icgc-argo/song-qc-module

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

song-qc-module's Issues

Implement docker-compose

docker-compose should spin up song, song-db, ego and the QC module. You can follow what was done with https://github.com/overture-stack/genomic-data-playground docker-compose

This ticket depends on the feature in song being implemented: overture-stack/SONG#601

Implement handler and wrapper

https://wiki.oicr.on.ca/display/icgcargotech/ARGO+QC+Module+for+Song

• The wrapper should take the incoming request, extract http method, headers and body, and just pass the body to the verification function.

• the verification function takes the body, does whatever validation, and returns a list of strings. Each string describes one issue that was found during validation. If no issues were found, the function returns the empty list.

• If the verification function doesn't follow its contract (eg. it returns a non-list, or a non-string in the list, or throws an exception, the wrapper should return an error describing the problem.

The verification function should be the only function in the file. When bioinfo updates the QC validation, they should only really be touching 1 file and not concern them self with the house keeping.

Create Jenkins pipeline

• refer to https://wiki.oicr.on.ca/pages/viewpage.action?spaceKey=icgcargotech&title=ARGO+QC+Module+for+Song#ARGOQCModuleforSong-CI/CDSpecs
• Jenkinsfile update and autodeployment
• connect properly with github

Create simple test infrastructure

The goal is to create an easy way for the qc module to be tested with minimal coding.

One way to do this, is create 2 directories:

• passing
• failing

the passing directory should contain passing payloads. When these payloads are run against the handler, assert there are no errors

the failing directory should contain payloads that are invalidated by the qc module. When these payloads are run against the handler, assert errors of the expected type are thrown.

tests should be written using pytest