adding SparkTestUtils.roundTripThroughJavaSerialization (#5257)

* adding in a new SparkTestUtils.roundTripThroughJavaSerialization method
* updating existing code to use the new method

Author: lbergelson

src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java

@@ -6,6 +6,7 @@
 import htsjdk.variant.vcf.VCFCodec;
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.testutils.SparkTestUtils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -210,22 +211,9 @@ public void testFeatureCodecCache() {
     @SuppressWarnings("unchecked")
     @Test
     public void testFeatureCodecCacheSerialization() throws IOException, ClassNotFoundException {
-        FeatureInput<VariantContext> featureInput = getVariantFeatureInputWithCachedCodec();
-
-        // serialize
-        byte[] serializedFeatureInput;
-        try (final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-             final ObjectOutputStream oos = new ObjectOutputStream(bos)) {
-            oos.writeObject(featureInput);
-            serializedFeatureInput = bos.toByteArray();
-        }
-        Assert.assertNotNull(serializedFeatureInput);
-
-        // deserialize
-        FeatureInput<VariantContext> roundTrippedFeatureInput;
-        try (final ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(serializedFeatureInput))) {
-            roundTrippedFeatureInput = (FeatureInput<VariantContext>) ois.readObject();
-        }
+        final FeatureInput<VariantContext>featureInput = getVariantFeatureInputWithCachedCodec();
+
+        final FeatureInput<VariantContext> roundTrippedFeatureInput = SparkTestUtils.roundTripThroughJavaSerialization(featureInput);
         Assert.assertNotNull(roundTrippedFeatureInput);
 
         // we expect to lose the cached feature codec class on serialization, but retain the feature path

src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReferenceFileSparkSourceUnitTest.java

@@ -2,14 +2,15 @@
 
 import com.google.common.jimfs.Configuration;
 import com.google.common.jimfs.Jimfs;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.testutils.SparkTestUtils;
+import org.testng.annotations.Test;
+
 import java.io.*;
 import java.nio.file.FileSystem;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import org.broadinstitute.hellbender.GATKBaseTest;
-import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource;
-import org.broadinstitute.hellbender.exceptions.UserException;
-import org.testng.annotations.Test;
 
 public class ReferenceFileSparkSourceUnitTest extends GATKBaseTest {
 
@@ -42,13 +43,9 @@ public void testDatasourcesReferenceSerializes() throws IOException, ClassNotFou
 
         final ReferenceFileSparkSource referenceFileSource = new ReferenceFileSparkSource(refPath);
 
-        // Can we serialize it?
-        final ByteArrayOutputStream baos = new ByteArrayOutputStream();
-        ObjectOutputStream os = new ObjectOutputStream(baos);
-        os.writeObject(referenceFileSource);
+        //can we serialize it?
+        ReferenceFileSparkSource otherSide = SparkTestUtils.roundTripThroughJavaSerialization(referenceFileSource);
 
-        ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(baos.toByteArray()));
-        ReferenceFileSparkSource otherSide = (ReferenceFileSparkSource)is.readObject();
         // After deserialization, will it crash?
         otherSide.getReferenceSequenceDictionary(null);
 

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

@@ -8,6 +8,8 @@
 import scala.reflect.ClassTag;
 import scala.reflect.ClassTag$;
 
+import java.io.*;
+
 public final class SparkTestUtils {
     private SparkTestUtils() {}
 
@@ -29,4 +31,28 @@ public static <T> T roundTripInKryo(final T input, final Class<?> inputClazz, fi
         final ClassTag<T> tag = ClassTag$.MODULE$.apply(inputClazz);
         return sparkSerializer.deserialize(sparkSerializer.serialize(input, tag), tag);
     }
+
+    /**
+     * Takes an input object and returns the value of the object after it has been serialized and then deserialized
+     * using Java's built in serialization.
+     *
+     * @param input an object to be serialized.  Never {@code null}
+     * @return serialized and deserialized instance of input, may throw if serialization fails
+     */
+    @SuppressWarnings("unchecked")
+    public static <T> T roundTripThroughJavaSerialization(T input) throws IOException, ClassNotFoundException {
+        Utils.nonNull(input);
+        final byte[] serializedBytes;
+        try(final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+            final ObjectOutputStream out = new ObjectOutputStream(baos)){
+            out.writeObject(input);
+            serializedBytes = baos.toByteArray();
+        }
+
+        try (final ByteArrayInputStream bais = new ByteArrayInputStream(serializedBytes);
+             final ObjectInputStream in = new ObjectInputStream(bais)){
+
+            return (T) in.readObject();
+        }
+    }
 }