removeBridge pass tests
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 2c85e42..eae94cb 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
@@ -83,12 +83,12 @@
private static void generateP4ForMergeGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
job.setVertexClass(P4ForPathMergeVertex.class);
- job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); //DataCleanInputFormat
+ job.setVertexInputFormatClass(DataCleanInputFormat.class); //NaiveAlgorithmForPathMergeInputFormat //
job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(PositionWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
- job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 3);
+ job.getConfiguration().setInt(P4ForPathMergeVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -100,7 +100,7 @@
private static void generateTipAddGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
job.setVertexClass(TipAddVertex.class);
- job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+ job.setVertexInputFormatClass(DataCleanOutputFormat.class);
job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(PositionWritable.class);
@@ -117,12 +117,12 @@
private static void generateTipRemoveGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
job.setVertexClass(TipRemoveVertex.class);
- job.setVertexInputFormatClass(DataCleanInputFormat.class);
+ job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(PositionWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
- job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+ job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -156,7 +156,7 @@
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(PositionWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
- job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+ job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -185,12 +185,12 @@
private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
job.setVertexClass(BubbleMergeVertex.class);
- job.setVertexInputFormatClass(DataCleanInputFormat.class);
+ job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(PositionWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
- job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
+ job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -203,7 +203,7 @@
//genNaiveAlgorithmForMergeGraph();
//genLogAlgorithmForMergeGraph();
//genP3ForMergeGraph();
- genTipAddGraph();
+ //genTipAddGraph();
genTipRemoveGraph();
genBridgeAddGraph();
genBridgeRemoveGraph();
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
index 5b641ff..397c514 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
@@ -43,26 +43,15 @@
public class BridgeRemoveSmallTestSuite extends TestSuite {
private static final Logger LOGGER = Logger.getLogger(BridgeRemoveSmallTestSuite.class.getName());
- public static final String PreFix = "data/input"; //"graphbuildresult";
+ public static final String PreFix = "data/actual"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "pathmerge_tip"};/*, PreFix + File.separator
- /*+ "CyclePath"};, PreFix + File.separator
- + "SimplePath", PreFix + File.separator
- + "SinglePath", PreFix + File.separator
- + "TreePath"};*/
- /* + "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 + "TwoKmer", PreFix + File.separator + "ThreeKmer",
- PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
- PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
- PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
- PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
- private static final String ACTUAL_RESULT_DIR = "actual";
+ + "pathmerge/P4ForMergeGraph/bin/tworeads"};
+ private static final String ACTUAL_RESULT_DIR = "data/actual/bridgeremove";
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";
private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
- private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+ private static final String PATH_TO_ONLY = "src/test/resources/only_bridgeremove.txt";
public static final String HDFS_INPUTPATH = "/PathTestSet";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
index 9e98cb6..a94d31c 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
@@ -45,24 +45,13 @@
public static final String PreFix = "data/input"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "pathmerge"};/*, PreFix + File.separator
- /*+ "CyclePath"};, PreFix + File.separator
- + "SimplePath", PreFix + File.separator
- + "SinglePath", PreFix + File.separator
- + "TreePath"};*/
- /* + "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 + "TwoKmer", PreFix + File.separator + "ThreeKmer",
- PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
- PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
- PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
- PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
- private static final String ACTUAL_RESULT_DIR = "actual";
+ + "graphs/bubblemerge/fr_bubble"};
+ private static final String ACTUAL_RESULT_DIR = "data/actual/bubblemerge";
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";
private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
- private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
+ private static final String PATH_TO_ONLY = "src/test/resources/only_bubblemerge.txt";
public static final String HDFS_INPUTPATH = "/PathTestSet";
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 44d24d6..79a13b3 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
@@ -43,10 +43,13 @@
public class PathMergeSmallTestSuite extends TestSuite {
private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
- public static final String PreFix = "data/PathTestSet_bidirection"; //"graphbuildresult";
+ public static final String PreFix = "data/actual"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "tworeads_6"};/*
- + "2", PreFix + File.separator
+ + "bubblemerge/BubbleMergeGraph/bin/small_bubble"};
+ //+ "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
@@ -54,21 +57,8 @@
+ "7", PreFix + File.separator
+ "8", PreFix + File.separator
+ "9", PreFix + File.separator
- + "tworeads"};
- /*+ "tipremove/TipRemoveGraph/bin/tworeads"};
- + "bridgeadd/BridgeAddGraph/bin/tworeads"};, PreFix + File.separator
- + "tipadd/TipAddGraph/bin/read"}, PreFix + File.separator
- /*+ "CyclePath"};, PreFix + File.separator
- + "SimplePath", PreFix + File.separator
- + "SinglePath", PreFix + File.separator
- + "TreePath"};*/
- /* + "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 + "TwoKmer", PreFix + File.separator + "ThreeKmer",
- PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
- PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
- PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
- PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
+ + "tworeads3", PreFix + File.separator
+ + "tworeads_6"};*/
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/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
index e174bd9..def24e4 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
@@ -43,20 +43,10 @@
public class TipRemoveSmallTestSuite extends TestSuite {
private static final Logger LOGGER = Logger.getLogger(TipRemoveSmallTestSuite.class.getName());
//P4ForMergeGraph/bin/read
- public static final String PreFix = "data/actual"; //"graphbuildresult";
+ public static final String PreFix = "data/input"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "bridgeadd/BridgeAddGraph/bin/tworeads"};/*, PreFix + File.separator
- /*+ "CyclePath"};, PreFix + File.separator
- + "SimplePath", PreFix + File.separator
- + "SinglePath", PreFix + File.separator
- + "TreePath"};*/
- /* + "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 + "TwoKmer", PreFix + File.separator + "ThreeKmer",
- PreFix + File.separator + "SinglePath", PreFix + File.separator + "SimplePath",
- PreFix + File.separator + "Path", PreFix + File.separator + "BridgePath",
- PreFix + File.separator + "CyclePath", PreFix + File.separator + "RingPath",
- PreFix + File.separator + "LongPath", PreFix + File.separator + "TreePath" };*/
+ + "graphs/tipremove/fr_with_tip"};
+ //+ "bridgeadd/BridgeAddGraph/bin/tworeads"};
private static final String ACTUAL_RESULT_DIR = "data/actual/tipremove";
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/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
index cc9e2d2..3531ec1 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
@@ -50,7 +50,7 @@
private static final String ACTUAL_RESULT_DIR = "actual";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
- private static final String DATA_INPUT_PATH = "data/input/singleread";
+ private static final String DATA_INPUT_PATH = "data/graphbuild.test/tworead3.txt";
private static final String HDFS_INPUT_PATH = "/webmap";
private static final String HDFS_OUTPUT_PATH = "/webmap_result";
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
index b36258a..f9b801a 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/BridgeRemoveGraph.xml
@@ -96,7 +96,7 @@
<property><name>io.sort.mb</name><value>100</value></property>
<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
<property><name>mapred.task.profile</name><value>false</value></property>
<property><name>job.end.retry.interval</name><value>30000</value></property>
<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
index 1b5cf0c..605a004 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/BubbleMergeGraph.xml
@@ -99,7 +99,7 @@
<property><name>mapred.task.profile</name><value>false</value></property>
<property><name>job.end.retry.interval</name><value>30000</value></property>
<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
-<property><name>BubbleMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BubbleMergeVertex.kmerSize</name><value>5</value></property>
<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
<property><name>webinterface.private.actions</name><value>false</value></property>
@@ -122,7 +122,7 @@
<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
<property><name>mapred.job.queue.name</name><value>default</value></property>
<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
<property><name>pregelix.incStateLength</name><value>true</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
index ae0dc7e..5ef1509 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/P4ForMergeGraph.xml
@@ -96,7 +96,7 @@
<property><name>io.sort.mb</name><value>100</value></property>
<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
<property><name>mapred.task.profile</name><value>false</value></property>
<property><name>job.end.retry.interval</name><value>30000</value></property>
<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
@@ -122,7 +122,7 @@
<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
<property><name>mapred.job.queue.name</name><value>default</value></property>
<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
<property><name>pregelix.incStateLength</name><value>true</value></property>
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
index 1fcacc9..588cc9f 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/TipRemoveGraph.xml
@@ -96,7 +96,7 @@
<property><name>io.sort.mb</name><value>100</value></property>
<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
<property><name>io.sort.factor</name><value>10</value></property>
-<property><name>BasicPathMergeVertex.kmerSize</name><value>3</value></property>
+<property><name>BasicPathMergeVertex.kmerSize</name><value>5</value></property>
<property><name>mapred.task.profile</name><value>false</value></property>
<property><name>job.end.retry.interval</name><value>30000</value></property>
<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
@@ -122,7 +122,7 @@
<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
<property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat</value></property>
<property><name>mapred.job.queue.name</name><value>default</value></property>
<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
<property><name>pregelix.incStateLength</name><value>true</value></property>