Upgrade GCS Connector to 1.9.17

build.gradle

@@ -69,7 +69,7 @@ final testNGVersion = '6.11'
 // Using the shaded version to avoid conflicts between its protobuf dependency
 // and that of Hadoop/Spark (either the one we reference explicitly, or the one
 // provided by dataproc).
-final googleCloudNioDependency = 'com.google.cloud:google-cloud-nio:0.81.0-alpha:shaded'
+final googleCloudNioDependency = 'com.google.cloud:google-cloud-nio:0.81.0-alpha'
 
 final baseJarName = 'gatk'
 final secondaryBaseJarName = 'hellbender'
@@ -148,7 +148,7 @@ ensureBuildPrerequisites(requiredJavaVersion, largeResourcesFolder, buildPrerequ
 configurations.all {
     resolutionStrategy {
         // the snapshot folder contains a dev version of guava, we don't want to use that.
-        force 'com.google.guava:guava:18.0'
+        force 'com.google.guava:guava:27.1-jre'
         // force the htsjdk version so we don't get a different one transitively
         force 'com.github.samtools:htsjdk:' + htsjdkVersion
         // later versions explode Hadoop
@@ -208,6 +208,9 @@ configurations {
         exclude module: 'spark-mllib_2.11'
         exclude group: 'org.scala-lang'
         exclude module: 'kryo'
+        exclude group: 'javax.jms'
+        exclude group: 'com.sun.jdmk'
+        exclude group: 'com.sun.jmx'
     }
 }
 
@@ -235,7 +238,7 @@ dependencies {
         exclude module: 'protobuf-java'
     }
     compile 'com.opencsv:opencsv:3.4'
-    compile 'com.google.guava:guava:18.0'
+    compile 'com.google.guava:guava:27.1-jre'
     compile 'com.github.samtools:htsjdk:'+ htsjdkVersion
     compile googleCloudNioDependency
 
@@ -244,7 +247,7 @@ dependencies {
     // this comes built-in when running on Google Dataproc, but the library
     // allows us to read from GCS also when testing locally (or on non-Dataproc clusters,
     // should we want to)
-    compile 'com.google.cloud.bigdataoss:gcs-connector:1.6.3-hadoop2'
+    compile 'com.google.cloud.bigdataoss:gcs-connector:hadoop2-1.9.17'
 
     compile 'org.apache.logging.log4j:log4j-api:2.3'
     compile 'org.apache.logging.log4j:log4j-core:2.3'

src/main/java/org/broadinstitute/hellbender/utils/gcs/BucketUtils.java

@@ -21,9 +21,9 @@
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
-import shaded.cloud_nio.com.google.api.gax.retrying.RetrySettings;
-import shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials;
-import shaded.cloud_nio.org.threeten.bp.Duration;
+import com.google.api.gax.retrying.RetrySettings;
+import com.google.auth.oauth2.GoogleCredentials;
+import org.threeten.bp.Duration;
 
 import java.io.*;
 import java.nio.file.Files;

src/main/java/org/broadinstitute/hellbender/utils/nio/SeekableByteChannelPrefetcher.java

@@ -21,7 +21,7 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
-import shaded.cloud_nio.com.google.common.util.concurrent.ThreadFactoryBuilder;
+import com.google.common.util.concurrent.ThreadFactoryBuilder;
 
 /**
  * SeekableByteChannelPrefetcher wraps an existing SeekableByteChannel to add prefetching.

src/test/java/org/broadinstitute/hellbender/utils/nio/GcsNioIntegrationTest.java

@@ -54,7 +54,7 @@ public void writePrivateFile() throws IOException {
             try (OutputStream os = Files.newOutputStream(outputPath)) {
                 os.write(42);
             }
-        } catch (shaded.cloud_nio.com.google.api.client.http.HttpResponseException forbidden) {
+        } catch (Exception forbidden) {
             helpDebugAuthError();
             throw forbidden;
         }