cognite-neat 0.123.12__py3-none-any.whl → 0.123.14__py3-none-any.whl

cognite/neat/_version.py

@@ -1,2 +1,2 @@
-__version__ = "0.123.12"
+__version__ = "0.123.14"
 __engine__ = "^2.0.4"

cognite/neat/core/_data_model/importers/_rdf/_owl2data_model.py

@@ -25,6 +25,8 @@ CLASSES_QUERY = """SELECT ?concept  ?name ?description ?implements
     }}
     """
 
+CLASSES_QUERY_PARAMETERS = {"concept", "name", "description", "implements"}
+
 PROPERTIES_QUERY = """
 
     SELECT ?concept  ?property_ ?name ?description ?value_type ?minCount ?maxCount ?default
@@ -44,34 +46,36 @@ PROPERTIES_QUERY = """
         FILTER (!bound(?description) || LANG(?description) = "" || LANGMATCHES(LANG(?description), "{language}"))
     }}
     """
+PROPERTIES_QUERY_PARAMETERS = {
+    "concept",
+    "property_",
+    "name",
+    "description",
+    "value_type",
+    "minCount",
+    "maxCount",
+    "default",
+}
 
 
 class OWLImporter(BaseRDFImporter):
     """Convert OWL ontology to unverified data model.
 
-        Args:
-            filepath: Path to OWL ontology
-
-    !!! Note
-        OWL Ontologies are information models which completeness varies. As such, constructing functional
-        data model directly will often be impossible, therefore the produced data model object will be ill formed.
-        To avoid this, neat will automatically attempt to make the imported data model compliant by adding default
-        values for missing information, attaching dangling properties to default containers based on the
-        property type, etc.
-
-        One has to be aware that NEAT will be opinionated about how to make the ontology
-        compliant, and that the resulting data model may not be what you expect.
-
+    Args:
+        filepath: Path to OWL ontology
     """
 
     def _to_data_model_components(
         self,
     ) -> dict:
-        concepts, issue_list = parse_concepts(self.graph, CLASSES_QUERY, self.language, self.issue_list)
+        concepts, issue_list = parse_concepts(
+            self.graph, CLASSES_QUERY, CLASSES_QUERY_PARAMETERS, self.language, self.issue_list
+        )
         self.issue_list = issue_list
 
-        # NeatError
-        properties, issue_list = parse_properties(self.graph, PROPERTIES_QUERY, self.language, self.issue_list)
+        properties, issue_list = parse_properties(
+            self.graph, PROPERTIES_QUERY, PROPERTIES_QUERY_PARAMETERS, self.language, self.issue_list
+        )
         self.issue_list = issue_list
 
         components = {

cognite/neat/core/_data_model/importers/_rdf/_shared.py

@@ -14,12 +14,17 @@ from cognite.neat.core._issues.warnings._resources import (
 from cognite.neat.core._utils.rdf_ import convert_rdflib_content
 
 
-def parse_concepts(graph: Graph, query: str, language: str, issue_list: IssueList) -> tuple[dict, IssueList]:
+def parse_concepts(
+    graph: Graph, query: str, parameters: set, language: str, issue_list: IssueList
+) -> tuple[dict, IssueList]:
     """Parse concepts from graph
 
     Args:
         graph: Graph containing concept definitions
+        query: SPARQL query to use for parsing concepts
+        parameters: Set of parameters to extract from the query results
         language: Language to use for parsing, by default "en"
+        issue_list: List to collect issues during parsing
 
     Returns:
         Dataframe containing owl classes
@@ -28,11 +33,10 @@ def parse_concepts(graph: Graph, query: str, language: str, issue_list: IssueLis
     concepts: dict[str, dict] = {}
 
     query = prepareQuery(query.format(language=language), initNs={k: v for k, v in graph.namespaces()})
-    expected_keys = [str(v) for v in query.algebra._vars]
 
     for raw in graph.query(query):
         res: dict = convert_rdflib_content(cast(ResultRow, raw).asdict(), True)
-        res = {key: res.get(key, None) for key in expected_keys}
+        res = {key: res.get(key, None) for key in parameters}
 
         # Quote the concept id to ensure it is web-safe
         res["concept"] = quote(res["concept"], safe="")
@@ -75,12 +79,17 @@ def parse_concepts(graph: Graph, query: str, language: str, issue_list: IssueLis
     return concepts, issue_list
 
 
-def parse_properties(graph: Graph, query: str, language: str, issue_list: IssueList) -> tuple[dict, IssueList]:
+def parse_properties(
+    graph: Graph, query: str, parameters: set, language: str, issue_list: IssueList
+) -> tuple[dict, IssueList]:
     """Parse properties from graph
 
     Args:
-        graph: Graph containing owl classes
+        graph: Graph containing property definitions
+        query: SPARQL query to use for parsing properties
+        parameters: Set of parameters to extract from the query results
         language: Language to use for parsing, by default "en"
+        issue_list: List to collect issues during parsing
 
     Returns:
         Dataframe containing owl classes
@@ -89,41 +98,40 @@ def parse_properties(graph: Graph, query: str, language: str, issue_list: IssueL
     properties: dict[str, dict] = {}
 
     query = prepareQuery(query.format(language=language), initNs={k: v for k, v in graph.namespaces()})
-    expected_keys = [str(v) for v in query.algebra._vars]
 
     for raw in graph.query(query):
         res: dict = convert_rdflib_content(cast(ResultRow, raw).asdict(), True)
-        res = {key: res.get(key, None) for key in expected_keys}
+        res = {key: res.get(key, None) for key in parameters}
 
         # Quote the concept id to ensure it is web-safe
         res["property_"] = quote(res["property_"], safe="")
         property_id = res["property_"]
 
-        # Safeguarding against incomplete semantic definitions
-        if not res["concept"] or isinstance(res["concept"], BNode):
+        # Skip Bnode
+        if isinstance(res["concept"], BNode):
             issue_list.append(
                 ResourceRetrievalWarning(
                     property_id,
                     "property",
-                    error=("Unable to determine to what concept property is being defined"),
+                    error="Cannot determine concept of property as it is a blank node",
                 )
             )
             continue
 
-        # Safeguarding against incomplete semantic definitions
-        if not res["value_type"] or isinstance(res["value_type"], BNode):
+        # Skip Bnode
+        if isinstance(res["value_type"], BNode):
             issue_list.append(
                 ResourceRetrievalWarning(
                     property_id,
                     "property",
-                    error=("Unable to determine value type of property"),
+                    error="Unable to determine value type of property as it is a blank node",
                 )
             )
             continue
 
         # Quote the concept and value_type to ensure they are web-safe
-        res["concept"] = quote(res["concept"], safe="")
-        res["value_type"] = quote(res["value_type"], safe="")
+        res["concept"] = quote(res["concept"], safe="") if res["concept"] else "#N/A"
+        res["value_type"] = quote(res["value_type"], safe="") if res["value_type"] else "#N/A"
 
         id_ = f"{res['concept']}.{res['property_']}"
 

cognite/neat/core/_data_model/models/conceptual/_unverified.py

@@ -78,7 +78,7 @@ class UnverifiedConceptualMetadata(UnverifiedComponent[ConceptualMetadata]):
 
 @dataclass
 class UnverifiedConceptualProperty(UnverifiedComponent[ConceptualProperty]):
-    concept: ConceptEntity | str
+    concept: ConceptEntity | str | UnknownEntity
     property_: str
     value_type: DataType | ConceptEntity | MultiValueTypeInfo | UnknownEntity | str
     name: str | None = None

cognite/neat/core/_data_model/models/conceptual/_validation.py

@@ -11,7 +11,11 @@ from cognite.neat.core._issues.errors._resources import (
     ResourceDuplicatedError,
     ResourceNotDefinedError,
 )
-from cognite.neat.core._issues.warnings._models import ConceptOnlyDataModelWarning, UndefinedConceptWarning
+from cognite.neat.core._issues.warnings._models import (
+    ConceptOnlyDataModelWarning,
+    DanglingPropertyWarning,
+    UndefinedConceptWarning,
+)
 from cognite.neat.core._issues.warnings._resources import (
     ResourceNotDefinedWarning,
     ResourceRegexViolationWarning,
@@ -47,6 +51,7 @@ class ConceptualValidation:
         self._referenced_classes_exist()
         self._referenced_value_types_exist()
         self._concept_only_data_model()
+        self._dangling_properties()
         self._regex_compliance_with_physical_data_model()
 
         return self.issue_list
@@ -56,6 +61,13 @@ class ConceptualValidation:
         if not self._properties:
             self.issue_list.append(ConceptOnlyDataModelWarning())
 
+    def _dangling_properties(self) -> None:
+        """Check if there are properties that do not reference any concept."""
+        dangling_properties = [prop for prop in self._properties if prop.concept == UnknownEntity()]
+        if dangling_properties:
+            for prop in dangling_properties:
+                self.issue_list.append(DanglingPropertyWarning(property_id=prop.property_))
+
     def _duplicated_resources(self) -> None:
         properties_sheet = self._read_info_by_spreadsheet.get("Properties")
         concepts_sheet = self._read_info_by_spreadsheet.get("Concepts")
@@ -119,7 +131,7 @@ class ConceptualValidation:
 
     def _undefined_classes(self) -> None:
         defined_concept = {concept.concept for concept in self._concepts}
-        referred_concepts = {property_.concept for property_ in self._properties}
+        referred_concepts = {property_.concept for property_ in self._properties} - {UnknownEntity()}
 
         if undefined_concepts := referred_concepts.difference(defined_concept):
             for concept in undefined_concepts:
@@ -153,7 +165,7 @@ class ConceptualValidation:
     def _referenced_classes_exist(self) -> None:
         # needs to be complete for this validation to pass
         defined_concept = {concept.concept for concept in self._concepts}
-        classes_with_explicit_properties = {property_.concept for property_ in self._properties}
+        classes_with_explicit_properties = {property_.concept for property_ in self._properties} - {UnknownEntity()}
 
         # USE CASE: models are complete
         if missing_classes := classes_with_explicit_properties.difference(defined_concept):
@@ -199,7 +211,7 @@ class ConceptualValidation:
                         PATTERNS.physical_property_id_compliance.pattern,
                     )
                 )
-            if not PATTERNS.view_id_compliance.match(prop_.concept.suffix):
+            if prop_.concept != UnknownEntity() and not PATTERNS.view_id_compliance.match(prop_.concept.suffix):
                 self.issue_list.append(
                     ResourceRegexViolationWarning(
                         prop_.concept,

cognite/neat/core/_data_model/models/conceptual/_verified.py

@@ -123,7 +123,7 @@ class ConceptualProperty(SheetRow):
               knowledge graph. Defaults to None (no transformation)
     """
 
-    concept: ConceptEntityType = Field(
+    concept: ConceptEntityType | UnknownEntity = Field(
         alias="Concept",
         description="Concept id that the property is defined for, strongly advise `PascalCase` usage.",
     )

cognite/neat/core/_issues/warnings/_models.py

@@ -109,6 +109,16 @@ class ConceptOnlyDataModelWarning(UserModelingWarning):
     fix = "Define properties for concepts or make sure that concepts implement other concepts that have properties."
 
 
+@dataclass(unsafe_hash=True)
+class DanglingPropertyWarning(UserModelingWarning):
+    """Property {property_id} is not defined for any concept.
+    This will likely cause issues when converting to a physical data model."""
+
+    fix = "Define the property for a concept or remove it from the data model."
+
+    property_id: str
+
+
 @dataclass(unsafe_hash=True)
 class UndefinedViewWarning(UserModelingWarning):
     """Undefined view {value_type} has been referred as value type for property <{view_property}> of view {view_id}."""

cognite/neat/core/_utils/spreadsheet.py

@@ -98,6 +98,10 @@ def read_individual_sheet(
         # Special handling for Value Type column, #N/A is treated specially by NEAT it means Unknown
         raw["Value Type"] = raw["Value Type"].replace(float("nan"), "#N/A")
 
+    if "Concept" in raw.columns:
+        # Special handling for Concept column, #N/A is treated specially by NEAT it means Unknown
+        raw["Concept"] = raw["Concept"].replace(float("nan"), "#N/A")
+
     output = raw.replace(float("nan"), None).to_dict(orient="records")
     if return_read_info:
         # If no rows are skipped, row 1 is the header row.

{cognite_neat-0.123.12.dist-info → cognite_neat-0.123.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cognite-neat
-Version: 0.123.12
+Version: 0.123.14
 Summary: Knowledge graph transformation
 Project-URL: Documentation, https://cognite-neat.readthedocs-hosted.com/
 Project-URL: Homepage, https://cognite-neat.readthedocs-hosted.com/

{cognite_neat-0.123.12.dist-info → cognite_neat-0.123.14.dist-info}/RECORD

@@ -1,5 +1,5 @@
 cognite/neat/__init__.py,sha256=12StS1dzH9_MElqxGvLWrNsxCJl9Hv8A2a9D0E5OD_U,193
-cognite/neat/_version.py,sha256=Mzqn-YIDR_mqLMU1RkQCFPerYxlahGnGKv-rz3QId68,47
+cognite/neat/_version.py,sha256=qLY0w9gF4NJv-QQnU8dofXCm32MMtagvnj-drOInmzU,47
 cognite/neat/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cognite/neat/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cognite/neat/core/_config.py,sha256=WT1BS8uADcFvGoUYOOfwFOVq_VBl472TisdoA3wLick,280
@@ -43,17 +43,17 @@ cognite/neat/core/_data_model/importers/_spreadsheet2data_model.py,sha256=2QqrxQ
 cognite/neat/core/_data_model/importers/_rdf/__init__.py,sha256=1yOjV2PKCxwH7uCTXVZhSdxtn5etmFX40cksvwtKcZ8,199
 cognite/neat/core/_data_model/importers/_rdf/_base.py,sha256=FKceKumKmhEGpMZvo1BwEewnUvfAsTF3Ax9fo1nxsGE,6020
 cognite/neat/core/_data_model/importers/_rdf/_inference2rdata_model.py,sha256=PCgM9-qGSLlupN7tYCFLHjivgICtMiahNry1ub8JCYk,28934
-cognite/neat/core/_data_model/importers/_rdf/_owl2data_model.py,sha256=WmncZNpELeZnt6mdw6X8yWnr7XsFXZGfoVe5wTd0HH4,3438
-cognite/neat/core/_data_model/importers/_rdf/_shared.py,sha256=KJz4HirSpWBXsOw8YGBJh-6Yj_pBjrMB9_K8UQ00sQg,6411
+cognite/neat/core/_data_model/importers/_rdf/_owl2data_model.py,sha256=l_89N1LewZVjSttcJkFAJj63JW8wI-THKJYjAxcNiDg,3093
+cognite/neat/core/_data_model/importers/_rdf/_shared.py,sha256=qibq94dFoy_g1ED5nIFYwHC_LYI4jI67HFVcMy7abrM,6665
 cognite/neat/core/_data_model/models/__init__.py,sha256=hmF7MDR1XmpLxYdMkOEuPuHUqOQKE4AgsuUqdc-ySSQ,1249
 cognite/neat/core/_data_model/models/_base_unverified.py,sha256=1Wfbp-tJaEF6hd1bFdp2FhTgPkInf-1ZokuEoVJRPxQ,6842
 cognite/neat/core/_data_model/models/_base_verified.py,sha256=nzPrlj7ZvYull_Fdh2zeDXz98hux-eQOdTGy9jhUtYA,15127
 cognite/neat/core/_data_model/models/_types.py,sha256=70E8fiLdZkVF2sDUGPuDhzXNA5niVECkVDI7YN0NF60,5488
 cognite/neat/core/_data_model/models/data_types.py,sha256=uQ_u9KxCetLjxo-VtFzOXSxQuuf97Kg-9lfTTGzY6hc,10150
 cognite/neat/core/_data_model/models/conceptual/__init__.py,sha256=9A6myEV8s0-LqdXejaljqPj8S0pIpUL75rNdRDZzyR8,585
-cognite/neat/core/_data_model/models/conceptual/_unverified.py,sha256=ufNHLd9czY0XHV_C2zbQDarKSPeew7ohRbmq6dyo-_o,6282
-cognite/neat/core/_data_model/models/conceptual/_validation.py,sha256=twgVP-SQypAf3R8RB5Rp8EjCgblePK_zUbUyYQfut28,13339
-cognite/neat/core/_data_model/models/conceptual/_verified.py,sha256=HPNjzASKP9hs8lI8Xxfvdl2a9MdlP-JoEtXFk0a2ISw,13700
+cognite/neat/core/_data_model/models/conceptual/_unverified.py,sha256=VswgnTSjSCRzBX3z5HvintBGaWBPexxIs-7z7S4J57c,6298
+cognite/neat/core/_data_model/models/conceptual/_validation.py,sha256=LOnLNArteqc9TlyyRNqQgMAKx2oZ8s91WePR8fqLRlE,13888
+cognite/neat/core/_data_model/models/conceptual/_verified.py,sha256=BUB4Ur4kpBoWiwTf57tjxJ2l0tDTSbY7zGrg1g0yVNQ,13716
 cognite/neat/core/_data_model/models/entities/__init__.py,sha256=UsW-_6fwd-TW0WcnShPKf40h75l1elVn80VurUwRAic,1567
 cognite/neat/core/_data_model/models/entities/_constants.py,sha256=GXRzVfArwxF3C67VCkzy0JWTZRkRJUYXBQaaecrqcWc,351
 cognite/neat/core/_data_model/models/entities/_loaders.py,sha256=PkrVtGlZWYLvAVIRABrgVSgkMvJYpBqdrHBfz-H0Ut8,2783
@@ -131,7 +131,7 @@ cognite/neat/core/_issues/errors/_wrapper.py,sha256=clhuSwUuHy-FQXQopFIQRY8c_NZM
 cognite/neat/core/_issues/warnings/__init__.py,sha256=lzNZrguzwXyifehsCilAXa5UL94DWHIeO-slyC-EYZc,3165
 cognite/neat/core/_issues/warnings/_external.py,sha256=w-1R7ea6DXTIWqwlwMMjY0YxKDMSJ8gKAbp_nIIM1AI,1324
 cognite/neat/core/_issues/warnings/_general.py,sha256=_6dAFaMz-LIv7GsBBIBq2d-kmbuxVXKvU4jZeb7tjAo,972
-cognite/neat/core/_issues/warnings/_models.py,sha256=mnoNxVvTifkIGxOxXAgdY-5ZDwy_IyxNsIxdTIcXdNY,4759
+cognite/neat/core/_issues/warnings/_models.py,sha256=dE8Ha96WtZ9m_Bozx64NCMuJY2gWZleicD5tnnOqbe8,5086
 cognite/neat/core/_issues/warnings/_properties.py,sha256=I3vqc1aL-ce_FRQNgQQy34RW7kQxcjbwhZIIVtGVmg8,3807
 cognite/neat/core/_issues/warnings/_resources.py,sha256=_iPRq0pRMmRu3LFjqZTaG3OqOzw4f8-Vc9G4Im__FHc,3578
 cognite/neat/core/_issues/warnings/user_modeling.py,sha256=Qn_S8TLw7MMYQaJcZBScJA48kz_PrTWz0NaepSR70Fk,4144
@@ -147,7 +147,7 @@ cognite/neat/core/_utils/collection_.py,sha256=zVrSmm4045pjw6Pt6y4VPTIJ4dXdMJPyO
 cognite/neat/core/_utils/graph_transformations_report.py,sha256=ORVH7lw357TPOq4elU5lH46Qx6GCLVrSj-1nX6Ggk1U,1235
 cognite/neat/core/_utils/io_.py,sha256=D2Mg8sOxfBoDg3fC0jBzaxO3vkXmr0QvZSgYIv6xRkM,386
 cognite/neat/core/_utils/rdf_.py,sha256=8AALp8H_nXEDSBo6jZ1idyT_x3K4PJT5ZyBEyxPmgxI,10403
-cognite/neat/core/_utils/spreadsheet.py,sha256=MMI_1zxeHEf9Ggu_-t_ryjj54ky085QIf8eArt5hXEY,5749
+cognite/neat/core/_utils/spreadsheet.py,sha256=VdjcCh339cKu9UwxJkYrmmnrbLguD71tdFmyd3MlIZA,5951
 cognite/neat/core/_utils/tarjan.py,sha256=IZvwaIITryGVNbo9Bv5EA9_sW3DyfUNAe7uYyPOCL0g,1357
 cognite/neat/core/_utils/text.py,sha256=ON4ihfscFJkQqQ-Rj46XXtf-9tAobwXbbfa3wuekSu4,8519
 cognite/neat/core/_utils/time_.py,sha256=7ayUm0OWZm1JDmy32E4ip8WRr2o0GLwrHwJA8sJ43Z4,357
@@ -186,7 +186,7 @@ cognite/neat/session/engine/__init__.py,sha256=D3MxUorEs6-NtgoICqtZ8PISQrjrr4dvc
 cognite/neat/session/engine/_import.py,sha256=1QxA2_EK613lXYAHKQbZyw2yjo5P9XuiX4Z6_6-WMNQ,169
 cognite/neat/session/engine/_interface.py,sha256=3W-cYr493c_mW3P5O6MKN1xEQg3cA7NHR_ev3zdF9Vk,533
 cognite/neat/session/engine/_load.py,sha256=g52uYakQM03VqHt_RDHtpHso1-mFFifH5M4T2ScuH8A,5198
-cognite_neat-0.123.12.dist-info/METADATA,sha256=U5jaZlc_AdCI7uML_9DBtq-V7bEIciJgBDxR8brvp0E,9172
-cognite_neat-0.123.12.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-cognite_neat-0.123.12.dist-info/licenses/LICENSE,sha256=W8VmvFia4WHa3Gqxq1Ygrq85McUNqIGDVgtdvzT-XqA,11351
-cognite_neat-0.123.12.dist-info/RECORD,,
+cognite_neat-0.123.14.dist-info/METADATA,sha256=OtegXPCjwnGT8EM8x8M1ekoHwwAhZ4NuNRKfz0uRxGM,9172
+cognite_neat-0.123.14.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+cognite_neat-0.123.14.dist-info/licenses/LICENSE,sha256=W8VmvFia4WHa3Gqxq1Ygrq85McUNqIGDVgtdvzT-XqA,11351
+cognite_neat-0.123.14.dist-info/RECORD,,