API update

datamodel_b07_tc/__init__.py

@@ -1,3 +1,3 @@
 
 __URL__ = "https://github.com/FAIRChemistry/datamodel_b07_tc.git"
-__COMMIT__ = "e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+__COMMIT__ = "0120803a8da7ad13c94e37b6f74dea33a9915fb8"

datamodel_b07_tc/core/author.py

@@ -29,5 +29,5 @@ class Author(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/calibration.py

@@ -47,5 +47,5 @@ class Calibration(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/chemical.py

@@ -6,8 +6,8 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .stoichiometry import Stoichiometry
 from .reactantrole import ReactantRole
+from .stoichiometry import Stoichiometry
 
 
 @forge_signature
@@ -65,5 +65,5 @@ class Chemical(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/data.py

@@ -5,8 +5,8 @@
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature, IDGenerator
 
-from astropy.units import UnitBase
 from datetime import datetime as Datetime
+from astropy.units import UnitBase
 
 from .quantity import Quantity
 
@@ -41,5 +41,5 @@ class Data(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/dataset.py

@@ -6,10 +6,10 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .speciesdata import SpeciesData
-from .generalinformation import GeneralInformation
 from .measurement import Measurement
 from .experiment import Experiment
+from .generalinformation import GeneralInformation
+from .speciesdata import SpeciesData
 from .plantsetup import PlantSetup
 
 
@@ -38,14 +38,14 @@ class Dataset(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_experiments(
         self,
         plant_setup: Optional[PlantSetup] = None,
         measurements: List[Measurement] = ListPlus(),
-        species_data: Optional[SpeciesData] = None,
+        species_data: List[SpeciesData] = ListPlus(),
         id: Optional[str] = None,
     ) -> None:
         """
@@ -55,7 +55,7 @@ def add_to_experiments(
             id (str): Unique identifier of the 'Experiment' object. Defaults to 'None'.
             plant_setup (): the individual plant setup that is used in this one experiment.. Defaults to None
             measurements (): different measurements that are made within the scope of one experiment.. Defaults to ListPlus()
-            species_data (): all provided and calculated data about a specific species.. Defaults to None
+            species_data (): all provided and calculated data about a specific species.. Defaults to ListPlus()
         """
 
         params = {

datamodel_b07_tc/core/device.py

@@ -39,5 +39,5 @@ class Device(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/experiment.py

@@ -6,12 +6,15 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .speciesdata import SpeciesData
 from .metadata import Metadata
 from .measurement import Measurement
+from .species import Species
 from .measurementtype import MeasurementType
+from .speciesdata import SpeciesData
 from .data import Data
 from .plantsetup import PlantSetup
+from .calibration import Calibration
+from .chemicalformula import ChemicalFormula
 
 
 @forge_signature
@@ -37,16 +40,17 @@ class Experiment(sdRDM.DataModel):
         ),
     )
 
-    species_data: Optional[SpeciesData] = Field(
-        default=SpeciesData(),
+    species_data: List[SpeciesData] = Field(
+        default_factory=ListPlus,
+        multiple=True,
         description="all provided and calculated data about a specific species.",
     )
 
     __repo__: Optional[str] = PrivateAttr(
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_measurements(
@@ -78,3 +82,42 @@ def add_to_measurements(
         self.measurements.append(Measurement(**params))
 
         return self.measurements[-1]
+
+    def add_to_species_data(
+        self,
+        species: Optional[Species] = None,
+        chemical_formula: Optional[ChemicalFormula] = None,
+        calibration: Optional[Calibration] = None,
+        correction_factor: Optional[Data] = None,
+        faraday_coefficient: Optional[Data] = None,
+        faraday_efficiency: Optional[Data] = None,
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'SpeciesData' to attribute species_data
+
+        Args:
+            id (str): Unique identifier of the 'SpeciesData' object. Defaults to 'None'.
+            species (): name of the species.. Defaults to None
+            chemical_formula (): chemical formula of the species.. Defaults to None
+            calibration (): calibration measurement.. Defaults to None
+            correction_factor (): correction factors of the individual species.. Defaults to None
+            faraday_coefficient (): Faraday coefficients of the individual species.. Defaults to None
+            faraday_efficiency (): Faraday efficiencies of the individual species.. Defaults to None
+        """
+
+        params = {
+            "species": species,
+            "chemical_formula": chemical_formula,
+            "calibration": calibration,
+            "correction_factor": correction_factor,
+            "faraday_coefficient": faraday_coefficient,
+            "faraday_efficiency": faraday_efficiency,
+        }
+
+        if id is not None:
+            params["id"] = id
+
+        self.species_data.append(SpeciesData(**params))
+
+        return self.species_data[-1]

datamodel_b07_tc/core/generalinformation.py

@@ -39,7 +39,7 @@ class GeneralInformation(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_authors(

datamodel_b07_tc/core/input.py

@@ -7,8 +7,8 @@
 
 
 from .stoichiometry import Stoichiometry
-from .chemical import Chemical
 from .reactantrole import ReactantRole
+from .chemical import Chemical
 
 
 @forge_signature
@@ -31,7 +31,7 @@ class Input(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_component(

datamodel_b07_tc/core/insulation.py

@@ -32,5 +32,5 @@ class Insulation(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/massflowmeter.py

@@ -4,8 +4,8 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .device import Device
 from .parameter import Parameter
+from .device import Device
 
 
 @forge_signature
@@ -32,5 +32,5 @@ class MassFlowMeter(Device):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/measurement.py

@@ -5,14 +5,14 @@
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature, IDGenerator
 
-from astropy.units import UnitBase
 from datetime import datetime as Datetime
+from astropy.units import UnitBase
 
-from .quantity import Quantity
 from .metadata import Metadata
+from .quantity import Quantity
+from .measurementtype import MeasurementType
 from .data import Data
 from .datatype import DataType
-from .measurementtype import MeasurementType
 
 
 @forge_signature
@@ -46,7 +46,7 @@ class Measurement(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_metadata(

datamodel_b07_tc/core/metadata.py

@@ -4,8 +4,8 @@
 from pydantic import Field, PrivateAttr
 from sdRDM.base.utils import forge_signature, IDGenerator
 
-from astropy.units import UnitBase
 from datetime import datetime as Datetime
+from astropy.units import UnitBase
 
 from .datatype import DataType
 
@@ -59,5 +59,5 @@ class Metadata(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/output.py

@@ -7,8 +7,8 @@
 
 
 from .stoichiometry import Stoichiometry
-from .chemical import Chemical
 from .reactantrole import ReactantRole
+from .chemical import Chemical
 
 
 @forge_signature
@@ -31,7 +31,7 @@ class Output(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_component(

datamodel_b07_tc/core/parameter.py

@@ -31,5 +31,5 @@ class Parameter(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/plantsetup.py

@@ -6,12 +6,12 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
+from .device import Device
+from .output import Output
 from .tubing import Tubing
 from .input import Input
-from .insulation import Insulation
-from .output import Output
-from .device import Device
 from .chemical import Chemical
+from .insulation import Insulation
 from .material import Material
 
 
@@ -53,7 +53,7 @@ class PlantSetup(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
 
     def add_to_devices(

datamodel_b07_tc/core/potentiostat.py

@@ -5,8 +5,8 @@
 
 
 from .metadata import Metadata
-from .measurement import Measurement
 from .device import Device
+from .measurement import Measurement
 
 
 @forge_signature
@@ -33,5 +33,5 @@ class Potentiostat(Device):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/pump.py

@@ -4,8 +4,8 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .device import Device
 from .pumptype import PumpType
+from .device import Device
 
 
 @forge_signature
@@ -27,5 +27,5 @@ class Pump(Device):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/speciesdata.py

@@ -5,10 +5,10 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .calibration import Calibration
-from .chemicalformula import ChemicalFormula
 from .data import Data
 from .species import Species
+from .calibration import Calibration
+from .chemicalformula import ChemicalFormula
 
 
 @forge_signature
@@ -55,5 +55,5 @@ class SpeciesData(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/stoichiometry.py

@@ -59,5 +59,5 @@ class Stoichiometry(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )

datamodel_b07_tc/core/thermocouple.py

@@ -27,5 +27,5 @@ class Thermocouple(Device):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )