added allow_equivalents: all as per #3

berkeleybop · May 26, 2022 · 2bdc217 · 2bdc217
1 parent 9ef0261
commit 2bdc217
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -64,7 +64,7 @@ all: odkversion test all_assets
 
 .PHONY: test
 test: odkversion sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
-	$(ROBOT) reason --input $(SRC) --reasoner ELK  --equivalent-classes-allowed asserted-only --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success"
+	$(ROBOT) reason --input $(SRC) --reasoner ELK  --equivalent-classes-allowed all --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success"
 
 .PHONY: odkversion
 odkversion:
@@ -516,7 +516,7 @@ $(ONT)-base.owl: $(SRC) $(OTHER_SRC)
 # Full: The full artefacts with imports merged, reasoned
 $(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT) merge --input $< \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
+		reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
 		relax \
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@

diff --git a/src/ontology/bero-odk.yaml b/src/ontology/bero-odk.yaml
@@ -11,6 +11,7 @@ export_formats:
   - owl
   - obo
   - json
+allow_equivalents: all
 import_group:
   module_type: mirror
   products: 

diff --git a/src/ontology/bero.Makefile b/src/ontology/bero.Makefile
@@ -7,7 +7,7 @@ MESH_TERMS_FILE = imports/mesh_terms.txt
 
 $(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) $(patsubst %, -i %, $(IMPORT_FILES)) \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
+		reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
 		relax \
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@