pymetadata

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pymetadata: python utilities for metadata and COMBINE archives

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pymetadata is a collection of python utilities for working with metadata in the context of COMBINE standards with source code available from https://github.com/matthiaskoenig/pymetadata <https://github.com/matthiaskoenig/pymetadata>__.

Features include among others

• COMBINE archive version 1 support (OMEX)
• annotation classes and helpers
• SBO and KISAO ontology enums

If you have any questions or issues please open an issue <https://github.com/matthiaskoenig/pymetadata/issues>__.

Documentation

Documentation is still work in progress. For an example usage of the COMBINE archive see src/pymetadata/examples/omex_example.py <src/pymetadata/examples/omex_example.py>__.

How to cite

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg :target: https://doi.org/10.5281/zenodo.5308801 :alt: Zenodo DOI

Contributing

Contributions are always welcome! Please read the contributing guidelines <https://github.com/matthiaskoenig/pymetadata/blob/develop/.github/CONTRIBUTING.rst>__ to get started.

License

• Source Code: LGPLv3 <http://opensource.org/licenses/LGPL-3.0>__
• Documentation: CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>__

The pymetadata source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection

• A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

Installation

pymetadata is available from pypi <https://pypi.python.org/pypi/pymetadata>__ and can be installed via::

pip install pymetadata

Develop version

The latest develop version can be installed via::

pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop

Or via cloning the repository and installing via::

git clone https://github.com/matthiaskoenig/pymetadata.git
cd pymetadata
pip install -e .

To install for development use::

pip install -e .[development]

Cache path

pymetadata caches some information for faster retrieval. The cache path is set to::

CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"

To use a custom cache path use::

import pymetadata
pymetadata.CACHE_PATH = <cache_path>

© 2021-2024 Matthias König