drugbank-downloader 0.2.0

A tool for reproducibly downloading and extracting DrugBank data

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.

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

git clone git+https://github.com/cthoyt/drugbank-downloader.git
cd drugbank-downloader
pip install -e .

Updating Package Boilerplate

This project uses cruft to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Update with the following:

pip install cruft
cruft update

More info on Cruft's update command is available here.

🥼 Testing

After cloning the repository and installing tox with pip install tox tox-uv, the unit tests in the tests/ folder can be run reproducibly with:

tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

git clone git+https://github.com/cthoyt/drugbank-downloader.git
cd drugbank-downloader
tox -e docs
open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the pyproject.toml. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .readthedocs.yml YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with tox -e docs-test) but also that ReadTheDocs can build it too.

Configuring ReadTheDocs

1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
4. Click next, and you're good to go!

📦 Making a Release

Configuring Zenodo

Zenodo is a long-term archival system that assigns a DOI to each release of your package.

1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this

After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/cthoyt/drugbank-downloader to see the DOI for the release and link to the Zenodo record for it.

Registering with the Python Package Index (PyPI)

You only have to do the following steps once.

1. Register for an account on the Python Package Index (PyPI)
2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token

Configuring your machine's connection to PyPI

You have to do the following steps once per machine. Create a file in your home directory called .pypirc and include the following:

[distutils]
index-servers =
    pypi
    testpypi

[pypi]
username = __token__
password = <the API token you just got>

# This block is optional in case you want to be able to make test releases to the Test PyPI server
[testpypi]
repository = https://test.pypi.org/legacy/
username = __token__
password = <an API token from test PyPI>

Note that since PyPI is requiring token-based authentication, we use __token__ as the user, verbatim. If you already have a .pypirc file with a [distutils] section, just make sure that there is an index-servers key and that pypi is in its associated list. More information on configuring the .pypirc file can be found here.

Uploading to PyPI

After installing the package in development mode and installing tox with pip install tox tox-uv, run the following from the shell:

tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the pyproject.toml, CITATION.cff, src/drugbank_downloader/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine.
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.

Releasing on GitHub

1. Navigate to https://github.com/cthoyt/drugbank-downloader/releases/new to draft a new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button

This will trigger Zenodo to assign a DOI to your release as well.