fairsharing-client

FAIRsharing Client

A client to the FAIRsharing API.

💪 Getting Started

FAIRsharing is a registry of high-quality metadata about standards, databases, and policies. However, there are two aspects to FAIRsharing's data that make it difficult to use:

1. It's licensed under the restrictive CC-BY-SA 4.0 license ( see https://fairsharing.org/licence). This makes it difficult to redistribute the data, even in part. Better options for community reuse are CC-BY 4.0 or ideally CC0. However, keep in mind that FAIR and Open are emphatically not the same thing.
2. Instead of offering a bulk download, there is an API that requires authentication using JWT.

While there's nothing wrong with JWT, it requires several steps that make programmatic access inconvenient for less seasoned programmers. The fairsharing_client package provides a way to automatically bulk download all contents from the API and store them locally in a reproducible way, so you can write code that relies on FAIRsharing data without having to worry about how to interact with its API nor redistribute its data yourself. Further, this package does some preprocessing on the content to make it more useful.

import fairsharing_client as fc

# Download the data and return the path of the YAML file
# This takes about 4 minutes and gets around 4K records.
path = fc.ensure_fairsharing()

# Download the data and open it for use
data = fc.load_fairsharing() 

# Get data for a given record
chebi_record = data["FAIRsharing.62qk8w"]

There are a few ways to do authentication:

1. Envionment Variables: set the FAIRSHARING_LOGIN and FAIRSHARING_PASSWORD envionrment variables
2. Configuration: in the ~/.config/fairshairing.ini file, add the following configuration:

   [fairsharing]
   login = [e-mail]
   password = ...
   

3. Keyword arguments: pass the login and password keywords to either of the example functions.

A reminder: this repository does NOT redistribute FAIRsharing's data, it only provides code for you to get it yourself.

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install fairsharing_client

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/cthoyt/fairsharing-client.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/fairsharing-client.git
$ cd fairsharing-client
$ pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action .

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/cthoyt/fairsharing-client.git
$ cd fairsharing-client
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the setup.cfg. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, src/fairsharing_client/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.