hadoop for contrail graph
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java
new file mode 100644
index 0000000..2880b6c
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java
@@ -0,0 +1,40 @@
+package edu.uci.ics.genomix.hadoop.contrailgraphbuilding;
+
+import java.io.IOException;
+
+import org.apache.commons.cli.Options;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+
+
+public class GenomixDriver {
+
+ private static class Options {
+ @Option(name = "-inputpath", usage = "the input path", required = true)
+ public String inputPath;
+
+ @Option(name = "-outputpath", usage = "the output path", required = true)
+ public String outputPath;
+
+ @Option(name = "-num-reducers", usage = "the number of reducers", required = true)
+ public int numReducers;
+
+ @Option(name = "-kmer-size", usage = "the size of kmer", required = true)
+ public int sizeKmer;
+
+ @Option(name = "-read-length", usage = "the length of read", required = true)
+ public int readLength;
+ }
+
+ public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength) throws IOException{
+
+ }
+
+ public static void main(String[] args) throws Exception {
+ Options options = new Options();
+ CmdLineParser parser = new CmdLineParser(options);
+ parser.parseArgument(args);
+ GenomixDriver driver = new GenomixDriver();
+ driver.run(options.inputPath, options.outputPath, options.numReducers, options.sizeKmer, options.readLength);
+ }
+}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
new file mode 100644
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--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
@@ -0,0 +1,64 @@
+package edu.uci.ics.genomix.hadoop.contrailgraphbuilding;
+
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MiniMRCluster;
+
+public class GraphBuildingTest {
+
+ private JobConf conf = new JobConf();
+ private static final String ACTUAL_RESULT_DIR = "actual1";
+ private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+ private static final String DATA_PATH = "data/webmap/text.txt";
+ private static final String HDFS_PATH = "/webmap";
+ private static final String RESULT_PATH = "/result1";
+ private static final String EXPECTED_PATH = "expected/";
+ private static final int COUNT_REDUCER = 2;
+ private static final int SIZE_KMER = 5;
+ private static final int READ_LENGTH = 8;
+
+ private MiniDFSCluster dfsCluster;
+ private MiniMRCluster mrCluster;
+ private FileSystem dfs;
+
+ public void test() throws Exception {
+ FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+ FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+ startHadoop();
+ cleanupHadoop();
+ }
+
+ private void startHadoop() throws IOException {
+ FileSystem lfs = FileSystem.getLocal(new Configuration());
+ lfs.delete(new Path("build"), true);
+ System.setProperty("hadoop.log.dir", "logs");
+ dfsCluster = new MiniDFSCluster(conf, 2, true, null);
+ dfs = dfsCluster.getFileSystem();
+ mrCluster = new MiniMRCluster(4, dfs.getUri().toString(), 2);
+
+ Path src = new Path(DATA_PATH);
+ Path dest = new Path(HDFS_PATH + "/");
+ dfs.mkdirs(dest);
+ dfs.copyFromLocalFile(src, dest);
+
+ DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
+ conf.writeXml(confOutput);
+ confOutput.flush();
+ confOutput.close();
+ }
+
+ private void cleanupHadoop() throws IOException {
+ mrCluster.shutdown();
+ dfsCluster.shutdown();
+ }
+
+}