Allow to seed the ORCIDIO module from specific properties.

Update the ODK ROBOT plugin to version 0.3.3, where the default
behaviour of the `odk:extract-orcids` command is to extract ORCID
references from all IRI-valued annotations.

Add to the generated Makefile a ORCIDIO_PROPERTIES variable, intended to
list the properties to use when extracting ORCID references. The
variable is set to an empty list, which triggers the default behaviour
of the `odk:extract-orcids` command (extract from all annotations
regardless of the property). The variable is intended to allow the
ontology owner to tweak that behaviour, by overriding its definition in
the custom Makefile.

Author: gouttegd

src/incatools/odk/setup.py

@@ -24,7 +24,7 @@
 SSSOM_SOURCE = "https://github.com/gouttegd/sssom-java/releases/download/sssom-java-1.11.2/sssom-cli-1.11.2.jar"
 DOSDP_SOURCE = "https://github.com/INCATools/dosdp-tools/releases/download/v0.20.0/dosdp-tools-0.20.0.tgz"
 RELGR_SOURCE = "https://github.com/INCATools/relation-graph/releases/download/v2.3.4/relation-graph-cli-2.3.4.tgz"
-ODK_PLUGIN_SOURCE = "https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.2/odk.jar"
+ODK_PLUGIN_SOURCE = "https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.3/odk.jar"
 SSSOM_PLUGIN_SOURCE = "https://github.com/gouttegd/sssom-java/releases/download/sssom-java-1.11.2/sssom-robot-plugin-1.11.2.jar"
 OBO_EPM_SOURCE = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.epm.json"
 

src/incatools/odk/templates/src/ontology/Makefile.jinja2

@@ -791,10 +791,17 @@ no-mirror-refresh-%:
 # ORCIDIO module
 # ----------------------------------------
 
+# By default, the ORCIDIO module is seeded from ORCID references in ALL
+# IRI-valued annotations in the ontology, regardless of the annotation
+# property. To seed only from annotations using specific properties,
+# override the following variable with the desired list of properties.
+ORCIDIO_PROPERTIES =
+
 ifeq ($(IMP),true)
 $(IMPORTDIR)/orcidio_import.owl: $(SRCMERGED) $(MIRRORDIR)/orcidio.owl | all_robot_plugins
 	$(ROBOT) odk:extract-orcids --input $(SRCMERGED) \
 	                            --orcid-file $(MIRRORDIR)/orcidio.owl \
+	                            $(foreach p, $(ORCIDIO_PROPERTIES),--property $(p)) \
 		 $(ANNOTATE_CONVERT_FILE)
 
 endif