This repository provides infrastructure tools to run
omop_es and
omop-cascade in
containerised environments on the GAE.
In addition, the prefect/ directory provides data workflow orchestration with
Prefect to allow automatic scheduling of omop_es runs.
Use docker compose build to build all images, or specify the image to build.
docker compose build omop_esdocker compose build omop-cascadeSet environment variables:
# Copy the templates and fill out as needed
cp template.env .env
cp omop_es/template.env omop_es/.env
cp omop-cascade/template.env omop-cascade/.envdocker compose --project-name <PROJECT-NAME> run --build \
--env OMOP_ES_SETTINGS_ID=<SETTINGS_ID>
--env ... \
omop_esAdjust the .env files accordingly.
docker compose -f docker-compose.prod.yml --project-name <PROJECT-NAME> run --build \
--env OMOP_ES_SETTINGS_ID=<SETTINGS_ID> \
--env ... \
omop_esTo be able to clone GitHub repos on a GAE, create a new
fine-grained personal access token,
make sure the "Resource owner" is set to uclh-criu and then select the repositories you want to access.
Submit the request to generate the token and then make sure to copy the token to a safe place as it will not be shown again!
First store your PAT in a file on the GAE in the path ~/.pat.txt, then
configure git to use the token by running the following command:
git config --global credential.helper 'store --file ~/.pat.txt'This process needs to be repeated for every GAE.
Additionally record the token in the GITHUB_PAT environment variable in the .env file in this
repository's root.