update core with new sdrdm

FAIRChemistry · May 13, 2024 · 2db1d88 · 2db1d88
1 parent f700c12
commit 2db1d88
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Showing 16 changed files with 68 additions and 40,250 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/FAIRFlowChemistry.ipynb b/FAIRFlowChemistry.ipynb
diff --git a/FAIRFlowChemistry/__init__.py b/FAIRFlowChemistry/__init__.py
@@ -1,3 +1,3 @@
 
-__URL__ = "https://github.com/FAIRChemistry/FAIRFlowChemistry"
-__COMMIT__ = "f4222f6744222333280cdf737a377645a4c02321"
+__URL__ = ""
+__COMMIT__ = ""
diff --git a/FAIRFlowChemistry/core/calibration.py b/FAIRFlowChemistry/core/calibration.py
@@ -50,12 +50,6 @@ class Calibration(sdRDM.DataModel, search_mode="unordered"):
         tag="degree",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/component.py b/FAIRFlowChemistry/core/component.py
@@ -77,12 +77,6 @@ class Component(sdRDM.DataModel, search_mode="unordered"):
         tag="connections",
         json_schema_extra=dict(multiple=True),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/data.py b/FAIRFlowChemistry/core/data.py
@@ -44,12 +44,6 @@ class Data(sdRDM.DataModel, search_mode="unordered"):
         tag="unit",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/dataset.py b/FAIRFlowChemistry/core/dataset.py
@@ -8,10 +8,10 @@
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature
 from sdRDM.tools.utils import elem2dict
-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
@@ -34,12 +34,6 @@ class GeneralInformation(sdRDM.DataModel, search_mode="unordered"):
     purpose: Optional[str] = element(
         default=None, tag="purpose", json_schema_extra=dict()
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
@@ -81,12 +75,6 @@ class Dataset(sdRDM.DataModel, search_mode="unordered"):
         tag="experiments",
         json_schema_extra=dict(multiple=True),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/experiment.py b/FAIRFlowChemistry/core/experiment.py
@@ -10,16 +10,16 @@
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature
 from sdRDM.tools.utils import elem2dict
-from .measurementtype import MeasurementType
 from .component import Component
-from .datatype import DataType
-from .quantity import Quantity
 from .calibration import Calibration
-from .plantsetup import PlantSetup
+from .quantity import Quantity
 from .measurement import Measurement
+from .datatype import DataType
 from .metadata import Metadata
+from .measurementtype import MeasurementType
 from .data import Data
 from .speciesdata import SpeciesData
+from .plantsetup import PlantSetup
 
 
 @forge_signature
@@ -55,12 +55,6 @@ class Experiment(sdRDM.DataModel, search_mode="unordered"):
         tag="species_data",
         json_schema_extra=dict(multiple=True),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/genericattibute.py b/FAIRFlowChemistry/core/genericattibute.py
@@ -62,12 +62,6 @@ class GenericAttibute(sdRDM.DataModel, search_mode="unordered"):
         tag="units_uri",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/measurement.py b/FAIRFlowChemistry/core/measurement.py
@@ -10,11 +10,11 @@
 from sdRDM.base.datatypes import Unit
 from sdRDM.tools.utils import elem2dict
 from datetime import datetime as Datetime
-from .measurementtype import MeasurementType
 from .component import Component
-from .datatype import DataType
 from .quantity import Quantity
+from .datatype import DataType
 from .metadata import Metadata
+from .measurementtype import MeasurementType
 from .data import Data
 
 
@@ -56,12 +56,6 @@ class Measurement(sdRDM.DataModel, search_mode="unordered"):
         tag="source",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/metadata.py b/FAIRFlowChemistry/core/metadata.py
@@ -72,12 +72,6 @@ class Metadata(sdRDM.DataModel, search_mode="unordered"):
         tag="description",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/parameter.py b/FAIRFlowChemistry/core/parameter.py
@@ -35,12 +35,6 @@ class Parameter(sdRDM.DataModel, search_mode="unordered"):
         tag="unit",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/plantsetup.py b/FAIRFlowChemistry/core/plantsetup.py
@@ -46,12 +46,6 @@ class PlantSetup(sdRDM.DataModel, search_mode="unordered"):
         tag="output",
         json_schema_extra=dict(multiple=True),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/core/speciesdata.py b/FAIRFlowChemistry/core/speciesdata.py
@@ -64,12 +64,6 @@ class SpeciesData(sdRDM.DataModel, search_mode="unordered"):
         tag="faraday_efficiency",
         json_schema_extra=dict(),
     )
-    _repo: Optional[str] = PrivateAttr(
-        default="https://github.com/FAIRChemistry/FAIRFlowChemistry"
-    )
-    _commit: Optional[str] = PrivateAttr(
-        default="f4222f6744222333280cdf737a377645a4c02321"
-    )
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")

diff --git a/FAIRFlowChemistry/tools/reader.py b/FAIRFlowChemistry/tools/reader.py
@@ -286,9 +286,4 @@ def DEXPI2sdRDM(filepath: Path|str ):
                 component.connections.extend(connection)
                 component.connections.remove(component.component_id)
 
-<<<<<<< Updated upstream
-    #for component in components:
-    #    print(component.component_id, component.connections)
-=======
->>>>>>> Stashed changes
     return PlantSetup(components=components)