Additional fixes to get release working post #509

obophenotype · Jul 7, 2018 · a7ea836 · a7ea836
1 parent 64504c3
commit a7ea836
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -28,13 +28,13 @@ build/%: build/cl.owl
 cl.owl: build/cl.owl
 	cp $< $@
 cl.obo: build/cl.owl
-	owltools $(USECAT) $< --add-obo-shorthand-to-properties --merge-imports-closure -o -f obo $@
+	owltools $(USECAT) $< --add-obo-shorthand-to-properties --merge-imports-closure -o -f obo --no-check $@.tmp && grep -v ^owl-axioms $@.tmp > $@
 cl-base.owl: cl-edit.owl
-	owltools $(USECAT) $< --remove-imports-declarations --set-ontology-id -v $(RELEASE_URIBASE)/$@ $(OBO)/cl/$@ -o $@
+	owltools $(USECAT) $< --remove-imports-declarations --set-ontology-id -v $(RELEASE_URIBASE)/$@ $(OBO)/cl/$@ -o $@.tmp && mv $@.tmp $@
 cl-basic.owl: build/cl-simple.owl
-	owltools $< --remove-axioms -t DisjointClasses --set-ontology-id $(OBO)/cl/$@ -o $@
+	owltools $< --remove-axioms -t DisjointClasses --set-ontology-id $(OBO)/cl/$@ -o $@.tmp && mv $@.tmp $@
 cl-basic.obo: cl-basic.owl
-	owltools $< -o -f obo $@
+	owltools $< -o -f obo $@.tmp && mv $@.tmp $@
 
 %-obocheck: %.obo
 	obo2obo $< -o $@
@@ -98,7 +98,7 @@ imports/seed.tsv: cl-edit.owl imports/seed_edit.tsv
 	owltools $(USECAT) $< --merge-support-ontologies --export-table $@.tmp && cut -f1 $@.tmp imports/seed_edit.tsv > $@
 
 imports/%_import.owl: $(SRC) mirror/%.owl imports/seed.tsv
-	robot extract -i mirror/$*.owl -T imports/seed.tsv -m BOT -O $(OBO)/cl/$@ -o $@
+	robot extract -i mirror/$*.owl -T imports/seed.tsv -m BOT -O $(OBO)/cl/$@ -o $@.tmp.owl && owltools $@.tmp.owl --remove-annotation-assertions -r -l -s -d -o $@.tmp && mv $@.tmp $@
 
 imports/%_import.obo: imports/%_import.owl
 	owltools $(USECAT) $< -o -f obo $@