Merge pull request #408 from monarch-initiative/bug-sync-ancestor

Bug: Sync subclass: ancestor inconsistencies
monarch-initiative · Feb 1, 2024 · fc5fe2d · fc5fe2d
2 parents fb8bfb0 + 1ec9345
commit fc5fe2d
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/src/ontology/mondo-ingest.Makefile b/src/ontology/mondo-ingest.Makefile
@@ -340,13 +340,17 @@ documentation: j2 $(ALL_DOCS) unmapped-terms-docs mapped-deprecated-terms-docs s
 build-mondo-ingest:
 	$(MAKE) refresh-imports exclusions-all slurp-all mappings matches \
 		mapped-deprecated-terms mapping-progress-report \
-		recreate-unmapped-components sync documentation
-	$(MAKE) prepare_release
+		recreate-unmapped-components sync documentation \
+		prepare_release
 	echo "Mondo Ingest has been fully completed"
 
 .PHONY: build-mondo-ingest-no-imports
 build-mondo-ingest-no-imports:
-	$(MAKE_FAST) build-mondo-ingest
+	$(MAKE_FAST) exclusions-all slurp-all mappings matches \
+		mapped-deprecated-terms mapping-progress-report \
+		recreate-unmapped-components sync documentation \
+		prepare_release
+	echo "Mondo Ingest has been fully completed"
 
 DEPLOY_ASSETS_MONDO_INGEST=$(OTHER_SRC) $(ALL_MAPPINGS) ../../mondo-ingest.owl ../../mondo-ingest.obo
 
@@ -432,6 +436,7 @@ tmp/merged.owl: tmp/mondo.owl mondo-ingest.owl tmp/mondo.sssom.ttl
 $(MAPPINGSDIR)/mondo-sources-all-lexical.sssom.tsv: $(SCRIPTSDIR)/match-mondo-sources-all-lexical.py tmp/merged.db $(MAPPINGSDIR)/rejected-mappings.tsv
 	rm -f $(MAPPINGSDIR)/mondo-sources-all-lexical.sssom.tsv
 	rm -f $(MAPPINGSDIR)/mondo-sources-all-lexical-2.sssom.tsv
+	$(MAKE) pip-bioregistry
 	python $(SCRIPTSDIR)/match-mondo-sources-all-lexical.py run tmp/merged.db \
 		-c metadata/mondo.sssom.config.yml \
 		-r config/mondo-match-rules.yaml \

diff --git a/src/scripts/sync_subclassof.py b/src/scripts/sync_subclassof.py
@@ -309,7 +309,8 @@ def sync_subclassof(
     missing_ancestor_rels = rels_indirect_mondo_mondo.union(rels_direct_mondo_mondo).difference(ancestors_mondo_mondo)
     if missing_ancestor_rels:
         rels_for_printing =  [rel for rel in list(missing_ancestor_rels)[:5]]
-        logging.error(
+        # TODO: temp:
+        raise ValueError(
             'Detected error in consistency of sets of terms gathered from Mondo.\n'
             f'\n 1. Mondo SCR ancestors: {len(ancestors_mondo_mondo)}'
             f'\n 2. Mondo direct SCR relationships: {len(rels_direct_mondo_mondo)}'
@@ -499,3 +500,4 @@ def run_defaults(use_cache=True):  # todo: #remove-temp-defaults
 
 if __name__ == '__main__':
     cli()
+    #run_defaults()  # TODO temp