APICURON Client

An unofficial client for interacting with the APICURON curation metadatabase.

💪 Getting Started

The following example shows how you can prepare a submission of a new resource to APICURON. Because apicuron_client uses PyDantic under the hood, the JSON is validated and automatically converted into programmatic models. The Description.update_remote() function takes care of interacting with the API and loading the APICURON_TOKEN from the environment or a config file with pystow.

from apicuron_client import Description

payload = {
   "resource_id": "Biomappings",
   "resource_name": "Biomappings",
   "resource_uri": "https://biomappings.github.io/biomappings/",
   "resource_url": "https://biomappings.github.io/biomappings/",
   "resource_long_name": "Biomappings",
   "resource_description": "Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.",
   "terms_def": [
      {
         "activity_term": "novel_curation",
         "activity_name": "Curated novel mapping",
         "activity_category": "generation",
         "score": 50,
         "description": "Curated a novel mapping between two entities"
      },
      {
         "activity_term": "validate_prediction",
         "activity_name": "Validate predicted mapping",
         "activity_category": "generation",
         "score": 50,
         "description": "Affirmed the correctness of a predicted mapping"
      },
      {
         "activity_term": "invalidate_prediction",
         "activity_name": "Invalidate predicted mapping",
         "activity_category": "generation",
         "score": 50,
         "description": "Affirmed the incorrectness of a predicted mapping"
      }
   ],
   "achievements_def": [
      {
         "category": "1",
         "name": "Newbie curator",
         "count_threshold": 10,
         "type": "badge",
         "list_terms": [
            "novel_curation",
            "validate_prediction",
            "invalidate_prediction"
         ],
         "color_code": "#055701"
      }
   ]
}
description = Description(**payload)
description.update_remote()

The results can then be seen on the APICURON website at https://apicuron.org/database?resource_uri=https:%2F%2Fbiomappings.github.io%2Fbiomappings%2F.

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install apicuron_client

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

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

To install in development mode, use the following:

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

👐 Contributing

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

👀 Attribution

⚖️ License

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

📖 Citation

This project isn't officially from the APICURON team, but if you like it, please cite their paper:

@article{Hatos2021,
   author = {Hatos, Andr{\'{a}}s and Quaglia, Federica and Piovesan, Damiano and Tosatto, Silvio C E},
   doi = {10.1093/database/baab019},
   issn = {1758-0463},
   journal = {Database},
   month = {apr},
   title = {{APICURON: a database to credit and acknowledge the work of biocurators}},
   url = {https://academic.oup.com/database/article/doi/10.1093/database/baab019/6244733},
   volume = {2021},
   year = {2021}
}

Acknowledgements

🍪 Cookiecutter

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

🛠️ For Developers

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

❓ 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.

📦 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 BumpVersion to switch the version number in the setup.cfg and src/apicuron_client/version.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel
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.