diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java index 656000c25d9..efc73ce43b7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java @@ -116,11 +116,6 @@ public void testInsertLengthPileup(boolean useShuffle) throws Exception { @Test(dataProvider = "shuffle") public void testFeaturesPileupHdfs(boolean useShuffle) throws Exception { - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> { final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster); final Path vcfPath = new Path(workingDirectory, "dbsnp_138.b37.20.21.vcf"); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java index 59c4b7449f7..d4e96e3ed56 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java @@ -80,11 +80,6 @@ public void testReadAndWriteCRAMAndReferenceOnHDFS() throws Exception { final GATKPath testRefDict = new GATKPath(getTestFile("count_reads.dict").getAbsolutePath()); final GATKPath testRefIndex = new GATKPath(getTestFile("count_reads.fasta.fai").getAbsolutePath()); - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> { final org.apache.hadoop.fs.Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java index dae5597491f..1f1a5b67c9b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java @@ -71,11 +71,6 @@ public void testRunLocal(final CpxVariantReInterpreterSparkIntegrationTestArgs p @Test(groups = "sv", dataProvider = "forCpxVariantReInterpreterSparkIntegrationTest") public void testRunHDFS(final CpxVariantReInterpreterSparkIntegrationTestArgs params) throws Exception { - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> { final List argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() ); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java index a3dc96fdb9a..4c8c44daa0c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java @@ -68,11 +68,6 @@ public void testDiscoverVariantsRunnableLocal(final DiscoverVariantsFromContigAl @Test(dataProvider = "discoverVariantsFromContigAlignmentsSparkIntegrationTest", groups = "sv") public void testDiscoverVariantsRunnableMiniCluster(final DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTestArgs params) throws Exception { - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> { final List argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() ); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java index 2730d69b927..d814c50a3d7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java @@ -115,11 +115,6 @@ public void testFindBreakpointRunnableLocal(final FindBreakpointEvidenceSparkInt @Test(dataProvider = "findBreakpointEvidenceSparkIntegrationTest", groups = "sv") public void testFindBreakpointRunnableMiniCluster(final FindBreakpointEvidenceSparkIntegrationTestArgs params) throws Exception { - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> { final List argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() ); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java index 649b9206b92..7b7024d3403 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java @@ -116,11 +116,6 @@ public void testSVDiscoverPipelineRunnableLocal(final StructuralVariationDiscove @Test(dataProvider = "svDiscoverPipelineSparkIntegrationTest", groups = "sv") public void testSVDiscoverPipelineRunnableMiniCluster(final StructuralVariationDiscoveryPipelineSparkIntegrationTestArgs params) throws Exception { - if (isGATKDockerContainer()) { - // see https://github.com/eclipse/jetty.project/issues/8549 - // for the docker tests, the test dependencies are in a separate jar - throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)"); - } MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> { final List argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );