ARC export option
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We are right now starting a project to implement export of OMERO data to ARC format. I am assigned to implement the code, @pzentis from CECAD imaging facility leads this project as part of NFDI4BIOIMAGE
More details about the project here: https://forum.image.sc/t/exciting-freelance-opportunities-extend-omero-functionality/86637
Apart from the question how to map OMERO data to an ARC, there is the question how to make the exporter available.
From our side there are two ideas how we could implement the tool:
- include the ARC export into omero-cli-transfer e.g.
omero transfer pack --arc, where arc dependencies could be optionally installed with omero-cli-transferpip install omero-cli-transfer[arc] - Develop an independent OMERO CLI plugin for arc export.
The ARC exporter is just the first step, for next year an importer from ARC to OMERO is also planned.
I you think it is a good idea, to extend omero-cli-tranfer to transfer data from OMERO to ARC repositories and vice versa, I am happy to follow this path and submit a pull request within the next month.
All the best
Christoph
Hi Christoph,
I'm excited folks are enthusiastic about this tool! I think, in a perfect world where I created omero-cli-transfer in a more modular way from scratch, this would be a plugin - but right now a regular PR into the main omero-cli-transfer codebase (with optional dependencies) probably makes more sense. Let me know if you need any help from my end!
OK, cool, then I'll start implementing the "--arc" option for omero-cli-transfer. I am happy that you support that idea!
One question regarding running integration tests on my local machine: I want to run tests on my local installation to be able to debug interactively.
I started an omero test server with
sudo .omero/compose up
I copied the ice.config from the docker container to a local folder. Then I run tests with setting environment variables for ICE CONFIG and OMERODIR:
ICE_CONFIG=path/to/my/local/ice.config OMERODIR=. pytest
I have to set the OMERODIR environment variable, but the omero server runs inside the docker container. So I just set an existing "fake" directory as OMERODIR, which is working for most of the tests, but not for all of them.
I guess there is a better way to run the integration tests locally. Do you have an idea how to do this in a better way?
You shouldn't need any of that - simply running .omero/docker cli should do all of it: the docker-compose, using your local version and running tests. It takes a while for the compose/test environment to spin up and the tests are not particularly quick (the whole process is ~10 mins on my machine), but it should be a single-command for everything!
Great, thank you!
Closing this as complete.