drugbank-downloader 0.1.0

Write scripts that can get drugbank data without redistributing it

drugbank_downloader

Don't worry about DrugBank licensing and distribution rules - just use drugbank_downloader to write code that knows how to download it and use it automatically.

Installation

$ pip install drugbank-downloader

Download A Specific Version

import os
from drugbank_downloader import download_drugbank

username = ...  # suggestion: load from environment with os.getenv('DRUGBANK_USERNAME')
password = ...

path = download_drugbank(version='5.1.7', username=username, password=password)

# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')
assert expected_path == path.as_posix()

After it's been downloaded once, it's smart and doesn't need to download again. It gets stored using pystow automatically in the ~/.data/drugbank directory.

Automating Configuration of DrugBank Credentials

There are two ways to automatically set the username and password so you don't have to worry about getting it and passing it around in your python code:

1. Set DRUGBANK_USERNAME and DRUGBANK_PASSWORD in the environment
2. Create ~/.config/drugbank.ini and set in the [drugbank] section a username and password key.

from drugbank_downloader import download_drugbank

# Same path as before
path = download_drugbank(version='5.1.7')

The username and password keyword arguments are available for all functions in this package, but will be omitted in the tutorial for brevity.

Download the Latest Version

First, you'll have to install bioversions with pip install bioversions, whose job it is to look up the latest version of many databases. Then, you can modify the previous code slightly by omitting the version keyword argument:

import os
from drugbank_downloader import download_drugbank

path = download_drugbank()

# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip based on the latest
# version, as of December 14th, 2020.
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')
assert expected_path == path.as_posix()

The version keyword argument is available for all functions in this package, but like the username and password will be omitted for brevity.

Don't Bother Unpacking - read full database.xml.zip Directly

DrugBank is a single XML (could be JSON in a better future) file inside a zip archive. Normally, people manually unzip this folder then do something with the resulting file. Don't do this, it's not reproducible! Instead, it can be opened as a file object in Python with the following code.

import zipfile
from drugbank_downloader import download_drugbank

path = download_drugbank()

with zipfile.ZipFile(path) as zip_file:
    with zip_file.open('full database.xml') as file:
        pass  # do something with the file

You don't have time to remember this. Just use drugbank_downloader.open_drugbank() instead:

from drugbank_downloader import open_drugbank

with open_drugbank() as file:
    pass  # do something with the file, same as above

Reading DrugBank's XML

After you've opened the file, you probably want to read it with an XML parser like:

from xml.etree import ElementTree
from drugbank_downloader import open_drugbank

with open_drugbank() as file:
    tree = ElementTree.parse(file)

You don't have time to remember this either. Just use drugbank_downloader.parse_drugbank() instead:

from xml.etree import ElementTree
from drugbank_downloader import parse_drugbank

tree = parse_drugbank()
root = tree.getroot()

If your first thing to do to the tree is always to get its root, just use drugbank_downloader.get_drugbank_root():

from drugbank_downloader import get_drugbank_root

root = get_drugbank_root()

You now know everything I can teach you. Please use these tools to do re-usable, reproducible science!

Store in a Different Place

If you want to store the data elsewhere using pystow (e.g., in pyobo I also keep a copy of this file), you can use the prefix argument.

import os
from drugbank_downloader import download_drugbank

path = download_drugbank(prefix=['pyobo', 'raw', 'drugbank'])

# This is where it gets downloaded: ~/.data/pyobo/raw/drugbank/5.1.7/full database.xml.zip
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'pyobo', 'raw', 'drugbank', '5.1.7',
                             'full database.xml.zip')
assert expected_path == path.as_posix()

See the pystow documentation on configuring the storage location further.

Download via CLI

After installing, run the following CLI command to ensure it and send the path to stdout

$ drugbank_downloader

If you haven't pre-configured the username and password, you can specify them with the --username and --password options.