BioGRID Biorxiv Fetcher

Take a list of BioRxiv DOIs and parse them out using the BioRxiv API

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
• Create a directory called <DOWNLOAD_PATH> (what you set download_path equal to in the config file)
• Run: python run.py -i <input_file>-o<sql_file>-e<excel_file>-swhereis replaced with the id you want to start counting from. So using125would start counting from888800000125`.
• Running this script will will create a file called <sql_file> and another file called <excel_file> in the <DOWNLOAD_PATH> folder

Example:

• python run.py -i dois.csv -o pubs.sql -e excel.csv -s 126