[ome-devel] Integration tests for importing a plate

[Etienne Dumoulin]

Hi Sebastien,

Thank you, it is exactly what I was looking for!

Regards,

Etienne

On Tue, May 29, 2018 at 8:58 PM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

> HI Etienne,
>
> On 29 May 2018, at 17:45, Etienne Dumoulin <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
> <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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>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Etienne Dumoulin
PhenomicAI
Lead software engineer
+1 (416)-471-8323
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