song-qc-module

A QC module for Song that performs icgc-argo specific validations of song submissions

Creating a verifier program

There is a sample verifier program (written in Python) named verifier.py -- just edit it to create whatever verifier program you like.

verifier.py must define a single function, called verify(). The verify() function must take a string containing JSON as input, and must return a list of issues (strings describing problems with the input). If there are no issues, verify() must return an empty list.

Testing:

Files which contain sample inputs for which the verifier program should fail (produce issues) should be placed into the directory tests/failing. Files which contain sample inputs for which it should produce no issues should be placed into the directory tests/passing.

To run the tests, run

python3 -m pytest -s -v

To run the REST Server

When the Dockerfile is run, it creates a REST server on port 8080 which calls verifier.py to verify JSON data which is POSTED to it, and which returns the issues detected in JSON format.

To run the dockerfile, run

docker build . -t sidecar
docker run -p 8080:8080 sidecar

To use with SONG

Add the URL of your REST Server to the SONG setting verifierURLs in application.properties or application.yaml configuration file.