A client to the FAIRsharing API.
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:
- 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.
- 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:
- Envionment Variables: set the
FAIRSHARING_LOGIN
andFAIRSHARING_PASSWORD
envionrment variables - Configuration: in the
~/.config/fairshairing.ini
file, add the following configuration:[fairsharing] login = cthoyt@gmail.com password = ...
- Keyword arguments: pass the
login
andpassword
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.
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
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/fairsharing-client.git
$ cd fairsharing-client
$ pip install -e .
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 .
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
.
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:
- Uses Bump2Version to switch the
version number in the
setup.cfg
,src/fairsharing_client/version.py
, anddocs/source/conf.py
to not have the-dev
suffix - Packages the code in both a tar archive and a wheel
using
build
- Uploads to PyPI using
twine
. Be sure to have a.pypirc
file configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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.