Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add data integrity tests #15

Merged
merged 13 commits into from
Oct 25, 2022
Merged

Add data integrity tests #15

merged 13 commits into from
Oct 25, 2022

Conversation

cthoyt
Copy link
Collaborator

@cthoyt cthoyt commented Oct 20, 2022

As a step towards addressing #11, this PR adds four data integrity tests:

  1. Test that prefixes are unique among canonical records in each context
  2. Test that namespaces are unique among canonical records in each context
  3. Test that the prefix appearing in each namespace_alias record has a corresponding prefix in a canonical record
  4. Test that the namespace appearing in each prefix record has a corresponding namespace in a canonical record

Most of these tests are failing, so having a second set of eyes on them (@caufieldjh ;)) will be great. We can start updating the content further until these tests pass, either in this PR or in a different one. However, it might also point out some more systematic issues in the ETL pipelines, so I would also suggest @hrshdhgd takes a careful look too.

Blockers

@cthoyt
Copy link
Collaborator Author

cthoyt commented Oct 20, 2022

I curated all of the remaining issues in Bioportal away in e29c159

cthoyt and others added 6 commits October 20, 2022 22:42
@caufieldjh
Copy link
Contributor

Great tests! I want to see if I can get that test_namespace_aliases working - some of those prefixes are already covered by other maps in this repo, and the remainder are instances which only don't have canonical prefixes because they aren't in Bioportal (but are imports)

@caufieldjh
Copy link
Contributor

I think this is probably sufficient for now, though I'll likely have further updates to the BP maps quite soon.

@cthoyt
Copy link
Collaborator Author

cthoyt commented Oct 25, 2022

@caufieldjh thanks for making the BioPortal updates and getting this up to date! It's now merged with master and done from my side.

@caufieldjh caufieldjh merged commit 47842b6 into linkml:main Oct 25, 2022
@cthoyt cthoyt deleted the add-guarantees branch October 25, 2022 20:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants