Metadata-Version: 2.1
Name: curies
Version: 0.4.5
Summary: Idiomatic conversion between URIs and compact URIs (CURIEs).
Home-page: https://github.com/cthoyt/curies
Download-URL: https://github.com/cthoyt/curies/releases
Author: Charles Tapley Hoyt
Author-email: cthoyt@gmail.com
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Project-URL: Bug Tracker, https://github.com/cthoyt/curies/issues
Project-URL: Source Code, https://github.com/cthoyt/curies
Keywords: snekpack,cookiecutter,semantic web,compact uniform resource identifiers,uniform resource identifiers,curies
Classifier: Development Status :: 1 - Planning
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Framework :: Pytest
Classifier: Framework :: tox
Classifier: Framework :: Sphinx
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: tests
Provides-Extra: pandas
Provides-Extra: bioregistry
Provides-Extra: flask
Provides-Extra: fastapi
Provides-Extra: rdflib
Provides-Extra: docs
License-File: LICENSE

<!--
<p align="center">
  <img src="https://github.com/cthoyt/curies/raw/main/docs/source/logo.png" height="150">
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<h1 align="center">
  curies
</h1>

<p align="center">
    <a href="https://github.com/cthoyt/curies/actions?query=workflow%3ATests">
        <img alt="Tests" src="https://github.com/cthoyt/curies/workflows/Tests/badge.svg" />
    </a>
    <a href="https://pypi.org/project/curies">
        <img alt="PyPI" src="https://img.shields.io/pypi/v/curies" />
    </a>
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        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/curies" />
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    <a href="https://github.com/cthoyt/curies/blob/main/LICENSE">
        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/curies" />
    </a>
    <a href='https://curies.readthedocs.io/en/latest/?badge=latest'>
        <img src='https://readthedocs.org/projects/curies/badge/?version=latest' alt='Documentation Status' />
    </a>
    <a href="https://codecov.io/gh/cthoyt/curies/branch/main">
        <img src="https://codecov.io/gh/cthoyt/curies/branch/main/graph/badge.svg" alt="Codecov status" />
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        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /> 
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        <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' />
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        <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/>
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</p>

Idiomatic conversion between URIs and compact URIs (CURIEs).

```python
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`.

Full documentation is available at [curies.readthedocs.io](https://curies.readthedocs.io).

### Standardization

The `curies.Converter` data structure supports prefix and URI prefix synonyms.
The following example loads the [Bioregistry](https://bioregistry.io) and demonstrates
using these synonyms to support standardizing prefixes, CURIEs, and URIs. Note below,
the colloquial prefix `gomf`, sometimes used to represent the subspace in the
[Gene Ontology (GO)](https://obofoundry.org/ontology/go) corresponding to molecular
functions, is upgraded to the preferred prefix, `GO`.

```python
from curies import Converter, Record

converter = Converter([
    Record(
        prefix="GO",
        prefix_synonyms=["gomf", "gocc", "gobp", "go", ...],
        uri_prefix="http://purl.obolibrary.org/obo/GO_",
        uri_prefix_synonyms=[
            "http://amigo.geneontology.org/amigo/term/GO:",
            "https://identifiers.org/GO:",
            ...
        ],
    ),
    # And so on
    ...
])

>>> converter.standardize_prefix("gomf")
'GO'
>>> converter.standardize_curie('gomf:0032571')
'GO:0032571'
>>> converter.standardize_uri('0032571')
'http://purl.obolibrary.org/obo/GO_0032571'
```

### Loading Prefix Maps

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:

```python
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:

```python
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()
```

### Bulk Operations

Apply in bulk to a `pandas.DataFrame` with `Converter.pd_expand` and
`Converter.pd_compress`:

```python
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):

```python
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)
```

### CLI Usage

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

```shell
$ python -m curies --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)

## 🚀 Installation

The most recent release can be installed from
[PyPI](https://pypi.org/project/curies/) with:

```bash
$ pip install curies
```

## 👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/curies/blob/master/.github/CONTRIBUTING.md) for more information on getting
involved.

## 👋 Attribution

### 🙏 Acknowledgements

This package heavily builds on the [trie](https://en.wikipedia.org/wiki/Trie)
data structure implemented in [`pytrie`](https://github.com/gsakkis/pytrie).

### ⚖️ License

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

### 🍪 Cookiecutter

This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.

## 🛠️ For Developers

<details>
  <summary>See developer instructions</summary>


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:

```bash
$ 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:

```shell
$ tox
```

Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/cthoyt/curies/actions?query=workflow%3ATests).

### 📖 Building the Documentation

The documentation can be built locally using the following:

```shell
$ 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`](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`](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:

```shell
$ tox -e finish
```

This script does the following:

1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,
   `src/curies/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/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.

</details>
