Currently a work in progress. Not yet part of any CanDIG stable release.
This repo implements a top-level API that provides access to all CanDIG data services, including clinical data in OMOP and blob data in an object store.
Implemeted using connextion and SQLAlchemy.
There are two OpenAPI schemas, both under development:
- schema.yml implements basic CRUD operations on clinical data objects (Datasets and Persons)
- beacon-schema.yml will implement a GA4GH Beacon v2 API for data discovery across datatypes (clinical, genomic).
The default branch is develop and the stable branch indicates a stable production release.
All development should be done on a fork or branch from the develop branch. Releases of new code to the 'stable' branch occur on an adhoc basis.
Following sections to be updated when we are ready to integrate into a full CanDIG stack.
Templates for two Github actions ymls are in the .github/workflows/ directory and should be edited to suit the needs of the microservice.
This action automatically makes a PR to the main CanDIGv2 repo stack to update the submodule each time a PR is merged into develop.
Edit this file with the appropriate submodule path on line 26.
This action assumes you have setup tests in the repo using pytest.
It automatically runs pytest on the repo each time a commit is pushed into the remote repo.