mgnifams-site

Dev setup

pip install -r requirements.txt
python manage.py migrate
python manage.py collectstatic
python manage.py runserver 8000

Deployment to EBI WebProd Kubernetes

Pre-requisites:

• Permission to push to a docker registry. We currently use a team quay.io.
• A kubeconfig that allows you to manage the EBI WebProd K8s cluster (e.g. in ~/mgnify-k8s-team-admin-hh.conf below)

Normal usage: Push to the main branch, and Quay.io will automatically build and tag the :latest container. Wait a few minutes for the build, and then restart the deployment to pull the image again:

 kubectl --kubeconfig ~/mgnify-k8s-team-admin-hh.conf rollout restart deployment mgnifams-site -n mgnifams-hl-exp

Non-normal usage: Secrets setup (one-time):

• Make a secrets .env file at k8s-hl/secrets.env with the database connection config (env vars read by settings.py) and the DJANGO_SECRET_KEY`.
  • Push it with e.g.: kubectl --kubeconfig ~/mgnify-k8s-team-admin-hh.conf --namespace mgnifams-hl-exp create secret generic mgnifams-secret --from-env-file=deployment/secrets.env
• Get authentication credentials for quay.io (the built image is private). You can get a Kubernetes secrets yaml file from your Quay.io user settings, in the "CLI Password" section.
  • Download the secrets yaml and name the secret name: quay-pull-secret in the metadata section. Put this into the k8s-hl folder as secrets-quayio.yml.

To redeploy with a manual build, or having changed the kubernetes config:

docker build -f Dockerfile -t quay.io/microbiome-informatics/mgnifams_site:ebi-wp-k8s-hl --load .
docker push quay.io/microbiome-informatics/mgnifams_site:ebi-wp-k8s-hl
kubectl --kubeconfig ~/mgnify-k8s-team-admin-hh.conf apply -f deployment/ebi-wp-k8s-hl.yaml