Ensure that exact synonyms in NCIT are preserved

matentzn commented 4 months ago

Resolves #612

Overview

This works because it prevents that remove -T config/properties.txt --select complement --select properties --trim true \ removes synonyms (they are removed because of these axiom annotations).

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

[ ] Yes
[ ] No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after docker pull obolibrary/odkfull:dev), and no errors occurred?

[ ] Yes
[ ] No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

New Packages

Were any new Python packages added?

[ ] Yes, requirements.txt.full was updated and an ODK issue submitted
[x] No

Were any other non-Python packages added?

[ ] Yes, Dockerfile updated and an ODK issue submitted
[x] No

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

[ ] Yes

twhetzel commented 3 months ago

I am running the test build on this now.

twhetzel commented 3 months ago

Test data build for this branch was reviewed and approved https://github.com/monarch-initiative/mondo-ingest/pull/631

monarch-initiative / mondo-ingest