upload the graph of the test case
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@3374 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
index e4ff126..133e7f8 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Kmer.java
@@ -197,7 +197,6 @@
byte in = (byte) (kmer[i - 1] & 0x03);
kmer[i] = (byte) (((kmer[i] >>> 2) & 0x3f) | (in << 6));
}
-
int pos = ((k - 1) % 4) << 1;
byte code = (byte) (GENE_CODE.getCodeFromSymbol(c) << pos);
kmer[0] = (byte) (((kmer[0] >>> 2) & 0x3f) | code);
@@ -295,4 +294,5 @@
.getCodeFromSymbol(c));
return (byte) (1 << output);
}
+
}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
index 8dacea1..d9c1846 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
@@ -24,7 +24,7 @@
@Test
public void TestMoveKmer(){
byte[] kmer = Kmer.compressKmer(k, array, 0);
- String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+ String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
Assert.assertEquals(result, "AATAGAA");
for (int i = k; i < array.length-1; i++) {
@@ -36,8 +36,8 @@
Assert.assertEquals(out, Kmer.GENE_CODE.getAdjBit((byte) 'A'));
result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
Assert.assertEquals(result, "ATAGAAG");
-
}
+
@Test
public void TestReverseKmer(){
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
index f9bf5b0..5a64f78 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
@@ -37,7 +37,7 @@
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_PATH = "src/test/resources/data/webmap/text.txt";
+ private static final String DATA_PATH = "src/test/resources/data/mergeTest/ThreeKmer";
private static final String HDFS_INPUT_PATH = "/webmap";
private static final String HDFS_OUTPUT_PATH = "/webmap_result";
@@ -195,11 +195,10 @@
BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
String partname = "/part-" + i;
-// FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
-// + partname), FileSystem.getLocal(new Configuration()),
-// new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + partname), false, conf);
-
-
+ FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
+ + partname), FileSystem.getLocal(new Configuration()),
+ new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + partname), false, conf);
+
Path path = new Path(HDFS_OUTPUT_PATH
+ partname);
FileSystem dfs = FileSystem.get(conf);
diff --git a/genomix/genomix-pregelix/graph/BridgePath b/genomix/genomix-pregelix/graph/BridgePath
new file mode 100644
index 0000000..c10ea60
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+++ b/genomix/genomix-pregelix/graph/BridgePath
@@ -0,0 +1,14 @@
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+CCACC T|C 1
+CCACT T|C 1
+CACCC C|C 1
+TTTCC |A 2
+CCCGT C|G 1
+TCCGT C|G 1
+CACTC C|C 1
diff --git a/genomix/genomix-pregelix/graph/BridgePath_out.ps b/genomix/genomix-pregelix/graph/BridgePath_out.ps
new file mode 100644
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diff --git a/genomix/genomix-pregelix/graph/CyclePath_out.ps b/genomix/genomix-pregelix/graph/CyclePath_out.ps
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new file mode 100644
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--- /dev/null
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\ No newline at end of file
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index 0000000..86790c6
--- /dev/null
+++ b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
@@ -0,0 +1,2 @@
+ACACT |G 1
+CACTG A| 1
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
new file mode 100644
index 0000000..128b0dc
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -0,0 +1,58 @@
+
+package edu.uci.ics.genomix.pregelix.client;
+
+import java.io.IOException;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
+import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.pregelix.core.base.IDriver.Plan;
+import edu.uci.ics.pregelix.core.driver.Driver;
+
+public class Client {
+
+ private static class Options {
+ @Option(name = "-inputpaths", usage = "comma seprated input paths", required = true)
+ public String inputPaths;
+
+ @Option(name = "-outputpath", usage = "output path", required = true)
+ public String outputPath;
+
+ @Option(name = "-ip", usage = "ip address of cluster controller", required = true)
+ public String ipAddress;
+
+ @Option(name = "-port", usage = "port of cluster controller", required = false)
+ public int port;
+
+ @Option(name = "-plan", usage = "query plan choice", required = false)
+ public Plan planChoice = Plan.OUTER_JOIN;
+
+ @Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
+ public String profiling = "false";
+ }
+
+ public static void run(String[] args, PregelixJob job) throws Exception {
+ Options options = prepareJob(args, job);
+ Driver driver = new Driver(Client.class);
+ driver.runJob(job, options.planChoice, options.ipAddress, options.port, Boolean.parseBoolean(options.profiling));
+ }
+
+ private static Options prepareJob(String[] args, PregelixJob job) throws CmdLineException, IOException {
+ Options options = new Options();
+ CmdLineParser parser = new CmdLineParser(options);
+ parser.parseArgument(args);
+
+ String[] inputs = options.inputPaths.split(";");
+ FileInputFormat.setInputPaths(job, inputs[0]);
+ for (int i = 1; i < inputs.length; i++)
+ FileInputFormat.addInputPaths(job, inputs[0]);
+ FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
+ return options;
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
index 84b342e..c00e996 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
@@ -1,11 +1,16 @@
package edu.uci.ics.genomix.pregelix.JobRun;
+import java.io.BufferedWriter;
import java.io.File;
+import java.io.FileWriter;
import junit.framework.TestCase;
+import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.FileUtil;
import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.junit.Test;
@@ -33,6 +38,8 @@
private final String resultFileName;
private final String expectedFileName;
private final String jobFile;
+
+
public RunJobTestCase(String hadoopConfPath, String jobName, String jobFile, String resultFile, String expectedFile)
throws Exception {
@@ -151,6 +158,16 @@
}
private void compareResults() throws Exception {
+ FileSystem.getLocal(new Configuration()).mkdirs(new Path("actual"));
+ //File filePathTo = new File(CONVERT_RESULT);
+ //BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
+ for (int i = 0; i < 1 * 2; i++) {
+ String partname = "/part-" + i;
+ FileUtil.copy(FileSystem.get(job.getConfiguration()), new Path(HDFS_OUTPUTPAH
+ + partname), FileSystem.getLocal(new Configuration()),
+ new Path("actual/test" + partname), false, job.getConfiguration());
+ }
+
TestUtils.compareWithResult(new File(resultFileName), new File(expectedFileName));
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
index fb698e5..e7589e3 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
@@ -187,4 +187,12 @@
return false;
}
+ public JobConf getConf() {
+ return conf;
+ }
+
+ public void setConf(JobConf conf) {
+ this.conf = conf;
+ }
+
}