BioGRID-Coronavirus-Biorxiv-Triage

A simple script to take the Biorxiv Coronavirus Collection and Triage it for interaction terms

Requirements

• Pipenv (https://pypi.org/project/pipenv/)
• Python 3.6.9 (https://www.python.org/)

Configuration

• You need to create a new file called config/config.yml containing the settings for your implementation. You can use the config/config.sample.yml file as a template.

How to Run

• Go into the directory containing this repository
• Run: pipenv shell
• Run: pipenv install
• Run: python -m spacy download en_core_web_sm
• Create a directory called <DOWNLOAD_PATH> (what you set download_path equal to in the config file)
• Run: python run.py -d -e <DATE> where <DATE> is replaced with the date you want to go back to. For example, to fetch papers back to August 15, 2020 use: 2020-08-15
• On subsequent runs, if you don't want to re-download the json, you can simply execute: python run.py
• Running this script will will create a file called results.csv in the <DOWNLOAD_PATH> folder