From ba186513e6746d8783529d29af76875d7bbd4965 Mon Sep 17 00:00:00 2001 From: sdRDM Bot Date: Wed, 6 Mar 2024 09:00:45 +0000 Subject: [PATCH] API update --- FAIRFlowChemistry/__init__.py | 2 +- FAIRFlowChemistry/core/__init__.py | 1 - FAIRFlowChemistry/core/calibration.py | 15 +++---- FAIRFlowChemistry/core/component.py | 23 +++-------- FAIRFlowChemistry/core/componenttype.py | 1 - FAIRFlowChemistry/core/data.py | 13 ++---- FAIRFlowChemistry/core/dataset.py | 48 ++++++----------------- FAIRFlowChemistry/core/datatype.py | 1 - FAIRFlowChemistry/core/experiment.py | 37 ++++++----------- FAIRFlowChemistry/core/genericattibute.py | 7 ++-- FAIRFlowChemistry/core/measurement.py | 37 +++++------------ FAIRFlowChemistry/core/measurementtype.py | 1 - FAIRFlowChemistry/core/metadata.py | 9 ++--- FAIRFlowChemistry/core/parameter.py | 8 ++-- FAIRFlowChemistry/core/plantsetup.py | 27 ++++--------- FAIRFlowChemistry/core/quantity.py | 1 - FAIRFlowChemistry/core/speciesdata.py | 9 ++--- 17 files changed, 67 insertions(+), 173 deletions(-) diff --git a/FAIRFlowChemistry/__init__.py b/FAIRFlowChemistry/__init__.py index e1dd7af..bec2ed5 100644 --- a/FAIRFlowChemistry/__init__.py +++ b/FAIRFlowChemistry/__init__.py @@ -1,3 +1,3 @@ __URL__ = "https://github.com/FAIRChemistry/FAIRFlowChemistry" -__COMMIT__ = "ff495cb3c7e3baec101ecf174569b19e722565cc" +__COMMIT__ = "c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" diff --git a/FAIRFlowChemistry/core/__init__.py b/FAIRFlowChemistry/core/__init__.py index 39c62e3..5ef3331 100644 --- a/FAIRFlowChemistry/core/__init__.py +++ b/FAIRFlowChemistry/core/__init__.py @@ -15,7 +15,6 @@ from .measurementtype import MeasurementType __doc__ = "" - __all__ = [ "Dataset", "Experiment", diff --git a/FAIRFlowChemistry/core/calibration.py b/FAIRFlowChemistry/core/calibration.py index 9ff91f1..4a86afd 100644 --- a/FAIRFlowChemistry/core/calibration.py +++ b/FAIRFlowChemistry/core/calibration.py @@ -1,14 +1,12 @@ import sdRDM -import numpy as np +import numpy as np from typing import List, Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - - from .data import Data @@ -16,7 +14,7 @@ class Calibration( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Calibration" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Calibration" }, ): """""" @@ -48,9 +46,7 @@ class Calibration( description="regression coefficients in order of increasing degree.", default_factory=ListPlus, tag="float", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -60,12 +56,11 @@ class Calibration( tag="degree", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def calibrate(self): diff --git a/FAIRFlowChemistry/core/component.py b/FAIRFlowChemistry/core/component.py index 9f44099..e5163b9 100644 --- a/FAIRFlowChemistry/core/component.py +++ b/FAIRFlowChemistry/core/component.py @@ -1,22 +1,20 @@ import sdRDM from typing import List, Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - - -from .genericattibute import GenericAttibute from .componenttype import ComponentType +from .genericattibute import GenericAttibute @forge_signature class Component( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Component" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Component" }, ): """""" @@ -72,9 +70,7 @@ class Component( description="a generic attribute as defined by DEXPI.", default_factory=ListPlus, tag="GenericAttibute", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -87,17 +83,14 @@ class Component( ), default_factory=ListPlus, tag="string", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def add_to_generic_attributes( @@ -122,7 +115,6 @@ def add_to_generic_attributes( units (): bla.. Defaults to None units_uri (): bla. Defaults to None """ - params = { "name": name, "attribute_uri": attribute_uri, @@ -131,10 +123,7 @@ def add_to_generic_attributes( "units": units, "units_uri": units_uri, } - if id is not None: params["id"] = id - self.generic_attributes.append(GenericAttibute(**params)) - return self.generic_attributes[-1] diff --git a/FAIRFlowChemistry/core/componenttype.py b/FAIRFlowChemistry/core/componenttype.py index 7b370e0..a0d6cf5 100644 --- a/FAIRFlowChemistry/core/componenttype.py +++ b/FAIRFlowChemistry/core/componenttype.py @@ -2,6 +2,5 @@ class ComponentType(Enum): - EQUIPMENT = "Equipment" PIPINGCOMPONENT = "Piping component" diff --git a/FAIRFlowChemistry/core/data.py b/FAIRFlowChemistry/core/data.py index 09c644e..778db89 100644 --- a/FAIRFlowChemistry/core/data.py +++ b/FAIRFlowChemistry/core/data.py @@ -1,15 +1,13 @@ import sdRDM from typing import Optional, Union, List -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - from sdRDM.base.datatypes import Unit from datetime import datetime as Datetime - from .quantity import Quantity @@ -17,7 +15,7 @@ class Data( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Data" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Data" }, ): """""" @@ -42,9 +40,7 @@ class Data( description="values.", default_factory=ListPlus, tag="float", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -54,10 +50,9 @@ class Data( tag="unit", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) diff --git a/FAIRFlowChemistry/core/dataset.py b/FAIRFlowChemistry/core/dataset.py index 869fb86..b829942 100644 --- a/FAIRFlowChemistry/core/dataset.py +++ b/FAIRFlowChemistry/core/dataset.py @@ -1,24 +1,22 @@ import sdRDM from typing import List, Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - - -from .experiment import Experiment from .measurement import Measurement -from .plantsetup import PlantSetup +from .experiment import Experiment from .speciesdata import SpeciesData +from .plantsetup import PlantSetup @forge_signature class GeneralInformation( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#GeneralInformation" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#GeneralInformation" }, ): """Small type for attribute 'general_information'""" @@ -29,36 +27,21 @@ class GeneralInformation( default_factory=lambda: str(uuid4()), xml="@id", ) - - title: Optional[str] = element( - default=None, - tag="title", - json_schema_extra=dict(), - ) - + title: Optional[str] = element(default=None, tag="title", json_schema_extra=dict()) project: Optional[str] = element( - default=None, - tag="project", - json_schema_extra=dict(), + default=None, tag="project", json_schema_extra=dict() ) - description: Optional[str] = element( - default=None, - tag="description", - json_schema_extra=dict(), + default=None, tag="description", json_schema_extra=dict() ) - purpose: Optional[str] = element( - default=None, - tag="purpose", - json_schema_extra=dict(), + default=None, tag="purpose", json_schema_extra=dict() ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) @@ -66,7 +49,7 @@ class GeneralInformation( class Dataset( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Dataset" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Dataset" }, ): """""" @@ -94,17 +77,14 @@ class Dataset( description="information about the individual experiment.", default_factory=ListPlus, tag="Experiment", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def add_to_experiments( @@ -123,16 +103,12 @@ def add_to_experiments( 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] diff --git a/FAIRFlowChemistry/core/datatype.py b/FAIRFlowChemistry/core/datatype.py index 38a3236..f75edf1 100644 --- a/FAIRFlowChemistry/core/datatype.py +++ b/FAIRFlowChemistry/core/datatype.py @@ -2,7 +2,6 @@ class DataType(Enum): - STRING = "string" FLOAT = "float" DATE = "date" diff --git a/FAIRFlowChemistry/core/experiment.py b/FAIRFlowChemistry/core/experiment.py index 99952de..4834eaf 100644 --- a/FAIRFlowChemistry/core/experiment.py +++ b/FAIRFlowChemistry/core/experiment.py @@ -2,31 +2,29 @@ import yaml import pandas as pd - from typing import List, Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - - -from .component import Component from .calibration import Calibration +from .measurementtype import MeasurementType +from .component import Component +from .datatype import DataType +from .speciesdata import SpeciesData from .plantsetup import PlantSetup from .metadata import Metadata from .measurement import Measurement -from .data import Data -from .datatype import DataType -from .speciesdata import SpeciesData -from .measurementtype import MeasurementType from .quantity import Quantity +from .data import Data + @forge_signature class Experiment( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Experiment" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Experiment" }, ): """""" @@ -54,9 +52,7 @@ class Experiment( ), default_factory=ListPlus, tag="Measurement", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -66,17 +62,14 @@ class Experiment( description="all provided and calculated data about a specific species.", default_factory=ListPlus, tag="SpeciesData", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def add_to_measurements( @@ -97,19 +90,15 @@ def add_to_measurements( experimental_data (): experimental data of a measurement.. Defaults to ListPlus() source (): measuring device the data stems from.. Defaults to None """ - params = { "measurement_type": measurement_type, "metadata": metadata, "experimental_data": experimental_data, "source": source, } - if id is not None: params["id"] = id - self.measurements.append(Measurement(**params)) - return self.measurements[-1] def add_to_species_data( @@ -134,7 +123,6 @@ def add_to_species_data( electron_transfer (): Number of transfered electrons 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, @@ -143,12 +131,9 @@ def add_to_species_data( "electron_transfer": electron_transfer, "faraday_efficiency": faraday_efficiency, } - if id is not None: params["id"] = id - self.species_data.append(SpeciesData(**params)) - return self.species_data[-1] def initialize_species_from_yaml(self, yaml_file: str): diff --git a/FAIRFlowChemistry/core/genericattibute.py b/FAIRFlowChemistry/core/genericattibute.py index 7102503..8351a24 100644 --- a/FAIRFlowChemistry/core/genericattibute.py +++ b/FAIRFlowChemistry/core/genericattibute.py @@ -1,8 +1,8 @@ import sdRDM from typing import Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element from sdRDM.base.utils import forge_signature @@ -11,7 +11,7 @@ class GenericAttibute( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#GenericAttibute" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#GenericAttibute" }, ): """""" @@ -64,10 +64,9 @@ class GenericAttibute( tag="units_uri", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) diff --git a/FAIRFlowChemistry/core/measurement.py b/FAIRFlowChemistry/core/measurement.py index 2486f79..b819a21 100644 --- a/FAIRFlowChemistry/core/measurement.py +++ b/FAIRFlowChemistry/core/measurement.py @@ -1,28 +1,26 @@ import sdRDM from typing import Optional, Union, List -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - from sdRDM.base.datatypes import Unit from datetime import datetime as Datetime - +from .measurementtype import MeasurementType +from .datatype import DataType from .component import Component -from .quantity import Quantity from .metadata import Metadata -from .datatype import DataType +from .quantity import Quantity from .data import Data -from .measurementtype import MeasurementType @forge_signature class Measurement( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Measurement" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Measurement" }, ): """""" @@ -47,9 +45,7 @@ class Measurement( description="metadata of a measurement.", default_factory=ListPlus, tag="Metadata", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -59,9 +55,7 @@ class Measurement( description="experimental data of a measurement.", default_factory=ListPlus, tag="Data", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -71,12 +65,11 @@ class Measurement( tag="source", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def add_to_metadata( @@ -103,7 +96,6 @@ def add_to_metadata( unit (): unit of the parameter.. Defaults to None description (): description of the parameter.. Defaults to None """ - params = { "parameter": parameter, "value": value, @@ -113,12 +105,9 @@ def add_to_metadata( "unit": unit, "description": description, } - if id is not None: params["id"] = id - self.metadata.append(Metadata(**params)) - return self.metadata[-1] def add_to_experimental_data( @@ -137,16 +126,8 @@ def add_to_experimental_data( values (): values.. Defaults to ListPlus() unit (): unit of the values.. Defaults to None """ - - params = { - "quantity": quantity, - "values": values, - "unit": unit, - } - + params = {"quantity": quantity, "values": values, "unit": unit} if id is not None: params["id"] = id - self.experimental_data.append(Data(**params)) - return self.experimental_data[-1] diff --git a/FAIRFlowChemistry/core/measurementtype.py b/FAIRFlowChemistry/core/measurementtype.py index fdb31a6..9e34214 100644 --- a/FAIRFlowChemistry/core/measurementtype.py +++ b/FAIRFlowChemistry/core/measurementtype.py @@ -2,7 +2,6 @@ class MeasurementType(Enum): - GALVANOSTATIC = "Galvanostatic measurement" GC = "GC measurement" MFM = "MFM measurement" diff --git a/FAIRFlowChemistry/core/metadata.py b/FAIRFlowChemistry/core/metadata.py index f489656..cc22f52 100644 --- a/FAIRFlowChemistry/core/metadata.py +++ b/FAIRFlowChemistry/core/metadata.py @@ -1,14 +1,12 @@ import sdRDM from typing import Optional, Union -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element from sdRDM.base.utils import forge_signature - from sdRDM.base.datatypes import Unit from datetime import datetime as Datetime - from .datatype import DataType @@ -16,7 +14,7 @@ class Metadata( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Metadata" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Metadata" }, ): """""" @@ -76,10 +74,9 @@ class Metadata( tag="description", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) diff --git a/FAIRFlowChemistry/core/parameter.py b/FAIRFlowChemistry/core/parameter.py index 706518e..49ab86d 100644 --- a/FAIRFlowChemistry/core/parameter.py +++ b/FAIRFlowChemistry/core/parameter.py @@ -1,11 +1,10 @@ import sdRDM from typing import Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element from sdRDM.base.utils import forge_signature - from sdRDM.base.datatypes import Unit @@ -13,7 +12,7 @@ class Parameter( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#Parameter" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#Parameter" }, ): """""" @@ -38,10 +37,9 @@ class Parameter( tag="unit", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) diff --git a/FAIRFlowChemistry/core/plantsetup.py b/FAIRFlowChemistry/core/plantsetup.py index a5f9b18..08c0a03 100644 --- a/FAIRFlowChemistry/core/plantsetup.py +++ b/FAIRFlowChemistry/core/plantsetup.py @@ -1,15 +1,13 @@ import sdRDM from typing import List, Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element, wrapped from sdRDM.base.listplus import ListPlus from sdRDM.base.utils import forge_signature - - -from .componenttype import ComponentType from .genericattibute import GenericAttibute +from .componenttype import ComponentType from .component import Component @@ -17,7 +15,7 @@ class PlantSetup( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#PlantSetup" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#PlantSetup" }, ): """""" @@ -35,9 +33,7 @@ class PlantSetup( description="bla.", default_factory=ListPlus, tag="Component", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -47,9 +43,7 @@ class PlantSetup( description="bla.", default_factory=ListPlus, tag="string", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) @@ -59,17 +53,14 @@ class PlantSetup( description="bla.", default_factory=ListPlus, tag="string", - json_schema_extra=dict( - multiple=True, - ), + json_schema_extra=dict(multiple=True), ), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" ) def add_to_components( @@ -96,7 +87,6 @@ def add_to_components( generic_attributes (): a generic attribute as defined by DEXPI.. Defaults to ListPlus() connections (): component id of other component this component is connected to via pipes, wires or similar.. Defaults to ListPlus() """ - params = { "component_type": component_type, "component_id": component_id, @@ -106,10 +96,7 @@ def add_to_components( "generic_attributes": generic_attributes, "connections": connections, } - if id is not None: params["id"] = id - self.components.append(Component(**params)) - return self.components[-1] diff --git a/FAIRFlowChemistry/core/quantity.py b/FAIRFlowChemistry/core/quantity.py index ece481b..b28cc71 100644 --- a/FAIRFlowChemistry/core/quantity.py +++ b/FAIRFlowChemistry/core/quantity.py @@ -2,7 +2,6 @@ class Quantity(Enum): - TIME = "Time" VOLTAGE = "Voltage" CURRENT = "Current" diff --git a/FAIRFlowChemistry/core/speciesdata.py b/FAIRFlowChemistry/core/speciesdata.py index 1cc5f75..3e8d7ed 100644 --- a/FAIRFlowChemistry/core/speciesdata.py +++ b/FAIRFlowChemistry/core/speciesdata.py @@ -1,12 +1,10 @@ import sdRDM from typing import Optional -from uuid import uuid4 from pydantic import PrivateAttr +from uuid import uuid4 from pydantic_xml import attr, element from sdRDM.base.utils import forge_signature - - from .calibration import Calibration from .data import Data @@ -15,7 +13,7 @@ class SpeciesData( sdRDM.DataModel, nsmap={ - "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@ff495cb3c7e3baec101ecf174569b19e722565cc#SpeciesData" + "": "https://github.com/FAIRChemistry/FAIRFlowChemistry@c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7#SpeciesData" }, ): """""" @@ -68,10 +66,9 @@ class SpeciesData( tag="faraday_efficiency", json_schema_extra=dict(), ) - _repo: Optional[str] = PrivateAttr( default="https://github.com/FAIRChemistry/FAIRFlowChemistry" ) _commit: Optional[str] = PrivateAttr( - default="ff495cb3c7e3baec101ecf174569b19e722565cc" + default="c41a0c1e08586e8cb4deff5d7a6e8b76d1e12ca7" )