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.
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
- 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 inRDAS/clinical/src/
- 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.
- Go to the root folder of the project ("RDAS") and run
nohup python3 -u start_test.py > {name_out_output_file}.txt &
- 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 &
If you have any feedback or questions, please reach out to us at [email protected]