add SingleNeuronSimulation and SingleNeuronSynaptomeSimulation (#73)

* add SingleNeuronSimulation and SingleNeuronSynaptomeSimulation

* add synaptome-related entities and NestedMEModel

Author: AurelienJaquier

src/entitysdk/models/__init__.py

@@ -17,7 +17,10 @@
 from entitysdk.models.mtype import MTypeClass
 from entitysdk.models.simulation import Simulation
 from entitysdk.models.simulation_campaign import SimulationCampaign
+from entitysdk.models.single_neuron_simulation import SingleNeuronSimulation
+from entitysdk.models.single_neuron_synaptome_simulation import SingleNeuronSynaptomeSimulation
 from entitysdk.models.subject import Subject
+from entitysdk.models.synaptome import SingleNeuronSynaptome
 from entitysdk.models.taxonomy import Species, Strain, Taxonomy
 from entitysdk.models.validation_result import ValidationResult
 
@@ -43,6 +46,9 @@
     "Role",
     "Simulation",
     "SimulationCampaign",
+    "SingleNeuronSimulation",
+    "SingleNeuronSynaptome",
+    "SingleNeuronSynaptomeSimulation",
     "Species",
     "Strain",
     "Subject",

src/entitysdk/models/memodel.py

@@ -4,7 +4,9 @@
 
 from pydantic import Field
 
+from entitysdk.models.base import BaseModel
 from entitysdk.models.contribution import Contribution
+from entitysdk.models.core import Identifiable
 from entitysdk.models.emodel import EModel
 from entitysdk.models.entity import Entity
 from entitysdk.models.etype import ETypeClass
@@ -20,7 +22,49 @@
 from entitysdk.types import ValidationStatus
 
 
-class MEModel(Entity):
+class MEModelBase(BaseModel):
+    """Base for simulatable neuron model."""
+
+    name: Annotated[
+        str | None,
+        Field(
+            examples=["Entity 1"],
+            description="The name of the entity.",
+        ),
+    ] = None
+    description: Annotated[
+        str | None,
+        Field(
+            examples=["This is entity 1"],
+            description="The description of the entity.",
+        ),
+    ] = None
+    validation_status: Annotated[
+        ValidationStatus,
+        Field(
+            description="The validation status of the memodel.",
+        ),
+    ]
+
+
+class NestedMEModel(MEModelBase, Identifiable):
+    """Nested simulatable neuron model."""
+
+    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
+
+
+class MEModel(MEModelBase, Entity):
     """Simulatable neuron model."""
 
     species: Annotated[
@@ -50,12 +94,6 @@ class MEModel(Entity):
             examples="1372346",
         ),
     ] = None
-    validation_status: Annotated[
-        ValidationStatus,
-        Field(
-            description="The validation status of the memodel.",
-        ),
-    ]
     holding_current: Annotated[
         float | None,
         Field(

src/entitysdk/models/single_neuron_simulation.py

@@ -0,0 +1,50 @@
+"""Single neuron simulation."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.entity import Entity
+from entitysdk.models.memodel import NestedMEModel
+from entitysdk.types import SingleNeuronSimulationStatus
+
+
+class SingleNeuronSimulation(Entity):
+    """Single neuron simulation."""
+
+    seed: Annotated[
+        int,
+        Field(
+            description="Random number generator seed used during the simulation.",
+            examples=42,
+        ),
+    ]
+    injection_location: Annotated[
+        list[str],
+        Field(
+            description="List of locations where the stimuli were injected, "
+            "in hoc-compatible format.",
+            examples="soma[0]",
+        ),
+    ]
+    recording_location: Annotated[
+        list[str],
+        Field(
+            description="List of locations where the stimuli were recorded, "
+            "in hoc-compatible format.",
+            examples="soma[0]",
+        ),
+    ]
+    status: Annotated[
+        SingleNeuronSimulationStatus,
+        Field(
+            description="Status of the simulation. Can be .started, .failure, .success",
+            examples=SingleNeuronSimulationStatus.success,
+        ),
+    ]
+    me_model: Annotated[
+        NestedMEModel,
+        Field(
+            description="The me-model (single cell model) that was simulated, in nested form.",
+        ),
+    ]

src/entitysdk/models/single_neuron_synaptome_simulation.py

@@ -0,0 +1,51 @@
+"""Single neuron synaptome simulation."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.entity import Entity
+from entitysdk.models.synaptome import NestedSynaptome
+from entitysdk.types import SingleNeuronSimulationStatus
+
+
+class SingleNeuronSynaptomeSimulation(Entity):
+    """Single neuron synaptome simulation."""
+
+    seed: Annotated[
+        int,
+        Field(
+            description="Random number generator seed used during the simulation.",
+            examples=42,
+        ),
+    ]
+    injection_location: Annotated[
+        list[str],
+        Field(
+            description="List of locations where the stimuli were injected, "
+            "in hoc-compatible format.",
+            examples="soma[0]",
+        ),
+    ]
+    recording_location: Annotated[
+        list[str],
+        Field(
+            description="List of locations where the stimuli were recorded, "
+            "in hoc-compatible format.",
+            examples="soma[0]",
+        ),
+    ]
+    status: Annotated[
+        SingleNeuronSimulationStatus,
+        Field(
+            description="Status of the simulation. Can be .started, .failure, .success",
+            examples=SingleNeuronSimulationStatus.success,
+        ),
+    ]
+    synaptome: Annotated[
+        NestedSynaptome,
+        Field(
+            description="The synaptome that was simulated, in nested form.",
+            examples="85663316-a7ff-4107-9eb9-236de8868c5c",
+        ),
+    ]

src/entitysdk/models/synaptome.py

@@ -0,0 +1,63 @@
+"""Single neuron synaptome."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.base import BaseModel
+from entitysdk.models.contribution import Contribution
+from entitysdk.models.core import Identifiable
+from entitysdk.models.entity import Entity
+from entitysdk.models.memodel import NestedMEModel
+from entitysdk.models.morphology import BrainRegion
+
+
+class SingleNeuronSynaptomeBase(BaseModel):
+    """Base for single neuron synaptome."""
+
+    name: Annotated[
+        str | None,
+        Field(
+            examples=["Entity 1"],
+            description="The name of the entity.",
+        ),
+    ] = None
+    description: Annotated[
+        str | None,
+        Field(
+            examples=["This is entity 1"],
+            description="The description of the entity.",
+        ),
+    ] = None
+    seed: Annotated[
+        int,
+        Field(
+            description="Random number generator seed.",
+            examples=42,
+        ),
+    ]
+
+
+class NestedSynaptome(SingleNeuronSynaptomeBase, Identifiable):
+    """Nested single neuron synaptome."""
+
+    pass
+
+
+class SingleNeuronSynaptome(SingleNeuronSynaptomeBase, Entity):
+    """Single neuron synaptome."""
+
+    brain_region: Annotated[
+        BrainRegion,
+        Field(description="The brain region where the memodel is used or applies."),
+    ]
+    contributions: Annotated[
+        list[Contribution] | None,
+        Field(description="List of contributions related to this memodel."),
+    ] = None
+    me_model: Annotated[
+        NestedMEModel,
+        Field(
+            description="The me-model (single cell model) the synaptome applies to.",
+        ),
+    ]

src/entitysdk/route.py

@@ -27,6 +27,9 @@
     "ReconstructionMorphology": "reconstruction-morphology",
     "Simulation": "simulation",
     "SimulationCampaign": "simulation-campaign",
+    "SingleNeuronSimulation": "single-neuron-simulation",
+    "SingleNeuronSynaptome": "single-neuron-synaptome",
+    "SingleNeuronSynaptomeSimulation": "single-neuron-synaptome-simulation",
     "Role": "role",
     "Species": "species",
     "Strain": "strain",

src/entitysdk/types.py

@@ -26,6 +26,14 @@ class ValidationStatus(StrEnum):
     error = auto()
 
 
+class SingleNeuronSimulationStatus(StrEnum):
+    """Single neuron simulation status."""
+
+    started = auto()
+    failure = auto()
+    success = auto()
+
+
 class ElectricalRecordingType(StrEnum):
     """Electrical cell recording type."""
 

tests/integration/test_searching.py

@@ -13,6 +13,9 @@
     Person,
     ReconstructionMorphology,
     Role,
+    SingleNeuronSimulation,
+    SingleNeuronSynaptome,
+    SingleNeuronSynaptomeSimulation,
     Species,
     Strain,
     ValidationResult,
@@ -37,6 +40,9 @@
         ElectricalCellRecording,
         ValidationResult,
         MEModelCalibrationResult,
+        SingleNeuronSimulation,
+        SingleNeuronSynaptomeSimulation,
+        SingleNeuronSynaptome,
     ],
 )
 def test_is_searchable(entity_type, client):