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Fix the minimal module type.#19

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gouttegd merged 1 commit into
mainfrom
fix-minimal-module
Jun 24, 2026
Merged

Fix the minimal module type.#19
gouttegd merged 1 commit into
mainfrom
fix-minimal-module

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@gouttegd

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This PR fixes a bug in the minimal module type (found when looking at the definition of that module while thinking about INCATools/ontology-development-kit#1352).

The code that generates the minimal module type is supposed, at some point, to select classes, individuals, and annotation properties.

However, the rule is incorrectly written as

--select "classes individual annotation-properties"

which is incorrect because the keyword that ROBOT expects to select individuals is individuals (with a final -s) -- individual without a -s is ignored.


Interestingly, nobody ever reported that bug, meaning either that nobody has ever used the minimal module type, or that nobody has ever noticed that individuals were not properly selected as they should!

The code that generates the `minimal` module type is supposed, at some
point, to select classes, individuals, and annotation properties.

However, the rule is incorrectly written as

  --select "classes individual annotation-properties"

which is incorrect because the keyword that ROBOT expects to select
individuals is `individuals` (with a final `-s`) -- `individual` without
a `-s` is ignored.
@gouttegd gouttegd requested a review from matentzn June 23, 2026 18:36
@gouttegd gouttegd merged commit db121c8 into main Jun 24, 2026
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@gouttegd gouttegd deleted the fix-minimal-module branch June 24, 2026 08:11
@matentzn

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@gouttegd

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Thanks for the search.

Projects that use module_type: minimal with CL, UBERON or PATO should not have been affected, since those ontologies don’t contain individuals anyway (at least I think PATO does not?).

But ELMO is using module_type: minimal with ENVO, which does contain individuals – individuals which would not have been included in the minimal module since the bug was introduced (by me, sorry about that) shortly before the 1.6 release.

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2 participants