p4 pass test
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index d2d3969..0e798fe 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -4,7 +4,6 @@
import java.io.FileOutputStream;
import java.io.IOException;
-import edu.uci.ics.genomix.oldtype.PositionWritable;
import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
@@ -19,6 +18,7 @@
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.pregelix.api.job.PregelixJob;
public class JobGenerator {
@@ -83,7 +83,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(PositionWritable.class);
+ job.setOutputKeyClass(KmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 2e67da2..5aedeb7 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -45,20 +45,14 @@
public static final String PreFix = "data/PathMergeTestSet"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "8"};
- //+ "tipremove/TipRemoveGraph/bin/fr_with_tip"};
- //+ "graphs/pathmerge/singleread"};
- //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
- /*+ "2", PreFix + File.separator
- + "3", PreFix + File.separator
- + "4", PreFix + File.separator
- + "5", PreFix + File.separator
- + "6", PreFix + File.separator
- + "7", PreFix + File.separator
- + "8", PreFix + File.separator
- + "9", PreFix + File.separator
- + "tworeads3", PreFix + File.separator
- + "tworeads_6"};*/
+// + "2", PreFix + File.separator
+// + "3", PreFix + File.separator
+// + "4", PreFix + File.separator
+// + "5", PreFix + File.separator
+// + "6", PreFix + File.separator
+// + "7", PreFix + File.separator
+// + "8", PreFix + File.separator
+ + "4"};
private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
index f20a863..597e5c3 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
@@ -58,7 +58,7 @@
<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
<property><name>fs.default.name</name><value>file:///</value></property>
-<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.oldtype.PositionWritable</value></property>
+<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.KmerBytesWritable</value></property>
<property><name>tasktracker.http.threads</name><value>40</value></property>
<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>