COB Revised

docs/odk-workflows/RepositoryFileStructure.md

@@ -16,8 +16,6 @@ These are the current imports in COB
 
 | Import | URL | Type |
 | ------ | --- | ---- |
-| ro | http://purl.obolibrary.org/obo/ro.owl | custom |
-| omo | http://purl.obolibrary.org/obo/omo.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:
@@ -26,9 +24,4 @@ Components, in contrast to imports, are considered full members of the ontology.
 2. A part of the ontology is managed in ROBOT templates
 3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may choose to manage logic that is beyond OBO in a specific OWL component.
 
-These are the components in COB
 
-| Filename | URL |
-| -------- | --- |
-| cob-annotations.owl | None |
-| cob-to-external.owl | None |

src/ontology/Makefile

@@ -19,7 +19,7 @@
 # 6. [Run everything (COB products and release pipeline)](all)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                5daef41d99e802417bd9ad0f378f72168e2d30f0488f5b2423330cbc561ec834
+CONFIG_HASH=                0cb0824fc712dd1bbe3e3067c8a9d6d4212a769da65f9ec96e0020e31e2cafb9
 
 
 # ----------------------------------------
@@ -62,13 +62,13 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output [email protected] && mv [email protected] $@
-OTHER_SRC =                 $(COMPONENTSDIR)/cob-annotations.owl $(COMPONENTSDIR)/cob-to-external.owl 
+OTHER_SRC =                 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
 FORMATS = $(sort  owl owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full cob-base-reasoned cob-examples-reasoned cob-native )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-root )
 
 ifeq ($(ODK_DEBUG),yes)
 ODK_DEBUG_FILE = debug.log
@@ -168,7 +168,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro omo
+IMPORTS = 
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -375,16 +375,6 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
-## Module for ontology: ro
-
-$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl
-	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in cob.Makefile!" && false
-## Module for ontology: omo
-
-$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_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:
@@ -406,39 +396,6 @@ refresh-%:
 no-mirror-refresh-%:
 	$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
 
-
-# ----------------------------------------
-# Components
-# ----------------------------------------
-# Some ontologies contain external and internal components. A component is included in the ontology in its entirety.
-
-COMP=true # Global parameter to bypass component generation
-
-.PHONY: all_components
-all_components: $(OTHER_SRC)
-
-.PHONY: recreate-components
-recreate-components:
-	$(MAKE) COMP=true IMP=false MIR=true PAT=true IMP_LARGE=false all_components -B
-
-.PHONY: no-mirror-recreate-components
-no-mirror-recreate-components:
-	$(MAKE) COMP=true IMP=false MIR=false PAT=true IMP_LARGE=false all_components -B
-
-.PHONY: recreate-%
-recreate-%:
-	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B
-
-.PHONY: no-mirror-recreate-%
-no-mirror-recreate-%:
-	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B
-
-$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)
-	test -f $@ || touch $@
-.PRECIOUS: $(COMPONENTSDIR)/%.owl
-
-
-
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------
@@ -450,22 +407,6 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 ifeq ($(strip $(MIR)),true)
 
 
-## ONTOLOGY: ro
-.PHONY: mirror-ro
-.PRECIOUS: $(MIRRORDIR)/ro.owl
-mirror-ro: | $(TMPDIR)
-	curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/[email protected]
-
-
-## ONTOLOGY: omo
-.PHONY: mirror-omo
-.PRECIOUS: $(MIRRORDIR)/omo.owl
-mirror-omo: | $(TMPDIR)
-	curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/[email protected]
-
-
 $(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
@@ -549,15 +490,6 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 		relax \
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@
-
-cob-base-reasoned.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
-
-cob-examples-reasoned.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
-
-cob-native.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
 # ----------------------------------------
 # Debugging Tools
 # ----------------------------------------