atlas-testing-docker

Docker compose for starting a local OMOP CDM Postgres database and a OHDSI Atlas instance

Status: WIP

Maintainer: Tim Bleimehl

Usage

requirements:

• git
• docker with docker compose

First time setup

• Clone this repo

git clone git@github.com:DZD-eV-Diabetes-Research/atlas-testing-docker.git

• Change to the new dir

cd atlas-testing-docker

• create a .env file

cp sample.env .env

Have a look into the .env file and adapt it to you needs.

You maybe want to copy some Athena Vocabulary exports CSVs into the directory ./athena-vocab/

First time start

• Pull the up2date docker images

docker compose pull

• Start the docker compose

docker compose up

• Wait some time to let the database be provisioned (created and filled with data). you will see some log message from omop-provision-1 | . If you load a large Athena Vocabulary on a slow machine, you even wait for more than a hour. But you will always see what happening in the log messages.

• When you see log messages from atlas-testing-docker-webapi-1 | wait at least one more minute. The Atlas WebAPI will now deploy its database scheme.

• Exit the compose with ctrl+c

• Shutdown the compose

docker compose down

Regular start

Your setup is now complete. Your database is ready. From now on you can simply start and stop the Atlas Setup as you like.

• Start with

docker compose up -d

• Stop with

docker compose down

If you need to troubleshot something check the logs with:

docker compose logs -f

(exit this by pressing the keys ctrl+c)

Access Atlas

Now visit http://localhost:8080/atlas/

optional visit http://localhost:8080/WebAPI for inspecting the

Known issues

• CORS disabled config is not applied by webapi process. At the moment this is mitigated by having an nginx as reverse proxy to server webapi and atlas from the same host.