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Suggestion for an order of IDs/links annotations#58

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galaxy-iuc:mainfrom
matuskalas:patch-1
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Suggestion for an order of IDs/links annotations#58
matuskalas wants to merge 1 commit into
galaxy-iuc:mainfrom
matuskalas:patch-1

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@matuskalas
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@matuskalas matuskalas commented Jul 23, 2020

... and added the missing xrefs.

This is based on a chat with @bgruening in winter 2020, and is also what I've been following when annotating example IUC tools. The idea was to have all the IDs a.k.a. external links a.k.a. upstream annotation next to each other: xrefs, edam_topics, edam_operations, citations.

If the order should be changed as suggested, it might be good to also change it in:
(I volunteer if green light)

And added the missing `xrefs`.
This is based on a chat with @bgruening in winter 2020, and is also what I've been following when annotating example IUC tools.
If the order should be changed as suggested, it might be good to also change it in https://docs.galaxyproject.org/en/latest/dev/schema.html.
@bgruening
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Thanks @matuskalas for bringing this up. This here needs also to be changed: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/linters/xml_order.py

@wm75
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wm75 commented Jul 24, 2020

👍 for grouping these elements
+0.5 for moving the group to the end of the tool definition because that would allow the citations element to stay in its familiar place

Within the group, I'd have a slight preference for moving xrefs below the edam elements and have it just above the citations. I think that may be more intuitive since the citations are typically for the command line tool pointed to by xrefs. It's also the order currently described in the tool xml syntax.

@Slugger70
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A good idea to put them all together. I agree with Wolfgang's order of placement.

@matuskalas
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matuskalas commented Jul 24, 2020

Excellent, thanks for the replies!

As I understood, the currently winning order would be edam_topics, edam_operations, xrefs, citations, all of it towards the end after help. Right?

(Another consideration would be having it all up between description (which they are kind-of extension of) and macros, but that would mean moving citations to the other end.)

I can fix it all over & PR, probably tonight...

@matuskalas matuskalas marked this pull request as draft July 24, 2020 09:30
@wm75
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wm75 commented Jul 24, 2020

As I understood, the currently winning order would be edam_topics, edam_operations, xrefs, citations, all of it towards the end after help. Right?

Yes, this is what I have in mind.

@annefou
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annefou commented Jul 24, 2020

@matuskalas As suggested by @bgruening I can add in the documentation some information about EDAM popovers. Does it make sense? If yes, what would be best: make a PR to matuskalas:patch-1 to get it in this PR or to make a separate PR.

@matuskalas
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Whichever you prefer @annefou :-)

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5 participants