Playing with the #GA4GH schemas and #Avro : my notebook

After watching David Haussler's talk "Beacon Project and Data Sharing ApIs", I wanted to play with Avro and the models and APIs defined by the Global Alliance for Genomics and Health (ga4gh) coalition Here is my notebook.

(Wikipedia) Avro: "Avro is a remote procedure call and data serialization framework developed within Apache's Hadoop project. It uses JSON for defining data types and protocols, and serializes data in a compact binary format. Its primary use is in Apache Hadoop, where it can provide both a serialization format for persistent data, and a wire format for communication between Hadoop nodes, and from client programs to the Hadoop services."

First, we download the java tools and libraries for apache Avro

curl -L -o avro-tools-1.7.7.jar "http://www.eng.lsu.edu/mirrors/apache/avro/avro-1.7.7/java/avro-tools-1.7.7.jar"

Next, we download the schemas defined by the ga4gh from github

curl -L -o schema.zip "https://github.com/ga4gh/schemas/archive/v0.5.1.zip"
unzip schema.zip
rm schema.zip

$ find -name "*.avdl"
./schemas-0.5.1/src/main/resources/avro/readmethods.avdl
./schemas-0.5.1/src/main/resources/avro/common.avdl
./schemas-0.5.1/src/main/resources/avro/wip/metadata.avdl
./schemas-0.5.1/src/main/resources/avro/wip/metadatamethods.avdl
./schemas-0.5.1/src/main/resources/avro/wip/variationReference.avdl
./schemas-0.5.1/src/main/resources/avro/variants.avdl
./schemas-0.5.1/src/main/resources/avro/variantmethods.avdl
./schemas-0.5.1/src/main/resources/avro/beacon.avdl
./schemas-0.5.1/src/main/resources/avro/references.avdl
./schemas-0.5.1/src/main/resources/avro/referencemethods.avdl
./schemas-0.5.1/src/main/resources/avro/reads.avdl

Those schema can be compiled to java using the avro-tools

$ java -jar avro-tools-1.7.7.jar compile protocol schemas-0.5.1/src/main/resources/avro/ ./generated
Input files to compile:
  schemas-0.5.1/src/main/resources/avro/variants.avpr
  
$ find generated/org/ -name "*.java"
generated/org/ga4gh/GAPosition.java
generated/org/ga4gh/GAVariantSetMetadata.java
generated/org/ga4gh/GACall.java
generated/org/ga4gh/GAException.java
generated/org/ga4gh/GACigarOperation.java
generated/org/ga4gh/GAVariantSet.java
generated/org/ga4gh/GAVariants.java
generated/org/ga4gh/GAVariant.java
generated/org/ga4gh/GACallSet.java
generated/org/ga4gh/GACigarUnit.java

As a test, the following java source uses the classes generated by avro to create nine variants and serialize them to Avro

Compile, archive and execute:

#compile classes
javac -d generated -cp avro-tools-1.7.7.jar -sourcepath generated:src generated/org/ga4gh/*.java src/test/TestAvro.java
# archive
jar cvf generated/ga4gh.jar -C generated org -C generated test
# run
java -cp avro-tools-1.7.7.jar:generated/ga4gh.jar test.TestAvro > variant.avro

We use the avro-tools to convert the generated file variant.avro to json

java -jar avro-tools-1.7.7.jar tojson variant.avro

Output:

The complete Makefile

That's it,
Pierre