curies

Idiomatic conversion between URIs and compact URIs (CURIEs).

import curies

converter = curies.load_prefix_map({
    "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
    # ... and so on
})

>>> converter.compress("http://purl.obolibrary.org/obo/CHEBI_1")
'CHEBI:1'

>>> converter.expand("CHEBI:1")
'http://purl.obolibrary.org/obo/CHEBI_1'

Full documentation is available at curies.readthedocs.io.

CLI Usage

This package comes with a built-in CLI for running a resolver web application or a IRI mapper web application:

# Run a resolver
python -m curies resolver --host 0.0.0.0 --port 8764 bioregistry

# Run a mapper
python -m curies mapper --host 0.0.0.0 --port 8764 bioregistry

The positional argument can be one of the following:

1. A pre-defined prefix map to get from the web (bioregistry, go, obo, monarch, prefixcommons)
2. A local file path or URL to a prefix map, extended prefix map, or one of several formats. Requires specifying a --format.

The framework can be swapped to use Flask (default) or FastAPI with --framework. The server can be swapped to use Werkzeug (default) or Uvicorn with --server. These functionalities are also available programmatically, see the docs for more information.

🧑‍🤝‍🧑 Related

Other packages that convert between CURIEs and URIs:

• https://github.com/prefixcommons/prefixcommons-py (Python)
• https://github.com/prefixcommons/curie-util (Java)
• https://github.com/geneontology/curie-util-py (Python)
• https://github.com/geneontology/curie-util-es5 (Node.js)
• https://github.com/endoli/curie.rs (Rust)
• https://github.com/cthoyt/curies4j (Java)
• https://github.com/biopragmatics/curies.rs (Rust, Node.js, Python)

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install curies

This package currently supports both Pydantic v1 and v2. See the Pydantic migration guide for updating your code.

👐 Contributing

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

👋 Attribution

🙏 Acknowledgements

This package heavily builds on the trie data structure implemented in pytrie.

⚖️ 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/curies.git
$ cd curies
$ 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/curies.git
$ cd curies
$ 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/curies/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.