entitysdk 0.2.2__tar.gz → 0.2.3__tar.gz

{entitysdk-0.2.2/src/entitysdk.egg-info → entitysdk-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.2.2
+Version: 0.2.3
 Summary: Python library for interacting with the entitycore service
 Author-email: Open Brain Institute <info@openbraininstitute.org>
 Maintainer-email: Open Brain Institute <info@openbraininstitute.org>

{entitysdk-0.2.2 → entitysdk-0.2.3}/examples/01_searching.ipynb

@@ -13,14 +13,15 @@
     "\n",
     "from entitysdk.client import Client\n",
     "from entitysdk.common import ProjectContext\n",
-    "from entitysdk.models.agent import Organization, Person\n",
-    "from entitysdk.models.contribution import Role\n",
-    "from entitysdk.models.morphology import (\n",
+    "from entitysdk.models import (\n",
+    "    MTypeClass,\n",
+    "    Organization,\n",
+    "    Person,\n",
     "    ReconstructionMorphology,\n",
+    "    Role,\n",
     "    Species,\n",
     "    Strain,\n",
     ")\n",
-    "from entitysdk.models.mtype import MTypeClass\n",
     "\n",
     "entitycore_api_url = \"http://127.0.0.1:8000\"\n",
     "project_context = ProjectContext(\n",

{entitysdk-0.2.2 → entitysdk-0.2.3}/examples/02_morphology.ipynb

@@ -16,7 +16,7 @@
     "\n",
     "from entitysdk.client import Client\n",
     "from entitysdk.common import ProjectContext\n",
-    "from entitysdk.models.morphology import (\n",
+    "from entitysdk.models import (\n",
     "    BrainLocation,\n",
     "    BrainRegion,\n",
     "    ReconstructionMorphology,\n",

{entitysdk-0.2.2 → entitysdk-0.2.3}/examples/03_contribution.ipynb

@@ -13,9 +13,7 @@
     "\n",
     "from entitysdk.client import Client\n",
     "from entitysdk.common import ProjectContext\n",
-    "from entitysdk.models.agent import Organization\n",
-    "from entitysdk.models.contribution import Contribution, Role\n",
-    "from entitysdk.models.morphology import ReconstructionMorphology\n",
+    "from entitysdk.models import Contribution, Organization, ReconstructionMorphology, Role\n",
     "\n",
     "entitycore_api_url = \"http://127.0.0.1:8000\"\n",
     "project_context = ProjectContext(\n",

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/client.py

@@ -13,7 +13,7 @@ from entitysdk.models.asset import Asset, LocalAssetMetadata
 from entitysdk.models.core import Identifiable
 from entitysdk.result import IteratorResult
 from entitysdk.token_manager import TokenManager
-from entitysdk.typedef import ID, DeploymentEnvironment
+from entitysdk.types import ID, DeploymentEnvironment
 from entitysdk.util import build_api_url
 
 

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/common.py

@@ -7,7 +7,7 @@ from uuid import UUID
 from pydantic import BaseModel
 
 from entitysdk.exception import EntitySDKError
-from entitysdk.typedef import DeploymentEnvironment
+from entitysdk.types import DeploymentEnvironment
 
 UUID_RE = "[0-9a-f]{8}(?:-[0-9a-f]{4}){3}-[0-9a-f]{12}"
 

entitysdk-0.2.3/src/entitysdk/models/__init__.py

@@ -0,0 +1,37 @@
+"""Models for entitysdk."""
+
+from entitysdk.models.agent import Organization, Person
+from entitysdk.models.asset import Asset
+from entitysdk.models.brain_location import BrainLocation
+from entitysdk.models.brain_region import BrainRegion
+from entitysdk.models.contribution import Contribution, Role
+from entitysdk.models.electrical_cell_recording import ElectricalCellRecording
+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
+
+__all__ = [
+    "Asset",
+    "BrainLocation",
+    "BrainRegion",
+    "Contribution",
+    "ElectricalCellRecording",
+    "EModel",
+    "IonChannelModel",
+    "License",
+    "MEModel",
+    "MTypeClass",
+    "NeuronBlock",
+    "Organization",
+    "Person",
+    "ReconstructionMorphology",
+    "Role",
+    "Species",
+    "Strain",
+    "Taxonomy",
+    "UseIon",
+]

entitysdk-0.2.3/src/entitysdk/models/brain_location.py

@@ -0,0 +1,33 @@
+"""Brain location model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.core import Struct
+
+
+class BrainLocation(Struct):
+    """BrainLocation model."""
+
+    x: Annotated[
+        float,
+        Field(
+            examples=[1.0, 2.0, 3.0],
+            description="The x coordinate of the brain location.",
+        ),
+    ]
+    y: Annotated[
+        float,
+        Field(
+            examples=[1.0, 2.0, 3.0],
+            description="The y coordinate of the brain location.",
+        ),
+    ]
+    z: Annotated[
+        float,
+        Field(
+            examples=[1.0, 2.0, 3.0],
+            description="The z coordinate of the brain location.",
+        ),
+    ]

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/models/brain_region.py

@@ -5,7 +5,7 @@ from typing import Annotated
 from pydantic import Field
 
 from entitysdk.models.core import Identifiable
-from entitysdk.typedef import ID
+from entitysdk.types import ID
 
 
 class BrainRegion(Identifiable):
@@ -29,8 +29,9 @@ class BrainRegion(Identifiable):
         ),
     ]
     parent_structure_id: Annotated[
-        ID, Field(examples=[], description="The parent region structure UUID.")
+        ID | None, Field(examples=[], description="The parent region structure UUID.")
     ]
     hierarchy_id: Annotated[
         ID, Field(examples=[], description="The brain hierarchy that includes this brain region.")
     ]
+    color_hex_triplet: Annotated[str, Field(description="Region's color hex triplet.")]

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/models/contribution.py

@@ -6,7 +6,6 @@ from pydantic import Field
 
 from entitysdk.models.agent import AgentUnion
 from entitysdk.models.core import Identifiable
-from entitysdk.models.entity import Entity
 
 
 class Role(Identifiable):
@@ -42,6 +41,12 @@ class Contribution(Identifiable):
         ),
     ]
     entity: Annotated[
-        Entity | None,
+        "Entity | None",
         Field(description="The entity that resulted in this contribution."),
     ] = None
+
+
+# Update forward reference for Entity
+from entitysdk.models.entity import Entity  # noqa: E402
+
+Contribution.model_rebuild(force=True)

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/models/core.py

@@ -6,7 +6,7 @@ from typing import Annotated
 from pydantic import Field
 
 from entitysdk.models.base import BaseModel
-from entitysdk.typedef import ID
+from entitysdk.types import ID
 
 
 class Struct(BaseModel):

entitysdk-0.2.3/src/entitysdk/models/electrical_cell_recording.py

@@ -0,0 +1,92 @@
+"""Electrical cell recording models."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.brain_region import BrainRegion
+from entitysdk.models.entity import Entity
+from entitysdk.models.license import License
+from entitysdk.models.subject import Subject
+from entitysdk.types import (
+    ElectricalRecordingOrigin,
+    ElectricalRecordingStimulusShape,
+    ElectricalRecordingStimulusType,
+    ElectricalRecordingType,
+)
+
+
+class ElectricalRecordingStimulus(Entity):
+    """Electrical cell recording stimulus model."""
+
+    dt: float | None = None
+    injection_type: ElectricalRecordingStimulusType
+    shape: ElectricalRecordingStimulusShape
+    start_time: float | None = None
+    end_time: float | None = None
+
+
+class ElectricalCellRecording(Entity):
+    """Electrical cell recording model."""
+
+    ljp: Annotated[
+        float,
+        Field(
+            title="Liquid Junction Potential",
+            description="Correction applied to the voltage trace, in mV",
+            examples=[0.1],
+        ),
+    ] = 0.0
+    recording_location: Annotated[
+        list[str],
+        Field(
+            title="Recording Location",
+            description=(
+                "Location on the cell where recording was performed, in hoc-compatible format."
+            ),
+        ),
+    ]
+    recording_type: Annotated[
+        ElectricalRecordingType,
+        Field(
+            title="Recording Type",
+            description="Recording type.",
+        ),
+    ]
+    recording_origin: Annotated[
+        ElectricalRecordingOrigin,
+        Field(
+            title="Recording Origin",
+            description="Recording origin.",
+        ),
+    ]
+    comment: Annotated[
+        str | None,
+        Field(
+            title="Comment",
+            description="Comment with further details.",
+        ),
+    ] = None
+    brain_region: Annotated[
+        BrainRegion,
+        Field(
+            description="The region of the brain where the morphology is located.",
+        ),
+    ]
+    subject: Annotated[
+        Subject,
+        Field(title="Subject", description="The subject of the electrical cell recording."),
+    ]
+    stimuli: Annotated[
+        list[ElectricalRecordingStimulus] | None,
+        Field(
+            title="Electrical Recording Stimuli",
+            description="List of stimuli applied to the cell with their respective time steps",
+        ),
+    ] = None
+    license: Annotated[
+        License | None,
+        Field(
+            description="The license attached to the morphology.",
+        ),
+    ] = None

entitysdk-0.2.3/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

entitysdk-0.2.3/src/entitysdk/models/entity.py

@@ -0,0 +1,74 @@
+"""Entity model."""
+
+from typing import Annotated
+from uuid import UUID
+
+from pydantic import Field
+
+from entitysdk.mixin import HasAssets
+from entitysdk.models.agent import AgentUnion
+from entitysdk.models.core import Identifiable
+from entitysdk.types import ID
+
+
+class Entity(Identifiable, HasAssets):
+    """Entity is a model with id and authorization."""
+
+    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
+    type: Annotated[
+        str | None,
+        Field(
+            examples=["license"],
+            description="The type of this Entity.",
+        ),
+    ] = None
+    createdBy: Annotated[
+        AgentUnion | None,
+        Field(description="The agent that created this entity."),
+    ] = None
+    updatedBy: Annotated[
+        AgentUnion | None,
+        Field(
+            description="The agent that updated this entity.",
+        ),
+    ] = None
+    authorized_public: Annotated[
+        bool | None,
+        Field(
+            examples=[True, False],
+            description="Whether the resource is authorized to be public.",
+        ),
+    ] = None
+    authorized_project_id: Annotated[
+        ID | None,
+        Field(
+            examples=[UUID("12345678-1234-1234-1234-123456789012")],
+            description="The project ID the resource is authorized to be public.",
+        ),
+    ] = None
+    contributions: Annotated[
+        "list[Contribution] | None", Field(description="The constributions for this entity.")
+    ] = None
+    legacy_id: Annotated[
+        list[str] | None,
+        Field(description="Legacy NEXUS ids."),
+    ] = None
+
+
+# Update forward reference for Contribution
+from entitysdk.models.contribution import Contribution  # noqa: E402
+
+Entity.model_rebuild(force=True)

entitysdk-0.2.3/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."),
+    ]

{entitysdk-0.2.2 → entitysdk-0.2.3}/src/entitysdk/models/ion_channel_model.py

@@ -4,7 +4,6 @@ from typing import Annotated
 
 from pydantic import Field
 
-from entitysdk.mixin import HasAssets
 from entitysdk.models.base import BaseModel
 from entitysdk.models.contribution import Contribution
 from entitysdk.models.entity import Entity
@@ -83,7 +82,7 @@ class NeuronBlock(BaseModel):
     ] = None
 
 
-class IonChannelModel(HasAssets, Entity):
+class IonChannelModel(Entity):
     """Ion channel mechanism model."""
 
     name: Annotated[

entitysdk-0.2.3/src/entitysdk/models/license.py

@@ -0,0 +1,33 @@
+"""License model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.core import Identifiable
+
+
+class License(Identifiable):
+    """License model."""
+
+    name: Annotated[
+        str,
+        Field(
+            examples=["Apache 2.0"],
+            description="The name of the license.",
+        ),
+    ]
+    description: Annotated[
+        str,
+        Field(
+            examples=["The 2.0 version of the Apache License"],
+            description="The description of the license.",
+        ),
+    ]
+    label: Annotated[
+        str,
+        Field(
+            examples=["Apache 2.0"],
+            description="The label of the license.",
+        ),
+    ]

entitysdk-0.2.3/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.types 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 | None,
+        Field(
+            description="The holding current of the memodel.",
+            examples=0.0,
+        ),
+    ] = None
+    threshold_current: Annotated[
+        float | None,
+        Field(
+            description="The threshold current of the memodel.",
+            examples=0.1,
+        ),
+    ] = None
+    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

entitysdk-0.2.3/src/entitysdk/models/morphology.py

@@ -0,0 +1,54 @@
+"""Morphology models."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.brain_location import BrainLocation
+from entitysdk.models.brain_region import BrainRegion
+from entitysdk.models.entity import Entity
+from entitysdk.models.license import License
+from entitysdk.models.mtype import MTypeClass
+from entitysdk.models.taxonomy import Species, Strain
+
+
+class ReconstructionMorphology(Entity):
+    """Morphology model."""
+
+    location: Annotated[
+        BrainLocation | None,
+        Field(
+            description="The location of the morphology in the brain.",
+        ),
+    ] = None
+    brain_region: Annotated[
+        BrainRegion | None,
+        Field(
+            description="The region of the brain where the morphology is located.",
+        ),
+    ] = None
+    species: Annotated[
+        Species | None,
+        Field(
+            description="The species of the morphology.",
+        ),
+    ] = None
+    strain: Annotated[
+        Strain | None,
+        Field(
+            description="The strain of the morphology.",
+        ),
+    ] = None
+    license: Annotated[
+        License | None,
+        Field(
+            description="The license attached to the morphology.",
+        ),
+    ] = None
+    mtypes: Annotated[
+        list[MTypeClass] | None,
+        Field(
+            description="The mtype classes of the morphology.",
+        ),
+    ] = None
+    legacy_id: list[str] | None = None