clean genomixMiniCluster
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
deleted file mode 100644
index 714d77e..0000000
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/GenomixMiniClusterTest.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package edu.uci.ics.genomix.hadoop.pmcommon;
-
-import java.io.BufferedWriter;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileStatus;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.FileUtil;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.hdfs.MiniDFSCluster;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MiniMRCluster;
-import org.apache.hadoop.util.ReflectionUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-
-import edu.uci.ics.genomix.hyracks.driver.Driver;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.hyracks.test.TestUtils;
-import edu.uci.ics.hyracks.hdfs.utils.HyracksUtils;
-
-/*
- * A base class providing most of the boilerplate for Genomix-based tests
- */
-@SuppressWarnings("deprecation")
-public class GenomixMiniClusterTest {
- protected int KMER_LENGTH = 5;
- protected int READ_LENGTH = 8;
-
- // subclass should modify this to include the HDFS directories that should be cleaned up
- protected ArrayList<String> HDFS_PATHS = new ArrayList<String>();
-
- protected static String EXPECTED_ROOT = "src/test/resources/expected/";
- protected static String ACTUAL_ROOT = "src/test/resources/actual/";
-
- protected static String HADOOP_CONF_ROOT = "src/test/resources/hadoop/conf/";
-
- protected static MiniDFSCluster dfsCluster;
- protected static MiniMRCluster mrCluster;
- private static FileSystem dfs;
- protected static JobConf conf = new JobConf();
- protected static int numberOfNC = 1;
- protected static int numPartitionPerMachine = 1;
- protected static Driver driver;
-
- @BeforeClass
- public static void setUpMiniCluster() throws Exception {
- cleanupStores();
- startHDFS();
- HyracksUtils.init();
- FileUtils.forceMkdir(new File(ACTUAL_ROOT));
- FileUtils.cleanDirectory(new File(ACTUAL_ROOT));
- driver = new Driver(HyracksUtils.CC_HOST, HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT, numPartitionPerMachine);
- }
-
- /*
- * Merge and copy a DFS directory to a local destination, converting to text if necessary.
- * Also locally store the binary-formatted result if available.
- */
- protected static void copyResultsToLocal(String hdfsSrcDir, String localDestFile, boolean resultsAreText,
- Configuration conf) throws IOException {
- if (resultsAreText) {
- // for text files, just concatenate them together
- FileUtil.copyMerge(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
- new Path(localDestFile), false, conf, null);
- } else {
- // file is binary
-// // save the entire binary output dir
-// FileUtil.copy(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
-// new Path(localDestFile + ".bindir"), false, conf);
-
- // also load the Nodes and write them out as text locally.
- FileSystem lfs = FileSystem.getLocal(new Configuration());
- lfs.mkdirs(new Path(localDestFile).getParent());
- File filePathTo = new File(localDestFile);
- BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-
- FileStatus[] files = dfs.globStatus(new Path(hdfsSrcDir + "*"));
- SequenceFile.Reader reader = new SequenceFile.Reader(dfs, files[0].getPath(), conf);
- String destBinDir = localDestFile.substring(0, localDestFile.lastIndexOf("."));
-// FileUtil.copy(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
-// new Path(destBinDir), false, conf);
- SequenceFile.Writer writer = new SequenceFile.Writer(lfs, new JobConf(), new Path(localDestFile
- + ".binmerge"), reader.getKeyClass(), reader.getValueClass());
-
- Writable key = (Writable) ReflectionUtils.newInstance(reader.getKeyClass(), conf);
- Writable value = (Writable) ReflectionUtils.newInstance(reader.getValueClass(), conf);
-
- for (FileStatus f : files) {
- if (f.getLen() == 0) {
- continue;
- }
- reader = new SequenceFile.Reader(dfs, f.getPath(), conf);
- while (reader.next(key, value)) {
- if (key == null || value == null) {
- break;
- }
- bw.write(key.toString() + "\t" + value.toString());
- System.out.println(key.toString() + "\t" + value.toString());
- bw.newLine();
- writer.append(key, value);
-
- }
- reader.close();
- }
- writer.close();
- bw.close();
- }
-
- }
-
- protected static boolean checkResults(String expectedPath, String actualPath, int[] poslistField) throws Exception {
- File dumped = new File(actualPath);
- if (poslistField != null) {
- TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
- } else {
- TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
- }
- return true;
- }
-
- protected static void cleanupStores() throws IOException {
- FileUtils.forceMkdir(new File("teststore"));
- FileUtils.forceMkdir(new File("build"));
- FileUtils.cleanDirectory(new File("teststore"));
- FileUtils.cleanDirectory(new File("build"));
- }
-
- protected static void startHDFS() throws IOException {
- conf.addResource(new Path(HADOOP_CONF_ROOT + "core-site.xml"));
- // conf.addResource(new Path(HADOOP_CONF_ROOT + "mapred-site.xml"));
- conf.addResource(new Path(HADOOP_CONF_ROOT + "hdfs-site.xml"));
-
- FileSystem lfs = FileSystem.getLocal(new Configuration());
- lfs.delete(new Path("build"), true);
- System.setProperty("hadoop.log.dir", "logs");
- dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
- dfs = dfsCluster.getFileSystem();
- mrCluster = new MiniMRCluster(4, dfs.getUri().toString(), 2);
- System.out.println(dfs.getUri().toString());
-
- DataOutputStream confOutput = new DataOutputStream(
- new FileOutputStream(new File(HADOOP_CONF_ROOT + "conf.xml")));
- conf.writeXml(confOutput);
- confOutput.close();
- }
-
- protected static void copyLocalToDFS(String localSrc, String hdfsDest) throws IOException {
- Path dest = new Path(hdfsDest);
- dfs.mkdirs(dest);
- dfs.copyFromLocalFile(new Path(localSrc), dest);
- }
-
- /*
- * Remove the local "actual" folder and any hdfs folders in use by this test
- */
- public void cleanUpOutput() throws IOException {
-// // local cleanup
-// FileSystem lfs = FileSystem.getLocal(new Configuration());
-// if (lfs.exists(new Path(ACTUAL_ROOT))) {
-// lfs.delete(new Path(ACTUAL_ROOT), true);
-// }
- // dfs cleanup
- for (String path : HDFS_PATHS) {
- if (dfs.exists(new Path(path))) {
- dfs.delete(new Path(path), true);
- }
- }
- }
-
- @AfterClass
- public static void tearDown() throws Exception {
- HyracksUtils.deinit();
- cleanupHDFS();
- }
-
- protected static void cleanupHDFS() throws Exception {
- dfsCluster.shutdown();
- mrCluster.shutdown();
- }
-}