Generalise QC check that ensures that all terms fall under preferred root

[matentzn]

If there is a preferred root declaration, then all terms in the base-namespace must fall under at least one class with a preferred root tag. See obophenotype/cell-ontology#725 (comment)

[gouttegd]

@matentzn Do you want to add that to the odk:validate command already used for #1175?

[matentzn]

Yes. i think as for the general pattern - we can try the feature in the ODK robot plugin, and if we think its useful, migrate it to ROBOT core?

[gouttegd]

we can try the feature in the ODK robot plugin, and if we think its useful, migrate it to ROBOT core?

Sounds good.

I think this should be the general pattern for ROBOT plugins:

(1) Is the command highly specific to one project?

Then make your own plugin. It’s easy, and we don’t want ROBOT to end up with a command for every single task imaginable (that was the mistake of OWLTools).

Typical examples would be Uberon’s uberon:merge-species and uberon:create-species-subset commands.

(2) Can the command be useful for a handful of projects?

Then maybe consider making a distinct plugin, that is not tied to any single project.

(3) Can the command be useful for many projects?

Then consider adding it to the ODK plugin – especially if you think that command should be used as part of any standard ODK workflow.

Once the command had been in the ODK plugin for a while (let’s say at least a full ODK major release cycle), consider submitting it to upstream ROBOT.

(4) Is the command intended to work around a bug in upstream ROBOT?

Then submit a proper fix to ROBOT first! And then only add the command to the ODK plugin (or any other plugin) as a temporary workaround that should be removed as soon as a version of ROBOT is available in which the bug is fixed.

Typical example would the current’s odk:normalize --merge-axioms true, which I hope to remove if/when ontodev/robot#1240 is merged (or ontodev/robot#1239 is fixed by any other means).

Likewise if the command implements a new feature that would fit nicely into one of the existing ROBOT commands (like odk:normalize --add-source, which I hope is a temporary workaround until ontodev/robot#1242 is merged).

[matentzn]

I agree, this is a great way to put it!