From a7ea8362d3a1000534f72bdc34f7f78dd81d7b33 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Fri, 6 Jul 2018 17:23:32 -0700
Subject: [PATCH] Additional fixes to get release working post #509

---
 src/ontology/Makefile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index e484da8fa..748218ae8 100644
--- 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 $@