From 96248cdec4278da529b890c15e770846feb253e1 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 14 Apr 2009 19:14:53 +0000 Subject: [PATCH] Added some output to all the classes, including build in runtime analysis git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/BaseTest.java | 9 ++++--- .../shards/ShardStrategyFactoryTest.java | 4 ++++ .../SAMBAMDataSourceTest.java | 8 ++++--- .../sting/utils/GenomeLocTest.java | 16 +++++++------ .../utils/cmdLine/ArgumentParserTest.java | 10 ++++++++ .../utils/fasta/FastaSequenceFile2Test.java | 16 +++++++++++++ .../utils/fasta/FastaSequenceIndexTest.java | 24 +++++++++++++------ 7 files changed, 67 insertions(+), 20 deletions(-) diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index 5455c310a..fad28eead 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -44,6 +44,7 @@ public abstract class BaseTest { protected static String oneKGLocation = "/broad/1KG"; protected static boolean alreadySetup = false; + private static long startTime; /** before the class starts up */ @BeforeClass @@ -55,7 +56,7 @@ public abstract class BaseTest { // setup our log layout PatternLayout layout = new PatternLayout(); - layout.setConversionPattern("TEST %C{1} - %d{HH:mm:ss,SSS} - %m%n"); + layout.setConversionPattern("TEST %C{1}.%M - %d{HH:mm:ss,SSS} - %m%n"); // now set the layout of all the loggers to our layout Enumeration en = logger.getAllAppenders(); @@ -148,12 +149,14 @@ public abstract class BaseTest { // pass through to the junit 3 calls, which are not annotated @Before final public void baseSetup() throws Exception { - + startTime = System.currentTimeMillis(); } @After public void baseTearDown() throws Exception { - + long endTime = System.currentTimeMillis(); + + logger.warn(String.format("runtime: %dms", (endTime - startTime))); } } diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java index 44877a8c0..a2d69ed62 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java @@ -86,6 +86,8 @@ public class ShardStrategyFactoryTest extends BaseTest { /** Tests that we got a string parameter in correctly */ @Test public void testFullGenomeCycle() { + logger.warn("Executing testFullGenomeCycle"); + GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary()); ShardStrategy strategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000); @@ -111,6 +113,8 @@ public class ShardStrategyFactoryTest extends BaseTest { /** Tests that we got a string parameter in correctly */ @Test public void testIntervalGenomeCycle() throws InterruptedException { + logger.warn("Executing testIntervalGenomeCycle"); + SAMSequenceDictionary dic = seq.getSequenceDictionary(); SAMSequenceRecord s = dic.getSequence(1); // Character stream writing diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java index 9523374d0..0eecfb234 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java @@ -77,6 +77,7 @@ public class SAMBAMDataSourceTest extends BaseTest { /** Test out that we can shard the file and iterate over every read */ //@Test public void testLinearBreakIterateAll() { + logger.warn("Executing testLinearBreakIterateAll"); // the sharding strat. ShardStrategy strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000); int count = 0; @@ -114,12 +115,13 @@ public class SAMBAMDataSourceTest extends BaseTest { /** Test out that we can shard the file and iterate over every read */ @Test public void testMergingTwoBAMFiles() { + logger.warn("Executing testMergingTwoBAMFiles"); // the sharding strat. ShardStrategy strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000); // setup the test files - fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188.aligned.duplicates_marked.bam"); + fl.add(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188.aligned.duplicates_marked.bam"); ArrayList readcountPerShard = new ArrayList(); ArrayList readcountPerShard2 = new ArrayList(); @@ -156,8 +158,8 @@ public class SAMBAMDataSourceTest extends BaseTest { // setup the data and the counter before our second run fl.clear(); - fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam"); - fl.add(seqLocation + "/dirseq/analysis/cancer_exome/sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam"); + fl.add(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam"); + fl.add(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam"); count = 0; // the sharding strat. strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000); diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java index 4f4a64616..904523c4c 100644 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java @@ -4,25 +4,24 @@ package org.broadinstitute.sting.utils; // the imports for unit testing. -import org.junit.*; -import static org.junit.Assert.*; -import org.apache.commons.cli.ParseException; -import org.broadinstitute.sting.utils.cmdLine.ArgumentParser; +import org.junit.Assert; +import org.junit.BeforeClass; +import org.junit.Test; +import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2; -import java.util.ArrayList; import java.io.File; /** * Basic unit test for GenomeLoc */ -public class GenomeLocTest { +public class GenomeLocTest extends BaseTest { private static FastaSequenceFile2 seq; @BeforeClass public static void init() { // sequence - seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); } /** @@ -30,6 +29,7 @@ public class GenomeLocTest { */ @Test public void testIsBetween() { + logger.warn("Executing testIsBetween"); GenomeLoc.setupRefContigOrdering(seq); GenomeLoc locMiddle = new GenomeLoc("chr1", 3, 3); @@ -43,6 +43,7 @@ public class GenomeLocTest { } @Test public void testContigIndex() { + logger.warn("Executing testContigIndex"); GenomeLoc locOne = new GenomeLoc("chr1",1,1); Assert.assertEquals(locOne.getContigIndex(), 1); Assert.assertEquals(locOne.getContig(), "chr1"); @@ -60,6 +61,7 @@ public class GenomeLocTest { @Test public void testCompareTo() { + logger.warn("Executing testCompareTo"); GenomeLoc twoOne = new GenomeLoc("chr2", 1); GenomeLoc twoFive = new GenomeLoc("chr2", 5); GenomeLoc twoOtherFive = new GenomeLoc("chr2", 5); diff --git a/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java b/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java index f7c10cfa7..f42d8d2cb 100644 --- a/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java +++ b/java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java @@ -89,6 +89,7 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testStringParameter() { + logger.warn("Executing testStringParameter"); // setup the parameter list String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"}; @@ -111,6 +112,7 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testBooleanParameter() { + logger.warn("Executing testBooleanParameter"); // setup the parameter list String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"}; @@ -130,6 +132,8 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testFloatParameter() { + logger.warn("Executing testFloatParameter"); + // setup the parameter list String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"}; @@ -149,6 +153,8 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testIntegerParameter() { + logger.warn("Executing testIntegerParameter"); + // setup the parameter list String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"}; @@ -169,6 +175,8 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testForUnpassedParameter() { + logger.warn("Executing testForUnpassedParameter"); + // add a new required flag we won't send it m_parser.addRequiredArg("testNotTHere", "N", "our should be provided test", "testFloat"); @@ -190,6 +198,8 @@ public class ArgumentParserTest extends BaseTest { */ @Test public void testForBadArgFieldName() { + logger.warn("Executing testForBadArgFieldName"); + try { // add a new required flag we won't send it m_parser.addRequiredArg("testNotTHere", "N", "our should be provided test", "testDoesNotExist"); diff --git a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java index 2d6264cab..bf2950167 100755 --- a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java +++ b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java @@ -45,6 +45,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testOpenFile() { + logger.warn("Executing testOpenFile"); + long startTime = System.currentTimeMillis(); Assert.assertNotNull( sequenceFile ); long endTime = System.currentTimeMillis(); @@ -54,6 +56,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testFirstSequence() { + logger.warn("Executing testFirstSequence"); + long startTime = System.currentTimeMillis(); ReferenceSequence sequence = sequenceFile.nextSequence(); Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM"); @@ -67,6 +71,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testNextSequence() { + logger.warn("Executing testNextSequence"); + long startTime = System.currentTimeMillis(); ReferenceSequence sequence = null; @@ -92,6 +98,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testSeekToSequence() { + logger.warn("Executing testSeekToSequence"); + long startTime = System.currentTimeMillis(); boolean success = sequenceFile.seekToContig("chr8"); @@ -111,6 +119,8 @@ public class FastaSequenceFile2Test extends BaseTest { // TODO: Is NullPointerException *really* the right exception when a sequence is missing? @Test(expected=NullPointerException.class) public void testSeekToMissingSequence() { + logger.warn("Executing testSeekToMissingSequence"); + long startTime = 0L, endTime = 0L; try { @@ -125,6 +135,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testSeekBackward() { + logger.warn("Executing testSeekBackward"); + long startTime = System.currentTimeMillis(); boolean success = sequenceFile.seekToContig("chr9"); @@ -146,6 +158,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testInvalidSeekBackward() { + logger.warn("Executing testInvalidSeekBackward"); + long startTime = System.currentTimeMillis(); boolean success = sequenceFile.seekToContig("chr9"); @@ -161,6 +175,8 @@ public class FastaSequenceFile2Test extends BaseTest { @Test public void testSimultaneousAccess() { + logger.warn("Executing testSimultaneousAccess"); + long startTime = System.currentTimeMillis(); // FastaSequenceFile2 other = (FastaSequenceFile2)sequenceFile.clone(); diff --git a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java index afb304c1d..2556e07d5 100755 --- a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java +++ b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java @@ -1,17 +1,15 @@ package org.broadinstitute.sting.utils.fasta; -import org.junit.BeforeClass; -import org.junit.Before; -import org.junit.Test; -import org.junit.Assert; -import org.apache.log4j.BasicConfigurator; +import edu.mit.broad.picard.PicardException; import org.broadinstitute.sting.BaseTest; +import org.junit.Assert; +import org.junit.Before; +import org.junit.BeforeClass; +import org.junit.Test; import java.io.File; import java.io.FileNotFoundException; -import edu.mit.broad.picard.PicardException; - /** * Created by IntelliJ IDEA. * User: hanna @@ -35,6 +33,8 @@ public class FastaSequenceIndexTest extends BaseTest { @Test public void testInitialContig() { + logger.warn("Executing testInitialContig"); + Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM")); FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrM"); Assert.assertEquals("Contig chrM name is incorrect",entry.getContig(),"chrM"); @@ -46,6 +46,8 @@ public class FastaSequenceIndexTest extends BaseTest { @Test public void testMiddleContig() { + logger.warn("Executing testMiddleContig"); + Assert.assertTrue("Contig chr8 is not present", sequenceIndex.hasIndexEntry("chr8")); FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chr8"); Assert.assertEquals("Contig chr8 name is incorrect",entry.getContig(),"chr8"); @@ -57,6 +59,8 @@ public class FastaSequenceIndexTest extends BaseTest { @Test public void testLastContig() { + logger.warn("Executing testLastContig"); + Assert.assertTrue("Contig chrX_random is not present", sequenceIndex.hasIndexEntry("chrX_random")); FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrX_random"); Assert.assertEquals("Contig chrX_random name is incorrect",entry.getContig(),"chrX_random"); @@ -68,6 +72,8 @@ public class FastaSequenceIndexTest extends BaseTest { @Test public void testAllContigsPresent() { + logger.warn("Executing testAllContigsPresent"); + Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM")); Assert.assertTrue("Contig chr1 is not present", sequenceIndex.hasIndexEntry("chr1")); Assert.assertTrue("Contig chr2 is not present", sequenceIndex.hasIndexEntry("chr2")); @@ -117,11 +123,15 @@ public class FastaSequenceIndexTest extends BaseTest { @Test public void testHasInvalidEntry() { + logger.warn("Executing testHasInvalidEntry"); + Assert.assertFalse("Found an invalid entry", sequenceIndex.hasIndexEntry("invalid")); } @Test(expected= PicardException.class) public void testGetInvalidEntry() { + logger.warn("Executing testGetInvalidEntry"); + sequenceIndex.getIndexEntry("invalid"); }