omero-rdf

A plugin for exporting RDF from OMERO

Requirements

• OMERO 5.6.0 or newer
• Python 3.10, 3.11, or 3.12 (only versions with zeroc-ice binary wheels are supported; newer versions will be added when wheels are available)

Installing from PyPI

This section assumes that an OMERO.py is already installed.

Install the command-line tool using pip:

$ pip install -U omero-rdf

Developer guidelines

Using uv (recommended):

1. Fork/clone the repository (e.g. gh repo fork https://github.com/German-BioImaging/omero-rdf).

2. Create a virtualenv and activate it:

   uv venv .venv
   source .venv/bin/activate
   

   (or prefix commands with uv run instead of activating).

3. Install in editable mode with test dependencies (pulls the correct platform-specific zeroc-ice wheel):

   uv pip install -e ".[tests,dev]"
   

4. Run the test suite:

   pytest
   

5. Lint and format:

   ruff check
   ruff format --check
   ruff format
   

To run pre-commit hooks:

uv tool install pre-commit
pre-commit run --all-files

Quick check against IDR

Assuming you have the uv environment active (source .venv/bin/activate), use the public IDR server to confirm the CLI works (public/public credentials):

1. Log in once to create a session:

   omero login -s idr.openmicroscopy.org -u public -w public
   

2. Export RDF for a project on IDR (2902) and inspect the first triples:

   omero rdf -F=turtle Project:2902 -S=flat | head  -n 10
   

Release process

This repository uses versioneer to manage version numbers. A tag prefixed with v will be detected by the library and used as the current version at runtime.

Remember to git push all commits and tags.

Funding

Funded by the Delta Tissue Program of Wellcome Leap.

License

This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the GNU General Public License (GPL) v2 or later.

Copyright

2022-2024, German BioImaging