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curies-0.5.4
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مشاهده بیشترتوضیحات
Idiomatic conversion between URIs and compact URIs (CURIEs).
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | curies-0.5.4 |
| نام | curies |
| نسخه کتابخانه | 0.5.4 |
| نگهدارنده | ['Charles Tapley Hoyt'] |
| ایمیل نگهدارنده | ['cthoyt@gmail.com'] |
| نویسنده | Charles Tapley Hoyt |
| ایمیل نویسنده | cthoyt@gmail.com |
| آدرس صفحه اصلی | https://github.com/cthoyt/curies |
| آدرس اینترنتی | https://pypi.org/project/curies/ |
| مجوز | MIT |
<!--
<p align="center">
<img src="https://github.com/cthoyt/curies/raw/main/docs/source/logo.png" height="150">
</p>
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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>
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<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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<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" />
</a>
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<img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' />
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</a>
<a href="https://zenodo.org/badge/latestdoi/519905487">
<img src="https://zenodo.org/badge/519905487.svg" alt="DOI">
</a>
</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 exampl 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('http://amigo.geneontology.org/amigo/term/GO:0032571')
'http://purl.obolibrary.org/obo/GO_0032571'
```
Note: non-standard URIs can still be parsed with `converter.parse_uri()` and compressed
into CURIEs with `converter.compress()`.
### 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 or a IRI mapper web application:
```shell
# 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)
## 🚀 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>
نیازمندی
| مقدار | نام |
|---|---|
| - | pytrie |
| - | requests |
| >=0.5.136 | bioregistry |
| - | sphinx |
| - | sphinx-rtd-theme |
| - | sphinx-autodoc-typehints |
| - | sphinx-automodapi |
| - | fastapi |
| - | python-multipart |
| - | httpx |
| - | defusedxml |
| - | uvicorn |
| - | flask |
| - | defusedxml |
| - | pandas |
| - | rdflib |
| - | pytest |
| - | coverage |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl curies-0.5.4:
pip install curies-0.5.4.whl
نصب پکیج tar.gz curies-0.5.4:
pip install curies-0.5.4.tar.gz