From baf7aa8a5f7c9063b8b3a06afb3b9b9057715449 Mon Sep 17 00:00:00 2001 From: Chris Norman Date: Tue, 22 Nov 2022 17:15:19 -0500 Subject: [PATCH 1/3] Upgrade hadoop to 3.3.1. --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index e93d0adb272..f98654ba820 100644 --- a/build.gradle +++ b/build.gradle @@ -65,7 +65,7 @@ final picardVersion = System.getProperty('picard.version','2.27.5') final barclayVersion = System.getProperty('barclay.version','4.0.2') final sparkVersion = System.getProperty('spark.version', '2.4.5') final scalaVersion = System.getProperty('scala.version', '2.11') -final hadoopVersion = System.getProperty('hadoop.version', '3.2.1') +final hadoopVersion = System.getProperty('hadoop.version', '3.3.1') final disqVersion = System.getProperty('disq.version','0.3.6') final genomicsdbVersion = System.getProperty('genomicsdb.version','1.4.3') final bigQueryVersion = System.getProperty('bigQuery.version', '2.9.0') From b210bdb0f86f453abbc69c91e0542b2ec54f015a Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 23 Nov 2022 11:00:22 -0500 Subject: [PATCH 2/3] fix deprecated --- .../hellbender/tools/dragstr/CalibrateDragstrModel.java | 2 +- .../GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java | 2 +- .../cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java | 2 +- .../hellbender/testutils/VariantContextTestUtils.java | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java b/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java index 24bb5df696f..cd2b7cbb601 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java @@ -264,7 +264,7 @@ private void checkSequenceDictionaryCompatibility(final SAMSequenceDictionary re } private PrintWriter openSitesOutputWriter(final String sitesOutput) { - return sitesOutput == null ? new PrintWriter(new NullOutputStream()) + return sitesOutput == null ? new PrintWriter(NullOutputStream.NULL_OUTPUT_STREAM) : new PrintWriter(BucketUtils.createFile(sitesOutput)); } diff --git a/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java index e5ad4d233ac..d38369825fc 100644 --- a/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java @@ -36,7 +36,7 @@ public class GATKAnnotationPluginDescriptorUnitTest extends GATKBaseTest { // null print stream for the tests - private static final PrintStream nullMessageStream = new PrintStream(new NullOutputStream()); + private static final PrintStream nullMessageStream = new PrintStream(NullOutputStream.NULL_OUTPUT_STREAM); //====================================================================================================================== // Methods for computing individual annotations diff --git a/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java b/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java index 59269d0d440..22a83fd1f90 100644 --- a/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java +++ b/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java @@ -35,7 +35,7 @@ public class GATKReadFilterPluginDescriptorTest extends GATKBaseTest { // null print stream for the tests - private static final PrintStream nullMessageStream = new PrintStream(new NullOutputStream()); + private static final PrintStream nullMessageStream = new PrintStream(NullOutputStream.NULL_OUTPUT_STREAM); @DataProvider(name = "defaultFiltersForAllowedValues") public Object[][] defaultFiltersForAllowedValues() { diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java index 93918aa87f3..aa82d7e7b03 100644 --- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java @@ -640,7 +640,7 @@ public static List getAllAnnotations() { Collections.emptySet()); List args = new ArrayList<>(); args.add("--enable-all-annotations"); - clp.parseArguments(new PrintStream(new NullOutputStream()), args.toArray(new String[args.size()])); + clp.parseArguments(new PrintStream(NullOutputStream.NULL_OUTPUT_STREAM), args.toArray(new String[args.size()])); return instantiateAnnotations(clp); } From 54ee4d56f854ca0c6d0416eb99b670ee6b8d8366 Mon Sep 17 00:00:00 2001 From: Chris Norman Date: Mon, 28 Nov 2022 17:27:20 -0500 Subject: [PATCH 3/3] Pin our github actions Java 11 jobs to Java version 11.0.11+9. --- .github/workflows/gatk-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml index a908b98cd15..d6db7c385ac 100644 --- a/.github/workflows/gatk-tests.yml +++ b/.github/workflows/gatk-tests.yml @@ -73,12 +73,12 @@ jobs: needs: check-secrets strategy: matrix: - java: [ 8, 11 ] + java: [ 8, 11.0.11+9 ] experimental: [ false ] scalaVersion: [ 2.11, 2.12 ] testType: [ cloud, integration, unit ] exclude: - - java: 11 + - java: 11.0.11+9 scalaVersion: 2.11 - java: 8 scalaVersion: 2.12