encam

Encyclopedia of Cancer Microenvironment http://encima.one

Local development

docker-compose up --build

This starts a flask server serving a static version of the webpage using nginx on http://localhost:8080 using the development server (proxied via nginx).

Building and deploying

Make a new access token on https://github.com/settings/tokens/new It needs these permissions:

• repo
• write:packages
• read:packages

Set up github credentials on docker using the token as password:

docker login docker.pkg.github.com --username danr

Run the deploy script which will build the docker image, upload it as a github package and then tell our running SNIC machine to pull it and restart:

VERSION=0.0.12 ./deploy.sh

The server needs a token to pull the image. The permissions need to be:

• read:packages

Login on the server as well:

docker login docker.pkg.github.com --username danr

Moving to a new server

1. On the old server: copy the config, certbot and snap directories in $HOME.

2. On the new server:

   1. Install docker.
   2. Login with github API keys as above to be able to pull the docker image.
   3. Create a volume and attach it to the running instance.
   4. Mount the volume to the config directory of the instance. On SNIC this looks like:

   sudo mkfs.ext4 /dev/vdb
   mkdir -p ~/config
   sudo mount /dev/vdb ~/config
   

   Detailed instructions about mounting a volume: https://github.com/naturalis/openstack-docs/wiki/Howto:-Creating-and-using-Volumes-on-a-Linux-instance

   5. Put the old server's directories config, certbot and snap in $HOME.
   6. Make sure permissions on config/content are liberal:

   chmod 777 config/content
   chmod 666 config/content/*
   

3. Locally: update the deploy.sh script to point to the new server IP address.

4. Locally: run the deploy.sh script.

5. Update the DNS on .one to point to the new IP address.

Running backend tests

To run the tests for the encam project

python test.py

in the api folder. The expected output is no assertion errors.

This can be run in a virtualenv or with

docker-compose run api python test.py

To get the code coverage, install the coverage package with pip and run

coverage run test.py

To get the report from the code coverage

coverage report -m

and the annotated HTML listings detailing missed lines

coverage html

Running frontend tests

This can be done in the frontend directory with

yarn install
yarn run test

This can also be executed in the container with:

docker-compose run -w /app encam-frontend-devel yarn run test