s");
final byte[] METADATA_BYTES = Bytes.toBytes("mtdt");
final byte[] HR_BYTES = Bytes.toBytes("_hr_");
final byte[] TAB = Bytes.toBytes(TABLE_NAME);
Configuration conf = cluster.getConfiguration();
HTableDescriptor desc = new HTableDescriptor(TAB);
desc.addFamily(new HColumnDescriptor(OL_BYTES));
desc.addFamily(new HColumnDescriptor(S_BYTES));
desc.addFamily(new HColumnDescriptor(METADATA_BYTES));
HBaseAdmin hbaseAdmin = new HBaseAdmin(conf);
if (hbaseAdmin.isTableAvailable(TABLE_NAME)) {
hbaseAdmin.disableTable(TABLE_NAME);
hbaseAdmin.deleteTable(TABLE_NAME);
}
hbaseAdmin.createTable(desc);
/**
* Enter the initial data (a,b), (b,c), (a,c) a = 1.0 - google b = 1.0 - yahoo c = 1.0 - bing
*/
HTable table = new HTable(conf, TABLE_NAME);
Put p1 = new Put(Bytes.toBytes("com.google.www"));
p1.add(OL_BYTES, Bytes.toBytes("www.yahoo.com"), Bytes.toBytes("ab"));
Put p2 = new Put(Bytes.toBytes("com.google.www"));
p2.add(OL_BYTES, Bytes.toBytes("www.bing.com"), Bytes.toBytes("ac"));
p2.add(OL_BYTES, Bytes.toBytes("www.bing.com"), Bytes.toBytes("invalid1"));
p2.add(OL_BYTES, Bytes.toBytes("www.google.com"), Bytes.toBytes("invalid2"));
Put p3 = new Put(Bytes.toBytes("com.yahoo.www"));
p3.add(OL_BYTES, Bytes.toBytes("www.bing.com"), Bytes.toBytes("bc"));
// p3.add(OL_BYTES, Bytes.toBytes(""), Bytes.toBytes("invalid4"));
Put p4 = new Put(Bytes.toBytes("com.bing.www"));
// TODO: Handle below case. use apache isValid method.
p4.add(OL_BYTES, Bytes.toBytes("http://invalidurl"), Bytes.toBytes("invalid5"));
p4.add(S_BYTES, S_BYTES, Bytes.toBytes(10.0d));
Put p5 = new Put(Bytes.toBytes("dummy"));
p5.add(S_BYTES, S_BYTES, Bytes.toBytes(10.0d));
table.put(p1);
table.put(p2);
table.put(p3);
table.put(p4);
table.put(p5);
// Set Giraph configuration
// now operate over HBase using Vertex I/O formats
conf.set(TableInputFormat.INPUT_TABLE, TABLE_NAME);
conf.set(TableOutputFormat.OUTPUT_TABLE, TABLE_NAME);
// Start the giraph job
GiraphJob giraphJob = new GiraphJob(conf, BspCase.getCallingMethodName());
GiraphConfiguration giraphConf = giraphJob.getConfiguration();
giraphConf.setZooKeeperConfiguration(cluster.getMaster().getZooKeeper().getQuorum());
setupConfiguration(giraphJob);
giraphConf.setComputationClass(LinkRankComputation.class);
giraphConf.setMasterComputeClass(LinkRankVertexMasterCompute.class);
giraphConf.setOutEdgesClass(ByteArrayEdges.class);
giraphConf.setVertexInputFormatClass(Nutch2HostInputFormat.class);
giraphConf.setVertexOutputFormatClass(Nutch2HostOutputFormat.class);
giraphConf.setInt("giraph.linkRank.superstepCount", 10);
giraphConf.setInt("giraph.linkRank.scale", 10);
giraphConf.set("giraph.linkRank.family", "mtdt");
giraphConf.set("giraph.linkRank.qualifier", "_hr_");
giraphConf.setVertexInputFilterClass(HostRankVertexFilter.class);
assertTrue(giraphJob.run(true));
if (LOG.isInfoEnabled()) LOG.info("Giraph job successful. Checking output qualifier.");
/** Check the results * */
Result result;
String key;
byte[] calculatedScoreByte;
HashMap expectedValues = new HashMap<String, Double>();
expectedValues.put("com.google.www", 1.3515060339386287d);
expectedValues.put("com.yahoo.www", 4.144902009567587d);
expectedValues.put("com.bing.www", 9.063893290511482d);
for (Object keyObject : expectedValues.keySet()) {
key = keyObject.toString();
result = table.get(new Get(key.getBytes()));
calculatedScoreByte = result.getValue(METADATA_BYTES, HR_BYTES);
assertNotNull(calculatedScoreByte);
assertTrue(calculatedScoreByte.length > 0);
Assert.assertEquals(
"Scores are not the same",
(Double) expectedValues.get(key),
Bytes.toDouble(calculatedScoreByte),
DELTA);
}
} finally {
if (cluster != null) {
cluster.shutdown();
}
if (zkCluster != null) {
zkCluster.shutdown();
}
// clean test files
if (fs != null) {
fs.delete(hbaseRootdir);
}
}
}
public QueryResult getSimpleVariantsByRegion(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("stats") && !options.containsKey("effects")) {
includeStats = true;
includeEffects = true;
} else {
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("sources.sourceId", sourceId);
DBCollection collection = db.getCollection("variants");
dbstart = System.currentTimeMillis();
DBCursor variantInStudies = collection.find(query);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
for (DBObject result : variantInStudies) {
String[] rowkeyParts = result.get("position").toString().split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
BasicDBList studies = (BasicDBList) result.get("sources");
BasicDBObject st = (BasicDBObject) studies.get(0);
String ref = (String) st.get("ref");
String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ",");
// TODO Needs rework
Variant variant = new Variant(chromosome, position, position, ref, alt);
// Set stats informations
if (includeStats) {
VariantStats stats = new VariantStats();
BasicDBObject mongoStats = (BasicDBObject) st.get("stats");
stats.setMaf((float) (double) mongoStats.get("maf"));
stats.setMafAllele((String) mongoStats.get("alleleMaf"));
stats.setMissingGenotypes((int) mongoStats.get("missing"));
List<Genotype> genotypeCount = new ArrayList<>();
for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) {
for (Map.Entry<String, Object> entry : s.entrySet()) {
Genotype genotype = new Genotype(entry.getKey());
genotype.setCount((Integer) entry.getValue());
genotypeCount.add(genotype);
}
}
stats.setGenotypes(genotypeCount);
variant.setStats(stats);
}
// TODO Set consequence type names
if (includeEffects) {
BasicDBList mongoEffects = (BasicDBList) st.get("effects");
if (mongoEffects != null) {
for (Object e : mongoEffects) {
String effectObo = e.toString();
VariantEffect effect = new VariantEffect();
effect.setConsequenceTypeObo(effectObo);
variant.addEffect(effect);
}
}
}
results.add(variant);
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
return queryResult;
}
public static void main(final String[] args) throws Exception {
final int res = ToolRunner.run(new Configuration(), new CrunchStockDateInserter(), args);
System.exit(res);
}