Update various dependencies and security patches (including docker images, python, and javascript) to reflect things that have changed in our first year of operation. This should clear the way for new planned features or docker build changes.
TODO
[x] Prepare this repo to be open sourced
[x] Update python version to python 3.8
[x] Update python dependencies and remove unused packages
[x] Migrate Manhattan and QQ plots to d3v5 (consistent with recent LocusZoom). Should reduce vendor.js bloat, as the frontend files are getting too big.
[x] Update base images (eg redis) in prod/local/portaldev.yml
FAQ changes:
[x] Add OSS links
[x] Reorganize to support direct links
[x] Add FAQs for "why no LD" and "rsid/ unrecognized variant"
Bonus items (while we're doing large scale testing):
Migrate celery backend from redis to rabbitmq and explore removing redis image from docker-compose. (revisit once celery has stabilized- the 5.0 release is still new and some things will change)
[x] Explore multistage builds so that yarn build step happens inside the container, for more reproducible deployments.
~Explore caching options for faster python dependency upgrades in docker / local-dev mode~
Deployment notes
On our main server, we use a modified copy of production.yml. Changes to base images (eg python3.8, redis 5.0) may need to be manually ported over during the deploy.
Database migrations will be required (based on auth model changes in addon)
When building the container, add --pull to ensure that our docker container receives security patches
Revise apache config proxy urls: celery flower URL behavior may have changed (we'll stick with Flower 0.9.3 for now; 0.9.5 isn't well documented and seems to be in flux)
Purpose
Update various dependencies and security patches (including docker images, python, and javascript) to reflect things that have changed in our first year of operation. This should clear the way for new planned features or docker build changes.
TODO
Bonus items (while we're doing large scale testing):
Migrate celery backend from redis to rabbitmq and explore removing redis image from docker-compose.(revisit once celery has stabilized- the 5.0 release is still new and some things will change)Deployment notes
--pullto ensure that our docker container receives security patchesRevise apache config proxy urls: celery flower URL behavior may have changed(we'll stick with Flower 0.9.3 for now; 0.9.5 isn't well documented and seems to be in flux)