From 1059e2d549ecfda6284f3b0622fb57b895ccdafe Mon Sep 17 00:00:00 2001 From: Nicole Deflaux Date: Wed, 11 May 2016 11:15:46 -0700 Subject: [PATCH 1/3] Get rid of "repackaged" imports. --- .../genomics/dataflow/pipelines/IdentifyPrivateVariants.java | 2 +- .../cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java | 2 +- .../google/cloud/genomics/dataflow/utils/GCSOutputOptions.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java index 73bb0b2..80e2369 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java @@ -19,7 +19,6 @@ import com.google.cloud.dataflow.sdk.options.Description; import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; import com.google.cloud.dataflow.sdk.options.Validation.Required; -import com.google.cloud.dataflow.sdk.repackaged.com.google.common.collect.ImmutableSet; import com.google.cloud.dataflow.sdk.transforms.Create; import com.google.cloud.dataflow.sdk.transforms.DoFn; import com.google.cloud.dataflow.sdk.transforms.ParDo; @@ -34,6 +33,7 @@ import com.google.common.base.CharMatcher; import com.google.common.base.Joiner; import com.google.common.base.Splitter; +import com.google.common.collect.ImmutableSet; import com.google.common.io.Files; import com.google.genomics.v1.StreamVariantsRequest; import com.google.genomics.v1.Variant; diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java index bc8db4b..b9dc391 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java @@ -13,7 +13,6 @@ */ package com.google.cloud.genomics.dataflow.pipelines; -import com.google.api.client.repackaged.com.google.common.base.Strings; import com.google.api.services.storage.Storage; import com.google.cloud.dataflow.sdk.Pipeline; import com.google.cloud.dataflow.sdk.coders.Coder; @@ -45,6 +44,7 @@ import com.google.cloud.genomics.utils.ShardUtils; import com.google.cloud.genomics.utils.ShardUtils.SexChromosomeFilter; import com.google.common.base.Preconditions; +import com.google.common.base.Strings; import com.google.common.collect.Lists; import com.google.genomics.v1.Read; import com.google.genomics.v1.StreamReadsRequest; diff --git a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java index b1233fa..214758c 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/utils/GCSOutputOptions.java @@ -13,11 +13,11 @@ */ package com.google.cloud.genomics.dataflow.utils; -import com.google.api.client.repackaged.com.google.common.base.Strings; import com.google.cloud.dataflow.sdk.options.Description; import com.google.cloud.dataflow.sdk.options.Validation; import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; import com.google.common.base.Preconditions; +import com.google.common.base.Strings; /** * A common options class for all pipelines that write their analysis results to GCS files. From 5aa809bde0b5772a9ca0bfb92a317b36f8f887e3 Mon Sep 17 00:00:00 2001 From: Nicole Deflaux Date: Thu, 12 May 2016 15:13:34 -0700 Subject: [PATCH 2/3] Bump guava dependency. --- pom.xml | 2 +- .../genomics/dataflow/pipelines/IdentifyPrivateVariants.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index cca3f0a..05c8c53 100644 --- a/pom.xml +++ b/pom.xml @@ -141,7 +141,7 @@ com.google.guava guava - 18.0 + 19.0 gov.nist.math.jama diff --git a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java index 80e2369..c41ab76 100644 --- a/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java +++ b/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java @@ -149,7 +149,7 @@ public static void main(String[] args) throws IOException, GeneralSecurityExcept ImmutableSet .builder() .addAll( - Splitter.on(CharMatcher.BREAKING_WHITESPACE).omitEmptyStrings().trimResults() + Splitter.on(CharMatcher.breakingWhitespace()).omitEmptyStrings().trimResults() .split(fileContents)).build(); LOG.info("The pipeline will identify and write to Cloud Storage variants " + "private to " + callSetIds.size() + " genomes with callSetIds: " + callSetIds); From d0b62f38eaed86125b488b33996d41d4f4fffd91 Mon Sep 17 00:00:00 2001 From: Nicole Deflaux Date: Thu, 12 May 2016 15:19:20 -0700 Subject: [PATCH 3/3] Also deploy a test jar. --- pom.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pom.xml b/pom.xml index 05c8c53..3b22adb 100644 --- a/pom.xml +++ b/pom.xml @@ -343,6 +343,13 @@ org.apache.maven.plugins maven-jar-plugin 2.6 + + + + test-jar + + +