Deploy Carrot Mapper

Get the example Compose file

Download the sample Carrot Mapper Compose file by running the command:

wget https://raw.githubusercontent.com/Health-Informatics-UoN/carrot/refs/heads/main/samples/Carrot-Mapper/compose/mapper.compose.yml

Environment configuration

For your convenience, the compose file is already configured with enough environment variables to run Carrot Mapper. For the reference, please see the Configuration section.

OMOP CDM configuration

Before getting Carrot Mapper running, you need to configure the OMOP CDM in its database.

By default, Carrot Mapper uses a synthetic OMOP CDM database which will be then loaded into the database thanks to the omop-lite service. If you want to use your own vocabularies in the OMOP CDM, you need to:

• Set the SYNTHETIC environment variable of the omop-lite service to false in the mapper.compose.yml file.

SYNTHETIC: false

• Create a folder named vocabs in the same directory as the mapper.compose.yml file.
• Download the desired vocabularies from Athena and place them in the vocabs folder.

Running Carrot Mapper

To run Carrot, you need to specify the release version of the Carrot Mapper application you want to deploy. You can find the list of available versions in the container registry.

At the directory containing the mapper.compose.yml file, run the command with the release version, for example 3.0.7, specified:

RELEASE_VERSION=<release-version> docker compose up -d

The command will pull and build the following services:

• Frontend: frontend
• Backend: api
• Database: db
• Minio: minio
• Airflow Webserver: airflow-webserver
• Airflow Scheduler: scheduler
• OMOP Lite: omop-lite - This service will load the vocabularies into the database depending on how you configured it in the last step. After the vocabularies are loaded, api service will be started, then frontend, airflow-webserver and scheduler.

After the services are up and running successfully, you can access the Carrot Mapper frontend at http://localhost:3000 and the backend at http://localhost:8000. Default admin credentials are admin and admin.

Please follow mentioned in step 5 of dev’s quickstart to create first instances of Carrot Mapper.

You can also access the Airflow webserver at http://localhost:8080 to monitor the DAGs running. Default admin credentials are admin and admin.

Try using Carrot by steps in the user quickstart to see if Carrot is running correctly. If you can successfully upload a new scan report, create mapping rules, and finally can export the Mapping rules JSON. That’s a sign that you have successfully install and run Carrot locally.