Fix tests that were consistently or intermittently failing when run in parallel on the farm
-Make MaxRuntimeIntegrationTest more lenient by assuming that startup overhead might be as long as 120 seconds on a very slow node, rather than the original assumption of 20 seconds -In TraverseActiveRegionsUnitTest, write temp bam file to the temp directory, not to the current working directory -SimpleTimerUnitTest: This test was internally inconsistent. It asserted that a particular operation should take no more than 10 milliseconds, and then asserted again that this same operation should take no more than 100 microseconds (= 0.1 millisecond). On a slow node it could take slightly longer than 100 microseconds, however. Changed the test to assert that the operation should require no more than 10000 microseconds (= 10 milliseconds) -change global default test timeout from 20 to 40 minutes (things just take longer on the farm!) -build.xml: allow runtestonly target to work with scala test classes
This commit is contained in:
David Roazen
parent
7d833256e8
commit
3ab78543a7
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@ -1473,6 +1473,7 @@
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<property name="testng.classpath" value="testng.default.classpath" />
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<property name="test.maxmemory" value="${test.default.maxmemory}"/>
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<property name="include.contracts" value="true" />
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<property name="include.scala" value="true" />
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<run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
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</target>
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@ -35,7 +35,7 @@ import java.lang.reflect.Method;
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/**
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* Provide default @Test values for GATK testng tests.
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*
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* Currently only sets the maximum runtime to 10 minutes, if it's not been specified.
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* Currently only sets the maximum runtime to 40 minutes, if it's not been specified.
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*
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* See http://beust.com/weblog/2006/10/18/annotation-transformers-in-java/
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*
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@ -44,7 +44,7 @@ import java.lang.reflect.Method;
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* @version 0.1
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*/
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public class TestNGTestTransformer implements IAnnotationTransformer {
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public static final long DEFAULT_TIMEOUT = 1000 * 60 * 20; // 20 minutes max per test
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public static final long DEFAULT_TIMEOUT = 1000 * 60 * 40; // 40 minutes max per test
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final static Logger logger = Logger.getLogger(TestNGTestTransformer.class);
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@ -39,7 +39,7 @@ import java.util.concurrent.TimeUnit;
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*
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*/
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public class MaxRuntimeIntegrationTest extends WalkerTest {
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private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(20, TimeUnit.SECONDS);
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private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(120, TimeUnit.SECONDS);
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private class MaxRuntimeTestProvider extends TestDataProvider {
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final long maxRuntime;
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@ -68,7 +68,7 @@ public class MaxRuntimeIntegrationTest extends WalkerTest {
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//
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// Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
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//
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@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
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@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 300 * 1000)
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public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T PrintReads -R " + hg18Reference
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@ -58,6 +58,7 @@ 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.io.IOException;
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import java.util.*;
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/**
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@ -86,11 +87,10 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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private List<GenomeLoc> intervals;
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private static final String testBAM = "TraverseActiveRegionsUnitTest.bam";
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private static final String testBAI = "TraverseActiveRegionsUnitTest.bai";
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private File testBAM;
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@BeforeClass
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private void init() throws FileNotFoundException {
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private void init() throws IOException {
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//reference = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")); // hg19Reference));
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reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
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dictionary = reference.getSequenceDictionary();
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@ -133,17 +133,18 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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createBAM(reads);
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}
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private void createBAM(List<GATKSAMRecord> reads) {
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File outFile = new File(testBAM);
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outFile.deleteOnExit();
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File indexFile = new File(testBAI);
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indexFile.deleteOnExit();
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private void createBAM(List<GATKSAMRecord> reads) throws IOException {
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testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam");
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testBAM.deleteOnExit();
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SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, outFile);
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SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM);
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for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {
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out.addAlignment(read);
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}
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out.close();
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new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
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new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit();
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}
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@Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider")
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@ -400,7 +401,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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return getActiveRegions(t, walker, intervals, testBAM);
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}
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private Map<GenomeLoc, ActiveRegion> getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List<GenomeLoc> intervals, final String bam) {
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private Map<GenomeLoc, ActiveRegion> getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List<GenomeLoc> intervals, final File bam) {
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for (LocusShardDataProvider dataProvider : createDataProviders(t, walker, intervals, bam))
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t.traverse(walker, dataProvider, 0);
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@ -466,13 +467,13 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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return record;
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}
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private List<LocusShardDataProvider> createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List<GenomeLoc> intervals, String bamFile) {
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private List<LocusShardDataProvider> createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List<GenomeLoc> intervals, File bamFile) {
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GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
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engine.setGenomeLocParser(genomeLocParser);
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traverseActiveRegions.initialize(engine, walker);
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Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
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SAMReaderID readerID = new SAMReaderID(new File(bamFile), new Tags());
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SAMReaderID readerID = new SAMReaderID(bamFile, new Tags());
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samFiles.add(readerID);
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SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
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@ -594,7 +595,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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walker.setStates(readStates);
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final TraverseActiveRegions traversal = new TraverseActiveRegions<Integer, Integer>();
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final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString());
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final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());
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final Set<String> alreadySeenReads = new HashSet<String>(); // for use with the primary / non-primary
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for ( final ActiveRegion region : activeRegionsMap.values() ) {
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@ -666,7 +667,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
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final DummyActiveRegionWalker walker = new DummyActiveRegionWalker(activeRegions, false);
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final TraverseActiveRegions traversal = new TraverseActiveRegions<Integer, Integer>();
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final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString());
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final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());
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final ActiveRegion region = activeRegionsMap.values().iterator().next();
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int nReadsExpectedInRegion = 0;
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@ -118,8 +118,8 @@ public class SimpleTimerUnitTest extends BaseTest {
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Assert.assertTrue(secs < 0.01, "Fast operation said to take longer than 10 milliseconds: elapsed time in seconds " + secs);
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Assert.assertTrue(nano > 0, "Nanosecond timer doesn't appear to count properly: elapsed time is " + nano);
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final long maxTimeInMicro = 100;
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final long maxTimeInNano = TimeUnit.MICROSECONDS.toNanos(100);
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final long maxTimeInMicro = 10000;
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final long maxTimeInNano = TimeUnit.MICROSECONDS.toNanos(maxTimeInMicro);
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Assert.assertTrue(nano < maxTimeInNano, "Fast operation said to take longer than " + maxTimeInMicro + " microseconds: elapsed time in nano " + nano + " micro " + TimeUnit.NANOSECONDS.toMicros(nano));
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}
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