path: root/python-drugbank-downloader.spec

%global _empty_manifest_terminate_build 0
Name:		python-drugbank-downloader
Version:	0.1.1
Release:	1
Summary:	Write scripts that can get drugbank data without redistributing it
License:	MIT
URL:		https://github.com/cthoyt/drugbank_downloader
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/9d/cb/658ba821ff969c61ecb280643c45e8d061db06ae5cec367f084998259b95/drugbank_downloader-0.1.1.tar.gz
BuildArch:	noarch

Requires:	python3-pystow
Requires:	python3-click
Requires:	python3-bioversions

%description
<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.




%package -n python3-drugbank-downloader
Summary:	Write scripts that can get drugbank data without redistributing it
Provides:	python-drugbank-downloader
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-drugbank-downloader
<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.




%package help
Summary:	Development documents and examples for drugbank-downloader
Provides:	python3-drugbank-downloader-doc
%description help
<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.




%prep
%autosetup -n drugbank-downloader-0.1.1

%build
%py3_build

%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .

%files -n python3-drugbank-downloader -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.1-1
- Package Spec generated