Don't worry about DrugBank licensing - write code that knows how to download it automatically
MIT License
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.
$ pip install drugbank-downloader
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.
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:
DRUGBANK_USERNAME
and DRUGBANK_PASSWORD
in the environment~/.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.
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.
full database.xml.zip
DirectlyDrugBank 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
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!
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.
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.
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
git clone git+https://github.com/cthoyt/drugbank-downloader.git
cd drugbank-downloader
pip install -e .
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.
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.
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.
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
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.
You only have to do the following steps once.
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.
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:
pyproject.toml
, CITATION.cff
, src/drugbank_downloader/version.py
,docs/source/conf.py
to not have the -dev
suffixbuild
twine
.tox -e bumpversion -- minor
after.This will trigger Zenodo to assign a DOI to your release as well.