Merge pull request #531 from ucoProject/Release-1.2.0

Release 1.2.0

.gitignore

@@ -2,3 +2,6 @@
 .*.ttl
 .git_submodule_init.done.log
 .lib.done.log
+.venv.done.log
+_*
+venv

CONTRIBUTE.md

@@ -1,6 +1,17 @@
-# Contributing to the CASE ontology
+# Contributing to the UCO ontology
 
 
 ## Testing prerelease states
 
 Practices for users interested in testing prerelease states are documented on the [Cyber Domain Ontology website](https://cyberdomainontology.org/ontology/development/#testing-prereleases).
+
+
+## Using Protégé catalog files
+
+Interested users of `catalog-v001.xml` files, e.g. users of [Protégé](https://protege.stanford.edu/), can use these XML files to interact with UCO as local files.  To do so, UCO must be `git-clone`'d with Git submodules also cloned.  This can be done with the following commands:
+
+* `git clone --recursive https://github.com/ucoProject/UCO.git` (all users)
+* `git clone https://github.com/ucoProject/UCO.git ; cd UCO ; make` (macOS or Linux users)
+   - The narrowest setup operation strictly for purposes of supporting the `catalog-v001.xml` files is to run `make .git_submodule_init.done.log` instead of the default `make all`.
+
+Protégé should not require network connectivity to load imported ontologies after the above commands are run.

Makefile

@@ -13,8 +13,11 @@
 
 SHELL := /bin/bash
 
+PYTHON3 ?= $(shell which python3)
+
 all: \
-  .lib.done.log
+  .lib.done.log \
+  .venv.done.log
 	$(MAKE) \
 	  --directory ontology
 
@@ -44,9 +47,31 @@ all: \
 	  --directory lib
 	touch $@
 
+# The two CASE-Utility... files are to trigger rebuilds based on command-line interface changes or version increments.
+.venv.done.log: \
+  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py \
+  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg \
+  requirements.txt
+	rm -rf venv
+	$(PYTHON3) -m venv \
+	  venv
+	source venv/bin/activate \
+	  && pip install \
+	    --upgrade \
+	    pip \
+	    setuptools \
+	    wheel
+	source venv/bin/activate \
+	  && pip install \
+	    dependencies/CASE-Utility-SHACL-Inheritance-Reviewer
+	source venv/bin/activate \
+	  && pip install \
+	    --requirement requirements.txt
+	touch $@
+
 check: \
-  .git_submodule_init.done.log \
-  .lib.done.log
+  .lib.done.log \
+  .venv.done.log
 	$(MAKE) \
 	  --directory ontology \
 	  check
@@ -59,7 +84,10 @@ clean: \
   clean-ontology
 	@rm -f \
 	  .git_submodule_init.done.log \
-	  .lib.done.log
+	  .lib.done.log \
+	  .venv.done.log
+	@rm -rf \
+	  venv
 
 clean-ontology:
 	@$(MAKE) \
@@ -70,3 +98,15 @@ clean-tests:
 	@$(MAKE) \
 	  --directory tests \
 	  clean
+
+# Maintain timestamp order.
+dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py: \
+  .git_submodule_init.done.log
+	touch -c $@
+	test -r $@
+
+# Maintain timestamp order.
+dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg: \
+  .git_submodule_init.done.log
+	touch -c $@
+	test -r $@

README.md

@@ -13,8 +13,8 @@ Through this approach not only are domain-focused representations defined consis
 The purpose of this repository is to provide a foundation for broader community involvement in defining what to represent and how.
 
 ### Current Release
-The current release of UCO is 1.1.0.
+The current release of UCO is 1.2.0.
 
-UCO 1.1.0 incorporates required refinements and updates, building on the stable 1.0.0 release.  Following [SemVer](https://semver.org/spec/v2.0.0.html), additive improvements will continue to be accepted, but backwards-incompatible changes will be scheduled only for the 2.0.0 release, which will come after at least 6 months to possibly 12 months.
+UCO 1.2.0 incorporates required refinements and updates, building on the stable 1.0.0 release.  Following [SemVer](https://semver.org/spec/v2.0.0.html), additive improvements will continue to be accepted, but backwards-incompatible changes will be scheduled only for the 2.0.0 release, which will come after at least 6 months to possibly 12 months.
 
-More detail of improvements is documented in the [UCO 1.1.0 release notes](https://unifiedcyberontology.org/releases/1.1.0/).
+More detail of improvements is documented in the [UCO 1.2.0 release notes](https://unifiedcyberontology.org/releases/1.2.0/).

etc/dependency_files.tsv

@@ -0,0 +1,2 @@
+http://purl.org/co/	${top_srcdir}/dependencies/collections-ontology/collections.owl
+http://purl.org/spar/error	${top_srcdir}/dependencies/error/docs/current/error.ttl

etc/domain_directories.tsv

@@ -0,0 +1 @@
+https://ontology.unifiedcyberontology.org/	${top_srcdir}/ontology/

ontology/co/Makefile

@@ -30,7 +30,8 @@ check_reference_basenames := $(foreach ttl_basename,$(ttl_basenames),.check-$(tt
 check_targets := $(foreach ttl_basename,$(ttl_basenames),check-$(ttl_basename))
 
 all: \
-  $(check_reference_basenames)
+  $(check_reference_basenames) \
+  catalog-v001.xml
 
 .check-%.ttl: \
   %.ttl \
@@ -43,8 +44,25 @@ all: \
 	  --target-format turtle
 	mv $@_ $@
 
+catalog-v001.xml: \
+  $(top_srcdir)/.venv.done.log \
+  $(top_srcdir)/etc/domain_directories.tsv \
+  $(top_srcdir)/etc/dependency_files.tsv \
+  $(top_srcdir)/src/create-catalog-v001.xml.py \
+  $(ttl_basenames)
+	rm -f _$@
+	source $(top_srcdir)/venv/bin/activate \
+	  && python3 $(top_srcdir)/src/create-catalog-v001.xml.py \
+	    _$@ \
+	    $(top_srcdir)/etc/domain_directories.tsv \
+	    $(top_srcdir)/etc/dependency_files.tsv \
+	    "$(top_srcdir)" \
+	    $(ttl_basenames)
+	mv _$@ $@
+
 check: \
-  $(check_targets)
+  $(check_targets) \
+  catalog-v001.xml
 
 # Reminder: diff exits non-0 on finding any differences.
 # Reminder: The $^ automatic Make variable is the name of all recipe prerequisites.
@@ -55,5 +73,6 @@ check-%.ttl: \
 	  || (echo "ERROR:ontology/co/Makefile:The local $< does not match the normalized version. If the above reported changes look fine, run 'cp .check-$< $<' while in the sub-folder ontology/co/ to get a file ready to commit to Git." >&2 ; exit 1)
 
 clean:
-	@rm -f $(check_reference_basenames)
-
+	@rm -f \
+	  $(check_reference_basenames) \
+	  catalog-v001.xml

ontology/co/catalog-v001.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../../dependencies/collections-ontology/collections.owl" name="http://purl.org/co"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/error/docs/current/error.ttl" name="http://purl.org/spar/error"/>
+    <uri id="User Entered Import Resolution" uri="co.ttl" name="https://ontology.unifiedcyberontology.org/co"/>
+</catalog>

ontology/co/co.ttl

@@ -12,10 +12,10 @@
 	a owl:Ontology ;
 	rdfs:label "uco-co"@en ;
 	rdfs:comment "This ontology defines SHACL shapes to supplement the OWL 2 DL definitions in the Collections Ontology."@en ;
-	owl:backwardCompatibleWith uco-co:1.0.0 ;
+	owl:backwardCompatibleWith uco-co:1.1.0 ;
 	owl:imports <http://purl.org/co> ;
-	owl:priorVersion uco-co:1.0.0 ;
-	owl:versionIRI uco-co:1.1.0 ;
+	owl:priorVersion uco-co:1.1.0 ;
+	owl:versionIRI uco-co:1.2.0 ;
 	.
 
 co:ListItem

ontology/owl/owl.ttl

@@ -10,9 +10,9 @@
 	rdfs:label "uco-owl"@en ;
 	rdfs:comment "This ontology defines SHACL shapes to perform conformance testing of OWL 2 DL.  Some of these shapes follow rules specified from the canonical, subtractive parsing process of Section 3 of the OWL 2 mapping to RDF.  From the last line of that document's Section 3, 'At the end of this process, the graph G MUST be empty,' anything not strictly matching patterns specified in that section cause the input graph to be non-conformant with OWL 2 DL."@en ;
 	rdfs:seeAlso <https://www.w3.org/TR/2012/REC-owl2-mapping-to-rdf-20121211/#Mapping_from_RDF_Graphs_to_the_Structural_Specification> ;
-	owl:backwardCompatibleWith uco-owl:1.0.0 ;
-	owl:priorVersion uco-owl:1.0.0 ;
-	owl:versionIRI uco-owl:1.1.0 ;
+	owl:backwardCompatibleWith uco-owl:1.1.0 ;
+	owl:priorVersion uco-owl:1.1.0 ;
+	owl:versionIRI uco-owl:1.2.0 ;
 	.
 
 uco-owl:Axiom-shape
@@ -226,6 +226,7 @@ uco-owl:ObjectProperty-shacl-constraints-shape
 			a sh:SPARQLConstraint ;
 			sh:message "An OWL Object Property must not permit a Literal value via SHACL consraints."@en ;
 			sh:select """
+				PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 				PREFIX sh: <http://www.w3.org/ns/shacl#>
 				SELECT $this ?value
 				WHERE {

ontology/uco/action/action.ttl

@@ -1,8 +1,8 @@
-# imports: https://ontology.unifiedcyberontology.org/uco/core/1.1.0
-# imports: https://ontology.unifiedcyberontology.org/uco/location/1.1.0
-# imports: https://ontology.unifiedcyberontology.org/uco/pattern/1.1.0
-# imports: https://ontology.unifiedcyberontology.org/uco/types/1.1.0
-# imports: https://ontology.unifiedcyberontology.org/uco/vocabulary/1.1.0
+# imports: https://ontology.unifiedcyberontology.org/uco/core/1.2.0
+# imports: https://ontology.unifiedcyberontology.org/uco/location/1.2.0
+# imports: https://ontology.unifiedcyberontology.org/uco/pattern/1.2.0
+# imports: https://ontology.unifiedcyberontology.org/uco/types/1.2.0
+# imports: https://ontology.unifiedcyberontology.org/uco/vocabulary/1.2.0
 
 @prefix action: <https://ontology.unifiedcyberontology.org/uco/action/> .
 @prefix core: <https://ontology.unifiedcyberontology.org/uco/core/> .
@@ -20,16 +20,16 @@
 	a owl:Ontology ;
 	rdfs:label "uco-action"@en ;
 	rdfs:comment "This ontology defines classes and properties for characterizing actions."@en-US ;
-	owl:backwardCompatibleWith action:1.0.0 ;
+	owl:backwardCompatibleWith action:1.1.0 ;
 	owl:imports
-		core:1.1.0 ,
-		location:1.1.0 ,
-		pattern:1.1.0 ,
-		types:1.1.0 ,
-		vocabulary:1.1.0
+		core:1.2.0 ,
+		location:1.2.0 ,
+		pattern:1.2.0 ,
+		types:1.2.0 ,
+		vocabulary:1.2.0
 		;
-	owl:priorVersion action:1.0.0 ;
-	owl:versionIRI action:1.1.0 ;
+	owl:priorVersion action:1.1.0 ;
+	owl:versionIRI action:1.2.0 ;
 	.
 
 action:Action

ontology/uco/action/catalog-v001.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../../../dependencies/collections-ontology/collections.owl" name="http://purl.org/co"/>
+    <uri id="User Entered Import Resolution" uri="../../../dependencies/error/docs/current/error.ttl" name="http://purl.org/spar/error"/>
+    <uri id="User Entered Import Resolution" uri="../../co/co.ttl" name="https://ontology.unifiedcyberontology.org/co/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../core/core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../location/location.ttl" name="https://ontology.unifiedcyberontology.org/uco/location/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../pattern/pattern.ttl" name="https://ontology.unifiedcyberontology.org/uco/pattern/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../types/types.ttl" name="https://ontology.unifiedcyberontology.org/uco/types/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../vocabulary/vocabulary.ttl" name="https://ontology.unifiedcyberontology.org/uco/vocabulary/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="action.ttl" name="https://ontology.unifiedcyberontology.org/uco/action"/>
+</catalog>

ontology/uco/analysis/analysis.ttl

@@ -1,4 +1,4 @@
-# imports: https://ontology.unifiedcyberontology.org/uco/action/1.1.0
+# imports: https://ontology.unifiedcyberontology.org/uco/action/1.2.0
 
 @prefix action: <https://ontology.unifiedcyberontology.org/uco/action/> .
 @prefix analysis: <https://ontology.unifiedcyberontology.org/uco/analysis/> .
@@ -14,8 +14,10 @@
 	rdfs:label "uco-analysis"@en ;
 	rdfs:comment "This ontology defines classes and properties for characterizing analytic actions and results."@en-US ;
 	rdfs:seeAlso <https://github.com/ucoProject/UCO/issues/400> ;
-	owl:imports action:1.1.0 ;
-	owl:versionIRI analysis:1.1.0 ;
+	owl:backwardCompatibleWith analysis:1.1.0 ;
+	owl:imports action:1.2.0 ;
+	owl:priorVersion analysis:1.1.0 ;
+	owl:versionIRI analysis:1.2.0 ;
 	.
 
 analysis:Analysis

ontology/uco/analysis/catalog-v001.xml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../../../dependencies/collections-ontology/collections.owl" name="http://purl.org/co"/>
+    <uri id="User Entered Import Resolution" uri="../../../dependencies/error/docs/current/error.ttl" name="http://purl.org/spar/error"/>
+    <uri id="User Entered Import Resolution" uri="../../co/co.ttl" name="https://ontology.unifiedcyberontology.org/co/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../action/action.ttl" name="https://ontology.unifiedcyberontology.org/uco/action/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../core/core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../location/location.ttl" name="https://ontology.unifiedcyberontology.org/uco/location/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../pattern/pattern.ttl" name="https://ontology.unifiedcyberontology.org/uco/pattern/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../types/types.ttl" name="https://ontology.unifiedcyberontology.org/uco/types/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../vocabulary/vocabulary.ttl" name="https://ontology.unifiedcyberontology.org/uco/vocabulary/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="analysis.ttl" name="https://ontology.unifiedcyberontology.org/uco/analysis"/>
+</catalog>

ontology/uco/configuration/catalog-v001.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../core/core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="configuration.ttl" name="https://ontology.unifiedcyberontology.org/uco/configuration"/>
+</catalog>

ontology/uco/configuration/configuration.ttl

@@ -1,4 +1,4 @@
-# imports: https://ontology.unifiedcyberontology.org/uco/core/1.1.0
+# imports: https://ontology.unifiedcyberontology.org/uco/core/1.2.0
 
 @prefix configuration: <https://ontology.unifiedcyberontology.org/uco/configuration/> .
 @prefix core: <https://ontology.unifiedcyberontology.org/uco/core/> .
@@ -13,10 +13,10 @@
 	rdfs:label "uco-configuration"@en ;
 	rdfs:comment "This ontology defines classes and properties for characterizing configurations."@en-US ;
 	rdfs:seeAlso <https://github.com/ucoProject/UCO/issues/432> ;
-	owl:backwardCompatibleWith configuration:1.0.0 ;
-	owl:imports core:1.1.0 ;
-	owl:priorVersion configuration:1.0.0 ;
-	owl:versionIRI configuration:1.1.0 ;
+	owl:backwardCompatibleWith configuration:1.1.0 ;
+	owl:imports core:1.2.0 ;
+	owl:priorVersion configuration:1.1.0 ;
+	owl:versionIRI configuration:1.2.0 ;
 	.
 
 configuration:Configuration

ontology/uco/core/catalog-v001.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core"/>
+</catalog>

ontology/uco/core/core.ttl

@@ -10,9 +10,9 @@
 	a owl:Ontology ;
 	rdfs:label "uco-core"@en ;
 	rdfs:comment "This ontology defines classes and properties that are shared across the various UCO ontologies.  At a high-level, the UCO core ontology provides base classes, relationship-oriented classes, content-aggregation classes, and shared classes."@en ;
-	owl:backwardCompatibleWith core:1.0.0 ;
-	owl:priorVersion core:1.0.0 ;
-	owl:versionIRI core:1.1.0 ;
+	owl:backwardCompatibleWith core:1.1.0 ;
+	owl:priorVersion core:1.1.0 ;
+	owl:versionIRI core:1.2.0 ;
 	.
 
 core:Annotation
@@ -409,15 +409,16 @@ core:UcoThing
 	rdfs:subClassOf owl:Thing ;
 	rdfs:label "UcoThing"@en ;
 	rdfs:comment "UcoThing is the top-level class within UCO."@en ;
-	rdfs:seeAlso core:UcoThing-identifier-shape ;
+	rdfs:seeAlso core:UcoThing-identifier-regex-shape ;
 	sh:sparql [
 		a sh:SPARQLConstraint ;
 		sh:message "UcoThings are required to not be blank nodes."@en ;
 		sh:select """
-			PREFIX uco-core: <https://ontology.unifiedcyberontology.org/uco/core/>
+			PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+			PREFIX core: <https://ontology.unifiedcyberontology.org/uco/core/>
 			SELECT $this
 			WHERE {
-			        $this a/rdfs:subClassOf* uco-core:UcoThing .
+			        $this a/rdfs:subClassOf* core:UcoThing .
 			        FILTER isBlank ($this)
 			}
 		""" ;
@@ -435,10 +436,11 @@ core:UcoThing-identifier-regex-shape
 		rdfs:seeAlso <https://datatracker.ietf.org/doc/html/rfc4122#section-4.1.3> ;
 		sh:message "UcoThings are suggested to end with a UUID."@en ;
 		sh:select '''
-			PREFIX uco-core: <https://ontology.unifiedcyberontology.org/uco/core/>
+			PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+			PREFIX core: <https://ontology.unifiedcyberontology.org/uco/core/>
 			SELECT $this
 			WHERE {
-			        $this a/rdfs:subClassOf* uco-core:UcoThing .
+			        $this a/rdfs:subClassOf* core:UcoThing .
 			        FILTER (
 			                ! REGEX (
 			                        STR($this),

ontology/uco/identity/catalog-v001.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../core/core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../location/location.ttl" name="https://ontology.unifiedcyberontology.org/uco/location/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="identity.ttl" name="https://ontology.unifiedcyberontology.org/uco/identity"/>
+</catalog>