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Merge pull request #641 from broadinstitute/dr_post_test_cleanup 

Improve test suite tmp file cleanup
This commit is contained in:
Eric Banks 2014-05-27 15:59:03 -04:00
parent 400d19a126 74b51c5c7a
commit 3f694d61ee
3 changed files with 46 additions and 16 deletions
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38
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -126,7 +126,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
final List<File> outputFiles = executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator")
@ -142,7 +143,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
Arrays.asList(params.cutVCFMD5));
spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
executeTest("testApplyRecalibration-"+params.inVCF, spec);
final List<File> outputFiles = executeTest("testApplyRecalibration-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(dataProvider = "VRAggregateTest")
@ -163,7 +165,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibratorAggregate-"+params.inVCF, spec).getFirst();
final List<File> outputFiles = executeTest("testVariantRecalibratorAggregate-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(dataProvider = "VRAggregateTest",dependsOnMethods="testVariantRecalibratorAggregate")
@ -179,7 +182,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
Arrays.asList(params.cutVCFMD5));
spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
executeTest("testApplyRecalibrationAggregate-"+params.inVCF, spec);
final List<File> outputFiles = executeTest("testApplyRecalibrationAggregate-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
@ -212,7 +216,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
2,
Arrays.asList("bcf", "txt"),
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
final List<File> outputFiles = executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(dataProvider = "VRBCFTest", dependsOnMethods="testVariantRecalibratorWithBCF")
@ -228,7 +233,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
Arrays.asList(params.cutVCFMD5));
spec.disableShadowBCF();
executeTest("testApplyRecalibration-"+params.inVCF, spec);
final List<File> outputFiles = executeTest("testApplyRecalibration-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@ -266,7 +272,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibratorIndel-"+params.inVCF, spec).getFirst();
final List<File> outputFiles = executeTest("testVariantRecalibratorIndel-"+params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(dataProvider = "VRIndelTest",dependsOnMethods="testVariantRecalibratorIndel")
@ -283,7 +290,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
Arrays.asList(params.cutVCFMD5));
spec.disableShadowBCF(); // has to be disabled because the input VCF is missing LowQual annotation
executeTest("testApplyRecalibrationIndel-" + params.inVCF, spec);
final List<File> outputFiles = executeTest("testApplyRecalibrationIndel-" + params.inVCF, spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test
@ -299,7 +307,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
" -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
Arrays.asList("03a0ed00af6aac76d39e569f90594a02"));
executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
final List<File> outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@Test(enabled = true)
@ -317,13 +326,20 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
spec.disableShadowBCF();
final File VCF = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).first.get(0);
final List<File> outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).getFirst();
setPDFsForDeletion(outputFiles);
final File VCF = outputFiles.get(0);
for( final VariantContext VC : GATKVCFUtils.readAllVCs(VCF, new VCFCodec()).getSecond() ) {
if( VC != null ) {
Assert.assertTrue(VC.isNotFiltered()); // there should only be unfiltered records in the output VCF file
}
}
}
private void setPDFsForDeletion( final List<File> walkerOutputFiles ) {
for ( final File outputFile : walkerOutputFiles ) {
new File(outputFile.getAbsolutePath() + ".pdf").deleteOnExit();
}
}
}

15
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
View File

@ -319,9 +319,12 @@ public class WalkerTest extends BaseTest {
String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);
File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext);
// Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file:
new File(fl.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(fl.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION).deleteOnExit();
// Cleanup any potential shadow BCFs on exit too, if we're generating them
if ( spec.includeShadowBCF && GENERATE_SHADOW_BCF ) {
final File potentalShadowBCFFile = BCF2Utils.shadowBCF(fl);
potentalShadowBCFFile.deleteOnExit();
new File(potentalShadowBCFFile.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
}
tmpFiles.add(fl);
}
@ -336,10 +339,12 @@ public class WalkerTest extends BaseTest {
List<String> md5s = new LinkedList<String>();
md5s.addAll(spec.md5s);
// check to see if they included any auxillary files, if so add them to the list
// check to see if they included any auxillary files, if so add them to the list and set them to be deleted on exit
for (String md5 : spec.auxillaryFiles.keySet()) {
md5s.add(md5);
tmpFiles.add(spec.auxillaryFiles.get(md5));
final File auxFile = spec.auxillaryFiles.get(md5);
auxFile.deleteOnExit();
tmpFiles.add(auxFile);
}
return executeTest(name, spec.getTestClassName(), spec.getOutputFileLocation(), md5s, tmpFiles, args, null);
}

9
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
View File

@ -25,6 +25,8 @@
package org.broadinstitute.gatk.utils;
import htsjdk.tribble.Tribble;
import htsjdk.tribble.util.TabixUtils;
import org.apache.log4j.AppenderSkeleton;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
@ -291,6 +293,13 @@ public abstract class BaseTest {
try {
File file = File.createTempFile(name, extension);
file.deleteOnExit();
// Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file:
new File(file.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(file.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(file.getAbsolutePath() + ".bai").deleteOnExit();
new File(file.getAbsolutePath().replaceAll(extension + "$", ".bai")).deleteOnExit();
return file;
} catch (IOException ex) {
throw new ReviewedGATKException("Cannot create temp file: " + ex.getMessage(), ex);