Skip to main content

Write scripts that can get drugbank data without redistributing it

Project description

drugbank_downloader

DOI

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)
root = tree.getroot()

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

from drugbank_downloader import parse_drugbank

root = parse_drugbank()

You 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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

drugbank_downloader-0.0.3.tar.gz (7.0 kB view details)

Uploaded Source

Built Distribution

drugbank_downloader-0.0.3-py3-none-any.whl (7.1 kB view details)

Uploaded Python 3

File details

Details for the file drugbank_downloader-0.0.3.tar.gz.

File metadata

  • Download URL: drugbank_downloader-0.0.3.tar.gz
  • Upload date:
  • Size: 7.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.6.1 requests/2.25.1 setuptools/51.0.0 requests-toolbelt/0.9.1 tqdm/4.55.0 CPython/3.9.1

File hashes

Hashes for drugbank_downloader-0.0.3.tar.gz
Algorithm Hash digest
SHA256 5ec4a886418b700351bbe8ed17557b867339113616b143aaf1167db073ef93b4
MD5 b590126afa0d061141174e9702ded32c
BLAKE2b-256 ed80c3f99ba2db959392a69870a78dbfcf52d7f66d8c3035e5a4599e74269a89

See more details on using hashes here.

Provenance

File details

Details for the file drugbank_downloader-0.0.3-py3-none-any.whl.

File metadata

  • Download URL: drugbank_downloader-0.0.3-py3-none-any.whl
  • Upload date:
  • Size: 7.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.6.1 requests/2.25.1 setuptools/51.0.0 requests-toolbelt/0.9.1 tqdm/4.55.0 CPython/3.9.1

File hashes

Hashes for drugbank_downloader-0.0.3-py3-none-any.whl
Algorithm Hash digest
SHA256 9a92ab103640b62de0f3c4180a6fab161783bb4517b7178aed27081d6b5d48b2
MD5 1d85dba5944deff15a8a17a4dc7c6881
BLAKE2b-256 777bb160bc071faaf4b711c6b95be3d21b3cbc07a45fab86169fc1bf4d9a9816

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page