obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Automatically detect when imports need refreshing? #1853

Open gouttegd opened 1 year ago

gouttegd commented 1 year ago

We now have a policy that PR authors can ask the “tech-support” group to intervene on a PR to refresh the imports, for cases where the authors can’t do it themselves (#1852).

For now this requires that the authors (or whoever is reviewing the pull request) add the update-imports-required label to the PR, and that someone from the “tech-support” group notice the addition of such a label (it would be nice if one could “follow a label”, i.e. be notified every time a label is used on a ticket; it does not seem possible, though :( ).

Could/should we have a CI action that runs on every PR, detects if the PR introduces bare IRIs (not sure yet exactly how we would detect that, but that must be possible), and if so 1) automatically adds the update-imports-required label and 2) actively notify the “tech-support” group for good measure?

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically in one year from now if no action is taken.

lubianat commented 4 months ago

@gouttegd That is great!

I am always having trouble with imports; I'll try using the "bare IRI" path now, after failing to refresh the imports myself.

Also: would you be okay with me reorganizing the documentation of the guidelines in relation to that, just so it is a bit more clear for the ones ignorant of the tech details (like me)? Of course, not excluding anything, just rewording here and there.

gouttegd commented 4 months ago

Completely forgot about this proposal… ^^'

Sure, use the “bare IRI” path, then create a PR with the update-imports-required.

would you be okay with me reorganizing the documentation of the guidelines in relation to that, just so it is a bit more clear for the ones ignorant of the tech details (like me)?

I would never say no to better documentation. :D

lubianat commented 4 months ago

I am having trouble even adding the terms as bare IRIs on Protége; my ontology editing skills are rusty. The "class editor" naturally only accepts classes.

I'll add the Pull Request without the part of axioms just so it doesn't get lost, hopefully I'll get it at some other time.

gouttegd commented 4 months ago

I am having trouble even adding the terms as bare IRIs on Protége; my ontology editing skills are rusty. The "class editor" naturally only accepts classes.

To be clear, when I say “bare IRI”, I refer to what is also called a “Protégé-based declaration”. That is, creating a new class in Protégé, directly under owl:Thing, and pasting the full IRI of the term to import in the Name field of the class creation dialog. Once that is done, you should be able to refer to that class wherever you need it in the rest of the ontology.

lubianat commented 4 months ago

Awesome! I imagined it was something on those lines. I'll do it – and clarify the docs.