Drugbank Scraper

Run

1. See Pipenv & Virtual Environments guide to create a virtual environment and activate the virtual environment
2. Install graphviz brew install graphviz
3. Install requirements with pip install -r requirements.txt.
4. Create PostgreSQL database.
5. Create .env file with cp .env.template .env and fill environment variables.

Spiders

Drug

Run scrapy crawl drug to run drug spider and populate database. This will scrape data, create and populate database tables. Final data will be in drugbank schema. This will:

1. Scrape following data:
   • DrugBank ID
   • SMILES string
   • Gene name
   • Actions and alternative identifiers of every target.
2. Save scraped data into the previously created PostgreSQL database.

Development

1. See the virtual environment step above.
2. Install requirements with pip install -r requirements_dev.txt.
3. Run pre-commit install to install pre-commit hooks. This repo is already set up to use some pre-commit hooks for code quality purposes. Configuration file is available here. More information about pre-commit is available on their website.