Adopt case-utils 0.9.0, CASE 1.1.0, and strict static type review

This patch does not apply `pre-commit`; that will be applied in a
follow-on patch.

Concept typo-checking is now delegated to the `case_validate`
typo-checker.  This removes the CASE-Examples-QC dependency.

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

References:
* casework/CASE-Utilities-Python#77

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

Author: ajnelson-nist

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "dependencies/CASE-Examples-QC"]
-	path = dependencies/CASE-Examples-QC
-	url = https://github.com/ajnelson-nist/CASE-Examples-QC.git
 [submodule "dependencies/CASE-Utilities-Python"]
 	path = dependencies/CASE-Utilities-Python
 	url = https://github.com/casework/CASE-Utilities-Python.git

Makefile

@@ -27,12 +27,14 @@ all:
 	cd dependencies \
 	  && git diff . \
 	    | cat
-	git submodule init
-	git submodule update
+	git submodule update --init
+	$(MAKE) \
+	  --directory dependencies/CASE-Utilities-Python \
+	  .git_submodule_init.done.log
 	touch $@
 
 check: \
-  dependencies/CASE-Examples-QC/tests/ontology_vocabulary.txt
+  .git_submodule_init.done.log
 	$(MAKE) \
 	  PYTHON3=$(PYTHON3) \
 	  --directory tests \
@@ -46,39 +48,11 @@ clean:
 	@$(MAKE) \
 	  --directory tests \
 	  clean
-	@#A full clean here erases test files and causes unnecessary rebuilding for the purposes of testing GNU Time mapping.
 	@rm -f \
-	  dependencies/CASE-Examples-QC/.*.done.log
-	@test ! -d dependencies/CASE-Examples-QC/tests \
-	  || rm -f dependencies/CASE-Examples-QC/tests/ontology_vocabulary.txt
-
-dependencies/CASE-Examples-QC/tests/ontology_vocabulary.txt: \
-  .git_submodule_init.done.log
-	test ! -z "$(PYTHON3)" \
-	  || (echo "ERROR:Makefile:PYTHON3 not defined" >&2 ; exit 1)
-	$(MAKE) \
-	  PYTHON3=$(PYTHON3) \
-	  --directory dependencies/CASE-Examples-QC \
-	  .git_submodule_init.done.log \
-	  .venv.done.log
-	$(MAKE) \
-	  PYTHON3=$(PYTHON3) \
-	  --directory dependencies/CASE-Examples-QC/tests \
-	  ontology_vocabulary.txt
-	test -r $@
-
-distclean: \
-  clean
-	@rm -f \
-	  .git_submodule_init.done.log \
-	  dependencies/CASE-Examples-QC/.lib.done.log \
-	  dependencies/CASE-Examples-QC/lib/rdf-toolkit.jar
-	@$(MAKE) \
-	  --directory tests \
-	  distclean
+	  .git_submodule_init.done.log
 
 download: \
-  dependencies/CASE-Examples-QC/tests/ontology_vocabulary.txt
+  .git_submodule_init.done.log
 	test ! -z "$(PYTHON3)" \
 	  || (echo "ERROR:Makefile:PYTHON3 not defined" >&2 ; exit 1)
 	$(MAKE) \

README.md

@@ -47,8 +47,8 @@ This project follows [SEMVER 2.0.0](https://semver.org/) where versions are decl
 
 This repository supports the CASE and UCO ontology versions that are distributed with the [CASE-Utilities-Python repository](https://github.com/casework/CASE-Utilities-Python), at its submodule-tracked state [here](dependencies/CASE-Utilities-Python).  Currently, those ontology versions are:
 
-* CASE 0.5.0
-* UCO 0.7.0
+* CASE 1.1.0
+* UCO 1.1.0
 
 
 ## Repository locations
@@ -65,8 +65,7 @@ Releases and issue tracking will be handled at the [casework location](https://g
 Some `make` targets are defined for this repository:
 * `all` - No effect.
 * `check` - Run unit tests.  *NOTE*: The tests entail downloading some software to assist with formatting and conversion, from PyPI and from a [third party](https://github.com/edmcouncil/rdf-toolkit).  `make download` retrieves these files.
-* `clean` - Remove test build files, but not downloaded files or the `tests/venv` virtual environment.
-* `distclean` - Run `make clean` and further delete downloaded files and the `tests/venv` virtual environment.  Neither `clean` nor `distclean` will remove downloaded submodules.
+* `clean` - Remove test build files, but not downloaded files or the `tests/venv` virtual environment.  Will not remove downloaded submodules.
 * `download` - Download files sufficiently to run the unit tests offline.  This will *not* include the ontology repositories tracked as submodules.  Note if you do need to work offline, be aware touching the `setup.py` file in the root, or `tests/requirements.txt`, will trigger a virtual environment rebuild.
 
 

case_gnu_time/__init__.py

@@ -29,36 +29,32 @@
 import rdflib.util
 
 import case_utils
+from case_utils.namespace import NS_RDF, NS_UCO_CORE, NS_UCO_OBSERVABLE, NS_XSD
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
-NS_RDF = rdflib.RDF
-NS_UCO_CORE = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/core#")
-NS_UCO_OBSERVABLE = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/observable#")
-NS_XSD = rdflib.namespace.XSD
 
 class ProcessUCOObject(object):
-    def __init__(self, graph, ns_base, **kwargs) -> None:
+    def __init__(self, graph: rdflib.Graph, ns_base: rdflib.Namespace, *args: typing.Any, prefix_slug:str = "process-", **kwargs: typing.Any) -> None:
         """
         Initializing a ProcessUCOObject will create one triple in the graph.  To add data to the new node, call populate_from_gnu_time_log().
         """
 
         assert isinstance(graph, rdflib.Graph)
 
         self.graph = graph
-
-        prefix_slug = kwargs.get("prefix_slug", "process-")
+        self._ns_base = ns_base
 
         # Guarantee at least one triple enters the graph.
-        self._node = rdflib.URIRef(ns_base[prefix_slug + case_utils.local_uuid.local_uuid()])
+        self._node = ns_base[prefix_slug + case_utils.local_uuid.local_uuid()]
         self.graph.add((self.node, NS_RDF.type, NS_UCO_OBSERVABLE.Process))
 
-        self._bnode_process: typing.Optional[rdflib.BNode] = None
+        self._n_process_facet: typing.Optional[rdflib.URIRef] = None
         self._created_time: typing.Optional[str] = None
         self._exit_status: typing.Optional[int] = None
         self._exit_time: typing.Optional[str] = None
 
-    def populate_from_gnu_time_log(self, gnu_time_log) -> None:
+    def populate_from_gnu_time_log(self, gnu_time_log: str) -> None:
         """
         This method populates Process data from a GNU Time log file.  If self.exit_time is not set before this method is called, it will be set by reading the modification time of gnu_time_log.
         """
@@ -107,17 +103,6 @@ def populate_from_gnu_time_log(self, gnu_time_log) -> None:
 
         self.created_time = created_time_datetime.isoformat()
 
-    @property
-    def bnode_process(self) -> rdflib.BNode:
-        """
-        Created on first access.
-        """
-        if self._bnode_process is None:
-            self._bnode_process = rdflib.BNode()
-            self.graph.add((self._bnode_process, NS_RDF.type, NS_UCO_OBSERVABLE.ProcessFacet))
-            self.graph.add((self.node, NS_UCO_CORE.hasFacet, self._bnode_process))
-        return self._bnode_process
-
     @property
     def created_time(self) -> typing.Optional[str]:
         return self._created_time
@@ -132,7 +117,7 @@ def created_time(self, value: str) -> None:
         str_value = str(value) # For e.g. datetime objects.
         # Confirm text is ISO-8601.
         check_value = dateutil.parser.isoparse(str_value)
-        self.graph.add((self.bnode_process, NS_UCO_OBSERVABLE.observableCreatedTime, rdflib.Literal(str_value, datatype=NS_XSD.dateTime)))
+        self.graph.add((self.n_process_facet, NS_UCO_OBSERVABLE.observableCreatedTime, rdflib.Literal(str_value, datatype=NS_XSD.dateTime)))
         self._created_time = value
 
     @property
@@ -142,7 +127,7 @@ def exit_status(self) -> typing.Optional[int]:
     @exit_status.setter
     def exit_status(self, value: int) -> None:
         assert isinstance(value, int)
-        self.graph.add((self.bnode_process, NS_UCO_OBSERVABLE.exitStatus, rdflib.Literal(value)))
+        self.graph.add((self.n_process_facet, NS_UCO_OBSERVABLE.exitStatus, rdflib.Literal(value)))
 
     @property
     def exit_time(self) -> typing.Optional[str]:
@@ -159,17 +144,42 @@ def exit_time(self, value: str) -> None:
         # Confirm text is ISO-8601.
         check_value = dateutil.parser.isoparse(str_value)
         literal_time = rdflib.Literal(str_value, datatype=NS_XSD.dateTime)
-        self.graph.add((self.bnode_process, NS_UCO_OBSERVABLE.exitTime, literal_time))
+        self.graph.add((self.n_process_facet, NS_UCO_OBSERVABLE.exitTime, literal_time))
         self._exit_time = value
 
+    @property
+    def n_process_facet(self) -> rdflib.URIRef:
+        """
+        Created on first access.
+        """
+        if self._n_process_facet is None:
+            self._n_process_facet = self.ns_base["process-facet-" + case_utils.local_uuid.local_uuid()]
+            self.graph.add((self._n_process_facet, NS_RDF.type, NS_UCO_OBSERVABLE.ProcessFacet))
+            self.graph.add((self.node, NS_UCO_CORE.hasFacet, self._n_process_facet))
+        return self._n_process_facet
+
     @property
     def node(self) -> rdflib.URIRef:
         """
         Read-only property.
         """
         return self._node
 
-def build_process_object(graph, ns_base, gnu_time_log, mtime=None, prefix_slug=None) -> ProcessUCOObject:
+    @property
+    def ns_base(self) -> rdflib.Namespace:
+        """
+        No setter.
+        """
+        return self._ns_base
+
+
+def build_process_object(
+    graph: rdflib.Graph,
+    ns_base: rdflib.Namespace,
+    gnu_time_log: str,
+    mtime: typing.Optional[str] = None,
+    prefix_slug: typing.Optional[str] = None
+) -> ProcessUCOObject:
     """
     This function builds a Process UCO Object from a file that contains the output of GNU Time's --verbose flag.
 
@@ -212,6 +222,7 @@ def main() -> None:
     graph.namespace_manager.bind("kb", NS_BASE)
     graph.namespace_manager.bind("uco-core", NS_UCO_CORE)
     graph.namespace_manager.bind("uco-observable", NS_UCO_OBSERVABLE)
+    graph.namespace_manager.bind("xsd", NS_XSD)
 
     mtime_str = None
     if args.done_log:

dependencies/CASE-Examples-QC

@@ -17,7 +17,7 @@ classifiers =
 
 [options]
 install_requires =
-    case_utils >= 0.3.0
+    case_utils >= 0.9.0, < 0.10.0
     python-dateutil
 packages = find:
 python_requires = >=3.7

dependencies/CASE-Utilities-Python

@@ -40,7 +40,6 @@ all: \
 
 .venv.done.log: \
   $(top_srcdir)/.git_submodule_init.done.log \
-  $(top_srcdir)/case_gnu_time/__init__.py \
   $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/requirements.txt \
   $(top_srcdir)/setup.cfg \
   $(top_srcdir)/setup.py \
@@ -54,21 +53,16 @@ all: \
 	    pip \
 	    setuptools \
 	    wheel
-	source venv/bin/activate \
-	  && cd $(top_srcdir)/dependencies/CASE-Utilities-Python \
-	    && pip install \
-	      .
 	source venv/bin/activate \
 	  && pip install \
 	    --requirement $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/requirements.txt
 	source venv/bin/activate \
-	  && cd $(top_srcdir) \
-	    && pip install \
-	      --editable \
-	      .
+	  && pip install \
+	    --editable \
+	    $(top_srcdir)
 	source venv/bin/activate \
 	  && pip install \
-	    -r requirements.txt
+	    --requirement requirements.txt
 	touch $@
 
 .venv_minimal.done.log: \
@@ -86,16 +80,12 @@ all: \
 	    pip \
 	    setuptools \
 	    wheel
-	source venv_minimal/bin/activate \
-	  && cd $(top_srcdir)/dependencies/CASE-Utilities-Python \
-	    && pip install \
-	      .
 	source venv_minimal/bin/activate \
 	  && pip install \
 	    --requirement $(top_srcdir)/dependencies/CASE-Utilities-Python/tests/requirements.txt
 	source venv_minimal/bin/activate \
 	  && pip install \
-	    -r requirements.txt
+	    --requirement requirements.txt
 	touch $@
 
 all-as_import: \
@@ -154,11 +144,9 @@ check-mypy: \
   .venv.done.log
 	source venv/bin/activate \
 	  && mypy \
+	    --strict \
 	    $(top_srcdir)/case_gnu_time \
-	    as_import \
-	    from_pip \
-	    gtime_and_done_log \
-	    gtime_log
+	    as_import
 
 clean:
 	@$(MAKE) \
@@ -175,9 +163,6 @@ clean:
 	  clean
 	@rm -rf \
 	  .pytest_cache
-
-distclean: \
-  clean
 	@rm -f \
 	  .venv.done.log \
 	  .venv_minimal.done.log