mustrd 0.3.0.0__py3-none-any.whl → 0.3.1a0__py3-none-any.whl

mustrd/mustrd.py

@@ -1,27 +1,3 @@
-"""
-MIT License
-
-Copyright (c) 2023 Semantic Partners Ltd
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-
 import os
 from typing import Tuple, List, Union
 
@@ -53,20 +29,21 @@ from collections import defaultdict
 from pyshacl import validate
 import logging
 from http.client import HTTPConnection
-from .steprunner import upload_given, run_when
+from .steprunner import upload_given, run_when_impl
 from multimethods import MultiMethod
 import traceback
+from functools import wraps
 
 log = logging.getLogger(__name__)
 
 requests.packages.urllib3.disable_warnings()
-requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += ':HIGH:!DH:!aNULL'
+requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += ":HIGH:!DH:!aNULL"
 
-logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
+logging.basicConfig(format="%(asctime)s %(message)s", level=logging.INFO)
 
 
 def debug_requests_on():
-    '''Switches on logging of the requests module.'''
+    """Switches on logging of the requests module."""
     HTTPConnection.debuglevel = 1
 
     logging.basicConfig()
@@ -77,7 +54,7 @@ def debug_requests_on():
 
 
 def debug_requests_off():
-    '''Switches off logging of the requests module, might be some side-effects'''
+    """Switches off logging of the requests module, might be some side-effects"""
     HTTPConnection.debuglevel = 0
 
     root_logger = logging.getLogger()
@@ -185,13 +162,14 @@ class UpdateSparqlQuery(SparqlAction):
 
 # https://github.com/Semantic-partners/mustrd/issues/19
 # Validate the specs found in spec_path
-def validate_specs(run_config: dict,
-                   triple_stores: List,
-                   shacl_graph: Graph,
-                   ont_graph: Graph,
-                   file_name: str = "*",
-                   selected_test_files: List[str] = [])\
-        -> Tuple[List, Graph, List]:
+def validate_specs(
+    run_config: dict,
+    triple_stores: List,
+    shacl_graph: Graph,
+    ont_graph: Graph,
+    file_name: str = "*",
+    selected_test_files: List[str] = [],
+) -> Tuple[List, Graph, List]:
     spec_graph = Graph()
     subject_uris = set()
     focus_uris = set()
@@ -199,10 +177,10 @@ def validate_specs(run_config: dict,
     ttl_files = []
 
     if not selected_test_files:
-        ttl_files = list(run_config['spec_path'].glob(
-            f'**/{file_name}.mustrd.ttl'))
+        ttl_files = list(run_config["spec_path"].glob(f"**/{file_name}.mustrd.ttl"))
         log.info(
-            f"Found {len(ttl_files)} {file_name}.mustrd.ttl files in {run_config['spec_path']}")
+            f"Found {len(ttl_files)} {file_name}.mustrd.ttl files in {run_config['spec_path']}"
+        )
     else:
         ttl_files = selected_test_files
 
@@ -221,23 +199,27 @@ def validate_specs(run_config: dict,
         except BadSyntax as e:
             template = "An exception of type {0} occurred when trying to parse a spec file. Arguments:\n{1!r}"
             message = template.format(type(e).__name__, e.args)
-            log.error(message)
-            error_messages += [f"Could not extract spec from {file} due to exception of type "
-                               f"{type(e).__name__} when parsing file"]
+            log.error(message, exc_info=True)
+            error_messages += [
+                f"Could not extract spec from {file} due to exception of type "
+                f"{type(e).__name__} when parsing file"
+            ]
             continue
 
         # run shacl validation
-        conforms, results_graph, results_text = validate(file_graph,
-                                                         shacl_graph=shacl_graph,
-                                                         ont_graph=ont_graph,
-                                                         inference='none',
-                                                         abort_on_first=False,
-                                                         allow_infos=False,
-                                                         allow_warnings=False,
-                                                         meta_shacl=False,
-                                                         advanced=True,
-                                                         js=False,
-                                                         debug=False)
+        conforms, results_graph, results_text = validate(
+            file_graph,
+            shacl_graph=shacl_graph,
+            ont_graph=ont_graph,
+            inference="none",
+            abort_on_first=False,
+            allow_infos=False,
+            allow_warnings=False,
+            meta_shacl=False,
+            advanced=True,
+            js=False,
+            debug=False,
+        )
         if str(file.name).endswith("_duplicate"):
             log.debug(f"Validation of {file.name} against SHACL shapes: {conforms}")
             log.debug(f"{results_graph.serialize(format='turtle')}")
@@ -251,13 +233,22 @@ def validate_specs(run_config: dict,
 
         # collect a list of uris of the tests in focus
         # If focus is found, only the spec in the focus will be executed
-        for focus_uri in file_graph.subjects(predicate=MUST.focus, object=Literal("true", datatype=XSD.boolean)):
+        for focus_uri in file_graph.subjects(
+            predicate=MUST.focus, object=Literal("true", datatype=XSD.boolean)
+        ):
             if focus_uri in focus_uris:
                 focus_uri = URIRef(str(focus_uri) + "_DUPLICATE")
             focus_uris.add(focus_uri)
 
-        add_spec_validation(file_graph, subject_uris, file,
-                            triple_stores, error_messages, invalid_specs, spec_graph)
+        add_spec_validation(
+            file_graph,
+            subject_uris,
+            file,
+            triple_stores,
+            error_messages,
+            invalid_specs,
+            spec_graph,
+        )
 
     valid_spec_uris = list(spec_graph.subjects(RDF.type, MUST.TestSpec))
 
@@ -282,8 +273,15 @@ def get_invalid_focus_spec(focus_uris: set, invalid_specs: list):
 # Detect duplicate,
 # If no error: associate the spec configuration and the file where this conf is stored
 # If error, aggregate the messages and mark spec as skipped
-def add_spec_validation(file_graph: Graph, subject_uris: set, file: Path, triple_stores: List,
-                        error_messages: list, invalid_specs: list, spec_graph: Graph):
+def add_spec_validation(
+    file_graph: Graph,
+    subject_uris: set,
+    file: Path,
+    triple_stores: List,
+    error_messages: list,
+    invalid_specs: list,
+    spec_graph: Graph,
+):
 
     for subject_uri in file_graph.subjects(RDF.type, MUST.TestSpec):
         # Always add file name and source file to the graph for error reporting
@@ -293,7 +291,8 @@ def add_spec_validation(file_graph: Graph, subject_uris: set, file: Path, triple
         # If we already collected a URI, then we tag it as duplicate and it won't be executed
         if subject_uri in subject_uris:
             log.warning(
-                f"Duplicate subject URI found: {file.name} {subject_uri}. File will not be parsed.")
+                f"Duplicate subject URI found: {file.name} {subject_uri}. File will not be parsed."
+            )
             error_messages += [f"Duplicate subject URI found in {file.name}."]
             subject_uri = URIRef(str(subject_uri) + "_DUPLICATE")
         if len(error_messages) == 0:
@@ -301,46 +300,81 @@ def add_spec_validation(file_graph: Graph, subject_uris: set, file: Path, triple
             this_spec_graph = Graph()
             this_spec_graph.parse(file)
             spec_uris_in_this_file = list(
-                this_spec_graph.subjects(RDF.type, MUST.TestSpec))
+                this_spec_graph.subjects(RDF.type, MUST.TestSpec)
+            )
             for spec in spec_uris_in_this_file:
                 this_spec_graph.add([spec, MUST.specSourceFile, Literal(file)])
-                this_spec_graph.add(
-                    [spec, MUST.specFileName, Literal(file.name)])
+                this_spec_graph.add([spec, MUST.specFileName, Literal(file.name)])
             spec_graph += this_spec_graph
         else:
             error_messages.sort()
             error_message = "\n".join(msg for msg in error_messages)
-            invalid_specs += [SpecSkipped(subject_uri, triple_store["type"], error_message, file.name, file)
-                              for triple_store in triple_stores]
-
-
-def get_specs(spec_uris: List[URIRef], spec_graph: Graph, triple_stores: List[dict],
-              run_config: dict):
+            invalid_specs += [
+                SpecSkipped(
+                    subject_uri, triple_store["type"], error_message, file.name, file
+                )
+                for triple_store in triple_stores
+            ]
+
+
+def get_specs(
+    spec_uris: List[URIRef],
+    spec_graph: Graph,
+    triple_stores: List[dict],
+    run_config: dict,
+):
     specs = []
     skipped_results = []
     try:
         for triple_store in triple_stores:
             if "error" in triple_store:
                 log.error(
-                    f"{triple_store['error']}. No specs run for this triple store.")
-                skipped_results += [SpecSkipped(spec_uri, triple_store['type'], triple_store['error'],
-                                                get_spec_file(spec_uri, spec_graph)) for spec_uri in
-                                    spec_uris]
+                    f"{triple_store['error']}. No specs run for this triple store."
+                )
+                skipped_results += [
+                    SpecSkipped(
+                        spec_uri,
+                        triple_store["type"],
+                        triple_store["error"],
+                        get_spec_file(spec_uri, spec_graph),
+                    )
+                    for spec_uri in spec_uris
+                ]
             else:
                 for spec_uri in spec_uris:
                     try:
-                        specs += [get_spec(spec_uri, spec_graph,
-                                           run_config, triple_store)]
+                        specs += [
+                            get_spec(spec_uri, spec_graph, run_config, triple_store)
+                        ]
                     except (ValueError, FileNotFoundError, ConnectionError) as e:
                         # Try to get file name/path from the graph, but fallback to "unknown"
-                        file_name = spec_graph.value(subject=spec_uri, predicate=MUST.specFileName) or "unknown"
-                        file_path = spec_graph.value(subject=spec_uri, predicate=MUST.specSourceFile) or "unknown"
-                        skipped_results += [SpecSkipped(spec_uri, triple_store['type'],
-                                                        str(e), str(file_name), Path(file_path))]
+                        file_name = (
+                            spec_graph.value(
+                                subject=spec_uri, predicate=MUST.specFileName
+                            )
+                            or "unknown"
+                        )
+                        file_path = (
+                            spec_graph.value(
+                                subject=spec_uri, predicate=MUST.specSourceFile
+                            )
+                            or "unknown"
+                        )
+                        skipped_results += [
+                            SpecSkipped(
+                                spec_uri,
+                                triple_store["type"],
+                                str(e),
+                                str(file_name),
+                                Path(file_path),
+                            )
+                        ]
 
     except (BadSyntax, FileNotFoundError) as e:
-        template = "An exception of type {0} occurred when trying to parse the triple store configuration file. " \
-                   "Arguments:\n{1!r}"
+        template = (
+            "An exception of type {0} occurred when trying to parse the triple store configuration file. "
+            "Arguments:\n{1!r}"
+        )
         message = template.format(type(e).__name__, e.args)
         log.error(message)
         log.error("No specifications will be run.")
@@ -368,28 +402,52 @@ def get_spec_file(spec_uri: URIRef, spec_graph: Graph):
     return "default.mustrd.ttl"
 
 
-def get_spec(spec_uri: URIRef, spec_graph: Graph, run_config: dict, mustrd_triple_store: dict = None) -> Specification:
+def get_spec(
+    spec_uri: URIRef,
+    spec_graph: Graph,
+    run_config: dict,
+    mustrd_triple_store: dict = None,
+) -> Specification:
     try:
         if not mustrd_triple_store:
             mustrd_triple_store = {"type": TRIPLESTORE.RdfLib}
         components = []
         for predicate in MUST.given, MUST.when, MUST.then:
-            components.append(parse_spec_component(subject=spec_uri,
-                                                   predicate=predicate,
-                                                   spec_graph=spec_graph,
-                                                   run_config=run_config,
-                                                   mustrd_triple_store=mustrd_triple_store))
+            components.append(
+                parse_spec_component(
+                    subject=spec_uri,
+                    predicate=predicate,
+                    spec_graph=spec_graph,
+                    run_config=run_config,
+                    mustrd_triple_store=mustrd_triple_store,
+                )
+            )
 
         spec_file_name = get_spec_file(spec_uri, spec_graph)
-        spec_file_path = Path(spec_graph.value(
-            subject=spec_uri, predicate=MUST.specSourceFile, default=Path("default.mustrd.ttl")))
+        spec_file_path = Path(
+            spec_graph.value(
+                subject=spec_uri,
+                predicate=MUST.specSourceFile,
+                default=Path("default.mustrd.ttl"),
+            )
+        )
         # https://github.com/Semantic-partners/mustrd/issues/92
-        return Specification(spec_uri, mustrd_triple_store,
-                             components[0].value, components[1], components[2], spec_file_name, spec_file_path)
+        return Specification(
+            spec_uri,
+            mustrd_triple_store,
+            components[0].value,
+            components[1],
+            components[2],
+            spec_file_name,
+            spec_file_path,
+        )
 
     except (ValueError, FileNotFoundError) as e:
-        template = "An exception of type {0} occurred. Arguments:\n{1!r}"
-        message = template.format(type(e).__name__, e.args)
+        template = (
+            "An exception of type {0} occurred. Arguments:\n{1!r}\nStacktrace:\n{2}"
+        )
+        stacktrace = traceback.format_exc()
+        message = template.format(type(e).__name__, e.args, stacktrace)
         log.exception(message)
         raise
     except ConnectionError as e:
@@ -398,9 +456,10 @@ def get_spec(spec_uri: URIRef, spec_graph: Graph, run_config: dict, mustrd_tripl
 
 
 def check_result(spec: Specification, result: Union[str, Graph]):
-    
+
     log.debug(
-        f"check_result {spec.spec_uri=}, {spec.triple_store=}, {result=} {type(spec.then)}")
+        f"check_result {spec.spec_uri=}, {spec.triple_store=}, {result=} {type(spec.then)}"
+    )
     if isinstance(spec.then, TableThenSpec):
         log.debug("table_comparison")
         return table_comparison(result, spec)
@@ -417,10 +476,14 @@ def check_result(spec: Specification, result: Union[str, Graph]):
             log.debug("not isomorphic")
             if spec.when[0].queryType == MUST.ConstructSparql:
                 log.debug("ConstructSpecFailure")
-                return ConstructSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
+                return ConstructSpecFailure(
+                    spec.spec_uri, spec.triple_store["type"], graph_compare
+                )
             else:
                 log.debug("UpdateSpecFailure")
-                return UpdateSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
+                return UpdateSpecFailure(
+                    spec.spec_uri, spec.triple_store["type"], graph_compare
+                )
 
 
 def run_spec(spec: Specification) -> SpecResult:
@@ -431,29 +494,34 @@ def run_spec(spec: Specification) -> SpecResult:
         log.warning(f"check_result called with non-Specification: {type(spec)}")
         return spec
         # return SpecSkipped(getattr(spec, 'spec_uri', None), getattr(spec, 'triple_store', {}), "Spec is not a valid Specification instance")
-    
-    log.debug(
-        f"run_spec {spec=}")
+
+    log.debug(f"run_spec {spec=}")
     log.debug(
-        f"run_when {spec_uri=}, {triple_store=}, {spec.given=}, {spec.when=}, {spec.then=}")
+        f"run_when {spec_uri=}, {triple_store=}, {spec.given=}, {spec.when=}, {spec.then=}"
+    )
     if spec.given:
         given_as_turtle = spec.given.serialize(format="turtle")
         log.debug(f"{given_as_turtle}")
         upload_given(triple_store, spec.given)
     else:
-        if triple_store['type'] == TRIPLESTORE.RdfLib:
-            return SpecSkipped(spec_uri, triple_store['type'], "Unable to run Inherited State tests on Rdflib")
+        if triple_store["type"] == TRIPLESTORE.RdfLib:
+            return SpecSkipped(
+                spec_uri,
+                triple_store["type"],
+                "Unable to run Inherited State tests on Rdflib",
+            )
     try:
         for when in spec.when:
             log.info(
-                f"Running {when.queryType} spec {spec_uri} on {triple_store['type']}")
+                f"Running {when.queryType} spec {spec_uri} on {triple_store['type']}"
+            )
             try:
-                result = run_when(spec_uri, triple_store, when)
+                result = run_when_impl(spec_uri, triple_store, when)
                 log.info(
-                    f"run {when.queryType} spec {spec_uri} on {triple_store['type']} {result=}")
+                    f"run {when.queryType} spec {spec_uri} on {triple_store['type']} {result=}"
+                )
             except ParseException as e:
-                log.error(
-                    f"parseException {e}")
+                log.error(f"parseException {e}")
                 return SparqlParseFailure(spec_uri, triple_store["type"], e)
             except NotImplementedError as ex:
                 log.error(f"NotImplementedError {ex}")
@@ -462,15 +530,16 @@ def run_spec(spec: Specification) -> SpecResult:
         return check_result(spec, result)
     except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout, OSError) as e:
         # close_connection = False
+        stacktrace = traceback.format_exc()
         template = "An exception of type {0} occurred. Arguments:\n{1!r}"
         message = template.format(type(e).__name__, e.args)
-        log.error(message)
+        log.error(message, exc_info=True)
         return TripleStoreConnectionError(spec_uri, triple_store["type"], message)
     except (TypeError, RequestException) as e:
-        log.error(f"{type(e)} {e}")
+        log.error(f"{type(e)} {e}", exc_info=True)
         return SparqlExecutionError(spec_uri, triple_store["type"], e)
     except Exception as e:
-        log.error(f"Unexpected error {e}")
+        log.error(f"Unexpected error {e}", exc_info=True)
         return RuntimeError(spec_uri, triple_store["type"], f"{type(e).__name__}: {e}")
     # https://github.com/Semantic-partners/mustrd/issues/78
     # finally:
@@ -482,8 +551,9 @@ def get_triple_store_graph(triple_store_graph_path: Path, secrets: str):
     if secrets:
         return Graph().parse(triple_store_graph_path).parse(data=secrets)
     else:
-        secret_path = triple_store_graph_path.parent / Path(triple_store_graph_path.stem +
-                                                            "_secrets" + triple_store_graph_path.suffix)
+        secret_path = triple_store_graph_path.parent / Path(
+            triple_store_graph_path.stem + "_secrets" + triple_store_graph_path.suffix
+        )
         return Graph().parse(triple_store_graph_path).parse(secret_path)
 
 
@@ -491,32 +561,40 @@ def get_triple_store_graph(triple_store_graph_path: Path, secrets: str):
 def get_triple_stores(triple_store_graph: Graph) -> list[dict]:
     triple_stores = []
     shacl_graph = Graph().parse(
-        Path(os.path.join(get_mustrd_root(), "model/triplestoreshapes.ttl")))
+        Path(os.path.join(get_mustrd_root(), "model/triplestoreshapes.ttl"))
+    )
     ont_graph = Graph().parse(
-        Path(os.path.join(get_mustrd_root(), "model/triplestoreOntology.ttl")))
+        Path(os.path.join(get_mustrd_root(), "model/triplestoreOntology.ttl"))
+    )
     # SHACL validation of triple store configuration
     conforms, results_graph, results_text = validate(
         data_graph=triple_store_graph,
         shacl_graph=shacl_graph,
         ont_graph=ont_graph,
         advanced=True,
-        inference='none'
+        inference="none",
     )
     if not conforms:
-        raise ValueError(f"Triple store configuration not conform to the shapes. SHACL report: {results_text}",
-                         results_graph)
-    for triple_store_config, rdf_type, triple_store_type in triple_store_graph.triples((None, RDF.type, None)):
+        raise ValueError(
+            f"Triple store configuration not conform to the shapes. SHACL report: {results_text}",
+            results_graph,
+        )
+    for triple_store_config, rdf_type, triple_store_type in triple_store_graph.triples(
+        (None, RDF.type, None)
+    ):
         triple_store = {}
         triple_store["type"] = triple_store_type
         triple_store["uri"] = triple_store_config
         # Anzo graph via anzo
         if triple_store_type == TRIPLESTORE.Anzo:
             get_anzo_configuration(
-                triple_store, triple_store_graph, triple_store_config)
+                triple_store, triple_store_graph, triple_store_config
+            )
         # GraphDB
         elif triple_store_type == TRIPLESTORE.GraphDb:
             get_graphDB_configuration(
-                triple_store, triple_store_graph, triple_store_config)
+                triple_store, triple_store_graph, triple_store_config
+            )
 
         elif triple_store_type != TRIPLESTORE.RdfLib:
             triple_store["error"] = f"Triple store not implemented: {triple_store_type}"
@@ -525,48 +603,74 @@ def get_triple_stores(triple_store_graph: Graph) -> list[dict]:
     return triple_stores
 
 
-def get_anzo_configuration(triple_store: dict, triple_store_graph: Graph, triple_store_config: URIRef):
+def get_anzo_configuration(
+    triple_store: dict, triple_store_graph: Graph, triple_store_config: URIRef
+):
     triple_store["url"] = triple_store_graph.value(
-        subject=triple_store_config, predicate=TRIPLESTORE.url)
+        subject=triple_store_config, predicate=TRIPLESTORE.url
+    )
     triple_store["port"] = triple_store_graph.value(
-        subject=triple_store_config, predicate=TRIPLESTORE.port)
+        subject=triple_store_config, predicate=TRIPLESTORE.port
+    )
     try:
-        triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config,
-                                                                predicate=TRIPLESTORE.username))
-        triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config,
-                                                                predicate=TRIPLESTORE.password))
+        triple_store["username"] = str(
+            triple_store_graph.value(
+                subject=triple_store_config, predicate=TRIPLESTORE.username
+            )
+        )
+        triple_store["password"] = str(
+            triple_store_graph.value(
+                subject=triple_store_config, predicate=TRIPLESTORE.password
+            )
+        )
     except (FileNotFoundError, ValueError) as e:
         triple_store["error"] = e
-    triple_store["gqe_uri"] = triple_store_graph.value(subject=triple_store_config,
-                                                       predicate=TRIPLESTORE.gqeURI)
-    triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                           predicate=TRIPLESTORE.inputGraph)
-    triple_store["output_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                            predicate=TRIPLESTORE.outputGraph)
+    triple_store["gqe_uri"] = triple_store_graph.value(
+        subject=triple_store_config, predicate=TRIPLESTORE.gqeURI
+    )
+    triple_store["input_graph"] = triple_store_graph.value(
+        subject=triple_store_config, predicate=TRIPLESTORE.inputGraph
+    )
+    triple_store["output_graph"] = triple_store_graph.value(
+        subject=triple_store_config, predicate=TRIPLESTORE.outputGraph
+    )
     try:
         check_triple_store_params(
-            triple_store, ["url", "port", "username", "password", "input_graph"])
+            triple_store, ["url", "port", "username", "password", "input_graph"]
+        )
     except ValueError as e:
         triple_store["error"] = e
 
 
-def get_graphDB_configuration(triple_store: dict, triple_store_graph: Graph, triple_store_config: URIRef):
+def get_graphDB_configuration(
+    triple_store: dict, triple_store_graph: Graph, triple_store_config: URIRef
+):
     triple_store["url"] = triple_store_graph.value(
-        subject=triple_store_config, predicate=TRIPLESTORE.url)
+        subject=triple_store_config, predicate=TRIPLESTORE.url
+    )
     triple_store["port"] = triple_store_graph.value(
-        subject=triple_store_config, predicate=TRIPLESTORE.port)
+        subject=triple_store_config, predicate=TRIPLESTORE.port
+    )
     try:
-        triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config,
-                                                                predicate=TRIPLESTORE.username))
-        triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config,
-                                                                predicate=TRIPLESTORE.password))
+        triple_store["username"] = str(
+            triple_store_graph.value(
+                subject=triple_store_config, predicate=TRIPLESTORE.username
+            )
+        )
+        triple_store["password"] = str(
+            triple_store_graph.value(
+                subject=triple_store_config, predicate=TRIPLESTORE.password
+            )
+        )
     except (FileNotFoundError, ValueError) as e:
         log.error(f"Credential retrieval failed {e}")
         triple_store["error"] = e
-    triple_store["repository"] = triple_store_graph.value(subject=triple_store_config,
-                                                          predicate=TRIPLESTORE.repository)
-    triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                           predicate=TRIPLESTORE.inputGraph)
+    triple_store["repository"] = triple_store_graph.value(
+        subject=triple_store_config, predicate=TRIPLESTORE.repository
+    )
+    triple_store["input_graph"] = triple_store_graph.value(
+        subject=triple_store_config, predicate=TRIPLESTORE.inputGraph
+    )
     try:
         check_triple_store_params(triple_store, ["url", "repository"])
     except ValueError as e:
@@ -575,18 +679,26 @@ def get_graphDB_configuration(triple_store: dict, triple_store_graph: Graph, tri
 
 def check_triple_store_params(triple_store: dict, required_params: List[str]):
     missing_params = [
-        param for param in required_params if triple_store.get(param) is None]
+        param for param in required_params if triple_store.get(param) is None
+    ]
     if missing_params:
-        raise ValueError(f"Cannot establish connection to {triple_store['type']}. "
-                         f"Missing required parameter(s): {', '.join(missing_params)}.")
+        raise ValueError(
+            f"Cannot establish connection to {triple_store['type']}. "
+            f"Missing required parameter(s): {', '.join(missing_params)}."
+        )
 
 
-def get_credential_from_file(triple_store_name: URIRef, credential: str, config_path: Literal) -> str:
+def get_credential_from_file(
+    triple_store_name: URIRef, credential: str, config_path: Literal
+) -> str:
     log.info(
-        f"get_credential_from_file {triple_store_name}, {credential}, {config_path}")
+        f"get_credential_from_file {triple_store_name}, {credential}, {config_path}"
+    )
     if not config_path:
-        raise ValueError(f"Cannot establish connection defined in {triple_store_name}. "
-                         f"Missing required parameter: {credential}.")
+        raise ValueError(
+            f"Cannot establish connection defined in {triple_store_name}. "
+            f"Missing required parameter: {credential}."
+        )
     path = Path(config_path)
     log.info(f"get_credential_from_file {path}")
 
@@ -622,9 +734,11 @@ def json_results_to_panda_dataframe(result: str) -> pandas.DataFrame:
             else:
                 values.append(str(XSD.anyURI))
 
-        frames = pandas.concat(objs=[frames, pandas.DataFrame(
-            [values], columns=columns)], ignore_index=True)
-        frames.fillna('', inplace=True)
+        frames = pandas.concat(
+            objs=[frames, pandas.DataFrame([values], columns=columns)],
+            ignore_index=True,
+        )
+        frames.fillna("", inplace=True)
 
         if frames.size == 0:
             frames = pandas.DataFrame()
@@ -635,7 +749,8 @@ def table_comparison(result: str, spec: Specification) -> SpecResult:
     warning = None
     order_list = ["order by ?", "order by desc", "order by asc"]
     ordered_result = any(
-        pattern in spec.when[0].value.lower() for pattern in order_list)
+        pattern in spec.when[0].value.lower() for pattern in order_list
+    )
 
     # If sparql query doesn't contain order by clause, but order is define in then spec:
     # Then ignore order in then spec and print a warning
@@ -646,27 +761,40 @@ def table_comparison(result: str, spec: Specification) -> SpecResult:
     # If sparql query contains an order by clause and then spec is not order:
     # Spec is inconsistent
     if ordered_result and not spec.then.ordered:
-        message = "Actual result is ordered, must:then must contain sh:order on every row."
-        return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], None, message)
+        message = (
+            "Actual result is ordered, must:then must contain sh:order on every row."
+        )
+        return SelectSpecFailure(
+            spec.spec_uri, spec.triple_store["type"], None, message
+        )
 
     # Convert results to dataframe
     if is_json(result):
         df = json_results_to_panda_dataframe(result)
     else:
-        return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], None, "Sparql result is not in JSON")
+        return SelectSpecFailure(
+            spec.spec_uri,
+            spec.triple_store["type"],
+            None,
+            "Sparql result is not in JSON",
+        )
 
     # Compare result with expected
     df_diff, message = compare_table_results(df, spec)
 
     if df_diff.empty:
         if warning:
-            return SpecPassedWithWarning(spec.spec_uri, spec.triple_store["type"], warning)
+            return SpecPassedWithWarning(
+                spec.spec_uri, spec.triple_store["type"], warning
+            )
         else:
             return SpecPassed(spec.spec_uri, spec.triple_store["type"])
     else:
         log.error("\n" + df_diff.to_markdown())
         log.error(message)
-        return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], df_diff, message)
+        return SelectSpecFailure(
+            spec.spec_uri, spec.triple_store["type"], df_diff, message
+        )
 
 
 def compare_table_results_dispatch(resultDf: DataFrame, spec: Specification):
@@ -674,7 +802,8 @@ def compare_table_results_dispatch(resultDf: DataFrame, spec: Specification):
 
 
 compare_table_results = MultiMethod(
-    "compare_table_results", compare_table_results_dispatch)
+    "compare_table_results", compare_table_results_dispatch
+)
 
 
 # Scenario 1: expected a result and got a result
@@ -686,7 +815,8 @@ def _compare_results(resultDf: DataFrame, spec: Specification):
     sorted_then_cols = sorted(list(then))
     order_list = ["order by ?", "order by desc", "order by asc"]
     ordered_result = any(
-        pattern in spec.when[0].value.lower() for pattern in order_list)
+        pattern in spec.when[0].value.lower() for pattern in order_list
+    )
 
     if not ordered_result:
         resultDf.sort_values(by=list(resultDf.columns)[::2], inplace=True)
@@ -698,9 +828,11 @@ def _compare_results(resultDf: DataFrame, spec: Specification):
             if not ordered_result:
                 then.sort_values(by=columns[::2], inplace=True)
                 then.reset_index(drop=True, inplace=True)
-            if resultDf.shape == then.shape and (resultDf.columns == then.columns).all():
-                df_diff = then.compare(
-                    resultDf, result_names=("expected", "actual"))
+            if (
+                resultDf.shape == then.shape
+                and (resultDf.columns == then.columns).all()
+            ):
+                df_diff = then.compare(resultDf, result_names=("expected", "actual"))
             else:
                 df_diff = construct_df_diff(resultDf, then)
         else:
@@ -712,8 +844,12 @@ def _compare_results(resultDf: DataFrame, spec: Specification):
         resultDf = resultDf[sorted_columns]
         df_diff = construct_df_diff(resultDf, then)
 
-    message = build_summary_message(then.shape[0], round(
-        then.shape[1] / 2), resultDf.shape[0], round(resultDf.shape[1] / 2))
+    message = build_summary_message(
+        then.shape[0],
+        round(then.shape[1] / 2),
+        resultDf.shape[0],
+        round(resultDf.shape[1] / 2),
+    )
     return df_diff, message
 
 
@@ -723,7 +859,9 @@ def _unexpected_results(resultDf: DataFrame, spec: Specification):
     empty_then = create_empty_dataframe_with_columns(resultDf)
     df_diff = empty_then.compare(resultDf, result_names=("expected", "actual"))
 
-    return df_diff, build_summary_message(0, 0, resultDf.shape[0], round(resultDf.shape[1] / 2))
+    return df_diff, build_summary_message(
+        0, 0, resultDf.shape[0], round(resultDf.shape[1] / 2)
+    )
 
 
 # Scenario 3: expected a result, but got an empty result
@@ -747,8 +885,10 @@ def _no_results(resultDf: DataFrame, spec: Specification):
 
 
 def build_summary_message(expected_rows, expected_columns, got_rows, got_columns):
-    return f"Expected {expected_rows} row(s) and {expected_columns} column(s), " \
+    return (
+        f"Expected {expected_rows} row(s) and {expected_columns} column(s), "
         f"got {got_rows} row(s) and {got_columns} column(s)"
+    )
 
 
 def graph_comparison(expected_graph: Graph, actual_graph: Graph) -> GraphComparison:
@@ -756,9 +896,11 @@ def graph_comparison(expected_graph: Graph, actual_graph: Graph) -> GraphCompari
     in_both = diff[0]
     in_expected = diff[1]
     in_actual = diff[2]
-    in_expected_not_in_actual = (in_expected - in_actual)
-    in_actual_not_in_expected = (in_actual - in_expected)
-    return GraphComparison(in_expected_not_in_actual, in_actual_not_in_expected, in_both)
+    in_expected_not_in_actual = in_expected - in_actual
+    in_actual_not_in_expected = in_actual - in_expected
+    return GraphComparison(
+        in_expected_not_in_actual, in_actual_not_in_expected, in_both
+    )
 
 
 def get_then_update(spec_uri: URIRef, spec_graph: Graph) -> Graph:
@@ -786,11 +928,9 @@ def write_result_diff_to_log(res, info):
     if isinstance(res, UpdateSpecFailure) or isinstance(res, ConstructSpecFailure):
         info(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
         info(f"{Fore.BLUE} In Expected Not In Actual:")
-        info(
-            res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl"))
+        info(res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl"))
         info(f"{Fore.RED} in_actual_not_in_expected")
-        info(
-            res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl"))
+        info(res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl"))
         info(f"{Fore.GREEN} in_both")
         info(res.graph_comparison.in_both.serialize(format="ttl"))
 
@@ -799,11 +939,13 @@ def write_result_diff_to_log(res, info):
         info(res.message)
         info(res.table_comparison.to_markdown())
     if isinstance(res, SpecPassedWithWarning):
-        info(
-            f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}")
+        info(f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}")
         info(res.warning)
-    if isinstance(res, TripleStoreConnectionError) or isinstance(res, SparqlExecutionError) or \
-            isinstance(res, SparqlParseFailure):
+    if (
+        isinstance(res, TripleStoreConnectionError)
+        or isinstance(res, SparqlExecutionError)
+        or isinstance(res, SparqlParseFailure)
+    ):
         info(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
         info(res.exception)
     if isinstance(res, SpecSkipped):
@@ -811,16 +953,16 @@ def write_result_diff_to_log(res, info):
         info(res.message)
 
 
-def calculate_row_difference(df1: pandas.DataFrame,
-                             df2: pandas.DataFrame) -> pandas.DataFrame:
-    df_all = df1.merge(df2.drop_duplicates(), how='left', indicator=True)
-    actual_rows = df_all[df_all['_merge'] == 'left_only']
-    actual_rows = actual_rows.drop('_merge', axis=1)
+def calculate_row_difference(
+    df1: pandas.DataFrame, df2: pandas.DataFrame
+) -> pandas.DataFrame:
+    df_all = df1.merge(df2.drop_duplicates(), how="left", indicator=True)
+    actual_rows = df_all[df_all["_merge"] == "left_only"]
+    actual_rows = actual_rows.drop("_merge", axis=1)
     return actual_rows
 
 
-def construct_df_diff(df: pandas.DataFrame,
-                      then: pandas.DataFrame) -> pandas.DataFrame:
+def construct_df_diff(df: pandas.DataFrame, then: pandas.DataFrame) -> pandas.DataFrame:
     actual_rows = calculate_row_difference(df, then)
     expected_rows = calculate_row_difference(then, df)
     actual_columns = df.columns.difference(then.columns)
@@ -832,15 +974,19 @@ def construct_df_diff(df: pandas.DataFrame,
 
     if actual_columns.size > 0:
         modified_then = modified_then.reindex(
-            modified_then.columns.to_list() + actual_columns.to_list(), axis=1)
-        modified_then[actual_columns.to_list(
-        )] = modified_then[actual_columns.to_list()].fillna('')
+            modified_then.columns.to_list() + actual_columns.to_list(), axis=1
+        )
+        modified_then[actual_columns.to_list()] = modified_then[
+            actual_columns.to_list()
+        ].fillna("")
 
     if expected_columns.size > 0:
         modified_df = modified_df.reindex(
-            modified_df.columns.to_list() + expected_columns.to_list(), axis=1)
-        modified_df[expected_columns.to_list(
-        )] = modified_df[expected_columns.to_list()].fillna('')
+            modified_df.columns.to_list() + expected_columns.to_list(), axis=1
+        )
+        modified_df[expected_columns.to_list()] = modified_df[
+            expected_columns.to_list()
+        ].fillna("")
 
     modified_df = modified_df.reindex(modified_then.columns, axis=1)
 
@@ -852,29 +998,37 @@ def construct_df_diff(df: pandas.DataFrame,
     elif actual_rows.shape[0] > 0 or expected_rows.shape[0] > 0:
         df_diff = generate_row_diff(actual_rows, expected_rows)
     elif actual_columns.size > 0 or expected_columns.size > 0:
-        df_diff = modified_then.compare(modified_df, result_names=("expected", "actual"), keep_shape=True,
-                                        keep_equal=True)
+        df_diff = modified_then.compare(
+            modified_df,
+            result_names=("expected", "actual"),
+            keep_shape=True,
+            keep_equal=True,
+        )
     df_diff.fillna("", inplace=True)
     return df_diff
 
 
-def generate_row_diff(actual_rows: pandas.DataFrame, expected_rows: pandas.DataFrame) -> pandas.DataFrame:
+def generate_row_diff(
+    actual_rows: pandas.DataFrame, expected_rows: pandas.DataFrame
+) -> pandas.DataFrame:
     df_diff_actual_rows = pandas.DataFrame()
     df_diff_expected_rows = pandas.DataFrame()
 
     if actual_rows.shape[0] > 0:
         empty_actual_copy = create_empty_dataframe_with_columns(actual_rows)
         df_diff_actual_rows = empty_actual_copy.compare(
-            actual_rows, result_names=("expected", "actual"))
+            actual_rows, result_names=("expected", "actual")
+        )
 
     if expected_rows.shape[0] > 0:
-        empty_expected_copy = create_empty_dataframe_with_columns(
-            expected_rows)
+        empty_expected_copy = create_empty_dataframe_with_columns(expected_rows)
         df_diff_expected_rows = expected_rows.compare(
-            empty_expected_copy, result_names=("expected", "actual"))
+            empty_expected_copy, result_names=("expected", "actual")
+        )
 
     df_diff_rows = pandas.concat(
-        [df_diff_actual_rows, df_diff_expected_rows], ignore_index=True)
+        [df_diff_actual_rows, df_diff_expected_rows], ignore_index=True
+    )
     return df_diff_rows
 
 
@@ -889,40 +1043,76 @@ def review_results(results: List[SpecResult], verbose: bool) -> None:
     # Init dictionaries
     status_dict = defaultdict(lambda: defaultdict(int))
     status_counts = defaultdict(lambda: defaultdict(int))
-    colours = {SpecPassed: Fore.GREEN,
-               SpecPassedWithWarning: Fore.YELLOW, SpecSkipped: Fore.YELLOW}
+    colours = {
+        SpecPassed: Fore.GREEN,
+        SpecPassedWithWarning: Fore.YELLOW,
+        SpecSkipped: Fore.YELLOW,
+    }
     # Populate dictionaries from results
     for result in results:
         status_counts[result.triple_store][type(result)] += 1
         status_dict[result.spec_uri][result.triple_store] = type(result)
 
     # Get the list of statuses and list of unique triple stores
-    statuses = list(status for inner_dict in status_dict.values()
-                    for status in inner_dict.values())
-    triple_stores = list(set(status for inner_dict in status_dict.values()
-                         for status in inner_dict.keys()))
+    statuses = list(
+        status for inner_dict in status_dict.values() for status in inner_dict.values()
+    )
+    triple_stores = list(
+        set(
+            status
+            for inner_dict in status_dict.values()
+            for status in inner_dict.keys()
+        )
+    )
 
     # Convert dictionaries to list for tabulate
-    table_rows = [[spec_uri] + [
-        f"""{colours.get(status_dict[spec_uri][triple_store], Fore.RED)}
+    table_rows = [
+        [spec_uri]
+        + [
+            f"""{colours.get(status_dict[spec_uri][triple_store], Fore.RED)}
         {status_dict[spec_uri][triple_store].__name__}{Style.RESET_ALL}"""
-        for triple_store in triple_stores] for spec_uri in set(status_dict.keys())]
-
-    status_rows = [[f"{colours.get(status, Fore.RED)}{status.__name__}{Style.RESET_ALL}"] +
-                   [f"{colours.get(status, Fore.RED)}{status_counts[triple_store][status]}{Style.RESET_ALL}"
-                    for triple_store in triple_stores] for status in set(statuses)]
+            for triple_store in triple_stores
+        ]
+        for spec_uri in set(status_dict.keys())
+    ]
+
+    status_rows = [
+        [f"{colours.get(status, Fore.RED)}{status.__name__}{Style.RESET_ALL}"]
+        + [
+            f"{colours.get(status, Fore.RED)}{status_counts[triple_store][status]}{Style.RESET_ALL}"
+            for triple_store in triple_stores
+        ]
+        for status in set(statuses)
+    ]
 
     # Display tables with tabulate
-    log.info(tabulate(table_rows, headers=[
-             'Spec Uris / triple stores'] + triple_stores, tablefmt="pretty"))
-    log.info(tabulate(status_rows, headers=[
-             'Status / triple stores'] + triple_stores, tablefmt="pretty"))
+    log.info(
+        tabulate(
+            table_rows,
+            headers=["Spec Uris / triple stores"] + triple_stores,
+            tablefmt="pretty",
+        )
+    )
+    log.info(
+        tabulate(
+            status_rows,
+            headers=["Status / triple stores"] + triple_stores,
+            tablefmt="pretty",
+        )
+    )
 
     pass_count = statuses.count(SpecPassed)
     warning_count = statuses.count(SpecPassedWithWarning)
     skipped_count = statuses.count(SpecSkipped)
     fail_count = len(
-        list(filter(lambda status: status not in [SpecPassed, SpecPassedWithWarning, SpecSkipped], statuses)))
+        list(
+            filter(
+                lambda status: status
+                not in [SpecPassed, SpecPassedWithWarning, SpecSkipped],
+                statuses,
+            )
+        )
+    )
 
     if fail_count:
         overview_colour = Fore.RED
@@ -932,8 +1122,10 @@ def review_results(results: List[SpecResult], verbose: bool) -> None:
         overview_colour = Fore.GREEN
 
     logger_setup.flush()
-    log.info(f"{overview_colour}===== {fail_count} failures, {skipped_count} skipped, {Fore.GREEN}{pass_count} passed, "
-             f"{overview_colour}{warning_count} passed with warnings =====")
+    log.info(
+        f"{overview_colour}===== {fail_count} failures, {skipped_count} skipped, {Fore.GREEN}{pass_count} passed, "
+        f"{overview_colour}{warning_count} passed with warnings ====="
+    )
 
     if verbose and (fail_count or warning_count or skipped_count):
         display_verbose(results)
@@ -945,11 +1137,13 @@ def display_verbose(results: List[SpecResult]):
             log.info(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
             log.info(f"{Fore.BLUE} In Expected Not In Actual:")
             log.info(
-                res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl"))
+                res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl")
+            )
             log.info()
             log.info(f"{Fore.RED} in_actual_not_in_expected")
             log.info(
-                res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl"))
+                res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl")
+            )
             log.info(f"{Fore.GREEN} in_both")
             log.info(res.graph_comparison.in_both.serialize(format="ttl"))
 
@@ -961,12 +1155,33 @@ def display_verbose(results: List[SpecResult]):
             log.info(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
         if isinstance(res, SpecPassedWithWarning):
             log.info(
-                f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}")
+                f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}"
+            )
             log.info(res.warning)
-        if isinstance(res, TripleStoreConnectionError) or type(res, SparqlExecutionError) or \
-                isinstance(res, SparqlParseFailure):
+        if (
+            isinstance(res, TripleStoreConnectionError)
+            or type(res, SparqlExecutionError)
+            or isinstance(res, SparqlParseFailure)
+        ):
             log.info(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
             log.info(res.exception)
         if isinstance(res, SpecSkipped):
             log.info(f"{Fore.YELLOW}Skipped {res.spec_uri} {res.triple_store}")
             log.info(res.message)
+
+
+# Preserve the original run_when_impl multimethod
+original_run_when_impl = run_when_impl
+
+
+# Wrapper function for logging inputs and outputs of run_when
+def run_when_with_logging(*args, **kwargs):
+    log.debug(f"run_when called with args: {args}, kwargs: {kwargs}")
+    result = original_run_when_impl(*args, **kwargs)  # Call the original multimethod
+    log.debug(f"run_when returned: {result}")
+    return result
+
+
+# Replace the original run_when_impl with the wrapped version
+run_when_impl = run_when_with_logging
+run_when = run_when_impl