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

build.xml

@@ -1473,6 +1473,7 @@
         <property name="testng.classpath" value="testng.default.classpath" />
         <property name="test.maxmemory" value="${test.default.maxmemory}"/>
         <property name="include.contracts" value="true" />
+        <property name="include.scala" value="true" />
 
         <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
     </target>

public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java

@@ -35,7 +35,7 @@ import java.lang.reflect.Method;
 /**
  * Provide default @Test values for GATK testng tests.
  *
- * Currently only sets the maximum runtime to 10 minutes, if it's not been specified.
+ * Currently only sets the maximum runtime to 40 minutes, if it's not been specified.
  *
  * See http://beust.com/weblog/2006/10/18/annotation-transformers-in-java/
  *
@@ -44,7 +44,7 @@ import java.lang.reflect.Method;
  * @version 0.1
  */
 public class TestNGTestTransformer implements IAnnotationTransformer {
-    public static final long DEFAULT_TIMEOUT = 1000 * 60 * 20; // 20 minutes max per test
+    public static final long DEFAULT_TIMEOUT = 1000 * 60 * 40; // 40 minutes max per test
 
     final static Logger logger = Logger.getLogger(TestNGTestTransformer.class);
 

public/java/test/org/broadinstitute/sting/gatk/MaxRuntimeIntegrationTest.java

@@ -39,7 +39,7 @@ import java.util.concurrent.TimeUnit;
  *
  */
 public class MaxRuntimeIntegrationTest extends WalkerTest {
-    private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(20, TimeUnit.SECONDS);
+    private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(120, TimeUnit.SECONDS);
 
     private class MaxRuntimeTestProvider extends TestDataProvider {
         final long maxRuntime;
@@ -68,7 +68,7 @@ public class MaxRuntimeIntegrationTest extends WalkerTest {
     //
     // Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
     //
-    @Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
+    @Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 300 * 1000)
     public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T PrintReads -R " + hg18Reference

public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java

@@ -58,6 +58,7 @@ import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.*;
 
 /**
@@ -86,11 +87,10 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
 
     private List<GenomeLoc> intervals;
 
-    private static final String testBAM = "TraverseActiveRegionsUnitTest.bam";
+    private File testBAM;
-    private static final String testBAI = "TraverseActiveRegionsUnitTest.bai";
 
     @BeforeClass
-    private void init() throws FileNotFoundException {
+    private void init() throws IOException {
         //reference = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")); // hg19Reference));
         reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
         dictionary = reference.getSequenceDictionary();
@@ -133,17 +133,18 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         createBAM(reads);
     }
 
-    private void createBAM(List<GATKSAMRecord> reads) {
+    private void createBAM(List<GATKSAMRecord> reads) throws IOException {
-        File outFile = new File(testBAM);
+        testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam");
-        outFile.deleteOnExit();
+        testBAM.deleteOnExit();
-        File indexFile = new File(testBAI);
-        indexFile.deleteOnExit();
 
-        SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, outFile);
+        SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM);
         for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {
             out.addAlignment(read);
         }
         out.close();
+
+        new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
+        new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit();
     }
 
     @Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider")
@@ -400,7 +401,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         return getActiveRegions(t, walker, intervals, testBAM);
     }
 
-    private Map<GenomeLoc, ActiveRegion> getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List<GenomeLoc> intervals, final String bam) {
+    private Map<GenomeLoc, ActiveRegion> getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List<GenomeLoc> intervals, final File bam) {
         for (LocusShardDataProvider dataProvider : createDataProviders(t, walker, intervals, bam))
             t.traverse(walker, dataProvider, 0);
 
@@ -466,13 +467,13 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         return record;
     }
 
-    private List<LocusShardDataProvider> createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List<GenomeLoc> intervals, String bamFile) {
+    private List<LocusShardDataProvider> createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List<GenomeLoc> intervals, File bamFile) {
         GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
         engine.setGenomeLocParser(genomeLocParser);
         traverseActiveRegions.initialize(engine, walker);
 
         Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
-        SAMReaderID readerID = new SAMReaderID(new File(bamFile), new Tags());
+        SAMReaderID readerID = new SAMReaderID(bamFile, new Tags());
         samFiles.add(readerID);
 
         SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
@@ -594,7 +595,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         walker.setStates(readStates);
 
         final TraverseActiveRegions traversal = new TraverseActiveRegions<Integer, Integer>();
-        final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString());
+        final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());
 
         final Set<String> alreadySeenReads = new HashSet<String>(); // for use with the primary / non-primary
         for ( final ActiveRegion region : activeRegionsMap.values() ) {
@@ -666,7 +667,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
         final DummyActiveRegionWalker walker = new DummyActiveRegionWalker(activeRegions, false);
 
         final TraverseActiveRegions traversal = new TraverseActiveRegions<Integer, Integer>();
-        final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString());
+        final Map<GenomeLoc, ActiveRegion> activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile());
 
         final ActiveRegion region = activeRegionsMap.values().iterator().next();
         int nReadsExpectedInRegion = 0;

public/java/test/org/broadinstitute/sting/utils/SimpleTimerUnitTest.java

@@ -118,8 +118,8 @@ public class SimpleTimerUnitTest extends BaseTest {
         Assert.assertTrue(secs < 0.01, "Fast operation said to take longer than 10 milliseconds: elapsed time in seconds " + secs);
 
         Assert.assertTrue(nano > 0, "Nanosecond timer doesn't appear to count properly: elapsed time is " + nano);
-        final long maxTimeInMicro = 100;
+        final long maxTimeInMicro = 10000;
-        final long maxTimeInNano = TimeUnit.MICROSECONDS.toNanos(100);
+        final long maxTimeInNano = TimeUnit.MICROSECONDS.toNanos(maxTimeInMicro);
         Assert.assertTrue(nano < maxTimeInNano, "Fast operation said to take longer than " + maxTimeInMicro + " microseconds: elapsed time in nano " + nano + " micro " + TimeUnit.NANOSECONDS.toMicros(nano));
     }