Include closure in monolithic builds

A follow-on patch will regenerate Make-managed files.

References:
* #155

Signed-off-by: Alex Nelson <[email protected]>

Author: ajnelson-nist

case_utils/ontology/Makefile

@@ -40,15 +40,30 @@ $(case_srcdir)/.venv.done.log: \
 	touch -c $@
 	test -r $@
 
+# Build monolith including transitive import closure outside of
+# CDO-maintained ontologies, removing need for network retrieval for
+# non-CDO class and property definitions.
 case-$(case_version).ttl: \
   $(case_srcdir)/.venv.done.log \
   $(RDF_TOOLKIT_JAR)
 	$(MAKE) \
 	  --directory $(case_srcdir)/tests \
 	    case_monolithic.ttl
-	cp \
-	  $(case_srcdir)/tests/case_monolithic.ttl \
-	  $@
+	source $(case_srcdir)/venv/bin/activate \
+	  && rdfpipe \
+	    --output-format turtle \
+	    $(case_srcdir)/tests/case_monolithic.ttl \
+	    $(uco_srcdir)/dependencies/collections-ontology/collections.owl \
+	    $(uco_srcdir)/dependencies/error/docs/current/error.ttl \
+	    > __$@
+	java -jar $(RDF_TOOLKIT_JAR) \
+	  --inline-blank-nodes \
+	  --source __$@ \
+	  --source-format turtle \
+	  --target _$@ \
+	  --target-format turtle
+	rm __$@
+	mv _$@ $@
 
 case-$(case_version)-subclasses.ttl: \
   case-$(case_version).ttl \

case_utils/ontology/src/subclasses_ttl.py

@@ -18,7 +18,7 @@
 This script creates an excerpt of an ontology graph that consists solely of all rdfs:subClassOf statements.
 """
 
-__version__ = "0.1.1"
+__version__ = "0.2.0"
 
 import argparse
 
@@ -39,6 +39,10 @@ def main() -> None:
         in_graph.parse(in_ttl)
 
     for triple in in_graph.triples((None, rdflib.RDFS.subClassOf, None)):
+        # Avoid owl:Restrictions and set-complements, which would get
+        # emitted as empty blank nodes.
+        if isinstance(triple[2], rdflib.BNode):
+            continue
         out_graph.add(triple)
 
     out_graph.serialize(args.out_ttl)