update gitignore

.gitignore

@@ -20,7 +20,7 @@ datasets/*
 *.pyc
 
 # generated python objects
-datamodel_b07_tc/core
+# datamodel_b07_tc/core
 
 # compiled bython files
 datamodel_b07_tc/__pycache__

datamodel_b07_tc/core/__init__.py

@@ -0,0 +1,69 @@
+from .dataset import Dataset
+from .generalinformation import GeneralInformation
+from .author import Author
+from .experiment import Experiment
+from .plantsetup import PlantSetup
+from .device import Device
+from .pump import Pump
+from .thermocouple import Thermocouple
+from .massflowmeter import MassFlowMeter
+from .parameter import Parameter
+from .potentiostat import Potentiostat
+from .tubing import Tubing
+from .insulation import Insulation
+from .input import Input
+from .output import Output
+from .chemical import Chemical
+from .stoichiometry import Stoichiometry
+from .data import Data
+from .metadata import Metadata
+from .measurement import Measurement
+from .speciesdata import SpeciesData
+from .calibration import Calibration
+from .datatype import DataType
+from .thermocoupletype import ThermocoupleType
+from .material import Material
+from .pumptype import PumpType
+from .reactantrole import ReactantRole
+from .devicelist import DeviceList
+from .quantity import Quantity
+from .measurementtype import MeasurementType
+from .species import Species
+from .chemicalformula import ChemicalFormula
+
+__doc__ = ""
+
+__all__ = [
+    "Dataset",
+    "GeneralInformation",
+    "Author",
+    "Experiment",
+    "PlantSetup",
+    "Device",
+    "Pump",
+    "Thermocouple",
+    "MassFlowMeter",
+    "Parameter",
+    "Potentiostat",
+    "Tubing",
+    "Insulation",
+    "Input",
+    "Output",
+    "Chemical",
+    "Stoichiometry",
+    "Data",
+    "Metadata",
+    "Measurement",
+    "SpeciesData",
+    "Calibration",
+    "DataType",
+    "ThermocoupleType",
+    "Material",
+    "PumpType",
+    "ReactantRole",
+    "DeviceList",
+    "Quantity",
+    "MeasurementType",
+    "Species",
+    "ChemicalFormula",
+]

datamodel_b07_tc/core/analysis.py

@@ -0,0 +1,113 @@
+import sdRDM
+
+from typing import Optional, Union, List
+from pydantic import Field, PrivateAttr
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+from datetime import datetime as Datetime
+from astropy.units import UnitBase
+
+from .quantity import Quantity
+from .data import Data
+from .species import Species
+from .calibration import Calibration
+
+
+@forge_signature
+class Analysis(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("analysisINDEX"),
+        xml="@id",
+    )
+
+    calibrations: List[Calibration] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description="Calibration measurement.",
+    )
+
+    faraday_coefficients: List[Data] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description="Faraday coefficients.",
+    )
+
+    __repo__: Optional[str] = PrivateAttr(
+        default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
+    )
+    __commit__: Optional[str] = PrivateAttr(
+        default="a4c50b26815a02cca2986380d5aeb8c023e877eb"
+    )
+
+    def add_to_calibrations(
+        self,
+        species: Optional[Species] = None,
+        peak_areas: Optional[Data] = None,
+        concentrations: Optional[Data] = None,
+        slope: Optional[Data] = None,
+        intercept: Optional[Data] = None,
+        coefficient_of_determination: Optional[Data] = None,
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Calibration' to attribute calibrations
+
+        Args:
+            id (str): Unique identifier of the 'Calibration' object. Defaults to 'None'.
+            species (): Species for which the calibration was performed.. Defaults to None
+            peak_areas (): Recorded peak areas of the individual calibration solutions.. Defaults to None
+            concentrations (): concentrations of the individual calibration solutions.. Defaults to None
+            slope (): slopes of the (linear) calibration functions.. Defaults to None
+            intercept (): intercept of the (linear) calibration functions.. Defaults to None
+            coefficient_of_determination (): coefficients of the (linear) calibration functions.. Defaults to None
+        """
+
+        params = {
+            "species": species,
+            "peak_areas": peak_areas,
+            "concentrations": concentrations,
+            "slope": slope,
+            "intercept": intercept,
+            "coefficient_of_determination": coefficient_of_determination,
+        }
+
+        if id is not None:
+            params["id"] = id
+
+        self.calibrations.append(Calibration(**params))
+
+        return self.calibrations[-1]
+
+    def add_to_faraday_coefficients(
+        self,
+        quantity: Optional[Quantity] = None,
+        values: List[Union[float, str, Datetime]] = ListPlus(),
+        unit: Optional[UnitBase] = None,
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Data' to attribute faraday_coefficients
+
+        Args:
+            id (str): Unique identifier of the 'Data' object. Defaults to 'None'.
+            quantity (): quantity of a value.. Defaults to None
+            values (): values.. Defaults to ListPlus()
+            unit (): unit of the values.. Defaults to None
+        """
+
+        params = {
+            "quantity": quantity,
+            "values": values,
+            "unit": unit,
+        }
+
+        if id is not None:
+            params["id"] = id
+
+        self.faraday_coefficients.append(Data(**params))
+
+        return self.faraday_coefficients[-1]

datamodel_b07_tc/core/author.py

@@ -0,0 +1,33 @@
+import sdRDM
+
+from typing import Optional
+from pydantic import Field, PrivateAttr
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+@forge_signature
+class Author(sdRDM.DataModel):
+    """This is another object that represents the author of the dataset. Please note, that the options here contain all required fields but also custom ones. In this example, the ```Dataverse``` option specifies where each field should be mapped, when exported to a Dataverse format. Hence, these options allow you to link your dataset towards any other data model without writing code by yourself."""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("authorINDEX"),
+        xml="@id",
+    )
+
+    name: Optional[str] = Field(
+        default=None,
+        description="full name including given and family name.",
+    )
+
+    affiliation: Optional[str] = Field(
+        default=None,
+        description="organization the author is affiliated to.",
+    )
+
+    __repo__: Optional[str] = PrivateAttr(
+        default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
+    )
+    __commit__: Optional[str] = PrivateAttr(
+        default="84c47e3b42d9bd24447f9f5668612ba7a70e39c3"
+    )

datamodel_b07_tc/core/calibration.py

@@ -0,0 +1,51 @@
+import sdRDM
+
+from typing import Optional
+from pydantic import Field, PrivateAttr
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+from .data import Data
+
+
+@forge_signature
+class Calibration(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("calibrationINDEX"),
+        xml="@id",
+    )
+
+    peak_areas: Optional[Data] = Field(
+        default=Data(),
+        description="Recorded peak areas of the individual calibration solutions.",
+    )
+
+    concentrations: Optional[Data] = Field(
+        default=Data(),
+        description="concentrations of the individual calibration solutions.",
+    )
+
+    slope: Optional[Data] = Field(
+        default=Data(),
+        description="slopes of the (linear) calibration functions.",
+    )
+
+    intercept: Optional[Data] = Field(
+        default=Data(),
+        description="intercept of the (linear) calibration functions.",
+    )
+
+    coefficient_of_determination: Optional[Data] = Field(
+        default=Data(),
+        description="coefficients of the (linear) calibration functions.",
+    )
+
+    __repo__: Optional[str] = PrivateAttr(
+        default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
+    )
+    __commit__: Optional[str] = PrivateAttr(
+        default="84c47e3b42d9bd24447f9f5668612ba7a70e39c3"
+    )

datamodel_b07_tc/core/chemical.py

@@ -0,0 +1,69 @@
+import sdRDM
+
+from typing import List, Optional
+from pydantic import Field, PrivateAttr
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+from .stoichiometry import Stoichiometry
+from .reactantrole import ReactantRole
+
+
+@forge_signature
+class Chemical(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("chemicalINDEX"),
+        xml="@id",
+    )
+
+    name: List[str] = Field(
+        description="IUPAC name of the compound.",
+        default_factory=ListPlus,
+        multiple=True,
+    )
+
+    formula: Optional[str] = Field(
+        default=None,
+        description="molecular formula of the compound.",
+    )
+
+    pureness: Optional[float] = Field(
+        default=None,
+        description="pureness of the compound in percent.",
+    )
+
+    supplier: Optional[str] = Field(
+        default=None,
+        description="name of the supplier of the compound.",
+    )
+
+    stoichiometry: Optional[Stoichiometry] = Field(
+        default=Stoichiometry(),
+        description=(
+            "stoichiometric information like equivalents, mass, amount of substance,"
+            " volume"
+        ),
+    )
+
+    state_of_matter: Optional[str] = Field(
+        default=None,
+        description="s for solid, l for liquid and g for gaseous",
+    )
+
+    reactant_role: Optional[ReactantRole] = Field(
+        default=None,
+        description=(
+            "Role that a reactand plays in a chemical reaction or  in a process."
+        ),
+    )
+
+    __repo__: Optional[str] = PrivateAttr(
+        default="https://github.com/FAIRChemistry/datamodel_b07_tc.git"
+    )
+    __commit__: Optional[str] = PrivateAttr(
+        default="84c47e3b42d9bd24447f9f5668612ba7a70e39c3"
+    )

datamodel_b07_tc/core/chemicalformula.py

@@ -0,0 +1,10 @@
+from enum import Enum
+
+
+class ChemicalFormula(Enum):
+    H2 = "H2"
+    CO2 = "CO2"
+    CO = "CO"
+    CH4 = "CH4"
+    C2H4 = "C2H4"
+    C2H6 = "C2H6"