Idiomatic conversion between URIs and compact URIs (CURIEs).
Project description
curies
Idiomatic conversion between URIs and compact URIs (CURIEs).
from curies import Converter
converter = Converter.from_prefix_map({
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"MONDO": "http://purl.obolibrary.org/obo/MONDO_",
"GO": "http://purl.obolibrary.org/obo/GO_",
# ... and so on
"OBO": "http://purl.obolibrary.org/obo/",
})
>>> converter.compress("http://purl.obolibrary.org/obo/CHEBI_1")
'CHEBI:1'
>>> converter.expand("CHEBI:1")
'http://purl.obolibrary.org/obo/CHEBI_1'
# Unparsable
>>> assert converter.compress("http://example.com/missing:0000000") is None
>>> assert converter.expand("missing:0000000") is None
When some URI prefixes are partially overlapping (e.g.,
http://purl.obolibrary.org/obo/GO_ for GO and
http://purl.obolibrary.org/obo/ for OBO), the longest
URI prefix will always be matched. For example, compressing
http://purl.obolibrary.org/obo/GO_0032571
will return GO:0032571 instead of OBO:GO_0032571.
All loader function work on local file paths, remote URLs, and pre-loaded data structures. For example, a converter can be instantiated from a web-based resource in JSON-LD format:
from curies import Converter
url = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/semweb.context.jsonld"
converter = Converter.from_jsonld(url)
Several converters can be instantiated from pre-defined web-based resources:
import curies
# Uses the Bioregistry, an integrative, comprehensive registry
bioregistry_converter = curies.get_bioregistry_converter()
# Uses the OBO Foundry, a registry of ontologies
obo_converter = curies.get_obo_converter()
# Uses the Monarch Initative's project-specific context
monarch_converter = curies.get_monarch_converter()
Apply in bulk to a pandas.DataFrame with Converter.pd_expand and
Converter.pd_compress:
import curies
import pandas as pd
df = pd.read_csv(...)
obo_converter = curies.get_obo_converter()
obo_converter.pd_compress(df, column=0)
obo_converter.pd_expand(df, column=0)
Apply in bulk to a CSV file with Converter.file_expand and
Converter.file_compress (defaults to using tab separator):
import curies
path = ...
obo_converter = curies.get_obo_converter()
# modifies file in place
obo_converter.file_compress(path, column=0)
# modifies file in place
obo_converter.file_expand(path, column=0)
Full documentation is available here.
CLI Usage
This package comes with a built-in CLI for running a resolver web application:
$ python -m curies --host 0.0.0.0 --port 8764 bioregistry
The positional argument can be one of the following:
- A pre-defined prefix map to get from the web (bioregistry, go, obo, monarch, prefixcommons)
- 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)
🚀 Installation
The most recent release can be installed from PyPI with:
$ pip install curies
👐 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:
- Uses Bump2Version to switch the version number in the
setup.cfg,src/curies/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
build - Uploads to PyPI using
twine. Be sure to have a.pypircfile 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 minorafter.
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