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 and zeroc-ice is configured.

Install the command-line tool using pip:

$ pip install -U omero-rdf

Developer guidelines

Using uv (recommended):

Fork/clone the repository (e.g. gh repo fork https://github.com/German-BioImaging/omero-rdf).
Create a virtualenv and activate it:
```
uv venv .venv
source .venv/bin/activate
```
(or prefix commands with uv run instead of activating).
Install in editable mode with test dependencies:

::

uv pip install -r zeroc-ice-requirements.txt uv pip install -e “.[tests,dev]”

Run the test suite:

pytest test/unit
pytest test/integration/test_idr

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 credentials):

omero login -s idr.openmicroscopy.org -u [PUBLIC USER] -w [PUBLIC PASSWORD]

Export RDF for a project on IDR (2902) and inspect the first triples:
```
omero rdf -F=turtle Project:2902 -S=flat | head  -n 10
```

Mocking GitHub Actions checks

If you have gh installed, you can run the checks locally:
```
gh act push
```

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

2022-2026, German BioImaging

Metadata

Release files for omero-rdf 0.7.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for omero-rdf 0.7.2
File	Size	Uploaded
omero_rdf-0.7.2.tar.gz	24.7 kB	Feb 27, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for omero-rdf 0.7.2
File	Interpreter	ABI	Platform	Reset
omero_rdf-0.7.2-py3-none-any.whl 23.2 kB Feb 27, 2026	Python 3	none	any	Details

Total release size: 47.9 kB

Release files / omero_rdf-0.7.2.tar.gz

Download URL	omero_rdf-0.7.2.tar.gz
Size	24.7 kB
Tags	Source
SHA-256 checksum How to use checksums	`50813f10f4f4a0b382f7fefa5e6a531f16acc7b535ff86318559e40fbbc23430`
BLAKE2b-256 checksum How to use checksums	`075e1fe5f3b6f04a582dd506033aea834a81dcb7d240c5bc1d06216010c9f950`
Upload date	Feb 27, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.7`

Release files / omero_rdf-0.7.2-py3-none-any.whl

Download URL	omero_rdf-0.7.2-py3-none-any.whl
Size	23.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`3b890cdf1a2dd4f3085aceffdf30a2913df4f08da9c6adf9b4df8136d0382e02`
BLAKE2b-256 checksum How to use checksums	`e6b20961be09a7841e330e9ffc93ce9247b1e34bc45d8a0f9fb4e775bbb17675`
Upload date	Feb 27, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.7`