Remove unused synonym sync files

[joeflack4]

Overview

Removes unused synonym sync file: (i) the combined cases file, (ii) now the source-specific files so that they now go in tmp/ instead of being committed.

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 DO NOT MERGE: Remove unused synonym sync files - build #760
• 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
• 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

[twhetzel]

I checked out this branch and ran sh run.sh make sync-synonyms -B to check some things and the mini-build failed:

rm -f components/ordo.db.tmp && \
cat /usr/local/lib/python3.12/dist-packages/semsql/builder//sql_schema/semsql.sql | sqlite3 components/ordo.db.tmp && \
echo .exit | sqlite3 -echo components/ordo.db.tmp -cmd ".mode csv" -cmd ".import config/prefixes.csv prefix" && \
rdftab components/ordo.db.tmp < components/ordo.owl && \
sqlite3 components/ordo.db.tmp -cmd '.separator "\t"' ".import components/ordo-relation-graph.tsv entailed_edge" && \
gzip -f components/ordo-relation-graph.tsv && \
cat /usr/local/lib/python3.12/dist-packages/semsql/builder//indexes/*.sql | sqlite3 components/ordo.db.tmp && \
echo "ALTER TABLE statements ADD COLUMN graph TEXT;" | sqlite3 components/ordo.db.tmp && \
mv components/ordo.db.tmp components/ordo.db
.exit
rm components/ordo-min.owl components/ordo-prefixes.yaml components/ordo-properties.txt
make[1]: Leaving directory '/work/src/ontology'
robot --catalog catalog-v001.xml query -i components/ordo.owl --query ../sparql/synonyms-scope-type-xref.sparql tmp/ordo-synonyms-scope-type-xref.tsv
python3 ../scripts/sync_synonym.py \
--mondo-mappings-path tmp/mondo.sssom.tsv \
--ontology-db-path components/ordo.db \
--mondo-synonyms-path tmp/mondo-synonyms-scope-type-xref.tsv \
--mondo-exclusion-configs config/mondo-exclusion-configs.yml \
--onto-synonym-types-path tmp/ordo-synonyms-scope-type-xref.tsv \
--onto-config-path metadata/ordo.yml \
--outpath-added tmp/ordo.synonyms.added.robot.tsv \
--outpath-confirmed tmp/ordo.synonyms.confirmed.robot.tsv \
--outpath-updated tmp/ordo.synonyms.updated.robot.tsv \
   	--outpath-combined tmp/synonym_sync_combined_cases_ordo.tsv
awk '(NR == 1) || (NR == 2) || (FNR > 2)' reports/sync-synonym/*.synonyms.added.robot.tsv > reports/sync-synonym/sync-synonyms.added.robot.tsv
awk: cannot open "reports/sync-synonym/*.synonyms.added.robot.tsv" (No such file or directory)
make: *** [mondo-ingest.Makefile:598: reports/sync-synonym/sync-synonyms.added.robot.tsv] Error 2
rm tmp/icd10cm-synonyms-scope-type-xref.tsv tmp/icd10who-synonyms-scope-type-xref.tsv tmp/omim-synonyms-scope-type-xref.tsv tmp/doid-synonyms-scope-type-xref.tsv tmp/icd11foundation-synonyms-scope-type-xref.tsv tmp/ncit-synonyms-scope-type-xref.tsv tmp/ordo-synonyms-scope-type-xref.tsv
Command exited with non-zero status 2
### DEBUG STATS ###
Elapsed time: 33:55.56

[joeflack4]

@twhetzel Was more trouble than it was worth keeping this separate, so I merged it into:

• Synonym Sync: qc-duplicate-exact-synonym-no-abbrev related updates && Remove unused files #767