Merge pull request #61 from casework/release-0.6.0

Release 0.6.0

.github/workflows/cicd.yml

@@ -32,7 +32,7 @@ jobs:
       matrix:
         python-version:
         - '3.7'
-        - '3.10'
+        - '3.11'
 
     steps:
     - uses: actions/checkout@v2

.pre-commit-config.yaml

@@ -11,11 +11,11 @@
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 22.10.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 5.0.4
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort

case_prov/__init__.py

@@ -11,4 +11,4 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"

case_prov/case_prov_dot.py

@@ -21,7 +21,7 @@
 # get quoted.  This turns out to be a dot syntax error.  Need to report
 # this upstream to pydot.
 
-__version__ = "0.3.0"
+__version__ = "0.4.0"
 
 import argparse
 import collections
@@ -41,7 +41,7 @@
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
-NS_PROV = rdflib.Namespace("http://www.w3.org/ns/prov#")
+NS_PROV = rdflib.PROV
 NS_RDFS = rdflib.RDFS
 
 # This one isn't among the prov constants.
@@ -74,12 +74,6 @@ def iri_to_gv_node_id(iri: str) -> str:
     return "_" + hasher.hexdigest()
 
 
-def iri_to_short_iri(iri: str) -> str:
-    return iri.replace("http://example.org/kb/", "kb:").replace(
-        "http://www.w3.org/ns/prov#", "prov:"
-    )
-
-
 def main() -> None:
     parser = argparse.ArgumentParser()
     parser.add_argument("--debug", action="store_true")
@@ -145,7 +139,7 @@ def main() -> None:
     filter_iris: typing.Optional[typing.Set[str]] = None
     if args.from_empty_set:
         filter_iris = set()
-        filter_iris.add("http://www.w3.org/ns/prov#EmptyCollection")
+        filter_iris.add(str(NS_PROV.EmptyCollection))
         select_query_actions_text = """\
 SELECT ?nDerivingAction
 WHERE {
@@ -325,7 +319,7 @@ def main() -> None:
     for record in graph.query(select_query_object):
         (n_agent, l_label, l_comment) = record
         agent_iri = n_agent.toPython()
-        dot_label = "ID - " + iri_to_short_iri(agent_iri)
+        dot_label = "ID - " + graph.namespace_manager.qname(agent_iri)
         if l_label is not None:
             dot_label += "\n" + l_label.toPython()
         if l_comment is not None:
@@ -339,7 +333,7 @@ def main() -> None:
     # _logger.debug("nodes = %s." % pprint.pformat(nodes))
 
     # Find Collections, to adjust Entity rendering in the next block.
-    collection_iris = {"http://www.w3.org/ns/prov#EmptyCollection"}
+    collection_iris: typing.Set[str] = {str(NS_PROV.EmptyCollection)}
     select_query_text = """\
 SELECT ?nCollection
 WHERE {
@@ -357,9 +351,16 @@ def main() -> None:
 
     # Render Entities.
     # This loop operates differently from the others, to insert prov:EmptyCollection.
-    entity_iri_to_label_comment = dict()
+    entity_iri_to_label_comment: typing.Dict[
+        str,
+        typing.Tuple[
+            typing.Optional[str],
+            typing.Optional[str],
+            typing.Optional[str],
+        ],
+    ] = dict()
     if not args.omit_empty_set:
-        entity_iri_to_label_comment["http://www.w3.org/ns/prov#EmptyCollection"] = (
+        entity_iri_to_label_comment[str(NS_PROV.EmptyCollection)] = (
             None,
             None,
             None,
@@ -391,7 +392,7 @@ def main() -> None:
         entity_iri_to_label_comment[entity_iri] = (l_label, l_comment, l_exhibit_number)
     for entity_iri in sorted(entity_iri_to_label_comment):
         (l_label, l_comment, l_exhibit_number) = entity_iri_to_label_comment[entity_iri]
-        dot_label = "ID - " + iri_to_short_iri(entity_iri)
+        dot_label = "ID - " + graph.namespace_manager.qname(entity_iri)
         if l_exhibit_number is not None:
             dot_label += "\nExhibit - " + l_exhibit_number.toPython()
         if l_label is not None:
@@ -437,7 +438,7 @@ def main() -> None:
     for record in graph.query(select_query_object):
         (n_activity, l_label, l_comment, l_start_time, l_end_time) = record
         activity_iri = n_activity.toPython()
-        dot_label = "ID - " + iri_to_short_iri(activity_iri)
+        dot_label = "ID - " + graph.namespace_manager.qname(activity_iri)
         if l_label is not None:
             dot_label += "\n" + l_label.toPython()
         if l_start_time is not None or l_end_time is not None:

case_prov/case_prov_rdf.py

@@ -15,7 +15,7 @@
 This script executes CONSTRUCT queries, returning a supplemental graph.
 """
 
-__version__ = "0.2.1"
+__version__ = "0.3.0"
 
 import argparse
 import importlib.resources
@@ -34,7 +34,7 @@
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
-NS_PROV = rdflib.Namespace("http://www.w3.org/ns/prov#")
+NS_PROV = rdflib.PROV
 
 
 def main() -> None:

case_prov/queries/construct-wasDerivedFrom-map.sparql

@@ -11,6 +11,8 @@
 
 CONSTRUCT {
   ?x prov:wasDerivedFrom ?y .
+  ?x a prov:Entity .
+  ?y a prov:Entity .
 }
 WHERE {
   ?x case-investigation:wasDerivedFrom ?y .

case_prov/queries/construct-wasInformedBy-map.sparql

@@ -11,6 +11,8 @@
 
 CONSTRUCT {
   ?x prov:wasInformedBy ?y .
+  ?x a prov:Activity .
+  ?y a prov:Activity .
 }
 WHERE {
   ?x case-investigation:wasInformedBy ?y .

setup.cfg

@@ -19,7 +19,7 @@ license_files =
 [options]
 include_package_data = true
 install_requires =
-    case_utils >=0.7.0,< 0.8.0
+    case_utils >=0.9.0,< 0.10.0
     prov
     pydot
 packages = find:

tests/CASE-Examples/examples/illustrations/Makefile

@@ -13,6 +13,10 @@
 
 SHELL := /bin/bash
 
+top_srcdir := $(shell cd ../../../.. ; pwd)
+
+illustrations_srcdir := $(top_srcdir)/dependencies/CASE-Examples-QC/dependencies/CASE-Examples/examples/illustrations
+
 illdirs := $(shell find * -maxdepth 0 -type d | sort | egrep -v '^src$$')
 
 all_targets       := $(foreach illdir,$(illdirs),all-$(illdir))
@@ -28,6 +32,10 @@ all-%:
 
 check: \
   $(check_targets)
+	@diff \
+	  <(ls */prov-constraints.log | while read x; do dirname $$x ; done) \
+	  <(cd $(illustrations_srcdir) ; ls */*.json | while read x; do dirname $$x ; done | sort | uniq) \
+	  || (echo "ERROR:Makefile:The illustrations listed above do not have evaluation directories under $(top_srcdir)/tests/CASE-Examples/examples/illustrations." >&2 ; exit 1)
 
 check-%:
 	$(MAKE) \

tests/CASE-Examples/examples/illustrations/Oresteia/Makefile

@@ -32,12 +32,10 @@ all:
 	  $<
 	mv _$@ $@
 
-# TODO: Fix constraints errors, then uncomment the recipe to enforce unit testing.
 check:
-	@echo "ERROR:PROV constraints reports errors for forensic_lifecycle.json, which need fixing." >&2
-#	$(MAKE) \
-#	  --file ../src/illustration.mk \
-#	  check
+	$(MAKE) \
+	  --file ../src/illustration.mk \
+	  check
 
 clean:
 	@$(MAKE) \