Merge pull request #22 from casework/update_case_utils_usage

Update case_utils usage

Author: ajnelson-nist

case_gnu_time/__init__.py

@@ -49,7 +49,7 @@ def __init__(self, graph, ns_base, **kwargs):
 
         # Guarantee at least one triple enters the graph.
         self._node = rdflib.URIRef(ns_base[prefix_slug + case_utils.local_uuid.local_uuid()])
-        self.graph.add((self.node, NS_RDF.type, NS_UCO_OBSERVABLE.ObservableObject))
+        self.graph.add((self.node, NS_RDF.type, NS_UCO_OBSERVABLE.Process))
 
         self._bnode_process = None
         self._created_time = None
@@ -141,7 +141,7 @@ def exit_status(self):
     @exit_status.setter
     def exit_status(self, value):
         assert isinstance(value, int)
-        self.graph.add((self.bnode_process, NS_UCO_OBSERVABLE.exitStatus, rdflib.Literal(value, datatype=NS_XSD.long)))
+        self.graph.add((self.bnode_process, NS_UCO_OBSERVABLE.exitStatus, rdflib.Literal(value)))
         return self._exit_status
 
     @property

setup.cfg

@@ -17,15 +17,10 @@ classifiers =
 
 [options]
 install_requires =
-    case_utils
-    # TODO - This constraint on pyparsing can be removed when rdflib Issue #1190 is resolved.
-    # https://github.com/RDFLib/rdflib/issues/1190
-    pyparsing < 3.0.0
+    case_utils >= 0.3.0
     python-dateutil
-    rdflib
-    requests
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.7
 
 [options.entry_points]
 console_scripts =

tests/Makefile

@@ -62,7 +62,9 @@ all: \
 	    --requirement $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/requirements.txt
 	source venv/bin/activate \
 	  && cd $(top_srcdir) \
-	    && python3 setup.py install
+	    && pip install \
+	      --editable \
+	      .
 	source venv/bin/activate \
 	  && pip install \
 	    -r requirements.txt

tests/as_import/Makefile

@@ -40,10 +40,12 @@ endif
 RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
 
 all: \
-  undefined_vocabulary.txt
+  undefined_vocabulary.txt \
+  validation.ttl
 
 check: \
-  undefined_vocabulary.txt
+  undefined_vocabulary.txt \
+  validation.ttl
 	@test ! -s undefined_vocabulary.txt \
 	  || (echo "ERROR:tests/as_import/Makefile:The output in process.json has undefined CASE or UCO terms.  The first few are:" >&2 && head undefined_vocabulary.txt >&2 && exit 1)
 	source $(tests_srcdir)/venv/bin/activate \
@@ -82,7 +84,6 @@ echo.txt.time.log: \
 
 process.json: \
   process.ttl \
-  $(RDF_TOOLKIT_JAR) \
   $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/src/compact.py
 	java -jar $(RDF_TOOLKIT_JAR) \
 	  --infer-base-iri \
@@ -99,7 +100,9 @@ process.json: \
 	mv _$@ $@
 
 process.ttl: \
+  $(RDF_TOOLKIT_JAR) \
   $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/case_gnu_time/__init__.py \
   consumer.py \
   echo.txt.done.log \
   echo.txt.time.log
@@ -141,3 +144,23 @@ undefined_vocabulary.txt: \
 	    > $@_
 	rm $@__
 	mv $@_ $@
+
+validation.ttl: \
+  process.json
+	rm -f __$@
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_validate \
+	    --format turtle \
+	    --output __$@ \
+	    $< \
+	    ; rc=$$? ; test 1 -eq $$rc -o 0 -eq $$rc
+	test -s __$@
+	java -jar $(RDF_TOOLKIT_JAR) \
+	  --infer-base-iri \
+	  --inline-blank-nodes \
+	  --source __$@ \
+	  --source-format turtle \
+	  --target _$@ \
+	  --target-format turtle
+	rm __$@
+	mv _$@ $@

tests/as_import/process.json

@@ -7,11 +7,11 @@
         "xsd": "http://www.w3.org/2001/XMLSchema#"
     },
     "@id": "kb:custom-011a93fd-814b-537f-b111-ce4dceb373a6",
-    "@type": "uco-observable:ObservableObject",
+    "@type": "uco-observable:Process",
     "uco-core:hasFacet": {
         "@type": "uco-observable:ProcessFacet",
         "uco-observable:exitStatus": {
-            "@type": "xsd:long",
+            "@type": "xsd:integer",
             "@value": "0"
         },
         "uco-observable:exitTime": {

tests/as_import/process.ttl

@@ -7,10 +7,10 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 kb:custom-011a93fd-814b-537f-b111-ce4dceb373a6
-	a uco-observable:ObservableObject ;
+	a uco-observable:Process ;
 	uco-core:hasFacet [
 		a uco-observable:ProcessFacet ;
-		uco-observable:exitStatus "0"^^xsd:long ;
+		uco-observable:exitStatus "0"^^xsd:integer ;
 		uco-observable:exitTime "2020-10-14T14:07:39.267912-04:00"^^xsd:dateTime ;
 		uco-observable:observableCreatedTime "2020-10-14T14:07:39.267912-04:00"^^xsd:dateTime ;
 	] ;

tests/as_import/test_as_import.py

@@ -14,33 +14,27 @@
 import logging
 import os
 
-import rdflib
+import rdflib.plugins.sparql
+
+import case_utils.ontology
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
 srcdir = os.path.dirname(__file__)
 
-def _parse_graph(filename, format):
+def _parse_graph(filename):
     graph_filename = os.path.join(srcdir, filename)
     graph = rdflib.Graph()
-    graph.parse(graph_filename, format=format)
+    graph.parse(graph_filename)
+    case_utils.ontology.load_subclass_hierarchy(graph)
     return graph
 
-def _test_as_import_load(graph_filename, format):
-    graph = _parse_graph(graph_filename, format)
+def _test_as_import_load(graph_filename):
+    graph = _parse_graph(graph_filename)
     assert len(graph) > 0
 
-def _test_as_import_query(graph_filename, format):
-    #TODO This try block can be removed, and the import put at the script's top, when rdflib Issue #1190 is resolved.
-    # https://github.com/RDFLib/rdflib/issues/1190
-    try:
-        import rdflib.plugins.sparql
-    except:
-        import pyparsing
-        _logger.debug("pyparsing.__version__ = %r." % pyparsing.__version__)
-        raise
-
-    graph = _parse_graph(graph_filename, format)
+def _test_as_import_query(graph_filename):
+    graph = _parse_graph(graph_filename)
 
     nsdict = {k:v for (k,v) in graph.namespace_manager.namespaces()}
 
@@ -50,13 +44,13 @@ def _test_as_import_query(graph_filename, format):
 WHERE
 {
   ?nProcessObject
-    a uco-observable:ObservableObject ;
+    a/rdfs:subClassOf* uco-observable:ObservableObject ;
     uco-core:hasFacet ?nProcessFacet ;
     .
 
   ?nProcessFacet
     a uco-observable:ProcessFacet ;
-    uco-observable:exitStatus "0"^^xsd:long ;
+    uco-observable:exitStatus 0 ;
     .
 }
 """, initNs=nsdict)
@@ -73,13 +67,20 @@ def _test_as_import_query(graph_filename, format):
     assert len(iris) == 1
 
 def test_as_import_load_json():
-    _test_as_import_load("process.json", "json-ld")
+    _test_as_import_load("process.json")
 
 def test_as_import_load_turtle():
-    _test_as_import_load("process.ttl", "turtle")
+    _test_as_import_load("process.ttl")
 
 def test_as_import_query_json():
-    _test_as_import_query("process.json", "json-ld")
+    _test_as_import_query("process.json")
 
 def test_as_import_query_turtle():
-    _test_as_import_query("process.ttl", "turtle")
+    _test_as_import_query("process.ttl")
+
+def test_as_import_validation():
+    graph = _parse_graph("validation.ttl")
+    result = None
+    for triple in graph.triples((None, rdflib.SH.conforms, None)):
+        result = triple[2].toPython()
+    assert result

tests/as_import/validation.ttl

@@ -0,0 +1,11 @@
+@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 sh: <http://www.w3.org/ns/shacl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+[]
+	a sh:ValidationReport ;
+	sh:conforms "true"^^xsd:boolean ;
+	.
+

tests/from_pip/Makefile

@@ -40,12 +40,17 @@ endif
 RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar
 
 all: \
-  undefined_vocabulary.txt
+  undefined_vocabulary.txt \
+  validation.ttl
 
 check: \
-  undefined_vocabulary.txt
+  undefined_vocabulary.txt \
+  validation.ttl
 	@test ! -s undefined_vocabulary.txt \
 	  || (echo "ERROR:tests/from_pip/Makefile:The output in process.json has undefined CASE or UCO terms.  The first few are:" >&2 && head undefined_vocabulary.txt >&2 && exit 1)
+	source $(tests_srcdir)/venv/bin/activate \
+	  && pytest \
+	    --log-level=DEBUG
 
 clean:
 	@rm -f \
@@ -79,7 +84,6 @@ echo.txt.time.log: \
 
 process.json: \
   process.ttl \
-  $(RDF_TOOLKIT_JAR) \
   $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/src/compact.py
 	java -jar $(RDF_TOOLKIT_JAR) \
 	  --infer-base-iri \
@@ -96,7 +100,9 @@ process.json: \
 	mv _$@ $@
 
 process.ttl: \
+  $(RDF_TOOLKIT_JAR) \
   $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/case_gnu_time/__init__.py \
   echo.txt.done.log \
   echo.txt.time.log
 	rm -f _$@ __$@
@@ -137,3 +143,23 @@ undefined_vocabulary.txt: \
 	    > $@_
 	rm $@__
 	mv $@_ $@
+
+validation.ttl: \
+  process.json
+	rm -f __$@
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_validate \
+	    --format turtle \
+	    --output __$@ \
+	    $< \
+	    ; rc=$$? ; test 1 -eq $$rc -o 0 -eq $$rc
+	test -s __$@
+	java -jar $(RDF_TOOLKIT_JAR) \
+	  --infer-base-iri \
+	  --inline-blank-nodes \
+	  --source __$@ \
+	  --source-format turtle \
+	  --target _$@ \
+	  --target-format turtle
+	rm __$@
+	mv _$@ $@

tests/from_pip/process.json

@@ -7,11 +7,11 @@
         "xsd": "http://www.w3.org/2001/XMLSchema#"
     },
     "@id": "kb:process-e7498b28-74d7-5952-a0e3-2f9e924bd662",
-    "@type": "uco-observable:ObservableObject",
+    "@type": "uco-observable:Process",
     "uco-core:hasFacet": {
         "@type": "uco-observable:ProcessFacet",
         "uco-observable:exitStatus": {
-            "@type": "xsd:long",
+            "@type": "xsd:integer",
             "@value": "0"
         },
         "uco-observable:exitTime": {

tests/from_pip/process.ttl

@@ -7,10 +7,10 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 kb:process-e7498b28-74d7-5952-a0e3-2f9e924bd662
-	a uco-observable:ObservableObject ;
+	a uco-observable:Process ;
 	uco-core:hasFacet [
 		a uco-observable:ProcessFacet ;
-		uco-observable:exitStatus "0"^^xsd:long ;
+		uco-observable:exitStatus "0"^^xsd:integer ;
 		uco-observable:exitTime "2020-10-14T14:07:39.267912-04:00"^^xsd:dateTime ;
 		uco-observable:observableCreatedTime "2020-10-14T14:07:39.267912-04:00"^^xsd:dateTime ;
 	] ;

tests/from_pip/test_from_pip.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+
+# This software was developed at the National Institute of Standards
+# and Technology by employees of the Federal Government in the course
+# of their official duties. Pursuant to title 17 Section 105 of the
+# United States Code this software is not subject to copyright
+# protection and is in the public domain. NIST assumes no
+# responsibility whatsoever for its use by other parties, and makes
+# no guarantees, expressed or implied, about its quality,
+# reliability, or any other characteristic.
+#
+# We would appreciate acknowledgement if the software is used.
+
+import os
+
+import rdflib.plugins.sparql
+
+srcdir = os.path.dirname(__file__)
+
+def _parse_graph(filename):
+    graph_filename = os.path.join(srcdir, filename)
+    graph = rdflib.Graph()
+    graph.parse(graph_filename)
+    return graph
+
+def test_from_pip_validation():
+    graph = _parse_graph("validation.ttl")
+    result = None
+    for triple in graph.triples((None, rdflib.SH.conforms, None)):
+        result = triple[2].toPython()
+    assert result

tests/from_pip/validation.ttl

@@ -0,0 +1,11 @@
+@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 sh: <http://www.w3.org/ns/shacl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+[]
+	a sh:ValidationReport ;
+	sh:conforms "true"^^xsd:boolean ;
+	.
+