utils-java

This project's goal is to reduce duplicate code across different Google Genomics Java integrations.

If you have duplicate code appearing in your projects, or see useful functions in the other googlegenomics Java repositories that you want to depend on, please contribute!

##Depending on this project

Note: you can find the latest available version of this project in Maven's central repository.

Maven

Add the following to your pom.xml file:

<project>
  <dependencies>
    <dependency>
      <groupId>com.google.cloud.genomics</groupId>
      <artifactId>google-genomics-utils</artifactId>
      <version>v1beta2-0.1</version>
    </dependency>
  </dependencies>
</project>

Gradle

Add the following to your build.gradle file:

repositories {
    mavenCentral()
}

dependencies {
    compile 'com.google.cloud.genomics:google-genomics-utils:v1beta2-0.1'
}

##gRPC This project now includes code for calling the Genomics API using gRPC. Calling the API with gRPC should greatly improve performance but is still experimental (alpha). To use gRPC, you'll need a version of ALPN that matches your JRE version. See the ALPN documentation for a table of which ALPN JAR to use. The latest version (as of June 2015) is provided in the lib/ subdirectory, and is known to work with JRE 1.8.0_40. To run with ALPN:

java -Xbootclasspath/p:lib/alpn-boot-8.1.3.v20150130.jar

See Example.java for some example code that uses gRPC. The protocol buffer schema for the API can be found in src/main/proto/google/genomics/v1.

At the moment your project must be whitelisted to use gRPC. Please contact us if you are interested in testing gRPC.

###Generating gRPC code Users should typically not need to generate gRPC code themselves, as pre-generated code can be found in src/main/java/com/google/genomics/v1. For developers, code can be generated with Gradle by running

gradle :generateProto

which will create code in target/generated-sources/main.

##Code Layout

• com.google.cloud.genomics.utils
  • GenomicsFactory.java Makes it easier to construct an authenticated Genomics service.
  • Paginator.java Lazily paginates through readsets, reads, variants, callsets, etc...
• com.google.cloud.genomics.grpc
  • Channels.java Makes it easier to creating gRPC channels to the Google Genomics API.
  • Example.java Demonstrates usage of gRPC via a minimal example.
    • To run the example with Java 7:

    MAVEN_OPTS="-Xbootclasspath/p:./lib/alpn-boot-7.1.3.v20150130.jar" \
    mvn exec:java -Dexec.mainClass=com.google.cloud.genomics.grpc.Example
    

    • To run the example with Java 8:

    MAVEN_OPTS="-Xbootclasspath/p:./lib/alpn-boot-8.1.3.v20150130.jar" \
    mvn exec:java -Dexec.mainClass=com.google.cloud.genomics.grpc.Example
    

    • If you see error Caused by: io.grpc.StatusRuntimeException: NOT_FOUND: Method not found. your project has not been whitelisted. See the above grpc section for more detail.
• proto
  • Protocol Buffer files defing the gRPC interface to the Genomics API.
  • code auto-generated from the protobufs (do not edit, but easier to read than the protobuf files)
    • com.google.api
    • com.google.genomics.v1
    • com.google.longrunning
    • com.google.protobuf
    • com.google.rpc

##Releasing new versions

This section contains details on getting a new release into Maven central and can be safely ignored by most people. If you need a new release of this code, go ahead and just file an issue.

###Prereqs

• Create a Sonatype Jira Account
• File a ticket to get access to the Sonatype com.google.cloud.genomics group
• Setup gpg (Don't forget to publish a public key)
• Setup GitHub SSH keys (make sure ssh -T git@github.com works)
• Create a ~/.m2/settings.xml file which has the following:

<settings>
  <servers>
    <server>
      <id>ossrh</id>
      <username>sonatype-username</username>
      <password>sonatype-password</password>
    </server>
  </servers>
</settings> 

###Making a new release

1. Use Maven to tag the code, up the pom version and release into the Sonatype staging area.

mvn release:prepare && mvn release:perform

...
What is the release version for "Google Genomics Utils"?: <the next version, e.g. 'v1beta2-0.26'>
What is SCM release tag or label for "Google Genomics Utils"?: <ENTER>
What is the new development version for "Google Genomics Utils"? <the next, next version with a -SNAPSHOT suffix, e.g. v1beta2-0.27-SNAPSHOT>

2. Find the repository at https://oss.sonatype.org/#stagingRepositories and close it.
3. If closing succeeds, then release it. See the detailed instructions for more info.
4. As long as there aren't any errors - that's it! The new version will be synced to Maven central.