Merge branch 'master' into Merge-CNS-interneuron-interneuron-term

obophenotype · Dec 17, 2024 · 0c02d7b · 0c02d7b
2 parents db4f84b + 1fec991
commit 0c02d7b
Show file tree

Hide file tree

Showing 5 changed files with 211 additions and 202 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for cl
 # Generated using ontology-development-kit
-# ODK Version: v1.5.3
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead
 
@@ -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=                fe26dd231ab531dab5609c794de598d2a28083168916941a3276fe672cfe8be2
+CONFIG_HASH=                b8fef012ac2d7e3df8e8871cfa305bf6b9d5b6a56394a042bdf48a83d3d2e019
 
 
 # ----------------------------------------
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date def-not-only-xref id-format 
 SPARQL_EXPORTS =            cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs 
-ODK_VERSION_MAKEFILE =      v1.5.3
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -156,7 +156,7 @@ $(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
 
 $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar:
-	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
+	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar
 
 
 # ----------------------------------------

diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml
@@ -34,7 +34,7 @@ robot_plugins:
     - name: flybase
       mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar
     - name: uberon
-      mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
+      mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar
 subset_group:
   products:
     - id: BDS_subset

diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile
@@ -175,10 +175,10 @@ test: $(REPORTDIR)/taxon-constraint-check.txt
 # ----------------------------------------
 
 .PHONY: obocheck
-obocheck: $(SRC)
+obocheck: $(SRC) | all_robot_plugins
 	$(ROBOT) merge -i $(SRC) \
 		 remove --base-iri $(URIBASE)/CL_ --axioms external --trim false \
-		 convert -f obo --check false -o $(TMPDIR)/cl-check.obo
+		 uberon:obo-export --merge-comments --obo-output $(TMPDIR)/cl-check.obo
 	fastobo-validator $(TMPDIR)/cl-check.obo
 
 test_obsolete: $(ONT).obo
@@ -258,6 +258,36 @@ pattern_docs: $(ALL_PATTERN_FILES)
 		       -o ../../docs/patterns/
 
 
+# ----------------------------------------
+# CUSTOM OBO OUTPUT
+# ----------------------------------------
+OBO_EXPORT_OPTIONS = --merge-comments --strip-gci-axioms --strip-owl-axioms
+
+$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT).obo: $(ONT).owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-base.obo: $(ONT)-base.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-full.obo: $(ONT)-full.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-simple.obo: $(ONT)-simple.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-basic.obo: $(ONT)-basic.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-non-classified.obo: $(ONT)-non-classified.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+cl-plus.obo: cl-plus.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+
 # ----------------------------------------
 # DIFFS/REPORTS
 # ----------------------------------------