job generate frame complete
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
index fc968fd..d744bbe 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
@@ -32,7 +32,6 @@
public class AggregateKmerAggregateFactory implements IAggregatorDescriptorFactory {
-
/**
*
*/
@@ -114,7 +113,7 @@
public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
AggregateState state) throws HyracksDataException {
DataOutput fieldOutput = tupleBuilder.getDataOutput();
- NodeWritable localUniNode = (ArrayBackedValueSNodeWritabletorage) state.state;
+ NodeWritable localUniNode = (NodeWritable) state.state;
try {
fieldOutput.write(localUniNode.getByteArray(), localUniNode.getStartOffset(), localUniNode.getLength());
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
new file mode 100644
index 0000000..0371348
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -0,0 +1,116 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators;
+
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.uci.ics.genomix.hyracks.data.primitive.PositionReference;
+import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.data.std.util.ArrayBackedValueStorage;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+
+public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
+ private static final long serialVersionUID = 1L;
+ private static final Log LOG = LogFactory.getLog(MergeKmerAggregateFactory.class);
+
+ @Override
+ public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
+ RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
+ throws HyracksDataException {
+ final int frameSize = ctx.getFrameSize();
+ return new IAggregatorDescriptor() {
+
+ private PositionReference position = new PositionReference();
+
+ @Override
+ public AggregateState createAggregateStates() {
+ return new AggregateState(new ArrayBackedValueStorage());
+ }
+
+ @Override
+ public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+ AggregateState state) throws HyracksDataException {
+ ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+ inputVal.reset();
+ int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
+ for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
+ 1); offset += PositionReference.LENGTH) {
+ position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
+ inputVal.append(position);
+ }
+ //make a fake feild to cheat caller
+ tupleBuilder.addFieldEndOffset();
+ }
+
+ @Override
+ public void reset() {
+
+ }
+
+ @Override
+ public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
+ int stateTupleIndex, AggregateState state) throws HyracksDataException {
+ ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+ int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
+ for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
+ 1); offset += PositionReference.LENGTH) {
+ position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
+ inputVal.append(position);
+ }
+ }
+
+ @Override
+ public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+ AggregateState state) throws HyracksDataException {
+ throw new IllegalStateException("partial result method should not be called");
+ }
+
+ @Override
+ public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+ AggregateState state) throws HyracksDataException {
+ DataOutput fieldOutput = tupleBuilder.getDataOutput();
+ ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+ try {
+ if (inputVal.getLength() > frameSize / 2) {
+ LOG.warn("MergeKmer: output data kmerByteSize is too big: " + inputVal.getLength());
+ }
+ fieldOutput.write(inputVal.getByteArray(), inputVal.getStartOffset(), inputVal.getLength());
+ tupleBuilder.addFieldEndOffset();
+
+ } catch (IOException e) {
+ throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
+ }
+ }
+
+ @Override
+ public void close() {
+
+ }
+
+ };
+
+ }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
index abfff00..96e31b8 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
@@ -24,18 +24,53 @@
import org.apache.hadoop.mapred.InputSplit;
import org.apache.hadoop.mapred.JobConf;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.job.JobGen;
-import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
+import edu.uci.ics.genomix.hyracks.data.accessors.KmerNormarlizedComputerFactory;
+import edu.uci.ics.genomix.hyracks.data.accessors.ReadIDPartitionComputerFactory;
+import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
+import edu.uci.ics.genomix.hyracks.dataflow.ConnectorPolicyAssignmentPolicy;
+import edu.uci.ics.genomix.hyracks.dataflow.MapKmerPositionToReadOperator;
+import edu.uci.ics.genomix.hyracks.dataflow.MapReadToNodeOperator;
+import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.aggregators.AggregateKmerAggregateFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.aggregators.AggregateReadIDAggregateFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.aggregators.MergeKmerAggregateFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.aggregators.MergeReadIDAggregateFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.io.KMerSequenceWriterFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.io.KMerTextWriterFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.io.NodeSequenceWriterFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.io.NodeTextWriterFactory;
import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
import edu.uci.ics.hyracks.api.constraints.PartitionConstraintHelper;
import edu.uci.ics.hyracks.api.dataflow.IConnectorDescriptor;
import edu.uci.ics.hyracks.api.dataflow.IOperatorDescriptor;
+import edu.uci.ics.hyracks.api.dataflow.value.IBinaryComparatorFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunctionFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputerFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.ISerializerDeserializer;
+import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputerFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
import edu.uci.ics.hyracks.api.exceptions.HyracksException;
import edu.uci.ics.hyracks.api.job.JobSpecification;
+import edu.uci.ics.hyracks.data.std.accessors.PointableBinaryComparatorFactory;
+import edu.uci.ics.hyracks.data.std.accessors.PointableBinaryHashFunctionFactory;
+import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
+import edu.uci.ics.hyracks.data.std.primitive.IntegerPointable;
+import edu.uci.ics.hyracks.dataflow.common.data.partition.FieldHashPartitionComputerFactory;
+import edu.uci.ics.hyracks.dataflow.std.base.AbstractOperatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningConnectorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningMergingConnectorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.connectors.OneToOneConnectorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.HashSpillableTableFactory;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+import edu.uci.ics.hyracks.dataflow.std.group.external.ExternalGroupOperatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.preclustered.PreclusteredGroupOperatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.sort.ExternalSortOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.api.ITupleWriterFactory;
import edu.uci.ics.hyracks.hdfs.dataflow.ConfFactory;
import edu.uci.ics.hyracks.hdfs.dataflow.HDFSReadOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.dataflow.HDFSWriteOperatorDescriptor;
import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
@SuppressWarnings("deprecation")
@@ -85,7 +120,164 @@
}
initJobConfiguration(scheduler);
}
-
+
+ private ExternalGroupOperatorDescriptor newExternalGroupby(JobSpecification jobSpec, int[] keyFields,
+ IAggregatorDescriptorFactory aggeragater, IAggregatorDescriptorFactory merger,
+ ITuplePartitionComputerFactory partition, INormalizedKeyComputerFactory normalizer,
+ IPointableFactory pointable, RecordDescriptor outRed) {
+ return new ExternalGroupOperatorDescriptor(jobSpec, keyFields, frameLimits,
+ new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) }, normalizer,
+ aggeragater, merger, outRed, new HashSpillableTableFactory(new FieldHashPartitionComputerFactory(
+ keyFields,
+ new IBinaryHashFunctionFactory[] { PointableBinaryHashFunctionFactory.of(pointable) }),
+ tableSize), true);
+ }
+
+ private Object[] generateAggeragateDescriptorbyType(JobSpecification jobSpec, int[] keyFields,
+ IAggregatorDescriptorFactory aggregator, IAggregatorDescriptorFactory merger,
+ ITuplePartitionComputerFactory partition, INormalizedKeyComputerFactory normalizer,
+ IPointableFactory pointable, RecordDescriptor combineRed, RecordDescriptor finalRec)
+ throws HyracksDataException {
+
+ Object[] obj = new Object[3];
+
+ switch (groupbyType) {
+ case EXTERNAL:
+ obj[0] = newExternalGroupby(jobSpec, keyFields, aggregator, merger, partition, normalizer, pointable,
+ combineRed);
+ obj[1] = new MToNPartitioningConnectorDescriptor(jobSpec, partition);
+ obj[2] = newExternalGroupby(jobSpec, keyFields, merger, merger, partition, normalizer, pointable,
+ finalRec);
+ break;
+ case PRECLUSTER:
+ default:
+
+ obj[0] = new PreclusteredGroupOperatorDescriptor(jobSpec, keyFields,
+ new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) }, aggregator,
+ combineRed);
+ obj[1] = new MToNPartitioningMergingConnectorDescriptor(jobSpec, partition, keyFields,
+ new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) });
+ obj[2] = new PreclusteredGroupOperatorDescriptor(jobSpec, keyFields,
+ new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(pointable) }, merger,
+ finalRec);
+ jobSpec.setConnectorPolicyAssignmentPolicy(new ConnectorPolicyAssignmentPolicy());
+ break;
+ }
+ return obj;
+ }
+
+ public HDFSReadOperatorDescriptor createHDFSReader(JobSpecification jobSpec) throws HyracksDataException {
+ try {
+ InputSplit[] splits = hadoopJobConfFactory.getConf().getInputFormat()
+ .getSplits(hadoopJobConfFactory.getConf(), ncNodeNames.length);
+
+ return new HDFSReadOperatorDescriptor(jobSpec, ReadsKeyValueParserFactory.readKmerOutputRec,
+ hadoopJobConfFactory.getConf(), splits, readSchedule, new ReadsKeyValueParserFactory(readLength,
+ kmerSize, bGenerateReversedKmer));
+ } catch (Exception e) {
+ throw new HyracksDataException(e);
+ }
+ }
+
+ public static void connectOperators(JobSpecification jobSpec, IOperatorDescriptor preOp, String[] preNodes,
+ IOperatorDescriptor nextOp, String[] nextNodes, IConnectorDescriptor conn) {
+ PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, preOp, preNodes);
+ PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, nextOp, nextNodes);
+ jobSpec.connect(conn, preOp, 0, nextOp, 0);
+ }
+
+ public AbstractOperatorDescriptor generateGroupbyKmerJob(JobSpecification jobSpec,
+ AbstractOperatorDescriptor readOperator) throws HyracksDataException {
+ int[] keyFields = new int[] { 0 }; // the id of grouped key
+
+ ExternalSortOperatorDescriptor sorter = new ExternalSortOperatorDescriptor(jobSpec, frameLimits, keyFields,
+ new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(KmerPointable.FACTORY) },
+ ReadsKeyValueParserFactory.readKmerOutputRec);
+ connectOperators(jobSpec, readOperator, ncNodeNames, sorter, ncNodeNames, new OneToOneConnectorDescriptor(
+ jobSpec));
+
+ RecordDescriptor combineKmerOutputRec = new RecordDescriptor(new ISerializerDeserializer[] { null, null });
+ jobSpec.setFrameSize(frameSize);
+
+ Object[] objs = generateAggeragateDescriptorbyType(jobSpec, keyFields, new AggregateKmerAggregateFactory(),
+ new MergeKmerAggregateFactory(), new KmerHashPartitioncomputerFactory(),
+ new KmerNormarlizedComputerFactory(), KmerPointable.FACTORY, combineKmerOutputRec, combineKmerOutputRec);
+ AbstractOperatorDescriptor kmerLocalAggregator = (AbstractOperatorDescriptor) objs[0];
+ logDebug("LocalKmerGroupby Operator");
+ connectOperators(jobSpec, sorter, ncNodeNames, kmerLocalAggregator, ncNodeNames,
+ new OneToOneConnectorDescriptor(jobSpec));
+
+ logDebug("CrossKmerGroupby Operator");
+ IConnectorDescriptor kmerConnPartition = (IConnectorDescriptor) objs[1];
+ AbstractOperatorDescriptor kmerCrossAggregator = (AbstractOperatorDescriptor) objs[2];
+ connectOperators(jobSpec, kmerLocalAggregator, ncNodeNames, kmerCrossAggregator, ncNodeNames, kmerConnPartition);
+ return kmerCrossAggregator;
+ }
+
+
+ public AbstractOperatorDescriptor generateKmerWritorOperator(JobSpecification jobSpec,
+ AbstractOperatorDescriptor kmerCrossAggregator) throws HyracksException {
+ // Output Kmer
+ ITupleWriterFactory kmerWriter = null;
+ switch (outputFormat) {
+ case TEXT:
+ kmerWriter = new KMerTextWriterFactory(kmerSize);
+ break;
+ case BINARY:
+ default:
+ kmerWriter = new KMerSequenceWriterFactory(hadoopJobConfFactory.getConf());
+ break;
+ }
+ logDebug("WriteOperator");
+ HDFSWriteOperatorDescriptor writeKmerOperator = new HDFSWriteOperatorDescriptor(jobSpec,
+ hadoopJobConfFactory.getConf(), kmerWriter);
+ connectOperators(jobSpec, kmerCrossAggregator, ncNodeNames, writeKmerOperator, ncNodeNames,
+ new OneToOneConnectorDescriptor(jobSpec));
+ return writeKmerOperator;
+ }
+
+ public AbstractOperatorDescriptor generateNodeWriterOpertator(JobSpecification jobSpec,
+ AbstractOperatorDescriptor mapEachReadToNode) throws HyracksException {
+ ITupleWriterFactory nodeWriter = null;
+ switch (outputFormat) {
+ case TEXT:
+ nodeWriter = new NodeTextWriterFactory(kmerSize);
+ break;
+ case BINARY:
+ default:
+ nodeWriter = new NodeSequenceWriterFactory(hadoopJobConfFactory.getConf());
+ break;
+ }
+ logDebug("WriteOperator");
+ // Output Node
+ HDFSWriteOperatorDescriptor writeNodeOperator = new HDFSWriteOperatorDescriptor(jobSpec,
+ hadoopJobConfFactory.getConf(), nodeWriter);
+ connectOperators(jobSpec, mapEachReadToNode, ncNodeNames, writeNodeOperator, ncNodeNames,
+ new OneToOneConnectorDescriptor(jobSpec));
+ return writeNodeOperator;
+ }
+
+ @Override
+ public JobSpecification generateJob() throws HyracksException {
+
+ JobSpecification jobSpec = new JobSpecification();
+ logDebug("ReadKmer Operator");
+
+ HDFSReadOperatorDescriptor readOperator = createHDFSReader(jobSpec);
+
+ logDebug("Group by Kmer");
+ AbstractOperatorDescriptor lastOperator = generateGroupbyKmerJob(jobSpec, readOperator);
+
+ // logDebug("Write kmer to result");
+ // generateRootByWriteKmerGroupbyResult(jobSpec, lastOperator);
+
+ logDebug("Write node to result");
+ lastOperator = generateNodeWriterOpertator(jobSpec, lastOperator);
+
+ jobSpec.addRoot(lastOperator);
+ return jobSpec;
+ }
+
protected void initJobConfiguration(Scheduler scheduler) throws HyracksDataException {
Configuration conf = confFactory.getConf();
readLength = conf.getInt(GenomixJobConf.READ_LENGTH, GenomixJobConf.DEFAULT_READLEN);
@@ -131,30 +323,5 @@
LOG.info("Frame limit" + frameLimits);
LOG.info("Frame kmerByteSize" + frameSize);
}
-
- public HDFSReadOperatorDescriptor createHDFSReader(JobSpecification jobSpec) throws HyracksDataException {
- try {
- InputSplit[] splits = hadoopJobConfFactory.getConf().getInputFormat()
- .getSplits(hadoopJobConfFactory.getConf(), ncNodeNames.length);
- return new HDFSReadOperatorDescriptor(jobSpec, ReadsKeyValueParserFactory.readKmerOutputRec,
- hadoopJobConfFactory.getConf(), splits, readSchedule, new ReadsKeyValueParserFactory(readLength,
- kmerSize, bGenerateReversedKmer));
- } catch (Exception e) {
- throw new HyracksDataException(e);
- }
- }
-
- public static void connectOperators(JobSpecification jobSpec, IOperatorDescriptor preOp, String[] preNodes,
- IOperatorDescriptor nextOp, String[] nextNodes, IConnectorDescriptor conn) {
- PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, preOp, preNodes);
- PartitionConstraintHelper.addAbsoluteLocationConstraint(jobSpec, nextOp, nextNodes);
- jobSpec.connect(conn, preOp, 0, nextOp, 0);
- }
-
- @Override
- public JobSpecification generateJob() throws HyracksException {
- // TODO Auto-generated method stub
- return null;
- }
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCreateKmerInfo.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCreateKmerInfo.java
new file mode 100644
index 0000000..35d053a
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCreateKmerInfo.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.hyracks.newgraph.job;
+
+import java.util.Map;
+
+import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.api.exceptions.HyracksException;
+import edu.uci.ics.hyracks.api.job.JobSpecification;
+import edu.uci.ics.hyracks.dataflow.std.base.AbstractOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.dataflow.HDFSReadOperatorDescriptor;
+import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
+
+public class JobGenCreateKmerInfo extends JobGenBrujinGraph {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public JobGenCreateKmerInfo(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
+ int numPartitionPerMachine) throws HyracksDataException {
+ super(job, scheduler, ncMap, numPartitionPerMachine);
+ }
+
+ @Override
+ public JobSpecification generateJob() throws HyracksException {
+
+ JobSpecification jobSpec = new JobSpecification();
+ logDebug("ReadKmer Operator");
+ HDFSReadOperatorDescriptor readOperator = createHDFSReader(jobSpec);
+
+ logDebug("Group by Kmer");
+ AbstractOperatorDescriptor lastOperator = generateGroupbyKmerJob(jobSpec, readOperator);
+
+ logDebug("Write kmer to result");
+ lastOperator = generateKmerWritorOperator(jobSpec, lastOperator);
+ jobSpec.addRoot(lastOperator);
+
+ return jobSpec;
+ }
+}