Moving to V1 of the API, updating all deps #26

iliat · Jul 25, 2016

Updating all the deps for Maven to reference latest versions of the API and other dependencies
Changing all urls to reference V1 API url
Adding support for default app credentials for auth.
Changing code to deal with API changes that return empty string instead of null for some REST APIs
Adding new ALPN jar required for a newer version of Java
Changing run_picard to use grpc

coveralls · Jul 25, 2016

Changes Unknown when pulling 5187415 on iliat:upgrade-api into * on googlegenomics:master*.

pgrosu · Jul 25, 2016

Welcome back Ilia :) Looks great!

Two small things, you might want to update the Readme.md, and the Picard Readme to use v1 in these examples:

$ java -jar dist/picard.jar ViewSam \
INPUT=https://www.googleapis.com/genomics/v1beta2/readgroupsets/CK256frpGBD44IWHwLP22R4/ \
GA4GH_CLIENT_SECRETS=../client_secrets.json

and

java \
-Xbootclasspath/p:../gatk-tools-java/lib/alpn-boot-8.1.3.v20150130.jar \
-Dga4gh.using_grpc=true \
-jar dist/picard.jar ViewSam \
INPUT=https://www.googleapis.com/genomics/v1beta2/readgroupsets/CK256frpGBD44IWHwLP22R4/ \
GA4GH_CLIENT_SECRETS=../client_secrets.json

Thanks,
~p

Yay! Thanks @iliat

s/v1-rev87-1.22.0/v1-rev93-1.22.0

Just tested it and it looks to be working with the version released today.

Here and elsewhere !Strings.isNullOrEmpty(readGroup.getReferenceSetId())

Much better, will do!

This can be removed. StreamReads and StreamVariants require authentication. Therefore an API key is not sufficient.

Ok, will remove API key support.

Why is the protoc plugin needed here? The utils-java release contains the classes.

jar -tvf ~/.m2/repository/com/google/cloud/genomics/google-genomics-utils/v1-0.6/google-genomics-utils-v1-0.6.jar | grep StreamVariant
 15847 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsRequest.class
 15880 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsResponse$Builder.class
  1546 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsRequest$1.class
 15861 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsRequest$Builder.class
 12018 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsResponse.class
   611 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsResponseOrBuilder.class
   700 Fri Jul 15 12:00:40 PDT 2016 com/google/genomics/v1/StreamVariantsRequestOrBuilder.class
  1553 Fri Jul 15 12:00:42 PDT 2016 com/google/genomics/v1/StreamVariantsResponse$1.class

With or without the plugin in pom.xml, the Jar file has the same exact size:

Without the plugin:

-rw-rw-r-- 1 pgrosu pgrosu 24397578 Jul 27 16:09 gatk-tools-java-v1-0.6-SNAPSHOT-jar-with-dependencies.jar

With the plugin:

-rw-rw-r-- 1 pgrosu pgrosu 24397578 Jul 27 16:38 gatk-tools-java-v1-0.6-SNAPSHOT-jar-with-dependencies.jar

Not needed - I got it in when I was fixing other build issues since I was not sure if I was missing some deps and plugins but you are right - its will work without it.

coveralls · Jul 28, 2016

Changes Unknown when pulling 33ad437 on iliat:upgrade-api into * on googlegenomics:master*.

iliat · Jul 28, 2016

@deflaux Addressed the comments. I'll clean up non def. cred. auth and update readme in the next PR.

pgrosu · Jul 29, 2016

Cool thanks - look forward to the next PR :)

deflaux · Jul 29, 2016

LGTM, thank you!

deflaux was assigned by iliat Jul 25, 2016

iliat merged commit 5521664 into googlegenomics:master Jul 29, 2016
3 checks passed

3 checks passed

cla/google All necessary CLAs are signed

continuous-integration/travis-ci/pr The Travis CI build passed
Details

coverage/coveralls First build on master at 0.0%
Details

@@ -357,8 +407,9 @@
          <jetty.version>6.1.26</jetty.version>
          <jackson.version>2.4.2</jackson.version>
          <junit.version>4.11</junit.version>
-    -    <google.api.version>1.19.0</google.api.version>
-    -    <google.api.genomics.version>v1beta2-rev7-1.19.0</google.api.genomics.version>
+    +    <google.api.version>1.22.0</google.api.version>
+    +    <google.api.genomics.version>v1-rev87-1.22.0</google.api.genomics.version>

                readGroupSet.getReferenceSetId());
            referenceSetIds.add(readGroupSet.getReferenceSetId());
          }
          if (readGroupSet.getReadGroups() != null) {
            LOG.info("Found read groups");
            for (ReadGroup readGroup : readGroupSet.getReadGroups()) {
-    -        if (readGroup.getReferenceSetId() != null) {
+    +        if (readGroup.getReferenceSetId() != null && readGroup.getReferenceSetId().length() > 0) {

          }
-    -
-    -    channelImpl = NettyChannelBuilder.forAddress("genomics.googleapis.com", 443)
-    -        .negotiationType(NegotiationType.TLS)
-    -        .streamWindowSize(1000000)
-    -        .sslContext(GrpcSslContexts.forClient().ciphers(performantCiphers).build())
-    -        .build();
-    -    /*userCredentials = userCredentials.createScoped(
-    -        Arrays.asList("https://www.googleapis.com/auth/genomics"));*/
-    -    ClientAuthInterceptor interceptor = new ClientAuthInterceptor(userCredentials,
-    -        Executors.newSingleThreadExecutor());
-    -    return ClientInterceptors.intercept(channelImpl, interceptor);
+    +    if (apiKey != null && apiKey.length() > 0) {

@@ -275,6 +300,31 @@
              <version>2.2.0</version>
            </plugin>
            <plugin>
+    +        <groupId>org.xolstice.maven.plugins</groupId>

googlegenomics/gatk-tools-java

Moving to V1 of the API, updating all deps #26

iliat commented Jul 25, 2016

deflaux was assigned by iliat Jul 25, 2016

coveralls commented Jul 25, 2016

pgrosu commented Jul 25, 2016

deflaux commented on the diff Jul 26, 2016

deflaux and 1 other commented on an outdated diff Jul 26, 2016

deflaux and 1 other commented on an outdated diff Jul 26, 2016

deflaux and 2 others commented on an outdated diff Jul 26, 2016

coveralls commented Jul 28, 2016

iliat commented Jul 28, 2016

pgrosu commented Jul 29, 2016

deflaux commented Jul 29, 2016

iliat merged commit `5521664` into googlegenomics:master Jul 29, 2016
3 checks passed

3 checks passed

googlegenomics/gatk-tools-java

Join GitHub today

Moving to V1 of the API, updating all deps #26

Conversation

iliat commented Jul 25, 2016

deflaux was assigned by iliat Jul 25, 2016

coveralls commented Jul 25, 2016

pgrosu commented Jul 25, 2016

deflaux commented on the diff Jul 26, 2016

Show 2 comments Hide comments deflaux and 1 other commented on an outdated diff Jul 26, 2016

Show 2 comments Hide comments deflaux and 1 other commented on an outdated diff Jul 26, 2016

Show 3 comments Hide comments deflaux and 2 others commented on an outdated diff Jul 26, 2016

All checks have passed

coveralls commented Jul 28, 2016

iliat commented Jul 28, 2016

pgrosu commented Jul 29, 2016

deflaux commented Jul 29, 2016

Hide details View details iliat merged commit 5521664 into googlegenomics:master Jul 29, 2016 3 checks passed

3 checks passed

deflaux and 1 other commented on an outdated diff Jul 26, 2016

deflaux and 1 other commented on an outdated diff Jul 26, 2016

deflaux and 2 others commented on an outdated diff Jul 26, 2016

iliat merged commit `5521664` into googlegenomics:master Jul 29, 2016
3 checks passed