README.md

chemcurator_test

(Experimental) test environment for ChemReg / ChemCurator

Assumes the chemcurator_django, chemcurator_vuejs, and resolver repos. can be clone with the info. in chemcurator_test_config.py.

Copy chemcurator_test_config.py.template to chemcurator_test_config.py and edit appropriately. For simplicity you can use a dedicated GitHub access token, so {auth} is replaced with <githubuser>:<accesstoken>. chemcurator_test_config.py should not be shared or committed to version control. BASE_PORT can be any port number, 9000 or 39000 or whatever.

chemcurator_test.py is a "bash script" written in Python which merges the docker-compose.yml and template.env files for chemcurator_django and resolver and adds entries for chemcurator_vuejs. It may handle branch management for testing later, but for now it's basically just merging. You provide a base port number X in chemcurator_test_config.py and the code assigns X, X+1, etc. as required as host ports exposing container ports.

Assuming you have Python 3

python -m venv venv
. venv/bin/activate
pip install -r requirements.txt
python chemcurator_test.py --help
python chemcurator_test.py config
docker-compose build
docker-compose up

The following containers are launched by default:

web             <- resolver
chemreg-admin   30006->8000
chemreg-api     30005->8000
db              <- resolver
chemreg-ketcher 30007->8002
postgresql      <- ChemReg DB
redis
chemreg-cypress 30008->22, 30009->8080
chemreg-ui      30004->8080
pgbouncer   

<username>_cr_ is prepended to images / containers to avoid conflicts with other users.

The chemreg-cypress is only for testing.

(Currently) manual steps

After bringing everything up,

docker-compose exec chemreg-api bash
python manage.py migrate
# compounds < substances < lists order matters
python manage.py loaddata chemreg/fixtures/users.yaml
python manage.py loaddata chemreg/fixtures/compounds.yaml
python manage.py loaddata chemreg/fixtures/substances.yaml
python manage.py loaddata chemreg/fixtures/lists.yaml

these changes should persist until the persistent DB volume is destroyed, so not needed often.

Working

chemcurator_test.py builds a usable .env and docker-compose.yml for deploying all ChemReg components in a single docker network.

To do

[x] add ketcher [ ] revisit chemcurator_test.py subcommands for managing branches for testing etc.

chemcurator_vuejs notes

Currently the test deployment code makes no changes to the component repos. So the chemcurator_vuejs Dockerfile builds static production assets. But the chemcurator_test docker-compose overwrites the CMD to "npm run serve", so the container runs in dev. mode.

The static production assets do not seem to use the right API URL, i.e. not reading VUE_APP_API_URL correctly, but it works in dev. mode.