Automatically generate text definitions from logical definitions (#2349)

This commit uses the FlyBase ROBOT plugin to automatically generate text
definitions for terms that do not have any (or that have a "."
definition). The generated definition is derived from the term's logical
definition.

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

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

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
 # ----------------------------------------