Fix H3 test case
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
new file mode 100644
index 0000000..97563de
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
@@ -0,0 +1,209 @@
+/*
+ * Copyright 2009-2012 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.hadoop.pmcommon;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.conf.Configured;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobClient;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hadoop.mapred.RunningJob;
+import org.apache.hadoop.mapred.SequenceFileInputFormat;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.util.Tool;
+import org.apache.hadoop.util.ToolRunner;
+
+import edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3.MergePathsH3.MessageFlag;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+
+/*
+ * A map-reduce job to find all nodes that are part of a simple path and the mark the nodes that
+ * form their heads and tails.
+ */
+@SuppressWarnings("deprecation")
+public class PathNodeInitial extends Configured implements Tool {
+
+ public static class PathNodeInitialMapper extends MapReduceBase implements
+ Mapper<NodeWritable, NullWritable, PositionWritable, MessageWritableNodeWithFlag> {
+
+ private int KMER_SIZE;
+ private PositionWritable outputKey;
+ private MessageWritableNodeWithFlag outputValue;
+ private int inDegree;
+ private int outDegree;
+ private NodeWritable emptyNode;
+
+ public PathNodeInitialMapper() {
+
+ }
+
+ public void configure(JobConf conf) {
+ KMER_SIZE = conf.getInt("sizeKmer", 0);
+ outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+ outputKey = new PositionWritable();
+ emptyNode = new NodeWritable();
+ }
+
+ @Override
+ public void map(NodeWritable key, NullWritable value,
+ OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+ throws IOException {
+ inDegree = key.inDegree();
+ outDegree = key.outDegree();
+ if (inDegree == 1 && outDegree == 1) {
+ // simple path nodes map themselves
+ outputValue.set(MessageFlag.FROM_SELF, key);
+ output.collect(key.getNodeID(), outputValue);
+ reporter.incrCounter("genomix", "path_nodes", 1);
+ } else if (outDegree == 1) {
+ // Not a path myself, but my successor might be one. Map forward successor
+ outputValue.set(MessageFlag.FROM_PREDECESSOR, emptyNode);
+ if (key.getFFList().getCountOfPosition() > 0) {
+ outputKey.set(key.getFFList().getPosition(0));
+ } else {
+ outputKey.set(key.getFRList().getPosition(0));
+ }
+ output.collect(outputKey, outputValue);
+ } else if (inDegree == 1) {
+ // Not a path myself, but my predecessor might be one.
+ outputValue.set(MessageFlag.FROM_SUCCESSOR, emptyNode);
+ if (key.getRRList().getCountOfPosition() > 0) {
+ outputKey.set(key.getRRList().getPosition(0));
+ } else {
+ outputKey.set(key.getRFList().getPosition(0));
+ }
+ output.collect(outputKey, outputValue);
+ }
+ else {
+ // TODO: all other nodes will not participate-- should they be collected in a "complete" output?
+ }
+ }
+ }
+
+ public static class PathNodeInitialReducer extends MapReduceBase implements
+ Reducer<PositionWritable, MessageWritableNodeWithFlag, PositionWritable, MessageWritableNodeWithFlag> {
+
+ private int KMER_SIZE;
+ private MessageWritableNodeWithFlag inputValue;
+ private MessageWritableNodeWithFlag outputValue;
+ private NodeWritable nodeToKeep;
+ private int count;
+ private byte flag;
+
+ public void configure(JobConf conf) {
+ KMER_SIZE = conf.getInt("sizeKmer", 0);
+ inputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+ outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+ nodeToKeep = new NodeWritable(KMER_SIZE);
+ }
+
+ @Override
+ public void reduce(PositionWritable key, Iterator<MessageWritableNodeWithFlag> values,
+ OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+ throws IOException {
+
+ inputValue.set(values.next());
+ if (!values.hasNext()) {
+ if ((inputValue.getFlag() & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+ // FROM_SELF => need to keep this PATH node
+ output.collect(key, inputValue);
+ }
+ } else {
+ // multiple inputs => possible HEAD or TAIL to a path node. note if HEAD or TAIL node
+ count = 0;
+ flag = MessageFlag.EMPTY_MESSAGE;
+ while (true) { // process values; break when no more
+ count++;
+ if ((inputValue.getFlag() & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+ // SELF -> keep this node
+ nodeToKeep.set(inputValue.getNode());
+ } else if ((inputValue.getFlag() & MessageFlag.FROM_SUCCESSOR) == MessageFlag.FROM_SUCCESSOR) {
+ flag |= MessageFlag.IS_TAIL;
+ reporter.incrCounter("genomix", "path_nodes_tails", 1);
+ } else if ((inputValue.getFlag() & MessageFlag.FROM_PREDECESSOR) == MessageFlag.FROM_PREDECESSOR) {
+ flag |= MessageFlag.IS_HEAD;
+ reporter.incrCounter("genomix", "path_nodes_heads", 1);
+ }
+ if (!values.hasNext()) {
+ break;
+ } else {
+ inputValue = values.next();
+ }
+ }
+ if (count < 2) {
+ throw new IOException("Expected at least two nodes in PathNodeInitial reduce; saw "
+ + String.valueOf(count));
+ }
+ if ((flag & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+ // only map simple path nodes
+ outputValue.set(flag, nodeToKeep);
+ output.collect(key, outputValue);
+ reporter.incrCounter("genomix", "path_nodes", 1);
+ }
+ }
+ }
+ }
+
+ /*
+ * Mark the head, tail, and simple path nodes in one map-reduce job.
+ */
+ public RunningJob run(String inputPath, String outputPath, JobConf baseConf) throws IOException {
+ JobConf conf = new JobConf(baseConf);
+ conf.setJarByClass(PathNodeInitial.class);
+ conf.setJobName("PathNodeInitial " + inputPath);
+
+ FileInputFormat.addInputPath(conf, new Path(inputPath));
+ FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+
+ conf.setInputFormat(SequenceFileInputFormat.class);
+ conf.setOutputFormat(SequenceFileOutputFormat.class);
+
+ conf.setMapOutputKeyClass(PositionWritable.class);
+ conf.setMapOutputValueClass(MessageWritableNodeWithFlag.class);
+ conf.setOutputKeyClass(PositionWritable.class);
+ conf.setOutputValueClass(MessageWritableNodeWithFlag.class);
+
+ conf.setMapperClass(PathNodeInitialMapper.class);
+ conf.setReducerClass(PathNodeInitialReducer.class);
+
+ FileSystem.get(conf).delete(new Path(outputPath), true);
+
+ return JobClient.runJob(conf);
+ }
+
+ @Override
+ public int run(String[] arg0) throws Exception {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ public static void main(String[] args) throws Exception {
+ int res = ToolRunner.run(new Configuration(), new PathNodeInitial(), args);
+ System.exit(res);
+ }
+}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
new file mode 100644
index 0000000..17c6b16
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
@@ -0,0 +1,79 @@
+package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobConf;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.hadoop.pmcommon.GenomixMiniClusterTest;
+import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial;
+import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
+import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
+
+@SuppressWarnings("deprecation")
+public class TestPathMergeH3 extends GenomixMiniClusterTest {
+ protected String LOCAL_SEQUENCE_FILE = "src/test/resources/data/webmap/text.txt";
+ protected String HDFS_SEQUENCE = "/00-sequence/";
+ protected String HDFS_GRAPHBUILD = "/01-graphbuild/";
+ protected String HDFS_MARKPATHS = "/02-pathmark/";
+ protected String HDFS_MERGED = "/03-pathmerge/";
+
+ protected String GRAPHBUILD_FILE = "result.graphbuild.txt";
+ protected String PATHMARKS_FILE = "result.markpaths.txt";
+ protected String PATHMERGE_FILE = "result.mergepath.txt";
+ protected boolean regenerateGraph = false;
+
+ {
+ KMER_LENGTH = 5;
+ READ_LENGTH = 8;
+ HDFS_PATHS = new ArrayList<String>(Arrays.asList(HDFS_SEQUENCE, HDFS_GRAPHBUILD, HDFS_MARKPATHS, HDFS_MERGED));
+ conf.setInt(GenomixJobConf.KMER_LENGTH, KMER_LENGTH);
+ conf.setInt(GenomixJobConf.READ_LENGTH, READ_LENGTH);
+ }
+
+ @Test
+ public void TestBuildGraph() throws Exception {
+ cleanUpOutput();
+ copyLocalToDFS(LOCAL_SEQUENCE_FILE, HDFS_SEQUENCE);
+ buildGraph();
+ }
+
+ @Test
+ public void TestMergeOneIteration() throws Exception {
+ cleanUpOutput();
+ if (regenerateGraph) {
+ copyLocalToDFS(LOCAL_SEQUENCE_FILE, HDFS_SEQUENCE);
+ buildGraph();
+ copyLocalToDFS(ACTUAL_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+ } else {
+ copyLocalToDFS(EXPECTED_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+ }
+
+ PathNodeInitial inith3 = new PathNodeInitial();
+ inith3.run(HDFS_GRAPHBUILD, HDFS_MARKPATHS, conf);
+ copyResultsToLocal(HDFS_MARKPATHS, ACTUAL_ROOT + PATHMARKS_FILE, false, conf);
+
+ MergePathsH3Driver h3 = new MergePathsH3Driver();
+// h3.run(HDFS_GRAPHBUILD, HDFS_MERGED, 2, KMER_LENGTH, 1, HADOOP_CONF_ROOT + "conf.xml", conf);
+ h3.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 10, HADOOP_CONF_ROOT + "conf.xml", null);
+ copyResultsToLocal(HDFS_MERGED, ACTUAL_ROOT + PATHMERGE_FILE, false, conf);
+ }
+
+
+
+ public void buildGraph() throws Exception {
+ JobConf buildConf = new JobConf(conf); // use a separate conf so we don't interfere with other jobs
+ FileInputFormat.setInputPaths(buildConf, HDFS_SEQUENCE);
+ FileOutputFormat.setOutputPath(buildConf, new Path(HDFS_GRAPHBUILD));
+ buildConf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
+ buildConf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+ driver.runJob(new GenomixJobConf(buildConf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+ String fileFormat = buildConf.get(GenomixJobConf.OUTPUT_FORMAT);
+ boolean resultsAreText = GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(fileFormat);
+ copyResultsToLocal(HDFS_GRAPHBUILD, ACTUAL_ROOT + GRAPHBUILD_FILE, resultsAreText, buildConf);
+ }
+}