Refactor auth.

pom.xml

@@ -127,7 +127,7 @@
     <dependency>
       <groupId>com.google.cloud.genomics</groupId>
       <artifactId>google-genomics-utils</artifactId>
-      <version>v1beta2-0.37</version>
+      <version>v1beta2-0.38</version>
       <exclusions>
         <!-- Exclude an old version of guava which is being pulled
              in by a transitive dependency google-api-client 1.19.0 -->
@@ -233,6 +233,24 @@
         </plugins>
       </build>
     </profile>
+    <profile>
+      <id>java7profile</id>
+        <activation>
+          <jdk>[1.7, 1.8)</jdk>
+        </activation>
+      <properties>
+        <alpn.jar>${basedir}/lib/alpn-boot-7.1.3.v20150130.jar</alpn.jar>
+      </properties>
+    </profile>
+    <profile>
+      <id>java8profile</id>
+        <activation>
+          <jdk>[1.8, 1.9)</jdk>
+        </activation>
+      <properties>
+        <alpn.jar>${basedir}/lib/alpn-boot-8.1.3.v20150130.jar</alpn.jar>
+      </properties>
+    </profile>
   </profiles>
 
   <build>
@@ -304,6 +322,7 @@
         <version>2.18.1</version>
         <configuration>
           <useSystemClassLoader>false</useSystemClassLoader>
+          <argLine>-Xbootclasspath/p:${alpn.jar}</argLine>
         </configuration>
         <executions>
           <execution>

src/main/java/com/google/cloud/genomics/dataflow/functions/AlleleSimilarityCalculator.java

@@ -16,15 +16,15 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import com.google.api.services.genomics.model.Call;
-import com.google.api.services.genomics.model.Variant;
 import com.google.cloud.dataflow.sdk.transforms.DoFn;
 import com.google.cloud.dataflow.sdk.values.KV;
 import com.google.cloud.genomics.dataflow.utils.CallFilters;
 import com.google.cloud.genomics.dataflow.utils.PairGenerator;
-import com.google.cloud.genomics.utils.VariantUtils;
+import com.google.cloud.genomics.utils.grpc.VariantUtils;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Maps;
+import com.google.genomics.v1.Variant;
+import com.google.genomics.v1.VariantCall;
 
 /**
  * For each pair of calls on any of the given variants, computes a score, a number between 0 and 1
@@ -55,14 +55,14 @@ public void processElement(ProcessContext context) {
     Variant variant = context.element();
     CallSimilarityCalculator callSimilarityCalculator =
         callSimilarityCalculatorFactory.get(isReferenceMajor(variant));
-    for (KV<Call, Call> pair : PairGenerator.WITHOUT_REPLACEMENT.allPairs(
+    for (KV<VariantCall, VariantCall> pair : PairGenerator.WITHOUT_REPLACEMENT.allPairs(
         getSamplesWithVariant(variant), VariantUtils.CALL_COMPARATOR)) {
       accumulateCallSimilarity(callSimilarityCalculator, pair.getKey(), pair.getValue());
     }
   }
 
   private void accumulateCallSimilarity(CallSimilarityCalculator callSimilarityCalculator,
-      Call call1, Call call2) {
+      VariantCall call1, VariantCall call2) {
     KV<String, String> callPair = KV.of(call1.getCallSetName(), call2.getCallSetName());
     KV<Double, Integer> callPairAccumulation = accumulator.get(callPair);
     if (callPairAccumulation == null) {
@@ -79,15 +79,15 @@ public void finishBundle(Context context) {
     output(context, accumulator);
   }
 
-  static ImmutableList<Call> getSamplesWithVariant(Variant variant) {
+  static ImmutableList<VariantCall> getSamplesWithVariant(Variant variant) {
     return CallFilters.getSamplesWithVariantOfMinGenotype(variant, 0);
   }
 
   static boolean isReferenceMajor(Variant variant) {
     int referenceAlleles = 0;
     int alternateAlleles = 0;
-    for (Call call : variant.getCalls()) {
-      for (Integer i : call.getGenotype()) {
+    for (VariantCall call : variant.getCallsList()) {
+      for (Integer i : call.getGenotypeList()) {
         if (i == 0) {
           ++referenceAlleles;
         } else if (i > 0) {

src/main/java/com/google/cloud/genomics/dataflow/functions/CallSimilarityCalculator.java

@@ -15,10 +15,10 @@
  */
 package com.google.cloud.genomics.dataflow.functions;
 
-import com.google.api.services.genomics.model.Call;
+import com.google.genomics.v1.VariantCall;
 
 public interface CallSimilarityCalculator {
 
-  double similarity(Call call1, Call call2);
+  double similarity(VariantCall call1, VariantCall call2);
 
 }

src/main/java/com/google/cloud/genomics/dataflow/functions/JoinNonVariantSegmentsWithVariants.java

@@ -31,7 +31,7 @@
 import com.google.cloud.dataflow.sdk.values.PCollection;
 import com.google.cloud.genomics.dataflow.readers.VariantReader;
 import com.google.cloud.genomics.dataflow.utils.GenomicsDatasetOptions;
-import com.google.cloud.genomics.utils.GenomicsFactory;
+import com.google.cloud.genomics.utils.OfflineAuth;
 import com.google.cloud.genomics.utils.ShardBoundary;
 import com.google.cloud.genomics.utils.VariantUtils;
 import com.google.common.base.Function;
@@ -71,7 +71,7 @@ public class JoinNonVariantSegmentsWithVariants {
    *     merged into the variants with which they overlap.
    */
   public static PCollection<Variant> joinVariantsTransform(
-      PCollection<SearchVariantsRequest> input, GenomicsFactory.OfflineAuth auth) {
+      PCollection<SearchVariantsRequest> input, OfflineAuth auth) {
     return joinVariants(input, auth, null);
   }
 
@@ -87,7 +87,7 @@ public static PCollection<Variant> joinVariantsTransform(
    *     merged into the variants with which they overlap.
    */
   public static PCollection<Variant> joinVariantsTransform(
-      PCollection<SearchVariantsRequest> input, GenomicsFactory.OfflineAuth auth, String fields) {
+      PCollection<SearchVariantsRequest> input, OfflineAuth auth, String fields) {
     for (String field : REQUIRED_FIELDS) {
       Preconditions
           .checkArgument(
@@ -99,7 +99,7 @@ public static PCollection<Variant> joinVariantsTransform(
   }
 
   private static PCollection<Variant> joinVariants(PCollection<SearchVariantsRequest> input,
-      GenomicsFactory.OfflineAuth auth, String fields) {
+      OfflineAuth auth, String fields) {
     return input
         .apply(
             ParDo.named(VariantReader.class.getSimpleName()).of(

src/main/java/com/google/cloud/genomics/dataflow/functions/SharedAllelesRatioCalculator.java

@@ -15,7 +15,7 @@
  */
 package com.google.cloud.genomics.dataflow.functions;
 
-import com.google.api.services.genomics.model.Call;
+import com.google.genomics.v1.VariantCall;
 
 /**
  * See <a href="http://konradjkarczewski.files.wordpress.com/2012/02/identity-howto.pdf">this
@@ -27,15 +27,15 @@ public class SharedAllelesRatioCalculator implements CallSimilarityCalculator {
   // TODO: Double check that the following is the right way of computing the IBS
   // scores when the number of alleles is different than 2 and when the genotypes are unphased.
   @Override
-  public double similarity(Call call1, Call call2) {
-    int minNumberOfGenotypes = Math.min(call1.getGenotype().size(), call2.getGenotype().size());
+  public double similarity(VariantCall call1, VariantCall call2) {
+    int minNumberOfGenotypes = Math.min(call1.getGenotypeCount(), call2.getGenotypeCount());
     int numberOfSharedAlleles = 0;
     for (int i = 0; i < minNumberOfGenotypes; ++i) {
-      if (call1.getGenotype().get(i) == call2.getGenotype().get(i)) {
+      if (call1.getGenotype(i) == call2.getGenotype(i)) {
         ++numberOfSharedAlleles;
       }
     }
-    int maxNumberOfGenotypes = Math.max(call1.getGenotype().size(), call2.getGenotype().size());
+    int maxNumberOfGenotypes = Math.max(call1.getGenotypeCount(), call2.getGenotypeCount());
     return (double) numberOfSharedAlleles / maxNumberOfGenotypes;
   }
 

src/main/java/com/google/cloud/genomics/dataflow/functions/SharedMinorAllelesCalculator.java

@@ -15,9 +15,9 @@
  */
 package com.google.cloud.genomics.dataflow.functions;
 
-import com.google.api.services.genomics.model.Call;
 import com.google.common.base.Predicate;
 import com.google.common.collect.Iterables;
+import com.google.genomics.v1.VariantCall;
 
 /**
  * Computes the similarity of two calls based on whether they share a minor allele or not.
@@ -30,8 +30,8 @@ public SharedMinorAllelesCalculator(boolean isReferenceMajor) {
     this.isReferenceMajor = isReferenceMajor;
   }
 
-  private boolean hasMinorAllele(Call call) {
-    return Iterables.any(call.getGenotype(), new Predicate<Integer>() {
+  private boolean hasMinorAllele(VariantCall call) {
+    return Iterables.any(call.getGenotypeList(), new Predicate<Integer>() {
 
       @Override
       public boolean apply(Integer genotype) {
@@ -46,7 +46,7 @@ public boolean apply(Integer genotype) {
   }
 
   @Override
-  public double similarity(Call call1, Call call2) {
+  public double similarity(VariantCall call1, VariantCall call2) {
     if (call1.getCallSetName().equals(call2.getCallSetName())) {
       return 1.0;
     }

src/main/java/com/google/cloud/genomics/dataflow/pipelines/AnnotateVariants.java

@@ -48,6 +48,7 @@
 import com.google.cloud.genomics.dataflow.utils.GenomicsDatasetOptions;
 import com.google.cloud.genomics.dataflow.utils.GenomicsOptions;
 import com.google.cloud.genomics.utils.GenomicsFactory;
+import com.google.cloud.genomics.utils.OfflineAuth;
 import com.google.cloud.genomics.utils.Paginator;
 import com.google.cloud.genomics.utils.ShardBoundary;
 import com.google.cloud.genomics.utils.ShardUtils;
@@ -87,11 +88,11 @@ public final class AnnotateVariants extends DoFn<SearchVariantsRequest, KV<Strin
   private static final String VARIANT_FIELDS
       = "nextPageToken,variants(id,referenceName,start,end,alternateBases,referenceBases)";
 
-  private final GenomicsFactory.OfflineAuth auth;
+  private final OfflineAuth auth;
   private final List<String> callSetIds, transcriptSetIds, variantAnnotationSetIds;
   private final Map<Range<Long>, String> refBaseCache;
 
-  public AnnotateVariants(GenomicsFactory.OfflineAuth auth,
+  public AnnotateVariants(OfflineAuth auth,
       List<String> callSetIds, List<String> transcriptSetIds,
       List<String> variantAnnotationSetIds) {
     this.auth = auth;
@@ -104,7 +105,7 @@ public AnnotateVariants(GenomicsFactory.OfflineAuth auth,
   @Override
   public void processElement(
       DoFn<SearchVariantsRequest, KV<String, VariantAnnotation>>.ProcessContext c) throws Exception {
-    Genomics genomics = auth.getGenomics(auth.getDefaultFactory());
+    Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth);
 
     SearchVariantsRequest request = c.element();
     LOG.info("processing contig " + request);
@@ -258,8 +259,8 @@ public static void main(String[] args) throws Exception {
     // Option validation is not yet automatic, we make an explicit call here.
     GenomicsDatasetOptions.Methods.validateOptions(opts);
 
-    GenomicsFactory.OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(opts);
-    Genomics genomics = auth.getGenomics(auth.getDefaultFactory());
+    OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(opts);
+    Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth);
 
     List<String> callSetIds = ImmutableList.of();
     if (!Strings.isNullOrEmpty(opts.getCallSetIds().trim())) {

src/main/java/com/google/cloud/genomics/dataflow/pipelines/CalculateCoverage.java

@@ -48,6 +48,7 @@
 import com.google.cloud.genomics.utils.Contig;
 import com.google.cloud.genomics.utils.GenomicsFactory;
 import com.google.cloud.genomics.utils.GenomicsUtils;
+import com.google.cloud.genomics.utils.OfflineAuth;
 import com.google.cloud.genomics.utils.RetryPolicy;
 import com.google.cloud.genomics.utils.ShardBoundary;
 import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter;
@@ -76,7 +77,7 @@ public class CalculateCoverage {
 
   private static CoverageOptions options;
   private static Pipeline p;
-  private static GenomicsFactory.OfflineAuth auth;
+  private static OfflineAuth auth;
 
   /**
    * Options required to run this pipeline.
@@ -192,10 +193,10 @@ public static void main(String[] args) throws GeneralSecurityException, IOExcept
 
   static class CheckMatchingReferenceSet extends DoFn<String, String> {
     private final String referenceSetIdForAllReadGroupSets;
-    private final GenomicsFactory.OfflineAuth auth;
+    private final OfflineAuth auth;
 
     public CheckMatchingReferenceSet(String referenceSetIdForAllReadGroupSets,
-        GenomicsFactory.OfflineAuth auth) {
+        OfflineAuth auth) {
       this.referenceSetIdForAllReadGroupSets = referenceSetIdForAllReadGroupSets;
       this.auth = auth;
     }
@@ -396,11 +397,11 @@ static class CreateAnnotations extends
       DoFn<KV<Position, Iterable<KV<PosRgsMq.MappingQuality, List<Double>>>>, Annotation> {
 
     private final String asId;
-    private final GenomicsFactory.OfflineAuth auth;
+    private final OfflineAuth auth;
     private final List<Annotation> currAnnotations;
     private final boolean write;
 
-    public CreateAnnotations(String asId, GenomicsFactory.OfflineAuth auth, boolean write) {
+    public CreateAnnotations(String asId, OfflineAuth auth, boolean write) {
       this.asId = asId;
       this.auth = auth;
       this.currAnnotations = Lists.newArrayList();
@@ -446,8 +447,8 @@ public void finishBundle(Context c) throws IOException, GeneralSecurityException
     }
 
     private void batchCreateAnnotations() throws IOException, GeneralSecurityException {
-      Genomics.Annotations.BatchCreate aRequest = auth.getGenomics(auth.getDefaultFactory())
-          .annotations().batchCreate(
+      Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth);
+      Genomics.Annotations.BatchCreate aRequest = genomics.annotations().batchCreate(
               new BatchCreateAnnotationsRequest().setAnnotations(currAnnotations));
       RetryPolicy retryP = RetryPolicy.nAttempts(4);
       retryP.execute(aRequest);
@@ -477,8 +478,8 @@ private static AnnotationSet createAnnotationSet(String referenceSetId)
     }
     as.setReferenceSetId(referenceSetId);
     as.setType("GENERIC");
-    Genomics.AnnotationSets.Create asRequest = auth.getGenomics(auth.getDefaultFactory())
-        .annotationSets().create(as);
+    Genomics genomics = GenomicsFactory.builder().build().fromOfflineAuth(auth);
+    Genomics.AnnotationSets.Create asRequest = genomics.annotationSets().create(as);
     AnnotationSet asWithId = asRequest.execute();
     return asWithId;
   }

src/main/java/com/google/cloud/genomics/dataflow/pipelines/CountReads.java

@@ -47,7 +47,7 @@
 import com.google.cloud.genomics.dataflow.utils.GenomicsDatasetOptions;
 import com.google.cloud.genomics.dataflow.utils.GenomicsOptions;
 import com.google.cloud.genomics.utils.Contig;
-import com.google.cloud.genomics.utils.GenomicsFactory;
+import com.google.cloud.genomics.utils.OfflineAuth;
 import com.google.cloud.genomics.utils.ShardBoundary;
 import com.google.cloud.genomics.utils.ShardUtils;
 import com.google.common.base.Strings;
@@ -63,7 +63,7 @@ public class CountReads {
   private static final Logger LOG = Logger.getLogger(CountReads.class.getName());
   private static CountReadsOptions options;
   private static Pipeline p;
-  private static GenomicsFactory.OfflineAuth auth;
+  private static OfflineAuth auth;
 
   public static interface CountReadsOptions extends GenomicsDatasetOptions, GCSOptions {
     @Description("The ID of the Google Genomics ReadGroupSet this pipeline is working with. "