rework of whole concept

datamodel/__init__.py

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+
+__URL__ = ""
+__COMMIT__ = ""

datamodel/core/author.py

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+import sdRDM
+
+from typing import Optional
+from pydantic import Field
+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.",
+    )

datamodel/core/calibration.py

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+import sdRDM
+
+from typing import Optional
+from pydantic import Field
+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.",
+    )

datamodel/core/chemical.py

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+import sdRDM
+
+from typing import List, Optional
+from pydantic import Field
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+from .reactantrole import ReactantRole
+from .stoichiometry import Stoichiometry
+
+
+@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."
+        ),
+    )

datamodel/core/data.py

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+import sdRDM
+
+from typing import Optional, Union, List
+from pydantic import Field
+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 .quantity import Quantity
+
+
+@forge_signature
+class Data(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("dataINDEX"),
+        xml="@id",
+    )
+
+    quantity: Optional[Quantity] = Field(
+        default=None,
+        description="quantity of a value.",
+    )
+
+    values: List[Union[float, str, Datetime]] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description="values.",
+    )
+
+    unit: Optional[UnitBase] = Field(
+        default=None,
+        description="unit of the values.",
+    )

datamodel/core/dataset.py

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+import sdRDM
+
+from typing import List, Optional
+from pydantic import Field
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+from .experiment import Experiment
+from .plantsetup import PlantSetup
+from .generalinformation import GeneralInformation
+from .measurement import Measurement
+from .speciesdata import SpeciesData
+
+
+@forge_signature
+class Dataset(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("datasetINDEX"),
+        xml="@id",
+    )
+
+    general_information: Optional[GeneralInformation] = Field(
+        default=GeneralInformation(),
+        description="general data about the data model.",
+    )
+
+    experiments: List[Experiment] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description="information about the individual experiment.",
+    )
+
+    def add_to_experiments(
+        self,
+        plant_setup: Optional[PlantSetup] = None,
+        measurements: List[Measurement] = ListPlus(),
+        species_data: List[SpeciesData] = ListPlus(),
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Experiment' to attribute experiments
+
+        Args:
+            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 ListPlus()
+        """
+        params = {
+            "plant_setup": plant_setup,
+            "measurements": measurements,
+            "species_data": species_data,
+        }
+        if id is not None:
+            params["id"] = id
+        self.experiments.append(Experiment(**params))
+        return self.experiments[-1]

datamodel/core/device.py

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+import sdRDM
+
+from typing import Optional
+from pydantic import Field
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+@forge_signature
+class Device(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("deviceINDEX"),
+        xml="@id",
+    )
+
+    manufacturer: Optional[str] = Field(
+        default=None,
+        description="name of the manufacturer of the device.",
+    )
+
+    device_type: Optional[str] = Field(
+        default=None,
+        description="type given by the manufacturer of the device.",
+    )
+
+    series: Optional[str] = Field(
+        default=None,
+        description="the series of the device.",
+    )
+
+    on_off: Optional[bool] = Field(
+        default=None,
+        description="operational mode of the flow module. True is on and False is off.",
+    )

datamodel/core/experiment.py

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+import sdRDM
+
+from typing import List, Optional
+from pydantic import Field
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+from .chemicalformula import ChemicalFormula
+from .data import Data
+from .measurementtype import MeasurementType
+from .plantsetup import PlantSetup
+from .species import Species
+from .metadata import Metadata
+from .measurement import Measurement
+from .calibration import Calibration
+from .speciesdata import SpeciesData
+
+
+@forge_signature
+class Experiment(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("experimentINDEX"),
+        xml="@id",
+    )
+
+    plant_setup: Optional[PlantSetup] = Field(
+        default=PlantSetup(),
+        description="the individual plant setup that is used in this one experiment.",
+    )
+
+    measurements: List[Measurement] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description=(
+            "different measurements that are made within the scope of one experiment."
+        ),
+    )
+
+    species_data: List[SpeciesData] = Field(
+        default_factory=ListPlus,
+        multiple=True,
+        description="all provided and calculated data about a specific species.",
+    )
+
+    def add_to_measurements(
+        self,
+        measurement_type: Optional[MeasurementType] = None,
+        metadata: List[Metadata] = ListPlus(),
+        experimental_data: List[Data] = ListPlus(),
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Measurement' to attribute measurements
+
+        Args:
+            id (str): Unique identifier of the 'Measurement' object. Defaults to 'None'.
+            measurement_type (): type of a measurement, e.g. potentiostatic or gas chromatography.. Defaults to None
+            metadata (): metadata of a measurement.. Defaults to ListPlus()
+            experimental_data (): experimental data of a measurement.. Defaults to ListPlus()
+        """
+        params = {
+            "measurement_type": measurement_type,
+            "metadata": metadata,
+            "experimental_data": experimental_data,
+        }
+        if id is not None:
+            params["id"] = id
+        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[float] = None,
+        faraday_coefficient: Optional[float] = 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]