From ec6567e40d7a9aa12c0dd5c4e55a2840e649abed Mon Sep 17 00:00:00 2001
From: sdRDM Bot <sdRDM@bot.com>
Date: Mon, 18 Sep 2023 17:30:14 +0000
Subject: [PATCH] API update

---
 datamodel_b07_tc/__init__.py                  |  2 +-
 datamodel_b07_tc/core/author.py               |  2 +-
 datamodel_b07_tc/core/calibration.py          |  2 +-
 datamodel_b07_tc/core/chemical.py             |  4 +-
 datamodel_b07_tc/core/data.py                 |  4 +-
 datamodel_b07_tc/core/dataset.py              | 10 ++--
 datamodel_b07_tc/core/device.py               |  2 +-
 datamodel_b07_tc/core/experiment.py           | 51 +++++++++++++++++--
 datamodel_b07_tc/core/generalinformation.py   |  2 +-
 datamodel_b07_tc/core/input.py                |  4 +-
 datamodel_b07_tc/core/insulation.py           |  2 +-
 datamodel_b07_tc/core/massflowmeter.py        |  4 +-
 datamodel_b07_tc/core/measurement.py          |  8 +--
 datamodel_b07_tc/core/metadata.py             |  4 +-
 datamodel_b07_tc/core/output.py               |  4 +-
 datamodel_b07_tc/core/parameter.py            |  2 +-
 datamodel_b07_tc/core/plantsetup.py           |  8 +--
 datamodel_b07_tc/core/potentiostat.py         |  4 +-
 datamodel_b07_tc/core/pump.py                 |  4 +-
 datamodel_b07_tc/core/speciesdata.py          |  6 +--
 datamodel_b07_tc/core/stoichiometry.py        |  2 +-
 datamodel_b07_tc/core/thermocouple.py         |  2 +-
 datamodel_b07_tc/core/tubing.py               |  4 +-
 .../schemes/datamodel_b07_tc_schema.md        |  2 +-
 24 files changed, 91 insertions(+), 48 deletions(-)

diff --git a/datamodel_b07_tc/__init__.py b/datamodel_b07_tc/__init__.py
index 6ae5b39..0f22ae3 100644
--- a/datamodel_b07_tc/__init__.py
+++ b/datamodel_b07_tc/__init__.py
@@ -1,3 +1,3 @@
 
 __URL__ = "https://github.com/FAIRChemistry/datamodel_b07_tc.git"
-__COMMIT__ = "e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+__COMMIT__ = "0120803a8da7ad13c94e37b6f74dea33a9915fb8"
diff --git a/datamodel_b07_tc/core/author.py b/datamodel_b07_tc/core/author.py
index 712efb9..c4c794f 100644
--- a/datamodel_b07_tc/core/author.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/calibration.py b/datamodel_b07_tc/core/calibration.py
index 59dcb00..53dbda3 100644
--- a/datamodel_b07_tc/core/calibration.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/chemical.py b/datamodel_b07_tc/core/chemical.py
index c599ff3..ccb1958 100644
--- a/datamodel_b07_tc/core/chemical.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/data.py b/datamodel_b07_tc/core/data.py
index 6c127f9..4106044 100644
--- a/datamodel_b07_tc/core/data.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/dataset.py b/datamodel_b07_tc/core/dataset.py
index c5e08ed..12ca605 100644
--- a/datamodel_b07_tc/core/dataset.py
+++ b/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 = {
diff --git a/datamodel_b07_tc/core/device.py b/datamodel_b07_tc/core/device.py
index f844ee2..7412936 100644
--- a/datamodel_b07_tc/core/device.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/experiment.py b/datamodel_b07_tc/core/experiment.py
index 256c673..595891b 100644
--- a/datamodel_b07_tc/core/experiment.py
+++ b/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
@@ -37,8 +40,9 @@ 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.",
     )
 
@@ -46,7 +50,7 @@ class Experiment(sdRDM.DataModel):
         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]
diff --git a/datamodel_b07_tc/core/generalinformation.py b/datamodel_b07_tc/core/generalinformation.py
index 5503af0..c20060d 100644
--- a/datamodel_b07_tc/core/generalinformation.py
+++ b/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(
diff --git a/datamodel_b07_tc/core/input.py b/datamodel_b07_tc/core/input.py
index 317b66c..1aa01bf 100644
--- a/datamodel_b07_tc/core/input.py
+++ b/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(
diff --git a/datamodel_b07_tc/core/insulation.py b/datamodel_b07_tc/core/insulation.py
index 2e25bd9..21d143f 100644
--- a/datamodel_b07_tc/core/insulation.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/massflowmeter.py b/datamodel_b07_tc/core/massflowmeter.py
index 4e74fdf..532af3e 100644
--- a/datamodel_b07_tc/core/massflowmeter.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/measurement.py b/datamodel_b07_tc/core/measurement.py
index 961681e..695a365 100644
--- a/datamodel_b07_tc/core/measurement.py
+++ b/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(
diff --git a/datamodel_b07_tc/core/metadata.py b/datamodel_b07_tc/core/metadata.py
index 7c3a63c..1230343 100644
--- a/datamodel_b07_tc/core/metadata.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/output.py b/datamodel_b07_tc/core/output.py
index 0c37cd4..bb743c6 100644
--- a/datamodel_b07_tc/core/output.py
+++ b/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(
diff --git a/datamodel_b07_tc/core/parameter.py b/datamodel_b07_tc/core/parameter.py
index 8d60609..984fa09 100644
--- a/datamodel_b07_tc/core/parameter.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/plantsetup.py b/datamodel_b07_tc/core/plantsetup.py
index ac3e387..98d12ef 100644
--- a/datamodel_b07_tc/core/plantsetup.py
+++ b/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(
diff --git a/datamodel_b07_tc/core/potentiostat.py b/datamodel_b07_tc/core/potentiostat.py
index 43bf9d8..6b18782 100644
--- a/datamodel_b07_tc/core/potentiostat.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/pump.py b/datamodel_b07_tc/core/pump.py
index 048a0d3..f65c002 100644
--- a/datamodel_b07_tc/core/pump.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/speciesdata.py b/datamodel_b07_tc/core/speciesdata.py
index 73f65a1..d0c3fb8 100644
--- a/datamodel_b07_tc/core/speciesdata.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/stoichiometry.py b/datamodel_b07_tc/core/stoichiometry.py
index 04ccaec..0094cd7 100644
--- a/datamodel_b07_tc/core/stoichiometry.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/thermocouple.py b/datamodel_b07_tc/core/thermocouple.py
index 7a07404..a08f78d 100644
--- a/datamodel_b07_tc/core/thermocouple.py
+++ b/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"
     )
diff --git a/datamodel_b07_tc/core/tubing.py b/datamodel_b07_tc/core/tubing.py
index 5b1caf6..1bd2158 100644
--- a/datamodel_b07_tc/core/tubing.py
+++ b/datamodel_b07_tc/core/tubing.py
@@ -5,8 +5,8 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 
 
-from .material import Material
 from .insulation import Insulation
+from .material import Material
 
 
 @forge_signature
@@ -48,5 +48,5 @@ class Tubing(sdRDM.DataModel):
         default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
     )
     __commit__: Optional[str] = PrivateAttr(
-        default="e5e1710ac1f9b36c9f229d0f0d69a96a081365ba"
+        default="0120803a8da7ad13c94e37b6f74dea33a9915fb8"
     )
diff --git a/datamodel_b07_tc/schemes/datamodel_b07_tc_schema.md b/datamodel_b07_tc/schemes/datamodel_b07_tc_schema.md
index 0d138f0..c899f20 100644
--- a/datamodel_b07_tc/schemes/datamodel_b07_tc_schema.md
+++ b/datamodel_b07_tc/schemes/datamodel_b07_tc_schema.md
@@ -56,7 +56,7 @@ classDiagram
     class Experiment {
         +PlantSetup plant_setup
         +Measurement[0..*] measurements
-        +SpeciesData species_data
+        +SpeciesData[0..*] species_data
     }
     
     class PlantSetup {