[ome-devel] Integration tests for importing a plate

[Sebastien Besson (Staff)]

HI Etienne,

On 29 May 2018, at 17:45, Etienne Dumoulin <etienne at phenomic.ai<mailto:etienne at phenomic.ai>> wrote:

Hi Omero developers,

I have just started using the OMERO platform and I have a couple of separate questions. I will send them in two different emails, I hope you don't mind.

No worries at all. Splitting unrelated topics using different threads makes complete sense.

I have just customized an import. My new import loads a screen (a set of plates) using "omero import" command line tool on a directory (I think it is the only way to do it in Python) and adds annotations on the wells, plates and screen. It is working quite nicely, however I am not too sure how to create my integration tests. All the plate directories I have are several gigabytes big and I don't know how to create my own XML metadata file for a plate. All my attempts create orphaned images at the import. Ideally, I would like to be able to load a mini-plate successfully in a few seconds, a minute top.

What would you do in my situation?

For integration testing, your requirements make complete sense. You might want to
use Bio-Formats test images [1] which have support for HCS layout e.g.

$ touch “test&screens=1.fake"
$ bin/omero import "test&screens=1.fake”

The OMERO integration tests are making heave use of this functionality for importing
images without the need for real data - see for instance the CLI import integration tests [2].

[1] https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/generating-test-images.html
[2] https://github.com/openmicroscopy/openmicroscopy/blob/v5.4.6/components/tools/OmeroPy/test/integration/clitest/test_import.py#L1042

Thanks,

Etienne

Hope this helps,
Sébastien

NB: the OME team is holding its annual Users Meeting for the next three days. Please bare with us
as we might come back to the two other threads you started as late as next Monday.

--
Etienne Dumoulin
PhenomicAI
Lead software engineer
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