@Test
public void testCountsFromLocusTraversal() {
final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
engine.setGenomeLocParser(genomeLocParser);
final Collection<SAMReaderID> samFiles = new ArrayList<>();
final SAMReaderID readerID = new SAMReaderID(testBAM, new Tags());
samFiles.add(readerID);
final SAMDataSource dataSource =
new SAMDataSource(
samFiles,
new ThreadAllocation(),
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
new ArrayList<ReadTransformer>(),
false,
(byte) 30,
false,
true);
engine.setReadsDataSource(dataSource);
final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());
final TraverseLociNano traverseLociNano = new TraverseLociNano(1);
final DummyLocusWalker walker = new DummyLocusWalker();
traverseLociNano.initialize(engine, walker, null);
for (final Shard shard : dataSource.createShardIteratorOverAllReads(new LocusShardBalancer())) {
final WindowMaker windowMaker =
new WindowMaker(
shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples);
for (WindowMaker.WindowMakerIterator window : windowMaker) {
final LocusShardDataProvider dataProvider =
new LocusShardDataProvider(
shard,
shard.getReadProperties(),
genomeLocParser,
window.getLocus(),
window,
reference,
new ArrayList<ReferenceOrderedDataSource>());
traverseLociNano.traverse(walker, dataProvider, 0);
dataProvider.close();
}
windowMaker.close();
}
// dataSource.close();
Assert.assertEquals(
engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
Assert.assertEquals(
engine.getCumulativeMetrics().getNumIterations(), contigs.size() * numReadsPerContig);
}
private void twoAddressesTest(
String shard1Id, String shard2Id, int node1Weight, int node2Weight) {
DataSource testDataSource =
new DataSource() {
public RedisConnection getConnection() {
return null;
}
};
TestNode node1 = new TestNode();
TestNode node2 = new TestNode();
expect(dataSourceFactoryMock.create("addr1", 1)).andReturn(testDataSource);
expect(nodeFactoryMock.create(testDataSource)).andReturn(node1);
expect(dataSourceFactoryMock.create("addr2", 2)).andReturn(testDataSource);
expect(nodeFactoryMock.create(testDataSource)).andReturn(node2);
replay(nodeFactoryMock, dataSourceFactoryMock);
List<Shard<TestNode>> shards = new ArrayList<Shard<TestNode>>(shardsFactory.create());
verify(nodeFactoryMock, dataSourceFactoryMock);
Shard<TestNode> shard = shards.get(0);
assertEquals(node1, shard.getNode());
assertEquals(shard1Id, shard.getShardId());
assertEquals(node1Weight, shard.getWeight());
shard = shards.get(1);
assertEquals(node2, shard.getNode());
assertEquals(shard2Id, shard.getShardId());
assertEquals(node2Weight, shard.getWeight());
}
/* (non-Javadoc)
* @see org.apache.hadoop.mapred.MapReduceBase#configure(org.apache.hadoop.mapred.JobConf)
*/
public void configure(JobConf job) {
iconf = new IndexUpdateConfiguration(job);
analyzer = (Analyzer) ReflectionUtils.newInstance(iconf.getDocumentAnalyzerClass(), job);
localAnalysis =
(ILocalAnalysis) ReflectionUtils.newInstance(iconf.getLocalAnalysisClass(), job);
localAnalysis.configure(job);
shards = Shard.getIndexShards(iconf);
distributionPolicy =
(IDistributionPolicy) ReflectionUtils.newInstance(iconf.getDistributionPolicyClass(), job);
distributionPolicy.init(shards);
LOG.info("sea.document.analyzer = " + analyzer.getClass().getName());
LOG.info("sea.local.analysis = " + localAnalysis.getClass().getName());
LOG.info(shards.length + " shards = " + iconf.getIndexShards());
LOG.info("sea.distribution.policy = " + distributionPolicy.getClass().getName());
}
public Shard unmarshall(JsonUnmarshallerContext context) throws Exception {
Shard shard = new Shard();
int originalDepth = context.getCurrentDepth();
String currentParentElement = context.getCurrentParentElement();
int targetDepth = originalDepth + 1;
JsonToken token = context.currentToken;
if (token == null) token = context.nextToken();
if (token == VALUE_NULL) return null;
while (true) {
if (token == null) break;
if (token == FIELD_NAME || token == START_OBJECT) {
if (context.testExpression("ShardId", targetDepth)) {
context.nextToken();
shard.setShardId(StringJsonUnmarshaller.getInstance().unmarshall(context));
}
if (context.testExpression("ParentShardId", targetDepth)) {
context.nextToken();
shard.setParentShardId(StringJsonUnmarshaller.getInstance().unmarshall(context));
}
if (context.testExpression("AdjacentParentShardId", targetDepth)) {
context.nextToken();
shard.setAdjacentParentShardId(StringJsonUnmarshaller.getInstance().unmarshall(context));
}
if (context.testExpression("HashKeyRange", targetDepth)) {
context.nextToken();
shard.setHashKeyRange(HashKeyRangeJsonUnmarshaller.getInstance().unmarshall(context));
}
if (context.testExpression("SequenceNumberRange", targetDepth)) {
context.nextToken();
shard.setSequenceNumberRange(
SequenceNumberRangeJsonUnmarshaller.getInstance().unmarshall(context));
}
} else if (token == END_ARRAY || token == END_OBJECT) {
if (context.getLastParsedParentElement() == null
|| context.getLastParsedParentElement().equals(currentParentElement)) {
if (context.getCurrentDepth() <= originalDepth) break;
}
}
token = context.nextToken();
}
return shard;
}
@SuppressWarnings("unchecked")
public GeneratorT withInstance(int aValue) {
instance.setInstance(aValue);
return (GeneratorT) this;
}
@SuppressWarnings("unchecked")
public GeneratorT withFloc(Floc aValue) {
instance.setFloc(aValue);
return (GeneratorT) this;
}
private void initBuffer() throws IOException, InterruptedException, DataArchivedException {
if (this.buf == null) {
this.hlAdded = false;
if (HashFunctionPool.max_hash_cluster > 1) {
this.buf = ByteBuffer.wrap(new byte[Main.CHUNK_LENGTH]);
final ArrayList<Shard> cks = new ArrayList<Shard>();
int i = 0;
// long fp = this.position;
for (HashLocPair p : ar) {
if (p.hashloc[1] != 0) {
Shard sh = new Shard();
sh.hash = p.hash;
sh.hashloc = p.hashloc;
sh.pos = p.pos;
sh.nlen = p.nlen;
sh.offset = p.offset;
sh.len = p.len;
sh.apos = i;
cks.add(i, sh);
} else break;
i++;
}
sz = cks.size();
AsyncChunkReadActionListener l =
new AsyncChunkReadActionListener() {
@Override
public void commandException(Exception e) {
SDFSLogger.getLog().error("error getting block", e);
this.incrementAndGetDNEX();
synchronized (this) {
this.notifyAll();
}
}
@Override
public void commandResponse(Shard result) {
cks.get(result.apos).ck = result.ck;
if (this.incrementandGetDN() >= sz) {
synchronized (this) {
this.notifyAll();
}
}
}
@Override
public void commandArchiveException(DataArchivedException e) {
this.incrementAndGetDNEX();
this.setDAR(e);
synchronized (this) {
this.notifyAll();
}
}
};
for (Shard sh : cks) {
sh.l = l;
executor.execute(sh);
}
int wl = 0;
int tm = 1000;
int al = 0;
while (l.getDN() < sz && l.getDNEX() == 0) {
if (al == 30) {
int nt = wl / 1000;
SDFSLogger.getLog()
.debug("Slow io, waited [" + nt + "] seconds for all reads to complete.");
al = 0;
}
if (Main.readTimeoutSeconds > 0 && wl > (Main.writeTimeoutSeconds * tm)) {
int nt = (tm * wl) / 1000;
throw new IOException(
"read Timed Out after ["
+ nt
+ "] seconds. Expected ["
+ sz
+ "] block read but only ["
+ l.getDN()
+ "] were completed");
}
if (l.getDAR() != null) {
throw l.getDAR();
}
if (l.getDNEX() > 0) throw new IOException("error while reading data");
synchronized (l) {
l.wait(1000);
}
wl += 1000;
al++;
}
if (l.getDAR() != null) {
throw l.getDAR();
}
if (l.getDNEX() > 0) {
throw new IOException("error while getting blocks " + l.getDNEX() + " errors found");
}
if (l.getDN() < sz) {
throw new IOException("thread timed out before read was complete ");
}
buf.position(0);
for (Shard sh : cks) {
if (sh.pos == -1) {
try {
buf.put(sh.ck);
} catch (Exception e) {
// SDFSLogger.getLog().info("pos = " + this.position
// + "ck sz=" + sh.ck.length + " hcb sz=" +
// hcb.position() + " cks sz=" +cks.size() + " len="
// + (hcb.position() +sh.ck.length));
throw new IOException(e);
}
} else {
try {
buf.position(sh.pos);
buf.put(sh.ck, sh.offset, sh.nlen);
} catch (Exception e) {
SDFSLogger.getLog()
.error(
"pos = "
+ this.position
+ " ck nlen="
+ sh.nlen
+ " ck offset="
+ sh.offset
+ " ck len="
+ sh.ck.length
+ " hcb pos="
+ buf.position()
+ " ck slen="
+ sh.len
+ " len="
+ (buf.capacity()));
throw new IOException(e);
}
}
}
} else {
this.buf =
ByteBuffer.wrap(HCServiceProxy.fetchChunk(this.ar.get(0).hash, this.ar.get(0).hashloc));
}
}
}
public void cacheChunk() throws IOException, InterruptedException, DataArchivedException {
if (this.buf == null) {
this.hlAdded = false;
if (HashFunctionPool.max_hash_cluster > 1) {
final ArrayList<Shard> cks = new ArrayList<Shard>();
int i = 0;
// long fp = this.position;
for (HashLocPair p : ar) {
if (p.hashloc[1] != 0) {
Shard sh = new Shard();
sh.hash = p.hash;
sh.hashloc = p.hashloc;
sh.cache = true;
sh.pos = p.pos;
sh.nlen = p.nlen;
sh.offset = p.offset;
sh.len = p.len;
sh.apos = i;
cks.add(i, sh);
} else break;
i++;
}
sz = cks.size();
AsyncChunkReadActionListener l =
new AsyncChunkReadActionListener() {
@Override
public void commandException(Exception e) {
this.incrementAndGetDNEX();
synchronized (this) {
this.notifyAll();
}
}
@Override
public void commandResponse(Shard result) {
cks.get(result.apos).ck = result.ck;
if (this.incrementandGetDN() >= sz) {
synchronized (this) {
this.notifyAll();
}
}
}
@Override
public void commandArchiveException(DataArchivedException e) {
this.incrementAndGetDNEX();
this.setDAR(e);
synchronized (this) {
this.notifyAll();
}
}
};
for (Shard sh : cks) {
sh.l = l;
executor.execute(sh);
}
int wl = 0;
int al = 0;
while (l.getDN() < sz && l.getDNEX() == 0) {
if (al == 30) {
int nt = wl / 1000;
SDFSLogger.getLog()
.debug("Slow io, waited [" + nt + "] seconds for all reads to complete.");
al = 0;
}
if (l.getDAR() != null) {
throw l.getDAR();
}
if (l.getDNEX() > 0) throw new IOException("error while reading data");
synchronized (l) {
l.wait(1000);
}
wl += 1000;
al++;
}
if (l.getDAR() != null) {
throw l.getDAR();
}
if (l.getDNEX() > 0) {
throw new IOException("error while getting blocks " + l.getDNEX() + " errors found");
}
if (l.getDN() < sz) {
throw new IOException("thread timed out before read was complete ");
}
}
}
}
public void deleteNode(Shard realShard) {
for (int i = 0; i < num_virtual; i++) {
virtual_nodes.remove(hash.hash(realShard.toString() + "_" + i));
}
}
public void addNode(Shard realShard) {
for (int i = 0; i < num_virtual; i++) {
virtual_nodes.put(hash.hash(realShard.toString() + "_" + i), realShard);
}
}