update generate_api

.github/workflows/generate_api.yaml

@@ -8,7 +8,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Generate sdRDM library
-      uses: JR-1991/generate-sdrdm-api@main
+      uses: JR-1991/generate-sdrdm-api@v3.1
       with:
         library_name: "FAIRFlowChemistry"
         schema_path: "./specifications/datamodel.md"

FAIRFlowChemistry/__init__.py

@@ -1,3 +1,3 @@
 
-__URL__ = "https://github.com/FAIRChemistry/FAIRFlowChemistry"
-__COMMIT__ = "8cd2a321d0f28e24e41c7a3ac5d90aa738b1646d"
+__URL__ = ""
+__COMMIT__ = ""

FAIRFlowChemistry/core/calibration.py

@@ -1,14 +1,13 @@
 import sdRDM
 
 import numpy as np
-from typing import Dict, List, Optional
-from pydantic import PrivateAttr, model_validator
+from typing import List, Optional
+from pydantic import model_validator
 from uuid import uuid4
-from pydantic_xml import attr, element
-from lxml.etree import _Element
+from pydantic_xml import attr, element, wrapped
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature
-from sdRDM.tools.utils import elem2dict
+from lxml.etree import _Element
 from .data import Data
 
 
@@ -37,11 +36,14 @@ class Calibration(sdRDM.DataModel):
         json_schema_extra=dict(),
     )
 
-    regression_coefficients: List[float] = element(
-        description="regression coefficients in order of increasing degree.",
-        default_factory=ListPlus,
-        tag="regression_coefficients",
-        json_schema_extra=dict(multiple=True),
+    regression_coefficients: List[float] = wrapped(
+        "regression_coefficients",
+        element(
+            description="regression coefficients in order of increasing degree.",
+            default_factory=ListPlus,
+            tag="float",
+            json_schema_extra=dict(multiple=True),
+        ),
     )
 
     degree: Optional[int] = element(
@@ -50,13 +52,6 @@ class Calibration(sdRDM.DataModel):
         tag="degree",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="8cd2a321d0f28e24e41c7a3ac5d90aa738b1646d"
-    )
-    _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
     def _parse_raw_xml_data(self):

FAIRFlowChemistry/core/component.py

@@ -1,13 +1,12 @@
 import sdRDM
 
-from typing import Dict, List, Optional
-from pydantic import PrivateAttr, model_validator
+from typing import List, Optional
+from pydantic import model_validator
 from uuid import uuid4
-from pydantic_xml import attr, element
-from lxml.etree import _Element
+from pydantic_xml import attr, element, wrapped
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature
-from sdRDM.tools.utils import elem2dict
+from lxml.etree import _Element
 from .genericattibute import GenericAttibute
 from .componenttype import ComponentType
 
@@ -61,29 +60,63 @@ class Component(sdRDM.DataModel):
         json_schema_extra=dict(),
     )
 
-    generic_attributes: List[GenericAttibute] = element(
-        description="a generic attribute as defined by DEXPI.",
-        default_factory=ListPlus,
-        tag="generic_attributes",
-        json_schema_extra=dict(multiple=True),
+    generic_attributes: List[GenericAttibute] = wrapped(
+        "generic_attributes",
+        element(
+            description="a generic attribute as defined by DEXPI.",
+            default_factory=ListPlus,
+            tag="GenericAttibute",
+            json_schema_extra=dict(multiple=True),
+        ),
     )
 
-    connections: List[str] = element(
-        description=(
-            "component id of other component this component is connected to via pipes,"
-            " wires or similar."
+    connections: List[str] = wrapped(
+        "connections",
+        element(
+            description=(
+                "component id of other component this component is connected to via"
+                " pipes, wires or similar."
+            ),
+            default_factory=ListPlus,
+            tag="string",
+            json_schema_extra=dict(multiple=True),
         ),
-        default_factory=ListPlus,
-        tag="connections",
-        json_schema_extra=dict(multiple=True),
-    )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="8cd2a321d0f28e24e41c7a3ac5d90aa738b1646d"
     )
-    _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
+
+    def add_to_generic_attributes(
+        self,
+        name: Optional[str] = None,
+        attribute_uri: Optional[str] = None,
+        value: Optional[str] = None,
+        format: Optional[str] = None,
+        units: Optional[str] = None,
+        units_uri: Optional[str] = None,
+        id: Optional[str] = None,
+    ) -> GenericAttibute:
+        """
+        This method adds an object of type 'GenericAttibute' to attribute generic_attributes
+
+        Args:
+            id (str): Unique identifier of the 'GenericAttibute' object. Defaults to 'None'.
+            name (): bla.. Defaults to None
+            attribute_uri (): bla.. Defaults to None
+            value (): bla.. Defaults to None
+            format (): bla.. Defaults to None
+            units (): bla.. Defaults to None
+            units_uri (): bla. Defaults to None
+        """
+        params = {
+            "name": name,
+            "attribute_uri": attribute_uri,
+            "value": value,
+            "format": format,
+            "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]
 
     @model_validator(mode="after")
     def _parse_raw_xml_data(self):

FAIRFlowChemistry/core/data.py

@@ -1,15 +1,14 @@
 import sdRDM
 
-from typing import Optional, Union, List, Dict
-from pydantic import PrivateAttr, model_validator
+from typing import Optional, Union, List
+from pydantic import model_validator
 from uuid import uuid4
-from pydantic_xml import attr, element
-from lxml.etree import _Element
+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 sdRDM.tools.utils import elem2dict
 from datetime import datetime as Datetime
+from sdRDM.base.datatypes import Unit
+from lxml.etree import _Element
 from .quantity import Quantity
 
 
@@ -31,11 +30,14 @@ class Data(sdRDM.DataModel):
         json_schema_extra=dict(),
     )
 
-    values: List[Union[float, str, Datetime]] = element(
-        description="values.",
-        default_factory=ListPlus,
-        tag="values",
-        json_schema_extra=dict(multiple=True),
+    values: List[Union[float, str, Datetime]] = wrapped(
+        "values",
+        element(
+            description="values.",
+            default_factory=ListPlus,
+            tag="float",
+            json_schema_extra=dict(multiple=True),
+        ),
     )
 
     unit: Optional[Unit] = element(
@@ -44,13 +46,6 @@ class Data(sdRDM.DataModel):
         tag="unit",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="8cd2a321d0f28e24e41c7a3ac5d90aa738b1646d"
-    )
-    _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
     def _parse_raw_xml_data(self):

FAIRFlowChemistry/core/dataset.py

@@ -3,15 +3,14 @@
 from typing import Dict, List, Optional
 from pydantic import PrivateAttr, model_validator
 from uuid import uuid4
-from pydantic_xml import attr, element
-from lxml.etree import _Element
+from pydantic_xml import attr, element, wrapped
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature
-from sdRDM.tools.utils import elem2dict
-from .measurement import Measurement
-from .plantsetup import PlantSetup
+from lxml.etree import _Element
 from .experiment import Experiment
 from .speciesdata import SpeciesData
+from .plantsetup import PlantSetup
+from .measurement import Measurement
 
 
 @forge_signature
@@ -31,13 +30,63 @@ class GeneralInformation(sdRDM.DataModel):
     description: Optional[str] = element(
         default=None, tag="description", json_schema_extra=dict()
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
+
+
+@forge_signature
+class Dataset(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = attr(
+        name="id",
+        description="Unique identifier of the given object.",
+        default_factory=lambda: str(uuid4()),
+        xml="@id",
     )
-    _commit: Optional[str] = PrivateAttr(
-        default="8cd2a321d0f28e24e41c7a3ac5d90aa738b1646d"
+
+    general_information: Optional[GeneralInformation] = element(
+        description=(
+            "general data about the datasetm like titel, project name, and description."
+        ),
+        default_factory=GeneralInformation,
+        tag="general_information",
+        json_schema_extra=dict(),
     )
-    _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
+
+    experiments: List[Experiment] = wrapped(
+        "experiments",
+        element(
+            description="information about the individual experiment.",
+            default_factory=ListPlus,
+            tag="Experiment",
+            json_schema_extra=dict(multiple=True),
+        ),
+    )
+
+    def add_to_experiments(
+        self,
+        plant_setup: Optional[PlantSetup] = None,
+        measurements: List[Measurement] = ListPlus(),
+        species_data: List[SpeciesData] = ListPlus(),
+        id: Optional[str] = None,
+    ) -> Experiment:
+        """
+        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]
 
     @model_validator(mode="after")
     def _parse_raw_xml_data(self):