OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
http://obofoundry.org
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Add check:`id` entry in metadata should be lower-case #1667

Closed cthoyt closed 2 years ago

cthoyt commented 2 years ago

While the preferred prefix can have mixed case, it seems that the id field for all OBO Foundry ontologies, even including ones with uppercase or mixed case preferred prefixes have been completely lowercased. The current testing suite does not check for this, and the merge of https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1646 is the first example where the id was uppercase.

I noticed this because it broke the Bioregistry build, which assumed that the ID fields would be lowercase.

cthoyt commented 2 years ago

The specific example for EPSO was fixed in https://github.com/OBOFoundry/OBOFoundry.github.io/commit/ef6aa8d4ea34421cb2b4b1e26e1a63456365d1f2, but this issue shouldn't be closed until there's a technical solution to guard against this in the future (e.g., implementing a new test run in CI that fails when appropriate)

matentzn commented 2 years ago

Yep we need a check

cthoyt commented 2 years ago

Could be trivially added to #1661.

nlharris commented 2 years ago

1661 was already merged; did the change include this new check?

cthoyt commented 2 years ago

No, it did not. I am still unsure how we will go about implementing new tests outside of the existing framework. Also, #1661 was merged into another branch that is the subject of another PR, not the main branch.

matentzn commented 2 years ago

Isnt there some thing in json schema to specify all lowercase?

cthoyt commented 2 years ago

A regex would work

nlharris commented 2 years ago

@cthoyt this seems like the sort of thing that you could do a PR for and then it'd be done...

matentzn commented 2 years ago

Weird, there already is a check:

https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/util/schema/registry_schema.json#L142

Trying now: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1818

Doesnt work the error was spurious. Any idea?

cthoyt commented 2 years ago

No idea, let's close this one, since some other improvements to the testing pipeline in the mean time might have fixed it