Use Java 11.0.11+9 for testing, upgrade hadoop to v3.3.1. (#8102)

* Upgrade hadoop to 3.3.1. 
* Pin our github actions Java 11 jobs to Java version 11.0.11+9.  
This is necessary because of 2 bugs that appear when moving to java 11.0.16.1
This first is an issue with Jetty which crashes when the java version has more than 2 periods in it, upgrading hadoop updates jetty which should fix that.
The second is a numerical issue where the output of ModelSegments changes on the new java version which is not yet understood.

Co-authored-by: Louis Bergelson <[email protected]>

.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

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')

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));
     }
 

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

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() {

src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java

@@ -640,7 +640,7 @@ public static List<Annotation> getAllAnnotations() {
                 Collections.emptySet());
         List<String> 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);
     }