معرفی شرکت ها
drugbank-downloader-0.1.1
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مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Write scripts that can get drugbank data without redistributing it
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | drugbank-downloader-0.1.1 |
| نام | drugbank-downloader |
| نسخه کتابخانه | 0.1.1 |
| نگهدارنده | ['Charles Tapley Hoyt'] |
| ایمیل نگهدارنده | ['cthoyt@gmail.com'] |
| نویسنده | Charles Tapley Hoyt |
| ایمیل نویسنده | cthoyt@gmail.com |
| آدرس صفحه اصلی | https://github.com/cthoyt/drugbank_downloader |
| آدرس اینترنتی | https://pypi.org/project/drugbank-downloader/ |
| مجوز | MIT |
<h1 align="center">
drugbank_downloader
</h1>
<p align="center">
<a href="https://pypi.org/project/drugbank_downloader">
<img alt="PyPI" src="https://img.shields.io/pypi/v/drugbank_downloader" />
</a>
<a href="https://pypi.org/project/drugbank_downloader">
<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/drugbank_downloader" />
</a>
<a href="https://github.com/cthoyt/drugbank_downloader/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/drugbank_downloader" />
</a>
<a href="https://zenodo.org/badge/latestdoi/321374043">
<img src="https://zenodo.org/badge/321374043.svg" alt="DOI" />
</a>
</p>
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.
نیازمندی
| مقدار | نام |
|---|---|
| >=0.1.12 | pystow |
| - | click |
| - | bioversions |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl drugbank-downloader-0.1.1:
pip install drugbank-downloader-0.1.1.whl
نصب پکیج tar.gz drugbank-downloader-0.1.1:
pip install drugbank-downloader-0.1.1.tar.gz