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ncbo / bioportal-project

Serves to consolidate (in Zenhub) all public issues in BioPortal
BSD 2-Clause "Simplified" License
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what is the proper way to handle ontology parsing errors for "Summary Only" ontologies #256

Open alexskr opened 1 year ago

alexskr commented 1 year ago

ncbo_cron processes "Summary Only" ontologies when running ncbo_cron --all-ontologies and in some cases runs into various parsing errors.
Is it ok to:

  1. remove all existing submissions of the ontology since ontology is marked as a summary only?
  2. should ncbo_cron handle those more gracefully - i.e skip processing ontology if its marked as summary only
graybeal commented 1 year ago

Why does ncbo_cron do that, because the ontology is sitting there as a leftover? Ideally ncbo_cron would skip the ontology if it is Summary Only.

alexskr commented 1 year ago

it usually happens when we reparse or reindex all ontologies but that can also happen when we manually request to parse specific ontologies which happen to be summary-only via ncbo_cron or admin web UI. ncbo_cron would gladly accept the challenge and eventually error out after running owlapi or another step.

We do not allow downloads of summary-only ontologies so is there a good reason to keep old submissions?

graybeal commented 1 year ago

I like that we have them because (a) the owner might someday say "ok make it available again" and then we would have the older history intact, and (b) if someone said "I have this emergency and the health record used terminology from your website and I need to get information about that term" we could look it up and save someone's life. Well, maybe not too likely…

I'm not convinced either of those is a good enough reason. Mostly I'm just a keeper.