add EModel

src/entitysdk/models/__init__.py

@@ -5,8 +5,10 @@
 from entitysdk.models.brain_location import BrainLocation
 from entitysdk.models.brain_region import BrainRegion
 from entitysdk.models.contribution import Contribution, Role
+from entitysdk.models.emodel import EModel
 from entitysdk.models.ion_channel_model import IonChannelModel, NeuronBlock, UseIon
 from entitysdk.models.license import License
+from entitysdk.models.memodel import MEModel
 from entitysdk.models.morphology import ReconstructionMorphology
 from entitysdk.models.mtype import MTypeClass
 from entitysdk.models.taxonomy import Species, Strain, Taxonomy
@@ -16,8 +18,10 @@
     "BrainLocation",
     "BrainRegion",
     "Contribution",
+    "EModel",
     "IonChannelModel",
     "License",
+    "MEModel",
     "MTypeClass",
     "NeuronBlock",
     "Organization",

src/entitysdk/models/emodel.py

@@ -0,0 +1,89 @@
+"""Electrical cell model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.contribution import Contribution
+from entitysdk.models.entity import Entity
+from entitysdk.models.etype import ETypeClass
+from entitysdk.models.ion_channel_model import IonChannelModel
+from entitysdk.models.morphology import (
+    BrainRegion,
+    License,
+    ReconstructionMorphology,
+    Species,
+    Strain,
+)
+from entitysdk.models.mtype import MTypeClass
+
+
+class EModel(Entity):
+    """Electrical cell model."""
+
+    species: Annotated[
+        Species,
+        Field(description="The species for which the emodel applies."),
+    ]
+    strain: Annotated[
+        Strain | None,
+        Field(description="The specific strain of the species, if applicable."),
+    ] = None
+    brain_region: Annotated[
+        BrainRegion,
+        Field(description="The brain region where the emodel is used or applies."),
+    ]
+    license: Annotated[
+        License | None,
+        Field(description="License under which the emodel is distributed."),
+    ] = None
+    contributions: Annotated[
+        list[Contribution] | None,
+        Field(description="List of contributions related to this emodel."),
+    ] = None
+    iteration: Annotated[
+        str,
+        Field(
+            description="The iteration of the emodel used during optimisation.",
+            examples="1372346",
+        ),
+    ]
+    score: Annotated[
+        float,
+        Field(
+            description="The score of the emodel gotten during validation.",
+            examples=54.0,
+        ),
+    ]
+    seed: Annotated[
+        int,
+        Field(
+            description="The RNG seed used during optimisation.",
+            examples=13,
+        ),
+    ]
+    exemplar_morphology: Annotated[
+        ReconstructionMorphology | None,
+        Field(
+            description="The morphology used during optimisation.",
+        ),
+    ] = None
+    etypes: Annotated[
+        list[ETypeClass] | None,
+        Field(
+            description="The etype classes of the emodel.",
+        ),
+    ] = None
+    mtypes: Annotated[
+        list[MTypeClass] | None,
+        Field(
+            description="The mtype classes of the emodel.",
+        ),
+    ] = None
+    ion_channel_models: Annotated[
+        list[IonChannelModel] | None,
+        Field(
+            description="List of ion channel models.",
+        ),
+    ] = None
+    legacy_id: list[str] | None = None

src/entitysdk/models/etype.py

@@ -0,0 +1,28 @@
+"""EType classification models."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.core import Identifiable
+
+
+class ETypeClass(Identifiable):
+    """EType model class."""
+
+    pref_label: Annotated[
+        str,
+        Field(
+            description="The preferred label of the etype class.",
+        ),
+    ]
+    definition: Annotated[
+        str,
+        Field(
+            description="The definition of the etype class.",
+        ),
+    ]
+    alt_label: Annotated[
+        str | None,
+        Field(description="The alternative label of th etype class."),
+    ]

src/entitysdk/models/memodel.py

@@ -0,0 +1,96 @@
+"""Simulatable neuron model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.contribution import Contribution
+from entitysdk.models.emodel import EModel
+from entitysdk.models.entity import Entity
+from entitysdk.models.etype import ETypeClass
+from entitysdk.models.morphology import (
+    BrainRegion,
+    License,
+    ReconstructionMorphology,
+    Species,
+    Strain,
+)
+from entitysdk.models.mtype import MTypeClass
+from entitysdk.typedef import ValidationStatus
+
+
+class MEModel(Entity):
+    """Simulatable neuron model."""
+
+    species: Annotated[
+        Species,
+        Field(description="The species for which the memodel applies."),
+    ]
+    strain: Annotated[
+        Strain | None,
+        Field(description="The specific strain of the species, if applicable."),
+    ] = None
+    brain_region: Annotated[
+        BrainRegion,
+        Field(description="The brain region where the memodel is used or applies."),
+    ]
+    license: Annotated[
+        License | None,
+        Field(description="License under which the memodel is distributed."),
+    ] = None
+    contributions: Annotated[
+        list[Contribution] | None,
+        Field(description="List of contributions related to this memodel."),
+    ] = None
+    iteration: Annotated[
+        str | None,
+        Field(
+            description="The iteration of the memodel used during optimisation.",
+            examples="1372346",
+        ),
+    ] = None
+    validation_status: Annotated[
+        ValidationStatus,
+        Field(
+            description="The validation status of the memodel.",
+        ),
+    ]
+    holding_current: Annotated[
+        float,
+        Field(
+            description="The holding current of the memodel.",
+            examples=0.0,
+        ),
+    ] = 0.0
+    threshold_current: Annotated[
+        float,
+        Field(
+            description="The threshold current of the memodel.",
+            examples=0.1,
+        ),
+    ] = 0.1
+    morphology: Annotated[
+        ReconstructionMorphology,
+        Field(
+            description="The morphology of the memodel.",
+        ),
+    ]
+    emodel: Annotated[
+        EModel,
+        Field(
+            description="The emodel of the memodel.",
+        ),
+    ]
+    etypes: Annotated[
+        list[ETypeClass] | None,
+        Field(
+            description="The etype classes of the memodel.",
+        ),
+    ] = None
+    mtypes: Annotated[
+        list[MTypeClass] | None,
+        Field(
+            description="The mtype classes of the memodel.",
+        ),
+    ] = None
+    legacy_id: list[str] | None = None

src/entitysdk/models/morphology.py

@@ -22,17 +22,17 @@ class ReconstructionMorphology(Entity):
         ),
     ] = None
     brain_region: Annotated[
-        BrainRegion,
+        BrainRegion | None,
         Field(
             description="The region of the brain where the morphology is located.",
         ),
-    ]
+    ] = None
     species: Annotated[
-        Species,
+        Species | None,
         Field(
             description="The species of the morphology.",
         ),
-    ]
+    ] = None
     strain: Annotated[
         Strain | None,
         Field(

src/entitysdk/route.py

@@ -22,6 +22,8 @@
     "Taxonomy": "taxonomy",
     "IonChannelModel": "ion-channel-model",
     "Ion": "ion",
+    "EModel": "emodel",
+    "MEModel": "memodel",
 }
 
 

src/entitysdk/typedef.py

@@ -1,7 +1,7 @@
 """Type definitions."""
 
 import uuid
-from enum import StrEnum
+from enum import StrEnum, auto
 
 ID = uuid.UUID
 
@@ -11,3 +11,13 @@ class DeploymentEnvironment(StrEnum):
 
     staging = "staging"
     production = "production"
+
+
+class ValidationStatus(StrEnum):
+    """Validation status."""
+
+    created = auto()
+    initialized = auto()
+    running = auto()
+    done = auto()
+    error = auto()

tests/integration/test_searching.py

@@ -2,8 +2,10 @@
 
 from entitysdk.models import (
     Contribution,
+    EModel,
     IonChannelModel,
     License,
+    MEModel,
     MTypeClass,
     Organization,
     Person,
@@ -27,6 +29,8 @@
         Species,
         Strain,
         Organization,
+        EModel,
+        MEModel,
     ],
 )
 def test_is_searchable(entity_type, client):