Added test/example data

Author: HendrikBorgelt

docs/schema/catcore.yaml

@@ -1043,14 +1043,15 @@ slots:
     mappings:
     - voc4cat:0000187
     slot_uri: voc4cat:0000187
-    owner: Characterization
+    owner: ProductIdentificationMethod
     domain_of:
     - Solvothermal
     - PlasmaAssisted
     - CombustionSynthesis
     - MicrowaveAssisted
     - MechanochemicalSynthesis
     - Characterization
+    - ProductIdentificationMethod
     range: string
     multivalued: true
   stirring_speed:
@@ -6343,6 +6344,7 @@ classes:
     abstract: true
     slots:
     - identifier
+    - equipment
     class_uri: catcore:ProductIdentificationMethod
   Simulation:
     name: Simulation
@@ -6667,7 +6669,7 @@ classes:
     class_uri: catcore:BandGap
 metamodel_version: 1.7.0
 source_file: catcore.yaml
-source_file_date: '2025-12-11T12:55:52'
-source_file_size: 83282
-generation_date: '2025-12-11T12:57:46'
+source_file_date: '2025-12-11T14:29:28'
+source_file_size: 83313
+generation_date: '2025-12-11T14:32:11'
 

src/catcore/datamodel/catcore.py

@@ -1,5 +1,5 @@
 # Auto generated from catcore.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-12-11T12:56:00
+# Generation date: 2025-12-11T14:30:24
 # Schema: catcore-metadata
 #
 # id: https://w3id.org/nfdi4cat/catcore
@@ -3007,6 +3007,7 @@ def __post_init__(self, *_: str, **kwargs: Any):
         super().__post_init__(**kwargs)
 
 
+@dataclass(repr=False)
 class ProductIdentificationMethod(CatCoreEntity):
     """
     Method used for product identification
@@ -3018,6 +3019,15 @@ class ProductIdentificationMethod(CatCoreEntity):
     class_name: ClassVar[str] = "ProductIdentificationMethod"
     class_model_uri: ClassVar[URIRef] = CATCORE.ProductIdentificationMethod
 
+    equipment: Optional[Union[str, list[str]]] = empty_list()
+
+    def __post_init__(self, *_: str, **kwargs: Any):
+        if not isinstance(self.equipment, list):
+            self.equipment = [self.equipment] if self.equipment is not None else []
+        self.equipment = [v if isinstance(v, str) else str(v) for v in self.equipment]
+
+        super().__post_init__(**kwargs)
+
 
 @dataclass(repr=False)
 class Simulation(CatCoreEntity):

src/catcore/datamodel/catcore_pydantic.py

@@ -550,7 +550,8 @@ class Solvothermal(PreparationMethod):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     stirring_speed: Optional[list[float]] = Field(default=[], description="""Speed of stirring""", json_schema_extra = { "linkml_meta": {'domain_of': ['Solvothermal', 'MolecularSynthesis'],
          'slot_uri': 'catcore:stirring_speed',
@@ -575,7 +576,8 @@ class PlasmaAssisted(PreparationMethod):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     atmosphere: Optional[list[str]] = Field(default=[], description="""Atmospheric conditions""", json_schema_extra = { "linkml_meta": {'domain_of': ['PlasmaAssisted',
                        'CombustionSynthesis',
@@ -645,7 +647,8 @@ class CombustionSynthesis(PreparationMethod):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     identifier: Optional[str] = Field(default=None, description="""Unique identifier for the entity""", json_schema_extra = { "linkml_meta": {'domain_of': ['CatCoreEntity'], 'slot_uri': 'catcore:identifier'} })
 
@@ -811,7 +814,8 @@ class MicrowaveAssisted(PreparationMethod):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     power: Optional[list[float]] = Field(default=[], description="""Power setting""", json_schema_extra = { "linkml_meta": {'domain_of': ['MicrowaveAssisted'],
          'slot_uri': 'catcore:power',
@@ -994,7 +998,8 @@ class MechanochemicalSynthesis(PreparationMethod):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     vessel_volume: Optional[list[float]] = Field(default=[], description="""Volume of vessel""", json_schema_extra = { "linkml_meta": {'domain_of': ['MechanochemicalSynthesis'],
          'slot_uri': 'catcore:vessel_volume',
@@ -1229,7 +1234,8 @@ class Characterization(CatCoreEntity):
                        'CombustionSynthesis',
                        'MicrowaveAssisted',
                        'MechanochemicalSynthesis',
-                       'Characterization'],
+                       'Characterization',
+                       'ProductIdentificationMethod'],
          'slot_uri': 'voc4cat:0000187'} })
     characterization_technique: list[CharacterizationTechnique] = Field(default=..., description="""Technique used for characterization""", json_schema_extra = { "linkml_meta": {'domain_of': ['Characterization'], 'slot_uri': 'voc4cat:0000066'} })
     sample_state: Optional[list[SampleStateEnum]] = Field(default=[], description="""State of the sample""", json_schema_extra = { "linkml_meta": {'domain_of': ['Characterization'], 'slot_uri': 'catcore:sample_state'} })
@@ -2569,6 +2575,14 @@ class ProductIdentificationMethod(CatCoreEntity):
     """
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'https://w3id.org/nfdi4cat/catcore'})
 
+    equipment: Optional[list[str]] = Field(default=[], description="""Equipment used""", json_schema_extra = { "linkml_meta": {'domain_of': ['Solvothermal',
+                       'PlasmaAssisted',
+                       'CombustionSynthesis',
+                       'MicrowaveAssisted',
+                       'MechanochemicalSynthesis',
+                       'Characterization',
+                       'ProductIdentificationMethod'],
+         'slot_uri': 'voc4cat:0000187'} })
     identifier: Optional[str] = Field(default=None, description="""Unique identifier for the entity""", json_schema_extra = { "linkml_meta": {'domain_of': ['CatCoreEntity'], 'slot_uri': 'catcore:identifier'} })
 
 

src/catcore/schema/catcore.yaml

@@ -823,6 +823,8 @@ classes:
   ProductIdentificationMethod:
     is_a: CatCoreEntity
     description: Method used for product identification
+    slots:
+      - equipment
     abstract: true
 
   # ==================== SIMULATION ====================

…ts/data/valid/characterization_test.yaml …sts/data/valid/Characterization-001.yamltests/data/valid/characterization_test.yaml renamed to tests/data/valid/Characterization-001.yaml tests/data/valid/characterization_test.yaml renamed to tests/data/valid/Characterization-001.yaml

@@ -5,16 +5,15 @@
 identifier: "CHAR_001_Pt_Al2O3"
 equipment: ["Bruker D8 Advance diffractometer", "Thermo Scientific K-Alpha XPS", "Micromeritics ASAP 2020"]
 sample_state: ["powder"]
-sample_description: ["5 wt% Pt/Al2O3 catalyst after calcination at 450°C"]
+sample_description: ["5 wt% Pt/Al2O3 catalyst after calcination at 450C"]
 detector_type: ["Lynxeye detector", "hemispherical analyzer", "thermal conductivity detector"]
 sample_preparation: ["pressed into sample holder without binder", "mounted on carbon tape", "degassed under vacuum"]
-sample_pretreatment: ["calcined at 450°C for 4 hours", "none", "degassed at 300°C for 6 hours"]
+sample_pretreatment: ["calcined at 450C for 4 hours", "none", "degassed at 300C for 6 hours"]
 
 characterization_technique:
   # Powder XRD
   - identifier: "CHAR_TECH_001"
-    class_uri: "CHMO:0000158"
-    xray_source: ["Cu Kα (λ = 1.5406 Å)"]
+    xray_source: ["Cu Kalpha (lambda = 1.5406 A)"]
     atmosphere: ["ambient air"]
     operation_mode: ["continuous scan"]
     minimum_2theta: [10.0]  # degrees
@@ -27,8 +26,7 @@ characterization_technique:
 
   # XPS
   - identifier: "CHAR_TECH_002"
-    class_uri: "CHMO:0000404"
-    xray_source: ["Al Kα (1486.6 eV)"]
+    xray_source: ["Al Kalpha (1486.6 eV)"]
     total_acquisition_time: [1800.0]  # seconds
     number_of_scans: [10]
     spot_size: [400.0]  # micrometers
@@ -38,27 +36,19 @@ characterization_technique:
     step_size: [0.1]  # eV
     pass_energy: [50.0]  # eV
     charge_compensation: ["flood gun, 1.0 eV electrons"]
-    atmosphere: ["ultra-high vacuum, 2×10⁻⁹ mbar"]
-    temperature: [25.0]  # Celsius
+    atmosphere: ["ultra-high vacuum, 2x10-9 mbar"]
 
   # BET Surface Area
   - identifier: "CHAR_TECH_003"
-    class_uri: "catcore:BET"
     adsorbate_gas: ["N2"]
     degassing_temperature: [300.0]  # Celsius
     measurement_temperature: [77.0]  # Kelvin
     pore_size_distribution_method: ["BJH method from desorption branch"]
     sample_mass: [150.0]  # mg
-    atmosphere: ["nitrogen"]
-    temperature: [-196.0]  # Celsius (liquid N2)
 
   # Temperature Programmed Reduction
   - identifier: "CHAR_TECH_004"
-    class_uri: "CHMO:0002908"
     reducing_gas_composition: ["5% H2/Ar"]
     heating_rate: [10.0]  # Celsius/min
     minimum_temperature: [50.0]  # Celsius
     maximum_temperature: [800.0]  # Celsius
-    flow_rate: [50.0]  # mL/min
-    sample_mass: [50.0]  # mg
-    detector_type: ["thermal conductivity detector"]

tests/data/valid/reaction_test.yaml tests/data/valid/Reaction-001.yamltests/data/valid/reaction_test.yaml renamed to tests/data/valid/Reaction-001.yaml

@@ -8,8 +8,6 @@ catalyst_type: ["5 wt% Pt/Al2O3, 250-355 μm sieve fraction"]
 
 reactor_design_type:
   - identifier: "REACTOR_001"
-    class_uri: "catcore:FixedBedReactor"
-
 reactant: 
   - "CO (1000 ppm)"
   - "O2 (5 vol%)"
@@ -22,19 +20,17 @@ operation_parameters:
     experiment_pressure: [1.0]  # bar (atmospheric)
     feed_composition_range: ["CO: 1000 ppm, O2: 5 vol%, N2: balance"]
     experiment_duration: [8.0]  # hours
-    flow_rate: [100.0]  # mL/min (total flow)
 
 product_identification_method:
   - identifier: "PROD_ID_001"
-    class_uri: "CHMO:0000497"
     equipment: ["Agilent 7890B GC with TCD and FID"]
-    column_type: ["HP-PLOT Q column, 30 m × 0.32 mm × 20 μm"]
-    carrier_gas: ["helium"]
-    carrier_gas_purity: ["99.999%"]
-    inlet_temperature: [200.0]  # Celsius
-    detector_type: ["thermal conductivity detector (TCD)", "flame ionization detector (FID)"]
-    minimum_oven_temperature: [40.0]  # Celsius
-    maximum_oven_temperature: [250.0]  # Celsius
-    heating_ramp: [10.0]  # Celsius/min
-    external_standard: ["CO calibration gas 1000 ppm"]
-    internal_standard: ["CH4 100 ppm"]
+#     column_type: ["HP-PLOT Q column, 30 m × 0.32 mm × 20 μm"]
+#     carrier_gas: ["helium"]
+#     carrier_gas_purity: ["99.999%"]
+#     inlet_temperature: [200.0]  # Celsius
+#     detector_type: ["thermal conductivity detector (TCD)", "flame ionization detector (FID)"]
+#     minimum_oven_temperature: [40.0]  # Celsius
+#     maximum_oven_temperature: [250.0]  # Celsius
+#     heating_ramp: [10.0]  # Celsius/min
+#     external_standard: ["CO calibration gas 1000 ppm"]
+#     internal_standard: ["CH4 100 ppm"]

tests/data/valid/simulation_test.yaml tests/data/valid/Simulation-001.yamltests/data/valid/simulation_test.yaml renamed to tests/data/valid/Simulation-001.yaml

@@ -7,44 +7,35 @@ software_package: ["VASP 6.3.0", "ASE 3.22.1"]
 
 simulation_method:
   - identifier: "SIM_METHOD_001"
-    class_uri: "catcore:DFT"
     exchange_correlation_functional: ["PBE (Perdew-Burke-Ernzerhof)"]
     energy_cutoff: [450.0]  # eV
-    convergence_criteria: ["energy: 1×10⁻⁵ eV, forces: 0.02 eV/Å"]
+    convergence_criteria: ["energy: 1x10-5 eV, forces: 0.02 eV/A"]
     dft_u_parameters: ["not applied"]
     spin_polarization: [true]
     total_energy_per_atom: [-5.234]  # eV
-    k_point_mesh: ["5×5×1 Monkhorst-Pack"]
-    smearing_method: ["Methfessel-Paxton, sigma=0.2 eV"]
 
 calculated_property:
   # Surface properties
   - identifier: "CALC_PROP_001"
-    class_uri: "catcore:Surfaces"
     surface_energy: [0.089]  # J/m²
     miller_indices: ["(111)"]
     slab_thickness: [12.75]  # Angstrom (5 layers)
     vacuum_spacing: [15.0]  # Angstrom
     surface_termination_method: ["symmetric, both surfaces Pt-terminated"]
-    material_composition: ["Pt"]
-    crystal_structure: ["fcc, a = 3.92 Å"]
 
   # Electronic structure
   - identifier: "CALC_PROP_002"
-    class_uri: "catcore:ElectronicStructure"
     material_composition: ["Pt(111) surface with adsorbed CO"]
     crystal_structure: ["fcc Pt substrate"]
-    k_point_mesh: ["5×5×1 for surface calculations"]
+    k_point_mesh: ["5x5x1 for surface calculations"]
     energy_cutoff: [450.0]  # eV
     smearing_method: ["Methfessel-Paxton, sigma=0.2 eV"]
     spin_polarized: [true]
-    band_path: ["Γ-M-K-Γ"]
+    band_path: ["|-M-K-|"]
     fermi_energy: [5.42]  # eV
-    convergence_criteria: ["SCF: 1×10⁻⁶ eV"]
 
   # Adsorption energies (as additional property)
   - identifier: "CALC_PROP_003"
-    class_uri: "catcore:ThermodynamicStability"
     formation_energy: [-1.68]  # eV (CO adsorption energy)
     reference_energies: ["E(Pt_slab) = -261.70 eV, E(CO_gas) = -14.84 eV, E(Pt_slab+CO) = -278.22 eV"]
     energy_above_hull: [0.0]  # eV (most stable configuration)

tests/data/valid/synthesis_test.yaml tests/data/valid/Synthesis-001.yamltests/data/valid/synthesis_test.yaml renamed to tests/data/valid/Synthesis-001.yaml

@@ -12,7 +12,6 @@ precursor:
 
 preparation_method:
   - identifier: "PREP_001"
-    class_uri: "catcore:Impregnation"
     impregnation_type: ["wet_impregnation"]
     impregnation_duration: [4.0]  # hours
     impregnation_temperature: [25.0]  # Celsius