BETTER-fairificator

The FAIRification tools for BETTER project.

Installation

From the root of the project, i.e., in BETTER-fairificator folder

1. Make sure to have a recent Python 3 version, e.g., Python 3.12 (tested with Python 3.12 only)
2. Run the configuration script: bash configure.sh
3. Activate the virtual environment: source .venv-better-fairificator/bin/activate
4. To run the ETL script: python3 src/main.py --hospital_name=<hospital_name> --database_name=<database_name> --metadata_filepath=<path/to/metadata.csv> --data_filepath=<path/to/data.csv> --drop=<drop> where:
   • --hospital_name ranges over: ["IT_BUZZI_UC1", "RS_IMGGE", "ES_HSJD", "IT_BUZZI_UC3", "ES_TERRASSA", "DE_UKK", "ES_LAFE", "IL_HMC"] (required)
   • --database_name is the database name (optional, default: better_default)
   • --metadata_filepath is the (absolute) path of the metadata file (required)
   • --data_filepath=datasets/data/BUZZI/screening.csv is the (absolute) path of the data file (required)
   • --drop=False ranges over ["True", "False"] and indicates whether to drop the database. WARNING: if set to True, this action is not reversible!
   • An example: python3 src/main.py --hospital_name=IT_BUZZI_UC1 --database_name=currenttest --metadata_filepath=datasets/metadata/IT-Buzzi-variables.csv --data_filepath=datasets/data/BUZZI/screening.csv --drop=False
5. To run the tests: python3 -m unittest discover