Slurp pipeline

- Update: direct_owned_parents methods: Temporarily commented out, pending OAK fixes. Currently doing this in batch using SPARQL for now.
- Add: Param --onto-exclusions-path: Now we no longer consider exluded terms to be possible slurp candidates.
- Bugfix: Labels: Now they are successfully being fetched using OAK.

src/ontology/mondo-ingest.Makefile

@@ -345,13 +345,13 @@ slurp/:
 
 # min-id: the next available Mondo ID
 # TODO: `pip install` stuff is temporary until ODK docker up to date w/ recent OAK updates
-# TODO: Check if removing --rf from run.sh will fix need for pip install. havent been able to try yet; docker issue
 slurp/%.tsv: $(COMPONENTSDIR)/%.owl $(TMPDIR)/mondo.sssom.tsv $(REPORTDIR)/mirror_signature-mondo.tsv | slurp/
-	# pip install --upgrade -r $(RELEASEDIR)/requirements-unlocked.txt
+	pip install --upgrade -r $(RELEASEDIR)/requirements-unlocked.txt
 	python $(SCRIPTSDIR)/migrate.py \
 	--ontology-path $(COMPONENTSDIR)/$*.owl \
 	--sssom-map-path $(TMPDIR)/mondo.sssom.tsv \
 	--onto-config-path metadata/$*.yml \
+	--onto-exclusions-path reports/$*_term_exclusions.txt \
 	--min-id 850000 \
 	--max-id 999999 \
 	--mondo-terms-path $(REPORTDIR)/mirror_signature-mondo.tsv \

src/ontology/slurp/icd10cm.tsv

@@ -18,8 +18,5 @@ MONDO:850015	ICD10CM:N00-N99
 MONDO:850016	ICD10CM:O00-O9A			
 MONDO:850017	ICD10CM:P00-P96			
 MONDO:850018	ICD10CM:Q00-Q99			
-MONDO:850019	ICD10CM:R00-R99			
-MONDO:850020	ICD10CM:S00-T88			
-MONDO:850021	ICD10CM:U00-U85			
-MONDO:850022	ICD10CM:V00-Y99			
-MONDO:850023	ICD10CM:Z00-Z99			
+MONDO:850019	ICD10CM:S00-T88			
+MONDO:850020	ICD10CM:U00-U85