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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
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Integrate another bioMLmodel (biomd0000001076) #1371

Closed anuprulez closed 6 months ago

anuprulez commented 6 months ago

ping @bgruening thanks!

Integrates one of the models from (https://github.com/bgruening/galaxytools/issues/1365): BIOMD0000001076

The docker container is at: docker.io/anupkumar/biomodels_biomd0000001076:1. I could not push it to quay.io/galaxy/...

The source for building docker is at: https://github.com/anuprulez/biomodelsml-docker/tree/master/prediction_bc_mlp

bgruening commented 6 months ago

Can you look at the failing test? Anup should we move the containers to usegalaxy-eu organisation.

anuprulez commented 6 months ago

Ok, tests are fixed. I have moved the containers repo to https://github.com/usegalaxy-eu/docker-biomodels-ml

anuprulez commented 6 months ago

I see that the CI's lxml package is now lxml-5.0.0-cp37-cp37m-manylinux_2_28_x86_64.whl.metadata updated but in the previous successful run (https://github.com/bgruening/galaxytools/actions/runs/7299086010/job/19891280680), it was lxml-4.9.4-cp37-cp37m-manylinux_2_28_x86_64.whl.metadata. Maybe that's the cause of failing tests in planemo lint step? Locally, I am using the same planemo==0.75.19 as the CI.

lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329
bgruening commented 6 months ago

This is a known problem due to a new lxml version. pip install 'lxml<5' will fix that or new Galaxy packages.

Why did you remove the creator tag?

anuprulez commented 6 months ago

Why did you remove the creator tag?

I was testing to resolve the lining error. I made a few changes to find the cause of the lining error in the XML like removing citations as well. Locally, planemo lint worked fine. It's all there now.

This is a known problem due to a new lxml version. pip install 'lxml<5' will fix that or new Galaxy packages.

ah, good to know :)

anuprulez commented 6 months ago

yes, I think so :)