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https://github.com/cthoyt/drugbank_downloader

Don't worry about DrugBank licensing - write code that knows how to download it automatically
https://github.com/cthoyt/drugbank_downloader

drugbank python reproducible-research

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Don't worry about DrugBank licensing - write code that knows how to download it automatically

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    drugbank_downloader






    

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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



```bash

$ pip install drugbank-downloader

```



## Download A Specific Version



```python

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`](https://github.com/cthoyt/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.



```python

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`](https://github.com/cthoyt/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:



```python

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.



```python

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:



```python

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:



```python

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:



```python

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()`:



```python

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`](https://github.com/pyobo/pyobo)

I also keep a copy of this file), you can use the `prefix` argument.



```python

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](https://github.com/cthoyt/pystow#%EF%B8%8F-configuration) 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



```bash

$ drugbank_downloader

```



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

options.