Change transitive imports management

This patch applies and adapts the effects of UCO-Profile-Example PR 4.

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

References:
* ucoProject/UCO-Profile-Example#4

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

Author: ajnelson-nist

.gitignore

@@ -4,4 +4,5 @@
 .venv-pre-commit
 _*.*
 __pycache__
+generated-*
 venv

Makefile

@@ -20,21 +20,27 @@ PYTHON3 ?= python3
 
 all: \
   .venv-pre-commit/var/.pre-commit-built.log \
-  all-ontology \
-  all-shapes
+  all-shapes \
+  all-tests
 
 .PHONY: \
   all-dependencies \
   all-ontology \
   all-shapes \
+  all-tests \
   check-dependencies \
   check-mypy \
   check-ontology \
   check-shapes \
   check-supply-chain \
   check-supply-chain-cdo-profile \
   check-supply-chain-pre-commit \
-  check-supply-chain-submodules
+  check-supply-chain-submodules \
+  check-tests \
+  clean-dependencies \
+  clean-ontology \
+  clean-shapes \
+  clean-tests
 
 # This Make target should be left in place, even if it does nothing.  It
 # has been found beneficial with profiles that have a submodule-based
@@ -53,7 +59,7 @@ all: \
 	# profile builds on a UCO profile.
 	$(MAKE) \
 	  --directory dependencies/UCO-Profile-Example \
-	  .git_submodule_init_imports.done.log
+	  .git_submodule_init.done.log
 	$(MAKE) \
 	  --directory dependencies/CASE \
 	  .git_submodule_init.done.log \
@@ -103,33 +109,28 @@ all-dependencies: \
   .git_submodule_init.done.log \
   .venv.done.log
 	$(MAKE) \
+	  PYTHON3=$(PYTHON3) \
 	  --directory dependencies
 
 all-ontology: \
   all-dependencies
 	$(MAKE) \
 	  --directory ontology
 
-# NOTE: For profiles that don't include shapes, the $(top_srcdir)/shapes
-# directory might be missing.  Checking for its existence first relieves
-# each profile of needing to modify the top Makefile when removing
-# shapes.
 all-shapes: \
-  all-dependencies
-	test ! -d shapes \
-	  || $(MAKE) \
-	    --directory shapes
+  all-ontology
+	$(MAKE) \
+	  --directory shapes
+
+all-tests: \
+  all-ontology
+	$(MAKE) \
+	  --directory tests
 
 check: \
   .venv-pre-commit/var/.pre-commit-built.log \
   check-mypy \
-  check-dependencies \
-  check-ontology \
-  check-shapes
-	$(MAKE) \
-	  PYTHON3=$(PYTHON3) \
-	  --directory tests \
-	  check
+  check-tests
 
 check-dependencies: \
   all-dependencies
@@ -147,21 +148,18 @@ check-mypy: \
 	    .
 
 check-ontology: \
-  all-ontology
+  all-ontology \
+  check-dependencies
 	$(MAKE) \
 	  --directory ontology \
 	  check
 
-# NOTE: For profiles that don't include shapes, the $(top_srcdir)/shapes
-# directory might be missing.  Checking for its existence first relieves
-# each profile of needing to modify the top Makefile when removing
-# shapes.
 check-shapes: \
-  all-shapes
-	test ! -d shapes \
-	  || $(MAKE) \
-	    --directory shapes \
-	    check
+  all-shapes \
+  check-ontology
+	$(MAKE) \
+	  --directory shapes \
+	  check
 
 # This target's dependencies potentially modify the working directory's
 # Git state, so it is intentionally not a dependency of check.
@@ -228,19 +226,37 @@ check-supply-chain-submodules: \
 	  --ignore-submodules=dirty \
 	  dependencies
 
-clean:
-	@$(MAKE) \
+check-tests: \
+  all-tests \
+  check-shapes
+	$(MAKE) \
 	  --directory tests \
+	  check
+
+clean: \
+  clean-tests \
+  clean-shapes \
+  clean-ontology \
+  clean-dependencies
+	@rm -f \
+	  .*.done.log
+
+clean-dependencies:
+	@$(MAKE) \
+	  --directory dependencies \
 	  clean
-	@test ! -d shapes \
-	  || $(MAKE) \
-	    --directory shapes \
-	    clean
+
+clean-ontology:
 	@$(MAKE) \
 	  --directory ontology \
 	  clean
+
+clean-shapes:
 	@$(MAKE) \
-	  --directory dependencies \
+	  --directory shapes \
+	  clean
+
+clean-tests:
+	@$(MAKE) \
+	  --directory tests \
 	  clean
-	@rm -f \
-	  .*.done.log

dependencies/Makefile

@@ -16,71 +16,26 @@
 
 SHELL := /bin/bash
 
-top_srcdir := $(shell cd .. ; pwd)
+PYTHON3 ?= python3
 
 case_srcdir := CASE
 
-uco_srcdir := $(case_srcdir)/dependencies/UCO
-
-RDF_TOOLKIT_JAR := $(uco_srcdir)/lib/rdf-toolkit.jar
-
 all: \
-  catalog-v001.xml
+  $(case_srcdir)/tests/case_monolithic.ttl
 
-$(RDF_TOOLKIT_JAR):
-	@echo "DEBUG:dependencies/Makefile:top_srcdir=$(top_srcdir)" >&2
-	@echo "ERROR:dependencies/Makefile:rdf-toolkit.jar not found.  Did you run `make` from the top source directory?" >&2
-	@test -r $@
+$(case_srcdir)/.venv.done.log:
+	$(MAKE) \
+	  PYTHON3=$(PYTHON3) \
+	  --directory $(case_srcdir) \
+	  .venv.done.log
 
-catalog-v001.xml: \
-  $(case_srcdir)/ontology/master/catalog-v001.xml \
-  $(top_srcdir)/.venv.done.log \
-  $(top_srcdir)/etc/domain_directories.tsv \
-  $(top_srcdir)/etc/dependency_files.tsv \
-  $(uco_srcdir)/src/create-catalog-v001.xml.py \
-  imports-transitive.ttl
-	rm -f _$@
-	source $(top_srcdir)/venv/bin/activate \
-	  && python3 $(uco_srcdir)/src/create-catalog-v001.xml.py \
-	    --catalog-xml $(case_srcdir)/ontology/master/catalog-v001.xml \
-	    _$@ \
-	    $(top_srcdir)/etc/domain_directories.tsv \
-	    $(top_srcdir)/etc/dependency_files.tsv \
-	    "$(top_srcdir)" \
-	    imports-transitive.ttl
-	mv _$@ $@
+$(case_srcdir)/tests/case_monolithic.ttl: \
+  $(case_srcdir)/.venv.done.log
+	$(MAKE) \
+	  --directory $(case_srcdir)/tests \
+	  case_monolithic.ttl
 
 check: \
-  catalog-v001.xml
+  all
 
-# TODO: This recipe deletes files generated by Make.  The line deleting
-# example.ttl should be adapted.
 clean:
-	@rm -f \
-	  catalog-v001.xml \
-	  imports-transitive.ttl
-
-# This recipe intentionally does not incorporate CDO ontologies (UCO,
-# CASE, etc.), to avoid redundant imports between multiple profiles.
-# TODO: Adapt this recipe to depend instead on the normalized file, as
-# well as any profile submodules' imports-transitive files.
-# Note that the piping command, analagous to the concatenate ('cat')
-# command but for RDF graph files, will combine all recipe dependencies
-# into one file, using the $^ ("all dependencies") Make variable.
-imports-transitive.ttl: \
-  UCO-Profile-Example/dependencies/example.ttl \
-  UCO-Profile-Example/dependencies/imports-transitive.ttl \
-  UCO-Profile-Example/ontology/uco-example.ttl
-	source $(top_srcdir)/venv/bin/activate \
-	  && rdfpipe \
-	    --output-format turtle \
-	    $^ \
-	    > __$@
-	java -jar $(RDF_TOOLKIT_JAR) \
-	  --inline-blank-nodes \
-	  --source __$@ \
-	  --source-format turtle \
-	  --target _$@ \
-	  --target-format turtle
-	rm __$@
-	mv _$@ $@

dependencies/UCO-Profile-Example

@@ -1,4 +1,5 @@
-http://example.org/ontology/example/0.0.1	${top_srcdir}/dependencies/UCO-Profile-Example/dependencies/example.ttl
+http://example.org/ontology/example/0.0.1	${top_srcdir}/dependencies/UCO-Profile-Example/dependencies/CDO-Shapes-Example/dependencies/formatted-example.ttl
 http://example.org/ontology/uco-example	${top_srcdir}/dependencies/UCO-Profile-Example/ontology/uco-example.ttl
 http://example.org/shapes/sh-case-example	${top_srcdir}/shapes/sh-case-example.ttl
+http://example.org/shapes/sh-example	${top_srcdir}/dependencies/UCO-Profile-Example/dependencies/CDO-Shapes-Example/shapes/sh-example.ttl
 http://example.org/shapes/sh-uco-example	${top_srcdir}/dependencies/UCO-Profile-Example/shapes/sh-uco-example.ttl

dependencies/catalog-v001.xml

@@ -0,0 +1,5 @@
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+