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MicheleBortol authored Sep 24, 2024
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## Sources

The main sources are:
The main sources this project relies on are:
- omero-vitessce from Will Moore: https://github.com/will-moore/omero-vitessce
- cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
- `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
- Vitessce python package used for generating config files http://python-docs.vitessce.io/
- omero-web-zarr to serve OME-NGFF images: https://github.com/ome/omero-web-zarr
- omero-openlink to serve images and other files: https://github.com/sukunis/OMERO.openlink
- omero-test-infra for testing: https://github.com/ome/omero-test-infra

## Tests

### Test dataset
The dataset used for automated testing is at: [test/data/MB266](test/data/MB266)
This is a cropped version derived from larger images and their associated data available at:
https://doi.org/10.5281/zenodo.13832665

The original data are available at:
https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093

The associated publication is available at:
https://www.biorxiv.org/content/10.1101/2024.04.03.586404v1

### omero-test-infra configuration
[omero-test-infra](https://github.com/ome/omero-test-infra) is used for automated tests with [github-actions](.github/workflows/omero_plugin.yml).
The workflow setups an omero installation in docker and then:
1) Runs [app-config](.omeroci/app-config) to set up the omero-web plugin configuration.
2) Runs [app-build](.omeroci/app-build) which:
- runs to create a test user/group and upload a [test dataset](test/data/MB266).
- runs pytest tests in: [test/integration](test/integration)

It is possible to perform these tests locally by:
1) Starting the docker daemon.
2) Cloning the omero-test infra repository inside the base folder of omero-vitessce: `git clone https://github.com/openmicroscopy/omero-test-infra .omero`
3) Running: `.omero/app-docker`

## React web app

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