Merge branch 'main' into classify_location

.gitignore

@@ -1,7 +1,6 @@
 *.jar
 *.swp
 .*.done.log
-.check-*.ttl
 .venv-pre-commit
 __pycache__
 venv

.pre-commit-config.yaml

@@ -4,11 +4,17 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
+  - repo: https://github.com/casework/rdf-toolkit-action
+    rev: 2.0.3
+    hooks:
+      - id: rdf-toolkit-normalizer
+        args:
+          - --autofix

ontology/Makefile

@@ -20,37 +20,11 @@ top_srcdir := $(shell cd .. ; pwd)
 
 uco_srcdir := $(top_srcdir)/dependencies/UCO
 
-RDF_TOOLKIT_JAR := $(uco_srcdir)/lib/rdf-toolkit.jar
-
 ttl_basenames := $(wildcard uco-*.ttl)
 
-check_ttl_targets := $(foreach ttl_basename,$(ttl_basenames),check-$(ttl_basename))
-
 all: \
   catalog-v001.xml
 
-.PHONY: \
-  check-%.ttl
-
-.PRECIOUS: \
-  .check-%.ttl
-
-$(RDF_TOOLKIT_JAR):
-	@echo "DEBUG:ontology/Makefile:top_srcdir=$(top_srcdir)" >&2
-	@echo "ERROR:ontology/Makefile:rdf-toolkit.jar not found.  Did you run `make` from the top source directory?" >&2
-	@test -r $@
-
-.check-%.ttl: \
-  %.ttl \
-  $(RDF_TOOLKIT_JAR)
-	java -jar $(RDF_TOOLKIT_JAR) \
-	  --inline-blank-nodes \
-	  --source $< \
-	  --source-format turtle \
-	  --target _$@ \
-	  --target-format turtle
-	mv _$@ $@
-
 catalog-v001.xml: \
   $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/etc/domain_directories.tsv \
@@ -69,15 +43,8 @@ catalog-v001.xml: \
 	mv _$@ $@
 
 check: \
-  $(check_ttl_targets) \
   catalog-v001.xml
 
-check-%.ttl: \
-  %.ttl \
-  .check-%.ttl
-	diff $^	\
-	  || (echo "ERROR:ontology/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/ to get a file ready to commit to Git." >&2 ; exit 1)
-
 clean:
 	@rm -f \
 	  _* \

ontology/uco-gufo.ttl

@@ -181,6 +181,13 @@ uco-core:Item
 		;
 	.
 
+uco-core:Relationship
+	rdfs:subClassOf
+		drafting:Endurant ,
+		gufo:Object
+		;
+	.
+
 uco-core:endTime
 	rdfs:seeAlso
 		gufo:hasEndPoint ,
@@ -226,6 +233,14 @@ uco-location:Location
 		;
 	.
 
+uco-observable:AlternateDataStream
+	a gufo:Kind ;
+	rdfs:subClassOf
+		drafting:Endurant ,
+		gufo:Object
+		;
+	.
+
 uco-observable:BluetoothAddressFacet
 	a drafting:SpecificFacetType ;
 	.
@@ -237,6 +252,10 @@ uco-observable:Device
 		;
 	.
 
+uco-observable:FileSystemObject
+	a gufo:Category ;
+	.
+
 uco-observable:MACAddressFacet
 	a drafting:GeneralFacetType ;
 	.
@@ -268,3 +287,37 @@ uco-types:Hash
 	owl:annotatedSubject uco-core:Assertion ;
 	.
 
+[]
+	a owl:NegativePropertyAssertion ;
+	rdfs:comment "If this specialization were introduced, a further specialization would be suggested for gufo:mediates.  A demonstration exists among the CASE examples that is incompatible: A Relationship, 'Mapped_Into', that relates two Actions together to demonstrate a lifecycle phase."@en ;
+	rdfs:seeAlso
+		<http://example.org/kb/lifecycle_phase-60a55e96-d39e-487e-9b39-3ba96e1ffc7a> ,
+		<https://github.com/casework/CASE-Examples/tree/dc6f6b901289c1684fd88e25e9bcec925974d155/examples/illustrations/forensic_lifecycle> ,
+		[
+			a owl:NegativePropertyAssertion ;
+			rdfs:comment "gufo:mediates has range gufo:Endurant, but a uco-core:Relationship is permitted to link any UcoObject, including perdurants."@en ;
+			rdfs:seeAlso
+				<http://example.org/kb/lifecycle_phase-60a55e96-d39e-487e-9b39-3ba96e1ffc7a> ,
+				<https://github.com/casework/CASE-Examples/tree/dc6f6b901289c1684fd88e25e9bcec925974d155/examples/illustrations/forensic_lifecycle>
+				;
+			owl:assertionProperty rdfs:subPropertyOf ;
+			owl:sourceInvididual uco-core:source ;
+			owl:targetInvididual gufo:mediates ;
+		] ,
+		[
+			a owl:NegativePropertyAssertion ;
+			rdfs:comment "gufo:mediates has range gufo:Endurant, but a uco-core:Relationship is permitted to link any UcoObject, including perdurants."@en ;
+			rdfs:seeAlso
+				<http://example.org/kb/lifecycle_phase-60a55e96-d39e-487e-9b39-3ba96e1ffc7a> ,
+				<https://github.com/casework/CASE-Examples/tree/dc6f6b901289c1684fd88e25e9bcec925974d155/examples/illustrations/forensic_lifecycle>
+				;
+			owl:assertionProperty rdfs:subPropertyOf ;
+			owl:sourceInvididual uco-core:target ;
+			owl:targetInvididual gufo:mediates ;
+		]
+		;
+	owl:assertionProperty rdfs:subClassOf ;
+	owl:sourceInvididual uco-core:Relationship ;
+	owl:targetInvididual gufo:Relator ;
+	.
+

shapes/Makefile

@@ -20,37 +20,11 @@ top_srcdir := $(shell cd .. ; pwd)
 
 uco_srcdir := $(top_srcdir)/dependencies/UCO
 
-RDF_TOOLKIT_JAR := $(uco_srcdir)/lib/rdf-toolkit.jar
-
 ttl_basenames := $(wildcard sh-*.ttl)
 
-check_ttl_targets := $(foreach ttl_basename,$(ttl_basenames),check-$(ttl_basename))
-
 all: \
   catalog-v001.xml
 
-.PHONY: \
-  check-%.ttl
-
-.PRECIOUS: \
-  .check-%.ttl
-
-$(RDF_TOOLKIT_JAR):
-	@echo "DEBUG:shapes/Makefile:top_srcdir=$(top_srcdir)" >&2
-	@echo "ERROR:shapes/Makefile:rdf-toolkit.jar not found.  Did you run `make` from the top source directory?" >&2
-	@test -r $@
-
-.check-%.ttl: \
-  %.ttl \
-  $(RDF_TOOLKIT_JAR)
-	java -jar $(RDF_TOOLKIT_JAR) \
-	  --inline-blank-nodes \
-	  --source $< \
-	  --source-format turtle \
-	  --target _$@ \
-	  --target-format turtle
-	mv _$@ $@
-
 catalog-v001.xml: \
   $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/etc/domain_directories.tsv \
@@ -69,15 +43,8 @@ catalog-v001.xml: \
 	mv _$@ $@
 
 check: \
-  $(check_ttl_targets) \
   catalog-v001.xml
 
-check-%.ttl: \
-  %.ttl \
-  .check-%.ttl
-	diff $^	\
-	  || (echo "ERROR:shapes/Makefile:The local $< does not match the normalized version. If the above reported changes look fine, run 'cp .check-$< $<' while in the sub-folder shapes/ to get a file ready to commit to Git." >&2 ; exit 1)
-
 clean:
 	@rm -f \
 	  _* \

tests/exemplars.ttl

@@ -25,16 +25,30 @@
 
 kb:Action-13c91d40-9ca0-4558-81a1-4f7db888c371
 	a uco-action:Action ;
-	uco-action:endTime "2021-02-03T04:05:06Z"^^xsd:dateTime ;
-	uco-action:startTime "2020-01-02T03:04:05Z"^^xsd:dateTime ;
 	gufo:hasBeginPointInXSDDateTimeStamp "2020-01-02T03:04:05Z"^^xsd:dateTimeStamp ;
 	gufo:hasEndPointInXSDDateTimeStamp "2021-02-03T04:05:06Z"^^xsd:dateTimeStamp ;
+	uco-action:endTime "2021-02-03T04:05:06Z"^^xsd:dateTime ;
+	uco-action:startTime "2020-01-02T03:04:05Z"^^xsd:dateTime ;
+	.
+
+kb:AlternateDataStream-e6ceee40-5614-4740-b08c-d21ce9b2356d
+	a
+		uco-observable:AlternateDataStream ,
+		uco-observable:FileSystemObject
+		;
+	rdfs:comment "TODO - The assignment of FileSystemObject is only necessary until UCO Issue 590 is incorporated."@en ;
+	rdfs:seeAlso <https://github.com/ucoProject/UCO/issues/590> ;
 	.
 
 kb:AnalyticResult-34fb92db-d576-45a7-9d62-dae04510968f
 	a uco-analysis:AnalyticResult ;
 	.
 
+kb:Bearing-74c2bb20-1e4f-40ac-807e-bc2c528e39da
+	a drafting:Bearing ;
+	gufo:inheresIn kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc ;
+	.
+
 kb:BluetoothAddress-53c6bc31-4f9c-4ca7-96cb-c9c61d7e4ca2
 	a uco-observable:BluetoothAddress ;
 	uco-core:hasFacet
@@ -43,30 +57,33 @@ kb:BluetoothAddress-53c6bc31-4f9c-4ca7-96cb-c9c61d7e4ca2
 		;
 	.
 
-kb:Bearing-74c2bb20-1e4f-40ac-807e-bc2c528e39da
-	a drafting:Bearing ;
-	gufo:inheresIn kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc ;
-	.
-
 kb:BluetoothAddressFacet-717b8cce-e9c2-4d59-81e4-1747d7e2d8ee
 	a uco-observable:BluetoothAddressFacet ;
 	.
 
+kb:ContentData-0571dfb7-889e-4e8c-bec7-47a62ab9286f
+	a uco-observable:ContentData ;
+	.
+
 kb:ContentData-179c7e84-f72d-47f7-b6f3-3f4a1f0938bd
 	a uco-observable:ContentData ;
 	uco-core:hasFacet kb:ContentDataFacet-a961d865-087b-43bd-ab31-0e33331c5628 ;
 	.
 
+kb:ContentData-3f13e43a-a3f4-4dcc-8db2-e934b24890ec
+	a uco-observable:ContentData ;
+	.
+
 kb:ContentDataFacet-a961d865-087b-43bd-ab31-0e33331c5628
 	a uco-observable:ContentDataFacet ;
 	.
 
 kb:Event-03a1a1db-0579-4427-9a51-448c32281146
 	a uco-core:Event ;
-	uco-core:endTime "2011-02-03T04:05:06Z"^^xsd:dateTime ;
-	uco-core:startTime "2010-01-02T03:04:05Z"^^xsd:dateTime ;
 	gufo:hasBeginPointInXSDDateTimeStamp "2010-01-02T03:04:05Z"^^xsd:dateTimeStamp ;
 	gufo:hasEndPointInXSDDateTimeStamp "2011-02-03T04:05:06Z"^^xsd:dateTimeStamp ;
+	uco-core:endTime "2011-02-03T04:05:06Z"^^xsd:dateTime ;
+	uco-core:startTime "2010-01-02T03:04:05Z"^^xsd:dateTime ;
 	.
 
 kb:Hash-4c3d0623-d365-4c69-a1a1-01523c6502fa
@@ -136,9 +153,12 @@ kb:QualityValueAttributionSituation-872b7dd1-b49a-4278-bfdf-df507493d63f
 	gufo:hasEndPoint kb:Instant-c9ae3fce-ddcb-416b-971b-559c2f5bee95 ;
 	.
 
-kb:Velocity-62bc6232-b570-45d7-b382-d4e0a36fceb9
-	a drafting:Velocity ;
-	gufo:inheresIn kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc ;
+kb:Relationship-2be6b54a-a051-499c-9dcd-63d17d813293
+	a uco-core:Relationship ;
+	uco-core:isDirectional "true"^^xsd:boolean ;
+	uco-core:kindOfRelationship "Contained_Within" ;
+	uco-core:source kb:ContentData-0571dfb7-889e-4e8c-bec7-47a62ab9286f ;
+	uco-core:target kb:ContentData-3f13e43a-a3f4-4dcc-8db2-e934b24890ec ;
 	.
 
 kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc
@@ -149,3 +169,8 @@ kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc
 		;
 	.
 
+kb:Velocity-62bc6232-b570-45d7-b382-d4e0a36fceb9
+	a drafting:Velocity ;
+	gufo:inheresIn kb:Vehicle-c7e910e8-4bed-473e-ad74-3df3eb63cbcc ;
+	.
+

tests/test_exemplar_coverage.py

@@ -20,6 +20,7 @@
 from typing import Optional, Set
 
 from rdflib import RDF, RDFS, Graph, URIRef
+from rdflib.query import ResultRow
 
 NS_RDF = RDF
 NS_RDFS = RDFS
@@ -34,6 +35,7 @@ def test_exemplar_coverage() -> None:
     ontologies) designated a subclass of some C', and each property P
     designated a subproperty of some P', C (/P) is used in the exemplars
     graph.
+    For gUFO, instances of a gufo:Type are also included in the review.
     """
     exemplar_graph = Graph()
     profile_graph = Graph()
@@ -66,6 +68,22 @@ def test_exemplar_coverage() -> None:
         assert isinstance(triple[0], URIRef)
         classes_mapped.add(triple[0])
 
+    gufo_type_query = """\
+PREFIX gufo: <http://purl.org/nemo/gufo#>
+SELECT ?nClass
+WHERE {
+  # owl:Class restriction is to not pick up Relators.
+  ?nClass
+    a owl:Class ;
+    a/rdfs:subClassOf* gufo:Type ;
+    .
+}
+"""
+    for gufo_type_query_result in tbox_graph.query(gufo_type_query):
+        assert isinstance(gufo_type_query_result, ResultRow)
+        assert isinstance(gufo_type_query_result[0], URIRef)
+        classes_mapped.add(gufo_type_query_result[0])
+
     result: Optional[bool]
 
     class_query = """\