diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 43010713d..5120698b4 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= c05ee03cdbebf8765f9f8f3ed1deb9ecde656b5e92390f6f64bfce43560a3c56 +CONFIG_HASH= 3ef44073feb4dd21f093356b564a51bd94638e4a757ed43c0c9ff69e9599cac2 # ---------------------------------------- @@ -132,7 +132,7 @@ custom_robot_plugins: .PHONY: extra_robot_plugins -extra_robot_plugins: +extra_robot_plugins: $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar # Install all ROBOT plugins to the runtime plugins directory @@ -152,6 +152,9 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar: # Specific rules for supplementary plugins defined in configuration +$(ROBOT_PLUGINS_DIRECTORY)/flybase.jar: + curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar + # ---------------------------------------- # Release assets diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml index e13353d95..310baccee 100644 --- a/src/ontology/cl-odk.yaml +++ b/src/ontology/cl-odk.yaml @@ -26,6 +26,10 @@ release_artefacts: - custom-cl-plus documentation: documentation_system: mkdocs +robot_plugins: + plugins: + - name: flybase + mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar subset_group: products: - id: BDS_subset diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile index 1d202e188..5025db23c 100644 --- a/src/ontology/cl.Makefile +++ b/src/ontology/cl.Makefile @@ -74,6 +74,14 @@ tmp/cl_signature.txt: tmp/$(ONT)-stripped.owl tmp/cl_terms.txt # Note that right now, TypeDefs that are CL native (like has_age) are included in the release! +# Preprocessing: automatically generate text definitions from logical definitions +$(EDIT_PREPROCESSED): $(SRC) all_robot_plugins + $(ROBOT) flybase:rewrite-def -i $< --dot-definitions --null-definitions \ + --no-ids --filter-prefix CL_ \ + --add-annotation "oboInOwl:hasDbXref FBC:Autogenerated" \ + -o $@ + + # ---------------------------------------- # SSSOM MAPPINGS # ----------------------------------------