Format of Search CV parameters about galaxytools HOT 12 OPEN

@anuprulez Thanks for exposing the issue. My intuition is that changes of Galaxy's tool infrastructure caused the issue. I will look deep into it soon.

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@anuprulez Unfortunately, I couldn't reproduce the issue shown in the shared history. I have correct list of parameters in the dropdown in my local instance. One thing worth mentioning: use only the list in the Search list, having parameter name in the front, like selectkbest__k: [5880, 5890, 5895, 5900], would lead to failure.

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As wrapped here https://github.com/bgruening/galaxytools/blob/master/tools/sklearn/search_model_validation.xml#L11-L17, lines starting with @ should be selected to be search parameters, i.e., showing as the dropdown options. The EU instance seems to do the opposite, excluding lines having @. I have no idea what causes that, since I can't reproduce the issue elsewhere.

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@qiagu thanks a lot for looking into it. I found a fix here: #1232
Without this change, most of the tool tests (that are expected to pass) were failing in my local instance. Two changes worked: either removing the entire attribute startswith="@" or adding quotes for @: startswith=" '@' ". I chose the latter option. I hope it works on the EU server. It seems to be related to parsing of special symbols I guess but not 100% sure.

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Adding quotes to @ symbol did not work, unfortunately. But, removing it did and the tests are now passing. Removing it will add a few extra params in the list of estimator params of which the most we already show using @ as a startwith filter. It looks like there is some issue with parsing of this special symbol on EU server in the tool form, not 100% sure though.

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Same issue on Galaxy Main as well. We should keep this issue open until it is fixed

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Ha, the startswith issue got fixed 29 days ago.
See: galaxyproject/galaxy@d642ce3

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Do you want to ask for a backport?

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My bad. I'd correct myself. The issue seems to be caused by the commit 29 days ago. We may need to revert the change.
galaxyproject/galaxy@d642ce3#diff-7a49a06712755de974dbcb43a317151e9ceee2af1e58914e28f2f4c7de9bdf9aL648-R648

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I guess you need to open an issue then.

ping @bernt-matthias we well.

Thanks @qiagu for finding this.

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As far as I see this repo is using 21.05 for testing PRs. So it should not be affected by galaxyproject/galaxy#14332 which was for 22.01, or?

Anyway, galaxyproject/galaxy#14332 brought the code in line with the docs. In the Galaxy tool xml docs you will find: startswith: Ignore lines starting with the given string. Unfortunately that was never what was implemented in Galaxy. So I changed the code. As alternative we might revert the code change (ie fix) the docs.

Edit: Actually the docs were wrong (just added approx a year ago .. but the code is approx 15 years old)

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Will be fixed in galaxyproject/galaxy#14440

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