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@@ -15,11 +15,11 @@ |
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*/
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package com.google.cloud.genomics.gatk.common.grpc;
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-import com.google.api.client.googleapis.auth.oauth2.GoogleClientSecrets;
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-import com.google.api.client.googleapis.util.Utils;
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-import com.google.auth.oauth2.UserCredentials;
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import com.google.cloud.genomics.gatk.common.GenomicsDataSourceBase;
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-import com.google.cloud.genomics.utils.GenomicsFactory.OfflineAuth;
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+import com.google.cloud.genomics.utils.CredentialFactory;
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+import com.google.cloud.genomics.utils.OfflineAuth;
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+import com.google.cloud.genomics.utils.grpc.GenomicsChannel;
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+import com.google.common.base.Strings;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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@@ -39,25 +39,14 @@ |
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import com.google.genomics.v1.StreamReadsResponse;
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import com.google.genomics.v1.StreamingReadServiceGrpc;
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import com.google.genomics.v1.StreamingReadServiceGrpc.StreamingReadServiceBlockingStub;
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-
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import io.grpc.Channel;
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-import io.grpc.ChannelImpl;
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-import io.grpc.ClientInterceptors;
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-import io.grpc.auth.ClientAuthInterceptor;
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-import io.grpc.transport.netty.GrpcSslContexts;
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-import io.grpc.transport.netty.NegotiationType;
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-import io.grpc.transport.netty.NettyChannelBuilder;
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-
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+import io.grpc.ManagedChannel;
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import java.io.FileNotFoundException;
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-import java.io.FileReader;
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import java.io.IOException;
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import java.security.GeneralSecurityException;
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-import java.util.ArrayList;
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import java.util.Iterator;
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-import java.util.List;
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import java.util.Map;
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import java.util.Set;
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-import java.util.concurrent.Executors;
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/**
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* Manages Genomics GRPC Api initialization and provides Read iterator based
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@@ -66,8 +55,7 @@ |
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public class GenomicsDataSource
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extends GenomicsDataSourceBase<Read, ReadGroupSet, Reference> {
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/** gRPC channel used for faster access to Genomics API */
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- private Channel channel;
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- private ChannelImpl channelImpl;
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+ private ManagedChannel channel;
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public GenomicsDataSource(String rootUrl,
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String clientSecretsFilename,
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@@ -83,41 +71,19 @@ private Channel getChannel() throws FileNotFoundException, IOException, GeneralS |
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return channel;
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}
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- private Channel initGenomicsChannel() throws FileNotFoundException, IOException, GeneralSecurityException {
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- checkParamsForAuth(AUTH_REQUIREMENTS.CLIENT_SECRETS_ONLY);
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- final GoogleClientSecrets secrets = GoogleClientSecrets.load(
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- Utils.getDefaultJsonFactory(),
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- new FileReader(clientSecretsFilename));
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- final OfflineAuth auth = getFactory()
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- .getOfflineAuthFromClientSecretsFile(clientSecretsFilename);
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- final UserCredentials userCredentials = new UserCredentials(
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- secrets.getInstalled().getClientId(),
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- secrets.getInstalled().getClientSecret(),
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- auth.refreshToken);
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-
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- // Java 8's implementation of GCM ciphers is extremely slow. Therefore we disable
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- // them here.
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- List<String> defaultCiphers =
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- GrpcSslContexts.forClient().ciphers(null).build().cipherSuites();
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- List<String> performantCiphers = new ArrayList<>();
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- for (String cipher : defaultCiphers) {
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- if (!cipher.contains("GCM")) {
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- performantCiphers.add(cipher);
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- }
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+ private ManagedChannel initGenomicsChannel() throws FileNotFoundException, IOException, GeneralSecurityException {
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+ if (clientSecretsFilename != null && clientSecretsFilename.length() > 0) {
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+ return GenomicsChannel.fromOfflineAuth(
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+ new OfflineAuth(
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+ CredentialFactory.getCredentialFromClientSecrets(
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+ clientSecretsFilename,
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+ "genomics_java_client")));
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}
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- channelImpl = NettyChannelBuilder.forAddress("genomics.googleapis.com", 443)
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- .negotiationType(NegotiationType.TLS)
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- .streamWindowSize(1000000)
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- .sslContext(GrpcSslContexts.forClient().ciphers(performantCiphers).build())
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- .build();
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- /*userCredentials = userCredentials.createScoped(
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- Arrays.asList("https://www.googleapis.com/auth/genomics"));*/
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- ClientAuthInterceptor interceptor = new ClientAuthInterceptor(userCredentials,
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- Executors.newSingleThreadExecutor());
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- return ClientInterceptors.intercept(channelImpl, interceptor);
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+ // API Key is not sufficient for StreamReads request.
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+ // TODO: All support for non default credentials will be removed in a subsequent PR.
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+ return GenomicsChannel.fromDefaultCreds();
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}
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-
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@Override
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public ReadIteratorResource getReads(
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@@ -183,15 +149,15 @@ public ReadIteratorResource getReads( |
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private Map<String, Reference> getReferences(ReadGroupSet readGroupSet)
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throws IOException, GeneralSecurityException {
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Set<String> referenceSetIds = Sets.newHashSet();
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- if (readGroupSet.getReferenceSetId() != null && !readGroupSet.getReferenceSetId().isEmpty()) {
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+ if (!Strings.isNullOrEmpty(readGroupSet.getReferenceSetId())) {
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LOG.info("Found reference set from read group set " +
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readGroupSet.getReferenceSetId());
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referenceSetIds.add(readGroupSet.getReferenceSetId());
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}
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if (readGroupSet.getReadGroupsCount() > 0) {
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LOG.info("Found read groups");
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for (ReadGroup readGroup : readGroupSet.getReadGroupsList()) {
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- if (readGroup.getReferenceSetId() != null && !readGroup.getReferenceSetId().isEmpty()) {
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+ if (!Strings.isNullOrEmpty(readGroup.getReferenceSetId())) {
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LOG.info("Found reference set from read group: " +
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readGroup.getReferenceSetId());
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referenceSetIds.add(readGroup.getReferenceSetId());
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@@ -217,7 +183,7 @@ public ReadIteratorResource getReads( |
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GetReferenceRequest getReferenceRequest = GetReferenceRequest
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.newBuilder().setReferenceId(referenceId).build();
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Reference reference = referenceSetStub.getReference(getReferenceRequest);
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- if (reference.getName() != null && !reference.getName().isEmpty()) {
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+ if (!Strings.isNullOrEmpty(reference.getName())) {
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references.put(reference.getName(), reference);
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LOG.fine("Adding reference " + reference.getName());
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}
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@@ -316,9 +282,8 @@ public void remove() { |
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@Override
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public void close() {
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- if (channelImpl != null ) {
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- channelImpl.shutdown();
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- channelImpl = null;
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+ if (channel != null ) {
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+ channel.shutdown();
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}
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channel = null;
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}
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