Bug fix: Synonym Sync: Entries without exact mappings

[joeflack4]

resolves #687

Note

• Draft while working on: DO NOT MERGE: Bug fix: Synonym Sync: Entries without exact mappings - mini build #696

Overview

The synonym sync template TSVs were being built incorrectly, and were sometimes adding synchronization outputs for cases where the Mondo term and source term had no exact mapping in mondo.sssom.tsv. The filtering was not being applied correctly.

The cause of these appearing in the first place is that these pairs of Mondo+source terms have synonyms on them, but they do not have exact mappings.

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

Mini-build:
Not a full build yet, but there is a mini-build which compares the only synonym sync outputs before and after.

• DO NOT MERGE: Bug fix: Synonym Sync: Entries without exact mappings - mini build #696

Build:

• DO NOT MERGE: Bug fix: Synonym Sync: Entries without exact mappings - Build #707

New Packages

Were any new Python packages added?

• Yes, requirements.txt.full was updated and an ODK issue submitted
• No

Were any other non-Python packages added?

• Yes, Dockerfile updated and an ODK issue submitted
• 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

[matentzn]

Assuming (which I cant see in the diff) that mappings_df is only exact matches, this LGTM!

[joeflack4]

Assuming... that mappings_df is only exact matches

Yep! in mondo.sssom.tsv that does seem the case, but it also does a filter for exact just in case.

[twhetzel]

Mainly approving on Nico's approval here (and a previous discussion where these code changes look like what was needed) since I have not had enough time to look at this and the results in as much detail as I would prefer.

[twhetzel]

@joeflack4 I'll this for you to merge

[joeflack4]

@twhetzel OK, I'll merge it now. I just got done reviewing the build #707 and it is fine, consistent with the preliminary mini-build #696.