Currently a work in progress. Not yet part of any CanDIG stable release.
This repo will hold a top-level API that provides access to all CanDIG data services, including clinical data in OMOP and blob data in an object store.
Will implement a GA4GH Beacon v2 API for data discovery.
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.
Microservice setup not started
If you are setting up a new microservice that will be a part of the CanDIGv2 stack, you will most likely need to edit the files below, otherwise they can be deleted from the repo.
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Edit the Dockerfile with the correct names and paths that are relevant to your microservice.
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Add or remove the installed packages as needed
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Choose between using alpine or debian as the base operating system - we have found alpine can be slow for some applications
If your service will be communicating with other services in the network using the web server gateway interface, you will need to edit the configuration file.
This sets the configuration for uwsgi. You will need to add the name of the app and the port number as a minimum. The processes and harakiri values can also be updated based on your needs.
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.