automatic import of python-drugbank-downloaderopeneuler20.03

3 files changed, 614 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..db98e91 100644
--- a/.gitignore
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@@ -0,0 +1 @@
+/drugbank_downloader-0.1.1.tar.gz
diff --git a/python-drugbank-downloader.spec b/python-drugbank-downloader.spec
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+%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
diff --git a/sources b/sources
new file mode 100644
index 0000000..e1e51c1
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+5598c3bbb48edfe6981bccd82583a681  drugbank_downloader-0.1.1.tar.gz