Merge pull request #254 from ApolloDev/update-iao-import

converted IAO import to proper ODK import

docs/odk-workflows/RepositoryFileStructure.md

@@ -17,11 +17,11 @@ These are the current imports in APOLLO_SV
 | Import | URL | Type |
 | ------ | --- | ---- |
 | ro | http://purl.obolibrary.org/obo/ro.owl | slme |
-| pno | http://purl.obolibrary.org/obo/iao/pno/dev/pno.owl | mirror |
 | geo | http://purl.obolibrary.org/obo/geo/dev/geo.owl | mirror |
 | ido | http://purl.obolibrary.org/obo/ido.owl | slme |
 | mf | http://purl.obolibrary.org/obo/mf.owl | slme |
 | go | http://purl.obolibrary.org/obo/go.owl | slme |
+| iao | http://purl.obolibrary.org/obo/iao.owl | mirror |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

src/ontology/Makefile

@@ -16,7 +16,7 @@
 # 3. [Update repo to latest ODK](update_repo)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                c731446a515442f3b378e0f8803a2a533d775453ddcf1c23a26ddaed7564e0a1
+CONFIG_HASH=                15f7592d9de34fe046ce12ec9f83ca39edbde7b087bef60e9c64a022551c8f57
 
 
 # ----------------------------------------
@@ -165,7 +165,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro pno geo ido mf go
+IMPORTS =  ro geo ido mf go iao
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -395,12 +395,6 @@ $(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.t
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
-## Module for ontology: pno
-
-$(IMPORTDIR)/pno_import.owl: $(MIRRORDIR)/pno.owl $(IMPORTDIR)/pno_terms_combined.txt
-	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
-    $(ANNOTATE_CONVERT_FILE); fi
-
 ## Module for ontology: geo
 
 $(IMPORTDIR)/geo_import.owl: $(MIRRORDIR)/geo.owl $(IMPORTDIR)/geo_terms_combined.txt
@@ -431,6 +425,12 @@ $(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.t
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+## Module for ontology: iao
+
+$(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl $(IMPORTDIR)/iao_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
+    $(ANNOTATE_CONVERT_FILE); fi
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -471,13 +471,6 @@ mirror-ro: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
 
 
-## ONTOLOGY: pno
-.PHONY: mirror-pno
-.PRECIOUS: $(MIRRORDIR)/pno.owl
-mirror-pno: | $(TMPDIR)
-	$(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/pno/dev/pno.owl -o $(TMPDIR)/$@.owl
-
-
 ## ONTOLOGY: geo
 .PHONY: mirror-geo
 .PRECIOUS: $(MIRRORDIR)/geo.owl
@@ -509,6 +502,14 @@ mirror-go: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: iao
+.PHONY: mirror-iao
+.PRECIOUS: $(MIRRORDIR)/iao.owl
+mirror-iao: | $(TMPDIR)
+	curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -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