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Replace File.createTempFile with IOUtils.createTempFile (#6780)
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* This ensure that temp files are deleted on shutdown
* Fixes #6771
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@lbergelson
lbergelson committed Dec 24, 2022
1 parent 16fc4f1 commit ba2b5b3
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Showing 31 changed files with 148 additions and 157 deletions.
3 changes: 1 addition & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
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Expand Up @@ -573,8 +573,7 @@ else if (getIntervalsFromExistingWorkspace){
IOUtils.assertPathsAreReadable(vcfHeader);
final String header = GenomicsDBUtils.readEntireFile(vcfHeader);
try {
File tempHeader = File.createTempFile("tempheader", ".vcf");
tempHeader.deleteOnExit();
File tempHeader = IOUtils.createTempFile("tempheader", ".vcf");
Files.write(tempHeader.toPath(), header.getBytes(StandardCharsets.UTF_8));
mergedHeaderSequenceDictionary = VCFFileReader.getSequenceDictionary(tempHeader);
} catch (final IOException e) {
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4 changes: 2 additions & 2 deletions ...va/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleSequenceReferenceAligner.java
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Expand Up @@ -9,6 +9,7 @@
import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner;
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
import org.broadinstitute.hellbender.utils.io.IOUtils;

import java.io.File;
import java.io.IOException;
Expand Down Expand Up @@ -64,8 +65,7 @@ public SingleSequenceReferenceAligner(final String name, final byte[] bases,
this.alignmentFilter = Utils.nonNull(alignmentFilter);
Utils.validate(bases.length > 0, "the reference contig bases sequence must have at least one base");
try {
final File fasta = File.createTempFile("ssvh-temp", ".fasta");
fasta.deleteOnExit();
final File fasta = IOUtils.createTempFile("ssvh-temp", ".fasta");
image = new File(fasta.getParentFile(), fasta.getName().replace(".fasta", ".img"));
image.deleteOnExit();
FastaReferenceWriter.writeSingleSequenceReference(fasta.toPath(), false, false, name, null, bases);
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12 changes: 3 additions & 9 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/AlleleFrequencyQC.java
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Expand Up @@ -6,6 +6,7 @@
import org.broadinstitute.hellbender.metrics.MetricsUtils;
import org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric;
import org.broadinstitute.hellbender.utils.R.RScriptExecutor;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.io.Resource;
import org.broadinstitute.hellbender.utils.report.GATKReport;
import org.broadinstitute.hellbender.utils.report.GATKReportTable;
Expand Down Expand Up @@ -59,15 +60,8 @@ public void onTraversalStart() {
metricOutput = outFile; // output file for summary metrics

// have to set the output file for variant eval; if not given a debug file to return the variant eval results
// from, this will just be a temporary file that wil lbe deleted after the tool runs
try {
outFile = debugFile == null ? File.createTempFile("variant_eval" ,".txt") : debugFile;
} catch (IOException e) {
throw new RuntimeException("Trouble creating temporary variant eval file", e);
}
if (debugFile == null) {
outFile.deleteOnExit();
}
// from, this will just be a temporary file that will be deleted after the tool runs
outFile = debugFile == null ? IOUtils.createTempFile("variant_eval" ,".txt") : debugFile;
sample = getHeaderForVariants().getOtherHeaderLine("sampleAlias").getValue();
super.onTraversalStart();
}
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/io/Resource.java
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Expand Up @@ -83,7 +83,7 @@ public InputStream getResourceContentsAsStream() {
* @throws IOException
*/
public static File getResourceContentsAsFile(final String resourcePath) throws IOException {
final File tmpResourceFile = File.createTempFile("tmp_read_resource_", ".config");
final File tmpResourceFile = IOUtils.createTempFile("tmp_read_resource_", ".config");
// use current classloader rather than system classloader to support dynamic environments like Spark executors
final InputStream resourceAsStream = Resource.class.getClassLoader().getResourceAsStream(resourcePath);

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3 changes: 1 addition & 2 deletions ...ava/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java
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Expand Up @@ -206,8 +206,7 @@ private List<VariantContext> readVariants(String vcf) throws IOException {
File actualVcf;
// work around TribbleIndexedFeatureReader not reading header from .bgz files
if (vcf.endsWith(".bgz")) {
actualVcf = File.createTempFile(vcf, ".gz");
actualVcf.deleteOnExit();
actualVcf = IOUtils.createTempFile(vcf, ".gz");
Files.copy(new File(vcf), actualVcf);
} else {
actualVcf = new File(vcf);
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55 changes: 27 additions & 28 deletions ...institute/hellbender/tools/copynumber/utils/CombineSegmentBreakpointsIntegrationTest.java
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Expand Up @@ -10,12 +10,12 @@
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
Expand Down Expand Up @@ -44,9 +44,9 @@ public final class CombineSegmentBreakpointsIntegrationTest extends CommandLineP
private static final String SEGMENT_CALL_2 = "Segment_Call";

@Test
public void testRunWithExactSegments() throws IOException {
public void testRunWithExactSegments() {
// Segment intervals are the same in the input files. Therefore, the union should only generate more columns.
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
final Set<String> columnSet = Sets.newHashSet("MEAN_LOG2_COPY_RATIO", "CALL", "Segment_Mean", "Segment_Call");
final List<String> arguments = new ArrayList<>();
arguments.add("--" + CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME);
Expand All @@ -71,13 +71,13 @@ public void testRunWithExactSegments() throws IOException {
Assert.assertEquals(regions.size(), 4);
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().size() == columnSet.size()));
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().keySet().containsAll(columnSet)));
Assert.assertTrue(regions.getRecords().stream().noneMatch(r -> r.getAnnotations().values().contains("")));
Assert.assertTrue(regions.getRecords().stream().noneMatch(r -> r.getAnnotations().containsValue("")));
}

@Test
public void testRunWithExactSameFiles() throws IOException {
public void testRunWithExactSameFiles() {
// Input files are exactly the same. Therefore, the union should only generate more columns.
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
final List<String> arguments = new ArrayList<>();
arguments.add("-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME);
arguments.add(REFERENCE_FILE);
Expand All @@ -100,14 +100,14 @@ public void testRunWithExactSameFiles() throws IOException {
Assert.assertEquals(regions.size(), 4);
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().size() == gtColumnSet.size()));
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().keySet().containsAll(gtColumnSet)));
Assert.assertTrue(regions.getRecords().stream().noneMatch(r -> r.getAnnotations().values().contains("")));
Assert.assertTrue(regions.getRecords().stream().noneMatch(r -> r.getAnnotations().containsValue("")));
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().get("MEAN_LOG2_COPY_RATIO_1").equals(r.getAnnotations().get("MEAN_LOG2_COPY_RATIO_2"))));
Assert.assertTrue(regions.getRecords().stream().allMatch(r -> r.getAnnotations().get("CALL_1").equals(r.getAnnotations().get("CALL_2"))));
}
@Test
public void testRunWithoutExactOverlaps() throws IOException {
public void testRunWithoutExactOverlaps() {
// This test is a bit more like the real world
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
final List<String> arguments = new ArrayList<>();
arguments.add("-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME);
arguments.add(REFERENCE_FILE);
Expand Down Expand Up @@ -135,9 +135,9 @@ public void testRunWithoutExactOverlaps() throws IOException {
}

@Test(expectedExceptions = UserException.BadInput.class)
public void testFailureIfNotAllColsOfInterestExist() throws IOException {
public void testFailureIfNotAllColsOfInterestExist() {
// This test is a bit more like the real world
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
final List<String> arguments = new ArrayList<>();
arguments.add("-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME);
arguments.add(REFERENCE_FILE);
Expand Down Expand Up @@ -187,11 +187,11 @@ private void assertUnionedSegFiles(final String segmentCall1, final String segme
}

@Test
public void testRunWithoutExactOverlapsAndLabels() throws IOException {
public void testRunWithoutExactOverlapsAndLabels() {
final String TEST = "test";
final String GT = "gt";
// This test is a bit more like the real world
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
final List<String> arguments = new ArrayList<>();
arguments.add("-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME);
arguments.add(REFERENCE_FILE);
Expand Down Expand Up @@ -224,18 +224,17 @@ public void testRunWithoutExactOverlapsAndLabels() throws IOException {
}

@Test(expectedExceptions = UserException.class)
public void testErrorWithoutSamHeadersAndNoReference() throws IOException {

final File outputFile = File.createTempFile("combineseg_", ".seg");
public void testErrorWithoutSamHeadersAndNoReference() {
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
runCombineSegmentBreakpoints(GROUND_TRUTH_SEGMENTS_FILE_NO_SAMHEADER, INPUT_SEGMENTS_FILE_NO_SAMHEADER,
outputFile, null);
}

@Test
public void testWithoutSamHeaderAndWithReference() throws IOException {
public void testWithoutSamHeaderAndWithReference() {

// This test is a bit more like the real world
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
runCombineSegmentBreakpoints(GROUND_TRUTH_SEGMENTS_FILE_NO_SAMHEADER, INPUT_SEGMENTS_FILE_NO_SAMHEADER, outputFile, REFERENCE_FILE);

Assert.assertTrue(outputFile.exists());
Expand All @@ -251,10 +250,10 @@ public void testWithoutSamHeaderAndWithReference() throws IOException {
}

@Test
public void testRunAndOneWithoutSamHeaderAndNoReference() throws IOException {
public void testRunAndOneWithoutSamHeaderAndNoReference() {

// This test is a bit more like the real world
final File outputFile = File.createTempFile("combineseg_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
runCombineSegmentBreakpoints(INPUT_SEGMENTS_FILE, GROUND_TRUTH_SEGMENTS_FILE_NO_SAMHEADER, outputFile, null);

Assert.assertTrue(outputFile.exists());
Expand All @@ -275,15 +274,15 @@ public void testRunAndOneWithoutSamHeaderAndNoReference() throws IOException {
}

@Test(expectedExceptions = UserException.BadInput.class)
public void testDisagreeingSamHeadersAndNoReference() throws IOException {
final File outputFile = File.createTempFile("combineseg_", ".seg");
public void testDisagreeingSamHeadersAndNoReference() {
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
runCombineSegmentBreakpoints(INPUT_SEGMENTS_FILE_ALT_SAMHEADER, GROUND_TRUTH_SEGMENTS_FILE, outputFile, null);
}

/** Reference is ignored if SAM Headers are specified. */
@Test(expectedExceptions = UserException.BadInput.class)
public void testDisagreeingSamHeadersAndReference() throws IOException {
final File outputFile = File.createTempFile("combineseg_", ".seg");
public void testDisagreeingSamHeadersAndReference() {
final File outputFile = IOUtils.createTempFile("combineseg_", ".seg");
runCombineSegmentBreakpoints(INPUT_SEGMENTS_FILE_ALT_SAMHEADER, GROUND_TRUTH_SEGMENTS_FILE, outputFile, REFERENCE_FILE);
}

Expand Down Expand Up @@ -324,8 +323,8 @@ public Object[][] provideOldFormats() {
}

@Test(dataProvider = "oldFormats")
public void testOldFormats(final String inputSegFile, final String oldFormatSegFile, final String meanColumn, final String callColumn, int numAnnotations) throws IOException {
final File outputFile = File.createTempFile("combineseg_old_formats_", ".seg");
public void testOldFormats(final String inputSegFile, final String oldFormatSegFile, final String meanColumn, final String callColumn, int numAnnotations) {
final File outputFile = IOUtils.createTempFile("combineseg_old_formats_", ".seg");
runCombineSegmentBreakpoints(inputSegFile, oldFormatSegFile, outputFile, REFERENCE_FILE, "MEAN_LOG2_COPY_RATIO", "CALL", meanColumn, callColumn);
final AnnotatedIntervalCollection regions = AnnotatedIntervalCollection.create(outputFile.toPath(),
Sets.newHashSet("MEAN_LOG2_COPY_RATIO", "CALL", meanColumn, callColumn));
Expand All @@ -335,9 +334,9 @@ public void testOldFormats(final String inputSegFile, final String oldFormatSegF
}

@Test(dataProvider = "realTsvFormats")
public void testRealFormats(final String segFile, final String externalSegFile, final String expectedResult, final String ... colsOfInterest) throws IOException {
public void testRealFormats(final String segFile, final String externalSegFile, final String expectedResult, final String ... colsOfInterest) {

final File outputFile = File.createTempFile("combineseg_realformats_gt_", ".seg");
final File outputFile = IOUtils.createTempFile("combineseg_realformats_gt_", ".seg");
runCombineSegmentBreakpoints(segFile, externalSegFile, outputFile, REFERENCE_FILE,
colsOfInterest);

Expand Down
6 changes: 3 additions & 3 deletions ...e/hellbender/tools/copynumber/utils/MergeAnnotatedRegionsByAnnotationIntegrationTest.java
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Expand Up @@ -4,6 +4,7 @@
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.testng.Assert;
import org.testng.annotations.Test;

Expand All @@ -23,11 +24,10 @@ public class MergeAnnotatedRegionsByAnnotationIntegrationTest extends CommandLin
* Very simple test, since this tool basically calls out to a class that does all the heavy lifting. Most testing
* is done in
* {@link org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtilsUnitTest}.
* @throws IOException
*/
@Test
public void testLegacySegFile() throws IOException {
final File outputFile = File.createTempFile("mergeannotatedregionsbyannotation", ".seg");
public void testLegacySegFile() {
final File outputFile = IOUtils.createTempFile("mergeannotatedregionsbyannotation", ".seg");
final String annotationToMatch = "Segment_Mean";
final List<String> arguments = new ArrayList<>();
arguments.add("--" + CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME);
Expand Down
8 changes: 3 additions & 5 deletions ...roadinstitute/hellbender/tools/copynumber/utils/MergeAnnotatedRegionsIntegrationTest.java
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Expand Up @@ -4,27 +4,25 @@
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.testutils.BaseTest;
import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval;
import org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.testutils.BaseTest;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.testng.Assert;
import org.testng.annotations.Test;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

public class MergeAnnotatedRegionsIntegrationTest extends CommandLineProgramTest {
private static final String TEST_SUB_DIR = publicTestDir + "org/broadinstitute/hellbender/tools/copynumber/utils/";
private static final String SIMPLE_TEST_FILE = TEST_SUB_DIR + "merge-annotated-regions-simple-test.seg";
private static final String REF = hg19MiniReference;

@Test
public void basicTest() throws IOException {
public void basicTest() {
// This test is a bit more like the real world
final File outputFile = BaseTest.createTempFile("mergeannotatedregions", ".seg");
final ArgumentsBuilder arguments = new ArgumentsBuilder();
Expand Down
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