Remove jetty workaround for some tests.

broadinstitute · Feb 28, 2023 · 347f528 · 347f528
1 parent 188b680
commit 347f528
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Showing 6 changed files with 0 additions and 30 deletions.
diff --git 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/...a/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java b/...a/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/...te/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java b/...te/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<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

diff --git a/...ols/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java b/...ols/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<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

diff --git a/...ute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java b/...ute/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<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

diff --git a/.../tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java b/.../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<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );