🌿 SageRx

SageRx is a medication ontology and medication-related data aggregator created from many different public sources of data.

Including data from DailyMed, FDA, RxNorm, Orange Book, and more!

SageRx uses Airflow to schedule jobs to extract, load, and transform (using dbt) open drug data.

Data ends up in a PostgreSQL database and can be queried using pgAdmin (included with SageRx) or via any SQL editor of your choice.

Additional Documentation

We will be moving documentation over to Github, but additional documentation exists on the SageRx Website.

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License

Contributing

We would love to see you contribute to SageRx. Join our Slack channel to get involved.

Style Guide: How we think about the structure and naming conventions of SageRx.

Development Quickstart

Prerequisites

• Install Docker.
  • Windows users will also install WSL 2 (a Linux subsystem that runs on Windows) as part of this process.

Installation

1. Clone the repo.
2. Add a .env file at the root of the repo.
3. Add ENV vars to the .env file.
   • AIRFLOW_UID=<uid> - UID can be found by running id -u on linux systems, typically the first user on the system is 1000 or 1001.
     • Windows users following the Docker Desktop install guide should have WSL 2 installed. You can open up command line, type wsl and then within WSL 2, you can enter id -u to see your UID.
   • UMLS_API=<umls_api_key> - if you want to use RxNorm, you need an API key from UMLS.
4. Make sure Docker is installed
5. Run docker-compose up airflow-init.
6. Run docker-compose up.

NOTE: if you have an M1 Mac export DOCKER_DEFAULT_PLATFORM=linux/amd64, and re-build your images

NOTE 2: if you're running WSL1/2 you may need to use docker compose rather than docker-compose per this

Server URLs

• Airflow UI is hosted on localhost:8001 or 0.0.0.0:8001
  • Username/password = airflow / airflow
• PgAdmin is hosted on localhost:8002 or 0.0.0.0:8002
  • Username/password = sagerx / sagerx

Using dbt

On docker-compose up a dbt container will be created to be used for cli commands. To enter commands run docker exec -it dbt /bin/bash. This will place you into a bash session in the dbt container. Then you can run dbt commands as you normally would.

To serve dbt documentation locally, enter the commands in the dbt container dbt docs generate then dbt docs serve --port 8081. They should generate on http://localhost:8081

Troubleshooting

If you get issues on folder permissions:

sudo chmod -R 777 postgres,data,extracts,logs,plugins

If you get trouble from the postgres container with errors such as password authentication failed for user "airflow" or role "airflow" does not exist, these are all from the same issue that postgres is not setting itself up correctly. This is because of a file permission issue solved by running chmod +x ./postgres/0_pg_stat_statement.sh. You might need to remove any existing database configuration with rm -rf airflow/data and docker-compose down --volumes.