smaller CARO import

VirtualFlyBrain · Feb 25, 2022 · e5e12fb · e5e12fb
1 parent 4c0339d
commit e5e12fb
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diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -262,6 +262,10 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
+## Module for ontology: caro
+
+$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl
+	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in vfbext.Makefile!" && false
 ## Module for ontology: obi
 
 $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt

diff --git a/src/ontology/vfbext-odk.yaml b/src/ontology/vfbext-odk.yaml
@@ -21,6 +21,7 @@ import_group:
   products:
     - id: ro
     - id: caro
+      module_type: custom
     - id: fbbt
     - id: obi
       module_type: minimal

diff --git a/src/ontology/vfbext.Makefile b/src/ontology/vfbext.Makefile
@@ -10,6 +10,13 @@ $(ONT).owl: $(ONT)-full.owl
 	$(ROBOT) annotate --input $@.tmp.owl --ontology-iri http://virtualflybrain.org/data/VFB/OWL/vfbext.owl \
 		convert -o $@.tmp.owl && mv $@.tmp.owl $@
 
+# smaller CARO import
+$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl
+	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
+		extract --method MIREOT --force true --copy-ontology-annotations true \
+		--lower-term "obo:CARO_0030002" \
+		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
+
 
 # Include copying import files
 .PHONY: prepare_release