Add image verification support to CI

[kostrykin]

For the contributor:

• I have read the CONTRIBUTING.md document.
• License permits unrestricted use (educational + commercial).
• This PR adds or updates a tool or tool collection.
  • This PR adds a new tool or tool collection.
  • This PR updates an existing tool or tool collection.
  • Tools added/updated by this PR comply with the Naming and Annotation Conventions for Tools in the Image Community in Galaxy (or explain why they do not).
• This PR does something else (explain below).

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This PR adds the image verification support from galaxyproject/galaxy#17581 and galaxyproject/galaxy#17556, until the new features become available in a recent Galaxy release.

This temporary change to the CI essentially adds the instructions

python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util

before linting and testing, and, in addition,

python -m pip install pillow

before testing.

The commit hash 5c1d045ce7b1e45f85608346baed5455324ee967 corresponds to the latest merged bug fix.

[bgruening]

Go for it!

[kostrykin]

There is something wrong with either this PR or another bug, I'll try to hunt this down before merging this

[kostrykin]

7154d16 is the same test as https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/image_diff.xml and it passes when run in Galaxy using ./run_tests.sh -framework -id image_diff. But the same test fails when run on in this branch, both locally and in CI:

https://github.com/BMCV/galaxy-image-analysis/actions/runs/8310797509?pr=117#summary-22743770060

The reason for failure is that the attribute values for eps and metric are not there in attributes in files_image_diff so the defaults are used. The values are not passed through to files_image_diff from XML.

But there is no difference between the tool_util/parser/xml.py file used in the test on this branch (installed via pip install, where the test fails) and the one in the Galaxy repo (where the test passes).

Any idea? @bgruening

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Update 1: Turns out, the new attributes eps and metric are already missing in the response of the tool test API received in GalaxyInteractorApi.get_tool_tests in tool_util/verify/interactor.py. So it looks like the new attributes get stripped off by the tool test API server.

Update 2: Yup, the attributes are there in GalaxyEngine._run_test_cases in planemo/engine/galaxy.py. Then, interactor.verify_tool() is called, but the attributes are not passed along. Instead, the .verify_tool() method uses .get_tool_tests() on an GalaxyInteractorApi object to request the tests from API.

This request seems to be answered by test_data() in webapps/galaxy/api/tools.py, however, there seems to be no webapps/galaxy/api/tools.py on my filesystem. I did a full system search for api/tools.py and there was nothing. So how is this API request handled when running planemo test?

[kostrykin]

Do you have any security concerns because of dba0717? @bgruening

[bgruening]

No not at all. We all trust you!