Instantiate CWL documents as Java objects

Run the following command in an environment with Maven 3 and Java 8 to demonstrate how to instantiate and work with CWL documents as Java objects.

mvn clean install

Generate Avro Schema

The process for generating the Java classes in the first place from the CWL specification involves the following considerations.

Background:

The CWL specification is defined in something similar to but not entirely like Avro Use the schema salad project to convert to an avro-ish schema document Generate the Java classes for the schema We cannot use these classes directly since CWL documents are not json or avro binaries, use cwl-tool to convert to json and then gson to convert from json due to some incompatibilities between CWL avro and normal avro.

To regenerate:

1. Get schema salad from the common-workflow-language organization and run python -mschema_salad --print-avro ~/common-workflow-language/draft-3/CommonWorkflowLanguage.yml > cwl.avsc
2. Edit the allowed symbols for CWL versions. The draft3 specification generates symbols like "draft-3.dev1" which the avro parser will reject with the error "Exception in thread "main" org.apache.avro.SchemaParseException: Illegal character in: draft-3.dev1". You can safety delete all the symbols which are designated "draft" versions.
3. Get the avro tools jar and CWL avsc and call java -jar avro-tools-1.7.7.jar compile schema cwl.avsc cwl
4. Copy them to the appropriate directory in dockstore-client (you will need to refactor to insert package names)

Since this is kinda involved, a travis-CI build is provided which demos the process at https://travis-ci.org/common-workflow-language/cwljava