modify the test for graph building
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java
index f700f6d..b7b7054 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/io/NodeTextWriterFactory.java
@@ -29,7 +29,7 @@
public class NodeTextWriterFactory implements ITupleWriterFactory {
/**
- *
+ * Write the node to Text
*/
private static final long serialVersionUID = 1L;
private final int kmerSize;
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index 6cc4475..bb0d131 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -8,7 +8,6 @@
import java.io.IOException;
import junit.framework.Assert;
-
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
@@ -41,11 +40,7 @@
private static final String HDFS_INPUT_PATH = "/webmap";
private static final String HDFS_OUTPUT_PATH = "/webmap_result";
- private static final String EXPECTED_DIR = "src/test/resources/expected/";
- private static final String EXPECTED_READER_RESULT = EXPECTED_DIR + "result_after_initial_read";
-
private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
- private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";;
private MiniDFSCluster dfsCluster;
@@ -65,6 +60,7 @@
cleanUpReEntry();
conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
driver.runJob(new GenomixJobConf(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+ dumpResult();
}
@Before
@@ -124,55 +120,13 @@
}
}
-/* private boolean checkResults(String expectedPath, int[] poslistField) throws Exception {
- File dumped = null;
+ private void dumpResult() throws Exception {
String format = conf.get(GenomixJobConf.OUTPUT_FORMAT);
if (GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(format)) {
FileUtil.copyMerge(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH),
FileSystem.getLocal(new Configuration()), new Path(DUMPED_RESULT), false, conf, null);
- dumped = new File(DUMPED_RESULT);
- } else {
-
- FileSystem.getLocal(new Configuration()).mkdirs(new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
- File filePathTo = new File(CONVERT_RESULT);
- 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);
-
- Path path = new Path(HDFS_OUTPUT_PATH + partname);
- FileSystem dfs = FileSystem.get(conf);
- if (dfs.getFileStatus(path).getLen() == 0) {
- continue;
- }
- SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path, conf);
-
- NodeWritable node = new NodeWritable(conf.getInt(GenomixJobConf.KMER_LENGTH, KmerSize));
- NullWritable value = NullWritable.get();
- while (reader.next(node, value)) {
- if (node == null) {
- break;
- }
- bw.write(node.toString());
- System.out.println(node.toString());
- bw.newLine();
- }
- reader.close();
- }
- bw.close();
- dumped = new File(CONVERT_RESULT);
- }
-
- if (poslistField != null) {
- TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
- } else {
- TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
- }
- return true;
- }*/
+ }
+ }
@After
public void tearDown() throws Exception {