The Rare Disease Alert System (RDAS) is a system designed for annotating and managing information related to rare diseases. Users may subscribe to specific rare diseases and get email alerts when new information becomes available.

Environment Variables

To run this project, you will need to add the following environment variables:

AWS_ACCESS_KEY_ID AWS_SECRET_ACCESS_KEY PALANTIR_KEY NEO4J_URI NEO4J_USERNAME NEO4J_PASSWORD OMIM_KEY METAMAP_EMAIL METAMAP_KEY AWS_PROFILE NCBI_KEY

AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY = Amazon AWS User Credentials (For email service)

AWS_PROFILE = AWS profile to be used for services (set to "default")

PALANTIR_KEY = Palantir API key used for retrieving GARD related information from the DataLake project

NEO4J_URI, NEO4J_USERNAME, NEO4J_PASSWORD = Neo4j Database Credentials (For Python driver)

OMIM_KEY = OMIM API key used to populate the PubMed article database with OMIM information

METAMAP_EMAIL, METAMAP_KEY = MetaMap API key used to send information to their batch MetaMap services

NCBI_KEY = NCBI Entrez Eutilz API key, used to populate PubMed article database with articles

Deployment

Do the following for all 3 required servers (dev, test, prod)

• Create a conda environment with Python v3.8.16
• Pull the GitHub Repo to a local directory
• Inside of sysvars.py, change the current_user variable to your linux server username
• Download all of the dependencies from requirements.txt (preferable to install these dependencies within a Conda environment)
• Make sure the chromedriver binary is installed in your environment. Located in RDAS/clinical/src/

Production Server

• Once the preceding steps have been completed, go to the root folder of the project ("RDAS") and run nohup python3 -u start_prod.py > {name_out_output_file}.txt &. This will run the start of the pipeline in the background as a process and send its output to the txt file.

Testing Server

• Go to the root folder of the project ("RDAS") and run nohup python3 -u start_test.py > {name_out_output_file}.txt &

Development Server

• Before you start the pipeline, check config.ini to make sure the last updated dates for the databases are correct
• Go to the root folder of the project ("RDAS") and run nohup python3 -u start_dev.py > {name_out_output_file}.txt &

Feedback

If you have any feedback or questions, please reach out to us at [email protected]