267 lines
9.8 KiB
Java
267 lines
9.8 KiB
Java
// our package
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package org.broadinstitute.sting.utils.threading;
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// the imports for unit testing.
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.Assert;
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import org.testng.annotations.BeforeMethod;
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import org.testng.annotations.BeforeTest;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import java.util.concurrent.Callable;
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import java.util.concurrent.ExecutorService;
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import java.util.concurrent.Future;
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import java.util.concurrent.TimeUnit;
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/**
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* Basic unit test for GenomeLoc
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*/
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public class GenomeLocProcessingTrackerUnitTest extends BaseTest {
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IndexedFastaSequenceFile fasta = null;
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GenomeLocParser genomeLocParser = null;
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File sharedFile = new File("synchronizationFile.txt");
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String chr1 = null;
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@BeforeTest
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public void before() {
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File referenceFile = new File(hg18Reference);
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try {
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fasta = new IndexedFastaSequenceFile(referenceFile);
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chr1 = fasta.getSequenceDictionary().getSequence(1).getSequenceName();
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genomeLocParser = new GenomeLocParser(fasta);
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}
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catch(FileNotFoundException ex) {
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throw new UserException.CouldNotReadInputFile(referenceFile,ex);
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}
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}
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@BeforeMethod
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public void cleanup() {
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if ( sharedFile.exists() ) {
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sharedFile.delete();
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}
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}
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abstract private class TestTarget {
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String name;
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int nShards;
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int shardSize;
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protected TestTarget(String name, int nShards, int shardSize) {
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this.name = name;
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this.nShards = nShards;
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this.shardSize = shardSize;
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}
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public abstract GenomeLocProcessingTracker getTracker();
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public List<GenomeLoc> getShards() {
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List<GenomeLoc> shards = new ArrayList<GenomeLoc>();
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for ( int i = 0; i < nShards; i++ ) {
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int start = shardSize * i;
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int stop = start + shardSize;
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shards.add(genomeLocParser.createGenomeLoc(chr1, start, stop));
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}
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return shards;
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}
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public String toString() {
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return String.format("TestTarget %s: nShards=%d shardSize=%d", name, nShards, shardSize);
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}
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}
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@DataProvider(name = "data")
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public Object[][] createData1() {
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List<TestTarget> params = new ArrayList<TestTarget>();
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// for ( int nShard : Arrays.asList(10) ) {
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// for ( int shardSize : Arrays.asList(10) ) {
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for ( int nShard : Arrays.asList(10, 100, 1000, 10000) ) {
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for ( int shardSize : Arrays.asList(10, 100) ) {
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// shared mem -- canonical implementation
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// params.add(new TestTarget(nShard, shardSize) {
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// SharedMemoryGenomeLocProcessingTracker tracker = new SharedMemoryGenomeLocProcessingTracker();
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// public GenomeLocProcessingTracker getTracker() { return tracker; }
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// });
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// shared file -- working implementation
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params.add(new TestTarget("SharedFile", nShard, shardSize) {
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SharedFileGenomeLocProcessingTracker tracker = new SharedFileGenomeLocProcessingTracker(sharedFile, genomeLocParser);
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public GenomeLocProcessingTracker getTracker() { return tracker; }
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});
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}
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}
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List<Object[]> params2 = new ArrayList<Object[]>();
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for ( TestTarget x : params ) params2.add(new Object[]{x});
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return params2.toArray(new Object[][]{});
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}
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private static final String NAME_ONE = "name1";
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private static final String NAME_TWO = "name2";
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@Test(dataProvider = "data", enabled = true)
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public void testSingleProcessTracker(TestTarget test) {
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GenomeLocProcessingTracker tracker = test.getTracker();
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List<GenomeLoc> shards = test.getShards();
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logger.warn("testSingleProcessTracker " + test);
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int counter = 0;
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for ( GenomeLoc shard : shards ) {
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counter++;
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Assert.assertNull(tracker.findOwner(shard));
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Assert.assertFalse(tracker.locIsOwned(shard));
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GenomeLocProcessingTracker.ProcessingLoc proc = tracker.claimOwnership(shard,NAME_ONE);
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Assert.assertNotNull(proc);
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Assert.assertNotNull(proc.getLoc());
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Assert.assertNotNull(proc.getOwner());
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Assert.assertEquals(proc.getLoc(), shard);
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Assert.assertEquals(proc.getOwner(), NAME_ONE);
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Assert.assertEquals(tracker.findOwner(shard), proc);
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Assert.assertTrue(tracker.locIsOwned(shard));
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Assert.assertNotNull(tracker.getProcessingLocs());
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Assert.assertEquals(tracker.getProcessingLocs().size(), counter);
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GenomeLocProcessingTracker.ProcessingLoc badClaimAttempt = tracker.claimOwnership(shard,NAME_TWO);
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Assert.assertFalse(badClaimAttempt.getOwner().equals(NAME_TWO));
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Assert.assertEquals(badClaimAttempt.getOwner(), NAME_ONE);
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}
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}
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@Test(dataProvider = "data", enabled = true)
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public void testMarkedProcesses(TestTarget test) {
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GenomeLocProcessingTracker tracker = test.getTracker();
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List<GenomeLoc> shards = test.getShards();
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logger.warn("testMarkedProcesses " + test);
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List<GenomeLoc> markedShards = new ArrayList<GenomeLoc>();
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for ( int i = 0; i < shards.size(); i++ ) {
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if ( i % 2 == 0 ) {
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markedShards.add(shards.get(i));
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tracker.claimOwnership(shards.get(i), NAME_TWO);
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}
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}
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for ( GenomeLoc shard : shards ) {
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GenomeLocProcessingTracker.ProcessingLoc proc = tracker.claimOwnership(shard,NAME_ONE);
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Assert.assertTrue(proc.isOwnedBy(NAME_ONE) || proc.isOwnedBy(NAME_TWO));
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if ( proc.isOwnedBy(NAME_ONE) )
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Assert.assertTrue(! markedShards.contains(shard));
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else
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Assert.assertTrue(markedShards.contains(shard));
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if ( ! markedShards.contains(shard) ) {
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Assert.assertEquals(tracker.findOwner(shard), proc);
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}
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}
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}
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public class TestThread implements Callable<Integer> {
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public TestTarget test;
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public String name;
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public List<GenomeLoc> ran;
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public TestThread(TestTarget test, int count) {
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this.test = test;
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this.name = "thread" + count;
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this.ran = new ArrayList<GenomeLoc>();
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}
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public Integer call() {
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int nShards = test.getShards().size();
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for ( GenomeLoc shard : test.getShards() ) {
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if ( ran.size() < nShards / 3 ) {
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GenomeLocProcessingTracker.ProcessingLoc proc = test.getTracker().claimOwnership(shard,name);
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if ( proc.isOwnedBy(name) )
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ran.add(proc.getLoc());
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//logger.warn(String.format("Thread %s on %s -> owned by %s", name, shard, proc.getOwner()));
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}
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}
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return 1;
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}
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}
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private static TestThread findOwner(String name, List<TestThread> threads) {
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for ( TestThread thread : threads ) {
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if ( thread.name.equals(name) )
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return thread;
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}
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return null;
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}
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private static final <T> void assertAllThreadsFinished(List<Future<T>> futures) {
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for ( Future f : futures )
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Assert.assertTrue(f.isDone(), "Thread never finished running");
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}
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@Test(dataProvider = "data", enabled = true)
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public void testThreadedProcesses(TestTarget test) {
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// start up 3 threads
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logger.warn("ThreadedTesting " + test);
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List<TestThread> threads = new ArrayList<TestThread>();
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for ( int i = 0; i < 4; i++) {
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TestThread thread = new TestThread(test, i);
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threads.add(thread);
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}
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ExecutorService exec = java.util.concurrent.Executors.newFixedThreadPool(threads.size());
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try {
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List<Future<Integer>> results = exec.invokeAll(threads, 300, TimeUnit.SECONDS);
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GenomeLocProcessingTracker tracker = test.getTracker();
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List<GenomeLoc> shards = test.getShards();
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for ( TestThread thread : threads )
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logger.warn(String.format("TestThread ran %d jobs", thread.ran.size()));
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assertAllThreadsFinished(results);
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// we ran everything
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Assert.assertEquals(tracker.getProcessingLocs().size(), shards.size(), "Not all shards were run");
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for ( GenomeLoc shard : shards ) {
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Assert.assertTrue(tracker.locIsOwned(shard), "Unowned shard");
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GenomeLocProcessingTracker.ProcessingLoc proc = tracker.findOwner(shard);
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Assert.assertNotNull(proc, "Proc was null");
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Assert.assertNotNull(proc.getOwner(), "Owner was null");
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Assert.assertEquals(proc.getLoc(), shard, "Shard loc doesn't make ProcessingLoc");
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TestThread owner = findOwner(proc.getOwner(), threads);
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Assert.assertNotNull(owner, "Couldn't find owner");
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Assert.assertTrue(owner.ran.contains(shard), "Owner doesn't contain ran shard");
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for ( TestThread thread : threads )
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if ( ! proc.isOwnedBy(thread.name) )
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Assert.assertFalse(thread.ran.contains(shard), "Shard appears in another run list");
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}
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} catch (InterruptedException e) {
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Assert.fail("Thread failure", e);
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}
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}
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} |