Merge pull request #2413 from obophenotype/issue2373-update-pro

Updating pro import

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.3.0
+# ODK Version: v1.3.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -41,7 +41,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.3.0
+ODK_VERSION_MAKEFILE =      v1.3.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -268,7 +268,7 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
 $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
 		extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
@@ -277,28 +277,29 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 
 $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_combined.txt
 	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/chebi_terms_combined.txt --force true --individuals include --method BOT \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
+
 .PHONY: refresh-imports
 refresh-imports:
-	make IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
+	$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
 
 .PHONY: no-mirror-refresh-imports
 no-mirror-refresh-imports:
-	make IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B
+	$(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B
 
 .PHONY: refresh-imports-excluding-large
 refresh-imports-excluding-large:
-	make IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B
+	$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B
 
 .PHONY: refresh-%
 refresh-%:
-	make IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B
+	$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B
 
 .PHONY: no-mirror-refresh-%
 no-mirror-refresh-%:
-	make IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
+	$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
 
 
 # ----------------------------------------
@@ -308,6 +309,17 @@ no-mirror-refresh-%:
 
 COMP=true # Global parameter to bypass component generation
 
+.PHONY: all_components
+all_components: $(OTHER_SRC)
+
+.PHONY: recreate-components
+recreate-components:
+	$(MAKE) IMP=true MIR=true PAT=true IMP_LARGE=true all_components -B
+
+.PHONY: recreate-%
+recreate-%:
+	$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B
+
 $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 	touch $@
 .PRECIOUS: $(COMPONENTSDIR)/%
@@ -497,7 +509,7 @@ mirror-caro: | $(TMPDIR)
 
 
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
-	if [ $(IMP) = true ] && [ $(MIR) = true ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." && cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
+	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." && cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
 
 
 
@@ -533,7 +545,7 @@ SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql
 .PHONY: custom_reports
 custom_reports: $(SRC) | $(REPORTDIR)
 ifneq ($(SPARQL_EXPORTS_ARGS),)
-	$(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS)
+	$(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS)
 endif
 # ----------------------------------------
 # DOSDP Templates/Patterns
@@ -556,9 +568,9 @@ pattern_clean:
 .PHONY: patterns
 patterns dosdp:
 	echo "Validating all DOSDP templates"
-	make dosdp_validation
+	$(MAKE) dosdp_validation
 	echo "Building $(PATTERNDIR)/definitions.owl"
-	make $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl
+	$(MAKE) $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl
 
 # DOSDP Template Validation
 
@@ -756,7 +768,7 @@ $(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 		relax \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
 		reduce -r ELK \
-		query --update ../sparql/inject-subset-declaration.ru \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 # foo-basic: A version of -simple containing only relationships using relations on a configurable whitelist (default = BFO:0000050 (?)). See above (David comment) for explanation.
 # removes any axioms that contains one of the ops that not in the whitelist file
@@ -812,7 +824,7 @@ validate-tsv: $(TSV) | $(TMPDIR)
 	done
 
 validate-all-tsv: $(ALL_TSV_FILES)
-	make validate-tsv TSV="$^"
+	$(MAKE) validate-tsv TSV="$^"
 
 # ----------------------------------------
 # Editors Utilities
@@ -843,7 +855,7 @@ update_docs:
 # the environment does not malicously set `CLEANFILES` to `\`.
 .PHONY: clean
 clean:
-	make pattern_clean
+	$(MAKE) pattern_clean
 	[ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/*
 	[ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/*
 	rm -f $(CLEANFILES)
@@ -870,6 +882,7 @@ Core commands:
 
 Imports management:
 * refresh-imports:			Refresh all imports and mirrors.
+* refresh-components:			Refresh all components.
 * no-mirror-refresh-imports:		Refresh all imports without downloading mirrors.
 * refresh-imports-excluding-large:	Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'.
 * refresh-%:				Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'.