Build and test on Java 11

.travis.yml

@@ -9,16 +9,16 @@ jdk:
 - openjdk8
 env:
   matrix:
-  - TEST_TYPE=cloud UPLOAD=true TESTS_REQUIRE_GCLOUD=true
-  - TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - TEST_TYPE=variantcalling TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - TEST_TYPE=python TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - RUN_CNV_GERMLINE_COHORT_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - RUN_CNV_GERMLINE_CASE_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - RUN_CNV_SOMATIC_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - RUN_M2_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - RUN_CNN_WDL=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 TEST_TYPE=cloud UPLOAD=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
+  - SCALA_VERSION=2.11 TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
+  - SCALA_VERSION=2.11 TEST_TYPE=variantcalling TEST_DOCKER=true TEST_VERBOSITY=minimal
+  - SCALA_VERSION=2.11 TEST_TYPE=python TEST_DOCKER=true TEST_VERBOSITY=minimal
+  - SCALA_VERSION=2.11 RUN_CNV_GERMLINE_COHORT_WDL=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 RUN_CNV_GERMLINE_CASE_WDL=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 RUN_CNV_SOMATIC_WDL=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 RUN_M2_WDL=true TESTS_REQUIRE_GCLOUD=true
+  - SCALA_VERSION=2.11 RUN_CNN_WDL=true TESTS_REQUIRE_GCLOUD=true
   global:
   #gradle needs this
   - TERM=dumb
@@ -47,7 +47,11 @@ matrix:
   fast_finish: true
   include:
      - jdk: oraclejdk8
-       env: TEST_TYPE=integration TEST_VERBOSITY=minimal TEST_REQUIRE_GCLOUD=true
+       env: SCALA_VERSION=2.11 TEST_TYPE=integration TEST_VERBOSITY=minimal TEST_REQUIRE_GCLOUD=true
+     - jdk: openjdk11
+       env: SCALA_VERSION=2.12 TEST_TYPE=integration TEST_VERBOSITY=minimal
+     - jdk: openjdk11
+       env: SCALA_VERSION=2.12 TEST_TYPE=unit TEST_VERBOSITY=minimal
 before_cache:
   - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
   - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
@@ -162,13 +166,13 @@ script:
     sudo mkdir -p build/reports/;
     sudo chmod -R a+w build/reports/;
     cp scripts/docker/dockertest.gradle .;
-    sudo docker run -v $(pwd):/gatkCloneMountPoint:cached -v $(pwd)/testJars:/jars:cached --rm -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh;
+    sudo docker run -v $(pwd):/gatkCloneMountPoint:cached -v $(pwd)/testJars:/jars:cached --rm -e "scala.version=${SCALA_VERSION}" -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh;
     TEST_EXIT_VALUE=$?;
     sudo mkdir build/reports/tests/test && sudo cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test && sudo rm -r build/reports/tests/testOnPackagedReleaseJar;
     $( exit ${TEST_EXIT_VALUE} );
   else
     ./gatk PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam;
-    travis_wait 50 ./gradlew jacocoTestReport;
+    travis_wait 50 ./gradlew -Dscala.version=${SCALA_VERSION} jacocoTestReport;
   fi;
 # This creates and uploads the gatk zip file to the nightly build bucket, only keeping the 10 newest entries
 # This also constructs the Docker image and uploads it to https://cloud.docker.com/u/broadinstitute/repository/docker/broadinstitute/gatk-nightly/

build.gradle

@@ -57,11 +57,11 @@ repositories {
     mavenLocal()
 }
 
-final requiredJavaVersion = "8"
 final htsjdkVersion = System.getProperty('htsjdk.version','2.20.3')
 final picardVersion = System.getProperty('picard.version','2.20.7')
 final barclayVersion = System.getProperty('barclay.version','2.1.0')
 final sparkVersion = System.getProperty('spark.version', '2.4.3')
+final scalaVersion = System.getProperty('scala.version', '2.11')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
 final disqVersion = System.getProperty('disq.version','0.3.3')
 final genomicsdbVersion = System.getProperty('genomicsdb.version','1.1.2')
@@ -131,15 +131,23 @@ def looksLikeWereInAGitRepository(){
     file(".git").isDirectory() || (file(".git").exists() && file(".git").text.startsWith("gitdir"))
 }
 
-// Ensure that we have the right JDK version, a clone of the git repository, and resolve any required git-lfs
+// Ensure that we have a clone of the git repository, and resolve any required git-lfs
 // resource files that are needed to run the build but are still lfs stub files.
-def ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequisitesMessage) {
-    // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
-    if (ToolProvider.getSystemToolClassLoader() == null) {
+def ensureBuildPrerequisites(largeResourcesFolder, buildPrerequisitesMessage) {
+    if (!JavaVersion.current().isJava8Compatible()) {
+        throw new GradleException(
+                "Java 8 or later is required to build GATK, but ${JavaVersion.current()} was found. "
+                        + "$buildPrerequisitesMessage")
+    }
+    // Make sure we can get a ToolProvider class loader (for Java 8). If not we may have just a JRE.
+    if (JavaVersion.current().isJava8() && ToolProvider.getSystemToolClassLoader() == null) {
         throw new GradleException(
                 "The ClassLoader obtained from the Java ToolProvider is null. "
                 + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
     }
+    if (!JavaVersion.current().isJava8() && !JavaVersion.current().isJava11()) {
+        println("Warning: using Java ${JavaVersion.current()} but only Java 8 and Java 11 have been tested.")
+    }
     if (!looksLikeWereInAGitRepository()) {
         throw new GradleException("This doesn't appear to be a git folder. " +
                 "The GATK Github repository must be cloned using \"git clone\" to run the build. " +
@@ -150,7 +158,7 @@ def ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPre
     resolveLargeResourceStubFiles(largeResourcesFolder, buildPrerequisitesMessage)
 }
 
-ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequisitesMessage)
+ensureBuildPrerequisites(largeResourcesFolder, buildPrerequisitesMessage)
 
 configurations.all {
     resolutionStrategy {
@@ -221,7 +229,7 @@ configurations {
 // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
 // test execution, and gatkDoc generation, but we don't want them as part of the runtime
 // classpath and we don't want to redistribute them in the uber jar.
-final javadocJDKFiles = files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())
+final javadocJDKFiles = ToolProvider.getSystemToolClassLoader() == null ? files([]) : files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())
 
 dependencies {
     // javadoc utilities; compile/test only to prevent redistribution of sdk jars
@@ -280,15 +288,16 @@ dependencies {
     compile ('org.ojalgo:ojalgo-commons-math3:1.0.0') {
         exclude group: 'org.apache.commons'
     }
-    compile ('org.apache.spark:spark-mllib_2.11:' + sparkVersion) {
+    compile ('org.apache.spark:spark-mllib_' + scalaVersion + ':' + sparkVersion) {
         // JUL is used by Google Dataflow as the backend logger, so exclude jul-to-slf4j to avoid a loop
         exclude module: 'jul-to-slf4j'
         exclude module: 'javax.servlet'
         exclude module: 'servlet-api'
     }
+    compile 'com.thoughtworks.paranamer:paranamer:2.8'
 
     compile 'org.bdgenomics.bdg-formats:bdg-formats:0.5.0'
-    compile('org.bdgenomics.adam:adam-core-spark2_2.11:0.20.0') {
+    compile('org.bdgenomics.adam:adam-core-spark2_' + scalaVersion + ':0.28.0') {
         exclude group: 'org.slf4j'
         exclude group: 'org.apache.hadoop'
         exclude group: 'org.scala-lang'
@@ -349,7 +358,7 @@ dependencies {
 
     testCompile sourceSets.testUtils.output
 
-    testCompile "org.mockito:mockito-core:2.10.0"
+    testCompile "org.mockito:mockito-core:2.28.2"
     testCompile "com.google.jimfs:jimfs:1.1"
 }
 

src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java

@@ -271,8 +271,8 @@ public FeatureDataSource(final FeatureInput<T> featureInput, final int queryLook
             Utils.nonNull(genomicsDBOptions, "GenomicsDBOptions must not be null. Calling tool may not read from a GenomicsDB data source.");
         }
 
-        final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
-        final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Function.identity());
+        final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Utils.identityFunction());
+        final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Utils.identityFunction());
 
         // Create a feature reader without requiring an index.  We will require one ourselves as soon as
         // a query by interval is attempted.
@@ -371,7 +371,7 @@ private static <T extends Feature> FeatureReader<T> getFeatureReader(final Featu
             if (BucketUtils.isCloudStorageUrl(featureInput)) {
                 return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, cloudWrapper, cloudIndexWrapper);
             } else {
-                return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, Function.identity(), Function.identity());
+                return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, Utils.identityFunction(), Utils.identityFunction());
             }
         } catch (final TribbleException e) {
             throw new GATKException("Error initializing feature reader for path " + featureInput.getFeaturePath(), e);

src/main/java/org/broadinstitute/hellbender/engine/spark/AssemblyRegionWalkerSpark.java

@@ -23,6 +23,7 @@
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -90,7 +91,7 @@ protected Broadcast<Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSu
     }
 
     private static Broadcast<Supplier<AssemblyRegionEvaluator>> assemblyRegionEvaluatorSupplierBroadcastFunction(final JavaSparkContext ctx, final AssemblyRegionEvaluator assemblyRegionEvaluator) {
-        Supplier<AssemblyRegionEvaluator> supplier = () -> assemblyRegionEvaluator;
+        Supplier<AssemblyRegionEvaluator> supplier = (Supplier<AssemblyRegionEvaluator> & Serializable) (() -> assemblyRegionEvaluator);
         return ctx.broadcast(supplier);
     }
 

src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSink.java

@@ -13,7 +13,7 @@
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.broadcast.Broadcast;
-import org.bdgenomics.adam.models.RecordGroupDictionary;
+import org.bdgenomics.adam.models.ReadGroupDictionary;
 import org.bdgenomics.adam.models.SequenceDictionary;
 import org.bdgenomics.formats.avro.AlignmentRecord;
 import org.broadinstitute.hellbender.exceptions.GATKException;
@@ -157,7 +157,7 @@ private static void writeReadsADAM(
             final JavaSparkContext ctx, final String outputFile, final JavaRDD<SAMRecord> reads,
             final SAMFileHeader header) throws IOException {
         final SequenceDictionary seqDict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
-        final RecordGroupDictionary readGroups = RecordGroupDictionary.fromSAMHeader(header);
+        final ReadGroupDictionary readGroups = ReadGroupDictionary.fromSAMHeader(header);
         final JavaPairRDD<Void, AlignmentRecord> rddAlignmentRecords =
                 reads.map(read -> {
                     read.setHeaderStrict(header);

src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceTwoBitSparkSource.java

@@ -6,15 +6,19 @@
 import org.bdgenomics.adam.models.ReferenceRegion;
 import org.bdgenomics.adam.util.TwoBitFile;
 import org.bdgenomics.adam.util.TwoBitRecord;
+import org.bdgenomics.formats.avro.Strand;
 import org.bdgenomics.utils.io.ByteAccess;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.reference.ReferenceBases;
+import scala.Tuple2;
 import scala.collection.JavaConversions;
+import scala.collection.immutable.IndexedSeq;
 
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -39,7 +43,10 @@ public ReferenceTwoBitSparkSource( String referenceURL) throws IOException {
         byte[] bytes = ByteStreams.toByteArray(BucketUtils.openFile(this.referenceURL));
         ByteAccess byteAccess = new DirectFullByteArrayByteAccess(bytes);
         this.twoBitFile = new TwoBitFile(byteAccess);
-        this.twoBitSeqEntries = JavaConversions.mapAsJavaMap(twoBitFile.seqRecords());
+        this.twoBitSeqEntries = new LinkedHashMap<>();
+        for (Tuple2<String, TwoBitRecord> pair: JavaConversions.seqAsJavaList(twoBitFile.seqRecords())) {
+            twoBitSeqEntries.put(pair._1, pair._2);
+        }
     }
 
     /**
@@ -74,7 +81,7 @@ private static ReferenceRegion simpleIntervalToReferenceRegion(SimpleInterval in
         String contig = interval.getContig();
         long start = interval.getGA4GHStart();
         long end = interval.getGA4GHEnd();
-        return new ReferenceRegion(contig, start, end, null);
+        return new ReferenceRegion(contig, start, end, Strand.UNKNOWN);
     }
 
     private SimpleInterval cropIntervalAtContigEnd( final SimpleInterval interval ) {

src/main/java/org/broadinstitute/hellbender/utils/Utils.java

@@ -19,6 +19,7 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.Serializable;
 import java.lang.reflect.Array;
 import java.math.BigInteger;
 import java.nio.file.Files;
@@ -1102,6 +1103,18 @@ public static <T> Stream<T> stream(final Iterator<T> iterator) {
         return stream(() -> iterator);
     }
 
+    /**
+     * Returns a function that always returns its input argument. Unlike {@link Function#identity()} the returned
+     * function is also serializable.
+     *
+     * @param <T> the type of the input and output objects to the function
+     * @return a function that always returns its input argument
+     */
+    @SuppressWarnings("unchecked")
+    public static <T> Function<T, T> identityFunction() {
+        return (Function & Serializable) t -> t;
+    }
+
     /**
      * Like Guava's {@link Iterators#transform(Iterator, com.google.common.base.Function)}, but runs a fixed number
      * ({@code numThreads}) of transformations in parallel, while maintaining ordering of the output iterator.

src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java

@@ -216,6 +216,7 @@ public static File writeTempResourceFromPath(final String resourcePath, final Cl
      * @param resource Embedded resource.
      * @param file File path to write.
      */
+    @SuppressWarnings("deprecation")
     public static void writeResource(Resource resource, File file) {
         String path = resource.getPath();
         InputStream inputStream = resource.getResourceContentsAsStream();

src/main/java/org/broadinstitute/hellbender/utils/read/BDGAlignmentRecordToGATKReadAdapter.java

@@ -3,8 +3,7 @@
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
 import org.bdgenomics.adam.converters.AlignmentRecordConverter;
-import org.bdgenomics.adam.models.RecordGroupDictionary;
-import org.bdgenomics.adam.models.SAMFileHeaderWritable;
+import org.bdgenomics.adam.models.ReadGroupDictionary;
 import org.bdgenomics.formats.avro.AlignmentRecord;
 
 /**
@@ -30,8 +29,8 @@ public final class BDGAlignmentRecordToGATKReadAdapter extends SAMRecordToGATKRe
     private final AlignmentRecord alignmentRecord;
 
     public BDGAlignmentRecordToGATKReadAdapter(final AlignmentRecord alignmentRecord, final SAMFileHeader header) {
-        super(new AlignmentRecordConverter().convert(alignmentRecord, SAMFileHeaderWritable.apply(header),
-                RecordGroupDictionary.fromSAMHeader(header)));
+        super(new AlignmentRecordConverter().convert(alignmentRecord, header,
+                ReadGroupDictionary.fromSAMHeader(header)));
         this.alignmentRecord = alignmentRecord;
     }
 

src/main/java/org/broadinstitute/hellbender/utils/read/GATKReadToBDGAlignmentRecordConverter.java

@@ -5,7 +5,7 @@
 import org.bdgenomics.formats.avro.AlignmentRecord;
 import org.bdgenomics.adam.converters.SAMRecordConverter;
 import org.bdgenomics.adam.models.SequenceDictionary;
-import org.bdgenomics.adam.models.RecordGroupDictionary;
+import org.bdgenomics.adam.models.ReadGroupDictionary;
 
 /**
  * Converts a GATKRead to a BDG AlignmentRecord
@@ -15,27 +15,27 @@ public class GATKReadToBDGAlignmentRecordConverter {
 
     private SAMFileHeader header;
     private SequenceDictionary dict;
-    private RecordGroupDictionary readGroups;
+    private ReadGroupDictionary readGroups;
 
     public GATKReadToBDGAlignmentRecordConverter(SAMFileHeader header) {
         this.header = header;
         this.dict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
-        this.readGroups = RecordGroupDictionary.fromSAMHeader(header);
+        this.readGroups = ReadGroupDictionary.fromSAMHeader(header);
     }
 
     public static AlignmentRecord convert( final GATKRead gatkRead, final SAMFileHeader header ) {
         SequenceDictionary dict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
-        RecordGroupDictionary readGroups = RecordGroupDictionary.fromSAMHeader(header);
+        ReadGroupDictionary readGroups = ReadGroupDictionary.fromSAMHeader(header);
         return GATKReadToBDGAlignmentRecordConverter.convert(gatkRead, header, dict, readGroups);
     }
 
     public static AlignmentRecord convert(
-            final GATKRead gatkRead, final SAMFileHeader header, final SequenceDictionary dict, final RecordGroupDictionary readGroups ) {
+            final GATKRead gatkRead, final SAMFileHeader header, final SequenceDictionary dict, final ReadGroupDictionary readGroups ) {
         return converter.convert(gatkRead.convertToSAMRecord(header));
     }
 
     public static AlignmentRecord convert(
-            final SAMRecord sam, final SequenceDictionary dict, final RecordGroupDictionary readGroups ) {
+            final SAMRecord sam, final SequenceDictionary dict, final ReadGroupDictionary readGroups ) {
         return converter.convert(sam);
     }
 }

src/main/java/org/broadinstitute/hellbender/utils/runtime/CapturedStreamOutput.java

@@ -92,6 +92,7 @@ public boolean isBufferTruncated() {
      *
      * @throws IOException When unable to read or write.
      */
+    @SuppressWarnings("deprecation")
     public void read() throws IOException {
         int readCount = 0;
         try {

src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessController.java

@@ -71,6 +71,7 @@ public static int exec(String[] command) {
      * @param settings Settings to be run.
      * @return The output of the command.
      */
+    @SuppressWarnings("deprecation")
     public ProcessOutput exec(ProcessSettings settings) {
         StreamOutput stdout;
         StreamOutput stderr;
@@ -161,6 +162,7 @@ public ProcessOutput exec(ProcessSettings settings) {
      * TODO: Try to use NIO to interrupt streams.
      */
     @Override
+    @SuppressWarnings("deprecation")
     protected void tryCleanShutdown() {
         destroyed = true;
 

src/main/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessController.java

@@ -349,6 +349,7 @@ private void startListeners() {
      * NOTE: capture threads may block on read.
      */
     @Override
+    @SuppressWarnings("deprecation")
     protected void tryCleanShutdown() {
         if (stdErrFuture != null && !stdErrFuture.isDone()) {
             boolean isCancelled = stdErrFuture.cancel(true);