Import Extended Relations Ontology

.github/workflows/release.yml

@@ -32,20 +32,13 @@ jobs:
         with:
           path: '*.jar'
           key: ${{ steps.cache-dependencies.outputs.cache-primary-key }}
-
-      - name: merge ontology
+      - name: make
         run: |
-          java -jar robot.jar \
-            --catalog src/ontology/catalog-v001.xml \
-            merge \
-              --input src/ontology/oto.ttl \
-            unmerge \
-              --input-iri https://raw.githubusercontent.com/BFO-ontology/BFO/v2.0/bfo.owl \
-              --output build/oto.ttl
+            make
       - name: build documentation
         run: |
           java -jar widoco.jar \
-            -ontFile build/oto.ttl \
+            -ontFile build/oto/$(cat VERSION)/oto-full.ttl \
             -rewriteAll \
             -uniteSections \
             -noPlaceHolderText \

.gitignore

@@ -1 +1,3 @@
 build/
+tmp/
+*.jar

Makefile

@@ -0,0 +1,205 @@
+ONTOLOGY_NAME := oto
+IRI_NAME := OpenTransportOntology
+
+IRI_PLACEHOLDER := http:\/\/w3id.org\/
+IRI_BASE := https:\/\/openenergyplatform.github.io\/
+
+IRI_ONTOLOGY_PLACEHOLDER := $(IRI_PLACEHOLDER)$(ONTOLOGY_NAME)
+IRI_ONTOLOGY := $(IRI_BASE)$(IRI_NAME)
+
+MKDIR_P = mkdir -p
+VERSION:= $(shell cat VERSION)
+VERSIONDIR := build/$(ONTOLOGY_NAME)/$(VERSION)
+ONTOLOGY_SOURCE := src/ontology
+SCRIPTS := src/scripts
+BFO_SOURCE := https://raw.githubusercontent.com/BFO-ontology/BFO/v2019-08-26/bfo_classes_only.owl
+TMP := tmp
+IMPORTS := $(ONTOLOGY_SOURCE)/imports
+
+UNAME_S := $(shell uname -s)
+ifeq ($(UNAME_S),Linux)
+	SED := sed
+endif
+ifeq ($(UNAME_S),Darwin)
+	SED := gsed
+endif
+
+
+subst_paths =	${subst $(ONTOLOGY_SOURCE),$(VERSIONDIR),${patsubst $(ONTOLOGY_SOURCE)/edits/%,$(ONTOLOGY_SOURCE)/modules/%,$(1)}}
+subst_paths_owl =	${subst $(VERSIONDIR),$(VERSIONDIR)/owl,${patsubst %.ttl,%.owl,$(1)}}
+
+OWL_FILES := $(call subst_paths,$(shell find $(ONTOLOGY_SOURCE)/* -type f -name "*.owl"))
+OMN_FILES := $(call subst_paths,$(shell find $(ONTOLOGY_SOURCE)/* -type f -name "*.omn"))
+TTL_FILES := $(call subst_paths,$(shell find $(ONTOLOGY_SOURCE)* -type f -name "*.ttl"))
+
+SEPARATOR := \/
+
+OWL_COPY := $(OWL_FILES)
+
+OMN_COPY :=	$(OMN_FILES)
+
+TTL_COPY :=	$(TTL_FILES)
+
+OMN_TRANSLATE := ${patsubst %.omn,%.owl,$(OMN_FILES)}
+TTL_TRANSLATE := $(call subst_paths_owl,$(TTL_COPY))
+
+
+RM=/bin/rm
+ROBOT_PATH := robot.jar
+ROBOT := java -jar $(ROBOT_PATH)
+
+define replace_devs
+	$(SED) -i -E "s/$(IRI_ONTOLOGY)\/dev\/([a-zA-Z/\.\-]+)/$(IRI_ONTOLOGY)\/releases\/$(VERSION)\/\1/m" $1
+endef
+
+define replace_oms
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/dev\/([a-zA-Z/\-]+)\.)omn/\1owl/m" $1
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/releases\/$(VERSION)\/([a-zA-Z/\-]+)\.)omn/\1owl/m" $1
+endef
+
+define replace_ttls
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/dev\/([a-zA-Z/\-]+)\.)ttl/\1owl/m" $1
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/releases\/$(VERSION)\/([a-zA-Z/\-]+)\.)ttl/\1owl/m" $1
+endef
+
+define replace_owls
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/dev\/([a-zA-Z/\-]+)\.)owl/\1ttl/m" $1
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/releases\/$(VERSION)\/([a-zA-Z/\-]+)\.)owl/\1ttl/m" $1
+endef
+
+define replace_ttls_owx
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/dev\/([a-zA-Z/\-]+)\.)ttl/\1owx/m" $1
+	$(SED) -i -E "s/($(IRI_ONTOLOGY)\/releases\/$(VERSION)\/([a-zA-Z/\-]+)\.)ttl/\1owx/m" $1
+endef
+
+define replace_ttls_owx
+	$(SED) -i -E "s/($(OEP_BASE)\/dev\/([a-zA-Z/\-]+)\.)ttl/\1owx/m" $1
+	$(SED) -i -E "s/($(OEP_BASE)\/releases\/$(VERSION)\/([a-zA-Z/\-]+)\.)ttl/\1owx/m" $1
+endef
+
+define translate_to_owl
+	$(ROBOT) convert --catalog $(VERSIONDIR)/catalog-v001.xml --input $2 --output $1 --format owl
+	$(call replace_ttls,$1)
+	$(call replace_devs,$1)
+endef
+
+define translate_to_ttl
+	$(ROBOT) convert --catalog $(VERSIONDIR)/catalog-v001.xml --input $2 --output $1 --format ttl
+	$(call replace_owls,$1)
+	$(call replace_devs,$1)
+endef
+
+define translate_to_omn
+	$(ROBOT) convert --catalog $(VERSIONDIR)/catalog-v001.xml --input $2 --output $1 --format omn
+	$(call replace_owls,$1)
+	$(call replace_devs,$1)
+endef
+
+define translate_to_owx
+	$(ROBOT) convert --catalog $(VERSIONDIR)/catalog-v001.xml --input $2 --output $1 --format owx
+	$(call replace_ttls_owx,$1)
+	$(call replace_devs,$1)
+endef
+
+define replace_placeholder
+	$(SED) -i -E "s/$(IRI_ONTOLOGY_PLACEHOLDER)\/([a-zA-Z/\.\-]+)/$(IRI_ONTOLOGY)\/\1/m" $1
+	$(SED) -i -E "s/$(IRI_ONTOLOGY_PLACEHOLDER)\//$(IRI_ONTOLOGY)\//m" $1
+endef
+
+.PHONY: all clean base merge directories
+
+all: base merge profiles closure owx
+
+imports: ${TMP} ${TMP}/catalog.xml $(IMPORTS) $(IMPORTS)/bfo_classes_only.owl $(IMPORTS)/cco-extracted.ttl
+
+base: | directories imports $(VERSIONDIR)/catalog-v001.xml robot.jar  $(TTL_COPY) $(OWL_COPY) $(OWLVERSION) $(TTL_TRANSLATE)
+
+merge: | $(VERSIONDIR)/$(ONTOLOGY_NAME)-full.ttl 
+
+owx: | $(VERSIONDIR)/$(ONTOLOGY_NAME)-full.owx 
+
+closure: | $(VERSIONDIR)/$(ONTOLOGY_NAME)-closure.ttl
+
+clean:
+	- $(RM) -r $(VERSIONDIR)
+	- $(RM) -r ${TMP}
+clean-imports:
+	- $(RM) -r $(IMPORTS)/*
+
+directories: ${VERSIONDIR}/imports ${VERSIONDIR}/modules ${TMP} $(VERSIONDIR)/owl
+
+
+$(IMPORTS):
+	${MKDIR_P} ${IMPORTS}
+
+$(IMPORTS)/bfo_classes_only.owl:
+	curl -L -o $@ $(BFO_SOURCE)
+
+$(IMPORTS)/cco-extracted.ttl: $(ROBOT_PATH)
+	bash src/scripts/cco-imports/cco-extracted.sh
+
+${TMP}:
+	${MKDIR_P} ${TMP}
+
+${TMP}/catalog.xml:
+	cp assets/catalog.xml  $@
+
+$(VERSIONDIR)/owl:
+	${MKDIR_P} $(VERSIONDIR)/owl
+
+${VERSIONDIR}/imports:
+	${MKDIR_P} ${VERSIONDIR}/imports
+
+${VERSIONDIR}/modules:
+	${MKDIR_P} ${VERSIONDIR}/modules
+
+$(VERSIONDIR)/catalog-v001.xml: $(ONTOLOGY_SOURCE)/catalog-v001.xml
+	cp $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+	$(SED) -i -E "s/edits\//modules\//m" $@
+
+$(ROBOT_PATH): | build
+	curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar
+
+$(VERSIONDIR)/owl/%.owl: $(VERSIONDIR)/%.ttl
+	$(call translate_to_owl,$@,$<)
+
+$(VERSIONDIR)/owl/modules/%.owl: $(VERSIONDIR)/edits/%.ttl
+	$(call translate_to_owl,$@,$<)
+
+$(VERSIONDIR)/owl/%.owl: $(ONTOLOGY_SOURCE)/%.owl
+	cp -a $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+
+$(VERSIONDIR)/owl/modules/%.owl: $(ONTOLOGY_SOURCE)/edits/%.owl
+	cp -a $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+
+$(VERSIONDIR)/modules/%.ttl: $(ONTOLOGY_SOURCE)/edits/%.ttl
+	cp -a $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+
+$(VERSIONDIR)/%.ttl: $(ONTOLOGY_SOURCE)/%.ttl
+	cp -a $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+
+$(VERSIONDIR)/%.owl: $(ONTOLOGY_SOURCE)/%.owl
+	cp -a $< $@
+	$(call replace_placeholder,$@)
+	$(call replace_devs,$@)
+
+$(VERSIONDIR)/$(ONTOLOGY_NAME)-full.ttl : | base
+	$(ROBOT) merge --catalog $(VERSIONDIR)/catalog-v001.xml $(foreach f, $(VERSIONDIR)/$(ONTOLOGY_NAME).ttl $(TTL_COPY) $(OWL_COPY), --input $(f)) annotate --ontology-iri $(IRI_ONTOLOGY)$(SEPARATOR) --version-iri $(IRI_ONTOLOGY)/releases/$(VERSION)/$(ONTOLOGY_NAME)-full.ttl --output $@
+	$(call replace_owls,$@)
+
+$(VERSIONDIR)/owl/$(ONTOLOGY_NAME)-full.owl : $(VERSIONDIR)/$(ONTOLOGY_NAME)-full.ttl
+	$(call translate_to_ttl,$@,$<)
+	$(call replace_ttls,$@)
+
+$(VERSIONDIR)/$(ONTOLOGY_NAME)-full.owx : $(VERSIONDIR)/$(ONTOLOGY_NAME)-full.ttl
+	$(call translate_to_owx,$@,$<)

assets/catalog.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+	<group xml:base="">
+		<uri name="https://www.commoncoreontologies.org/ExtendedRelationOntology" uri="ExtendedRelationOntology.ttl" />
+	</group>
+</catalog>