rnaget Microservice

Based on CanDIG demo projects: OpenAPI variant service demo, Python Model Service. This is a Proof-of-Concept implementation of the GA4GH rnaget API, used to query and download RNA quantification matrix data.

Schema info

For more information about the schemas used visit https://github.com/ga4gh-rnaseq/schema

Stack

• Connexion for implementing the API
• SQLAlchemy, using Sqlite3 for ORM
• Bravado-core for Python classes from the spec
• Dredd and Dredd-Hooks-Python for testing
• HDF5 for matrix store & operations
• Python 3
• Pytest, tox
• Travis-CI

Installation

The server software can be installed in a py3.6+ virtual environment:

pip install -r requirements.txt
pip install -r requirements_dev.txt
python setup.py develop

for automated testing you can install dredd; assuming you already have node and npm installed,

npm install -g dredd

Running

Once running, a Swagger UI can be accessed at: /rnaget/ui

To specify your own database & log output, the server can be started with:

candig_rnaget --host=0.0.0.0 --port=3005 --database=data/test.db --logfile=/path/to/logs --loglevel=WARN

For testing, the dredd config is currently set up to launch the service itself, so no server needs be running:

cd tests
dredd --hookfiles=dreddhooks.py