Merge pull request #16 from VirtualFlyBrain/base-imports

Base imports

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for vfbext
 # Generated using ontology-development-kit
-# ODK Version: v1.4.1
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead
 
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4.1
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -110,7 +110,7 @@ all_main: $(MAIN_FILES)
 
 IMPORTS =  ro caro fbbt obi
 
-IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
+IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
 IMPORT_FILES = $(IMPORT_OWL_FILES)
 
@@ -208,7 +208,7 @@ ASSETS = \
   $(MAPPING_FILES)
 
 RELEASE_ASSETS = \
-  $(MAIN_FILES) \
+  $(MAIN_FILES) $(IMPORT_FILES) \
   $(SUBSET_FILES)
 
 .PHONY: all_assets
@@ -306,30 +306,28 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
 	if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq >  $@; fi
 
 
+ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS))
+$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
+	if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq >  $@; fi
 
 
-$(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 \
+$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
+		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
-.PRECIOUS: $(IMPORTDIR)/%_import.owl
 
-## Module for ontology: caro
 
-$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl
-	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in vfbext.Makefile!" && false
-## Module for ontology: obi
 
-$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
+$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
-    extract -T $(IMPORTDIR)/obi_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
-		remove --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
-		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obi_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
+		extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+.PRECIOUS: $(IMPORTDIR)/%_import.owl
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -365,37 +363,44 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl
 mirror-ro: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: caro
 .PHONY: mirror-caro
 .PRECIOUS: $(MIRRORDIR)/caro.owl
 mirror-caro: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/CARO_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: fbbt
 .PHONY: mirror-fbbt
 .PRECIOUS: $(MIRRORDIR)/fbbt.owl
 mirror-fbbt: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/fbbt.owl --create-dirs -o $(MIRRORDIR)/fbbt.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/fbbt.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/fbbt/fbbt-base.owl --create-dirs -o $(MIRRORDIR)/fbbt.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/fbbt.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: obi
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl
 mirror-obi: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/OBI_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
+ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
+MERGE_MIRRORS = true
+
+$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
+	if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi
+.PRECIOUS: $(MIRRORDIR)/merged.owl
+
 
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	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." &&\

src/ontology/catalog-v001.xml

@@ -1,9 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
-  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/imports/ro_import.owl" uri="imports/ro_import.owl"/>
-  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/imports/caro_import.owl" uri="imports/caro_import.owl"/>
-  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/imports/fbbt_import.owl" uri="imports/fbbt_import.owl"/>
-  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/imports/obi_import.owl" uri="imports/obi_import.owl"/>
-  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
+  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/vfbext/imports/merged_import.owl" uri="imports/merged_import.owl"/>
     <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
 </catalog>