OMERO.biomero Plugin

🚀 This package is part of BIOMERO 2.0 — For complete deployment and FAIR infrastructure setup, start with the NL-BIOMERO Documentation 📖

Description

The OMERO.biomero plugin adds functionality to the OMERO web client, allowing users to upload images directly from the web client. The uploads are in-place, meaning that the data is not duplicated in OMERO but remains where it is. Users can monitor their uploads using a dashboard.

Additionally, the plugin provides a user-friendly interface to execute OMERO scripts and BioMero workflows and monitor their execution.

Features

• Image Uploads: Upload images directly from the OMERO web client without duplicating data.
• Upload Monitoring: Monitor the status and history of uploads using a dashboard.
• Script Execution: Execute OMERO scripts through a user-friendly interface and monitor their execution.
• Workflow Execution: Execute BIOMERO workflows on SLURM cluster and monitor their execution.
• Optional ROI Output: Import label-image results and convert them into Polygon or Mask ROIs on the original images. BIOMERO automatically matches results to source images and selects label-like outputs on a best-effort basis.

Technologies Used

• Frontend: React
• Backend: Python/Django

Group folder mapping compatibility

Administrators manage importer group-to-folder mappings in the importer Admin Settings page. Saving mappings always writes the complete mapping object to:

• group-mappings.json, configured by OMERO_BIOMERO_GROUP_MAPPINGS_FILE.

When biomero-config.json already exists, saving also replaces its group_mappings key. A missing legacy config is not created solely for group mappings. Its location is configured by OMERO_BIOMERO_CONFIG_FILE.

The conditional second write preserves compatibility with BIOMERO scripts that still read biomero-config.json["group_mappings"] directly. Both locations are replaced with the complete submitted object, so deleting a mapping in the UI also removes it from both files. Other top-level keys in biomero-config.json are preserved.

Reads remain backward compatible with deployments that only have biomero-config.json: mappings from both files are merged, and values from group-mappings.json take precedence when the same group exists in both.

Development

The following instructions assume Ubuntu OS. For development, we use NL-BIOMERO - dockerized OMERO setup.

Setup and development of plugin core/Django files

1. Install Docker.
2. Clone the omero-biomero.
3. Clone the NL-BIOMERO repository and enter it.
4. Folders with both repositories must be in the same parent folder.
5. Enter NL-BIOMERO repository and start OMERO containers: docker compose --file docker-compose-dev.yml up. This compose file enables restarting OMERO Webclient server without causing the container to exit. It does not automatically start the Webclient server. It also mounts omero-biomero as a volume in the Webclient container. Changes to the plugin code are automatically reflected in the Webclient because pip installs the plugin in editable mode (see below).
6. In new terminal, enter omero-biomero repository and execute ./omero-init.sh. This will start the OMERO Webclient server in background mode. It also installs the plugin in editable mode, so changes to the plugin code are automatically reflected in the Webclient.
7. After making changes to the code outside of the folder webapp, they should be automatically reflected in the webclient. You can also execute ./omero-update.sh to restart the Webclient server and apply changes.

Testing

To run tests, create virtual environment, activate it and install the package in editable mode (this automatically pulls all dependencies from setup.py):

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install -e .

Then you can run the tests using:

python manage.py test

Note: All dependencies (including biomero-importer>=1.0.0b5) are automatically installed from setup.py when you install with -e .

Setup and development of the plugin frontend

1. Install Node.js and Yarn.
   • For Windows, install Corepack as superuser, then you can run yarn commands like corepack yarn install
2. Enter omero-biomero repository and enter the webapp folder.
3. Run yarn install to install the necessary packages.
4. Run yarn watch to watch for changes in the code and automatically rebuild the code on save. Each time code is rebuilt, Webclient server will automatically restart (~30s), which will update JS bundle in the Webclient static folder. Reload the Webclient page to see changes.
5. To build the code for production, run yarn build. This will also copy the JS bundle to the Webclient static folder and restart the Webclient server.

Troubleshooting

• Sometimes the plugin page loading will fail after multiple server restarts and you will see 404 error in the console, informing that plugin JS bundle could not be found, even though the files *are present on the server at the correct location. We found that the only way to fix this is to restart NL-BIOMERO containers: docker compose --file docker-compose-dev.yml up in the NL-BIOMERO repository.