fall back to API key if no OfflineAuth was saved

src/main/java/org/broadinstitute/hellbender/engine/dataflow/DataflowCommandLineProgram.java

@@ -12,6 +12,7 @@
 import com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner;
 import com.google.cloud.dataflow.sdk.runners.PipelineRunner;
 import com.google.cloud.genomics.dataflow.utils.GCSOptions;
+import com.google.cloud.genomics.dataflow.utils.GenomicsOptions;
 import com.google.cloud.genomics.utils.GenomicsFactory;
 import com.google.common.annotations.VisibleForTesting;
 import org.broadinstitute.hellbender.cmdline.Argument;
@@ -28,13 +29,16 @@
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
 import java.io.Serializable;
+import java.security.GeneralSecurityException;
 
 
 public abstract class DataflowCommandLineProgram extends CommandLineProgram implements Serializable {
     private static final long serialVersionUID = 1l;
 
     // We need authentication options from GCSOptions, and Dataflow options from DataflowPipelineOptions.
     // Neither inherits from the other, so we have to put them together like this.
+    // This also includes code to save the OfflineAuth onto the pipelineoptions, so we can get to them later
+    // (even if they're via client-secrets.json, which workers otherwise wouldn't be able to load).
     public interface HellbenderDataflowOptions extends GCSOptions, DataflowPipelineOptions {
 
         static class Methods {
@@ -46,8 +50,15 @@ public static void setOfflineAuth(HellbenderDataflowOptions opts, GenomicsFactor
                 }
                 opts.setSerializedOfflineAuth(os.toByteArray());
             }
-            public static GenomicsFactory.OfflineAuth getOfflineAuth(HellbenderDataflowOptions opts) throws IOException, ClassNotFoundException {
-                try (ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(opts.getSerializedOfflineAuth()))) {
+            public static GenomicsFactory.OfflineAuth getOfflineAuth(HellbenderDataflowOptions opts) throws IOException, ClassNotFoundException, GeneralSecurityException {
+                byte[] serialized = opts.getSerializedOfflineAuth();
+                if (null==serialized && opts.getApiKey()!=null) {
+                    // fall back to using the API key only (even if a secrets file was also specified).
+                    GenomicsFactory.Builder builder =
+                        GenomicsFactory.builder(opts.getAppName()).setNumberOfRetries(opts.getNumberOfRetries());
+                    return builder.build().getOfflineAuthFromApiKey(opts.getApiKey());
+                }
+                try (ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(serialized))) {
                     return (GenomicsFactory.OfflineAuth)(is.readObject());
                 }
             }