Merge pull request #19 from nfdi4cat/fix_testdata_issues

Add product_identification_method and test fixtures

Author: HendrikBorgelt

docs/schema/coremeta4cat.yaml

@@ -715,9 +715,10 @@ slots:
     mappings:
     - VOC4CAT:0000187
     slot_uri: VOC4CAT:0000187
-    owner: ThermalSynthesisMixin
+    owner: Characterization
     domain_of:
     - ThermalSynthesisMixin
+    - Characterization
     range: string
     multivalued: true
   flow_rate:
@@ -3716,6 +3717,27 @@ slots:
     domain_of:
     - FluidizedBedReactor
     range: string
+  product_identification_method:
+    name: product_identification_method
+    definition_uri: https://w3id.org/nfdi4cat/coremeta4cat/product_identification_method
+    description: 'The analytical method used to identify and/or quantify reaction
+      products.
+
+      Should reference a CharacterizationTechnique instance (e.g. GCMS, HPLC_MS).
+
+      The abstract stub ProductIdentificationMethod is retained for backward compatibility.'
+    from_schema: https://w3id.org/nfdi4cat/coremeta4cat/reaction/
+    mappings:
+    - coremeta4cat:product_identification_method
+    slot_uri: coremeta4cat:product_identification_method
+    owner: Reaction
+    domain_of:
+    - Reaction
+    range: ProductIdentificationMethod
+    required: true
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
   software_package:
     name: software_package
     definition_uri: https://w3id.org/nfdi4cat/coremeta4cat/software_package
@@ -6975,23 +6997,6 @@ slots:
       binds_value_of: id
       description: Restricts the allowable defined terms to the QUDT Unit vocabulary.
     recommended: true
-  product_identification_method:
-    name: product_identification_method
-    description: 'The analytical method used to identify and/or quantify reaction
-      products.
-
-      Should reference a CharacterizationTechnique instance (e.g. a GCMS or
-
-      HPLC_MS object from coremeta4cat_characterization_ap). The abstract stub
-
-      ProductIdentificationMethod is retained for backward compatibility.'
-    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
-    slot_uri: coremeta4cat:product_identification_method
-    range: ProductIdentificationMethod
-    required: true
-    multivalued: true
-    inlined: true
-    inlined_as_list: true
   CatalysisDataset_rdf_type:
     name: CatalysisDataset_rdf_type
     definition_uri: https://w3id.org/nfdi-de/dcat-ap-plus/rdf_type
@@ -7442,6 +7447,7 @@ slots:
     inlined_as_list: true
   Reaction_product_identification_method:
     name: Reaction_product_identification_method
+    definition_uri: https://w3id.org/nfdi4cat/coremeta4cat/product_identification_method
     description: 'The analytical method used to identify and/or quantify reaction
       products.
 
@@ -7450,7 +7456,9 @@ slots:
       HPLC_MS object from coremeta4cat_characterization_ap). The abstract stub
 
       ProductIdentificationMethod is retained for backward compatibility.'
-    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
+    from_schema: https://w3id.org/nfdi4cat/coremeta4cat/reaction/
+    mappings:
+    - coremeta4cat:product_identification_method
     is_a: product_identification_method
     domain: Reaction
     slot_uri: coremeta4cat:product_identification_method
@@ -7511,7 +7519,6 @@ slots:
     usage_slot_name: realized_plan
     range: SimulationMethod
     required: true
-    multivalued: true
     inlined: true
     inlined_as_list: true
   Simulation_carried_out_by:
@@ -12192,12 +12199,12 @@ classes:
     - ClassifierMixin_type
     - evaluated_activity
     - occurred_in
+    - Characterization_equipment
     - sample_state
     - sample_description
     - sample_preparation
     - sample_pretreatment
     - detector_type
-    - Characterization_equipment
     - Characterization_evaluated_entity
     - Characterization_realized_plan
     - Characterization_rdf_type
@@ -12935,10 +12942,10 @@ classes:
     - experiment_pressure
     - feed_composition_range
     - experiment_duration
+    - Reaction_product_identification_method
     - Reaction_rdf_type
     - Reaction_carried_out_by
     - Reaction_had_input_entity
-    - Reaction_product_identification_method
     slot_usage:
       rdf_type:
         name: rdf_type
@@ -12972,12 +12979,9 @@ classes:
           HPLC_MS object from coremeta4cat_characterization_ap). The abstract stub
 
           ProductIdentificationMethod is retained for backward compatibility.'
-        from_schema: https://w3id.org/nfdi4cat/coremeta4cat
-        slot_uri: coremeta4cat:product_identification_method
         range: ProductIdentificationMethod
         required: true
         multivalued: true
-        inlined: true
         inlined_as_list: true
     class_uri: SIO:010345
   ProductIdentificationMethod:
@@ -13001,7 +13005,6 @@ classes:
     mappings:
     - OBI:0000272
     is_a: Plan
-    abstract: true
     slots:
     - title
     - description
@@ -13300,8 +13303,6 @@ classes:
         description: The SimulationMethod (protocol) realized in this Simulation.
         range: SimulationMethod
         required: true
-        multivalued: true
-        inlined_as_list: true
       carried_out_by:
         name: carried_out_by
         description: The simulation software used, provided as a Software agent instance.
@@ -17078,5 +17079,5 @@ metamodel_version: 1.7.0
 source_file: coremeta4cat.yaml
 source_file_date: '2026-03-09T16:14:14'
 source_file_size: 6730
-generation_date: '2026-03-09T17:32:19'
+generation_date: '2026-03-10T08:36:44'
 

src/coremeta4cat/datamodel/coremeta4cat.py

@@ -1,5 +1,5 @@
 # Auto generated from coremeta4cat.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-03-09T17:19:45
+# Generation date: 2026-03-10T09:36:20
 # Schema: coremeta4cat-metadata
 #
 # id: https://w3id.org/nfdi4cat/coremeta4cat
@@ -1572,7 +1572,7 @@ class Simulation(DataGeneratingActivity):
     id: Union[str, SimulationId] = None
     software_package: Union[str, list[str]] = None
     calculated_property: Union[Union[dict, "CalculatedProperty"], list[Union[dict, "CalculatedProperty"]]] = None
-    realized_plan: Union[Union[dict, "SimulationMethod"], list[Union[dict, "SimulationMethod"]]] = None
+    realized_plan: Union[dict, "SimulationMethod"] = None
     rdf_type: Optional[Union[dict, "DefinedTerm"]] = None
     carried_out_by: Optional[Union[dict[Union[str, AgenticEntityId], Union[dict, AgenticEntity]], list[Union[dict, AgenticEntity]]]] = empty_dict()
     evaluated_entity: Optional[Union[dict[Union[str, EvaluatedEntityId], Union[dict, "EvaluatedEntity"]], list[Union[dict, "EvaluatedEntity"]]]] = empty_dict()
@@ -1597,9 +1597,8 @@ def __post_init__(self, *_: str, **kwargs: Any):
 
         if self._is_empty(self.realized_plan):
             self.MissingRequiredField("realized_plan")
-        if not isinstance(self.realized_plan, list):
-            self.realized_plan = [self.realized_plan] if self.realized_plan is not None else []
-        self.realized_plan = [v if isinstance(v, SimulationMethod) else SimulationMethod(**as_dict(v)) for v in self.realized_plan]
+        if not isinstance(self.realized_plan, SimulationMethod):
+            self.realized_plan = SimulationMethod(**as_dict(self.realized_plan))
 
         if self.rdf_type is not None and not isinstance(self.rdf_type, DefinedTerm):
             self.rdf_type = DefinedTerm(**as_dict(self.rdf_type))
@@ -2579,8 +2578,8 @@ class Reaction(EvaluatedActivity):
     id: Union[str, ReactionId] = None
     catalyst_quantity: Union[float, list[float]] = None
     reactant: Union[str, list[str]] = None
-    carried_out_by: Union[dict[Union[str, ReactorDesignTypeId], Union[dict, ReactorDesignType]], list[Union[dict, ReactorDesignType]]] = empty_dict()
     product_identification_method: Union[Union[dict, "ProductIdentificationMethod"], list[Union[dict, "ProductIdentificationMethod"]]] = None
+    carried_out_by: Union[dict[Union[str, ReactorDesignTypeId], Union[dict, ReactorDesignType]], list[Union[dict, ReactorDesignType]]] = empty_dict()
     catalyst_type: Optional[Union[str, list[str]]] = empty_list()
     reactor_temperature_range: Optional[Union[str, list[str]]] = empty_list()
     atmosphere: Optional[Union[str, list[str]]] = empty_list()
@@ -2608,16 +2607,16 @@ def __post_init__(self, *_: str, **kwargs: Any):
             self.reactant = [self.reactant] if self.reactant is not None else []
         self.reactant = [v if isinstance(v, str) else str(v) for v in self.reactant]
 
-        if self._is_empty(self.carried_out_by):
-            self.MissingRequiredField("carried_out_by")
-        self._normalize_inlined_as_list(slot_name="carried_out_by", slot_type=ReactorDesignType, key_name="id", keyed=True)
-
         if self._is_empty(self.product_identification_method):
             self.MissingRequiredField("product_identification_method")
         if not isinstance(self.product_identification_method, list):
             self.product_identification_method = [self.product_identification_method] if self.product_identification_method is not None else []
         self.product_identification_method = [v if isinstance(v, ProductIdentificationMethod) else ProductIdentificationMethod(**as_dict(v)) for v in self.product_identification_method]
 
+        if self._is_empty(self.carried_out_by):
+            self.MissingRequiredField("carried_out_by")
+        self._normalize_inlined_as_list(slot_name="carried_out_by", slot_type=ReactorDesignType, key_name="id", keyed=True)
+
         if not isinstance(self.catalyst_type, list):
             self.catalyst_type = [self.catalyst_type] if self.catalyst_type is not None else []
         self.catalyst_type = [v if isinstance(v, str) else str(v) for v in self.catalyst_type]
@@ -9221,6 +9220,9 @@ class slots:
 slots.bubble_size_distribution = Slot(uri=COREMETA4CAT.bubble_size_distribution, name="bubble_size_distribution", curie=COREMETA4CAT.curie('bubble_size_distribution'),
                    model_uri=COREMETA4CAT.bubble_size_distribution, domain=None, range=Optional[str])
 
+slots.product_identification_method = Slot(uri=COREMETA4CAT.product_identification_method, name="product_identification_method", curie=COREMETA4CAT.curie('product_identification_method'),
+                   model_uri=COREMETA4CAT.product_identification_method, domain=None, range=Union[Union[dict, ProductIdentificationMethod], list[Union[dict, ProductIdentificationMethod]]])
+
 slots.software_package = Slot(uri=COREMETA4CAT.software_package, name="software_package", curie=COREMETA4CAT.curie('software_package'),
                    model_uri=COREMETA4CAT.software_package, domain=None, range=Union[str, list[str]])
 
@@ -9854,9 +9856,6 @@ class slots:
 slots.quantitativeAttribute__unit = Slot(uri=QUDT.unit, name="quantitativeAttribute__unit", curie=QUDT.curie('unit'),
                    model_uri=COREMETA4CAT.quantitativeAttribute__unit, domain=None, range=Optional[Union[str, DefinedTermId]])
 
-slots.product_identification_method = Slot(uri=COREMETA4CAT.product_identification_method, name="product_identification_method", curie=COREMETA4CAT.curie('product_identification_method'),
-                   model_uri=COREMETA4CAT.product_identification_method, domain=None, range=Union[Union[dict, ProductIdentificationMethod], list[Union[dict, ProductIdentificationMethod]]])
-
 slots.CatalysisDataset_rdf_type = Slot(uri=RDF.type, name="CatalysisDataset_rdf_type", curie=RDF.curie('type'),
                    model_uri=COREMETA4CAT.CatalysisDataset_rdf_type, domain=CatalysisDataset, range=Optional[Union[dict, "DefinedTerm"]])
 
@@ -9921,7 +9920,7 @@ class slots:
                    model_uri=COREMETA4CAT.Simulation_rdf_type, domain=Simulation, range=Optional[Union[dict, "DefinedTerm"]])
 
 slots.Simulation_realized_plan = Slot(uri=PROV.used, name="Simulation_realized_plan", curie=PROV.curie('used'),
-                   model_uri=COREMETA4CAT.Simulation_realized_plan, domain=Simulation, range=Union[Union[dict, "SimulationMethod"], list[Union[dict, "SimulationMethod"]]])
+                   model_uri=COREMETA4CAT.Simulation_realized_plan, domain=Simulation, range=Union[dict, "SimulationMethod"])
 
 slots.Simulation_carried_out_by = Slot(uri=PROV.wasAssociatedWith, name="Simulation_carried_out_by", curie=PROV.curie('wasAssociatedWith'),
                    model_uri=COREMETA4CAT.Simulation_carried_out_by, domain=Simulation, range=Optional[Union[dict[Union[str, AgenticEntityId], Union[dict, AgenticEntity]], list[Union[dict, AgenticEntity]]]])