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feat 29: ecephys results (#31)
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* adds models for different ecephys results

* base filters

* adds unit tests

* linters

* adds newline to end of metadata.py
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@mekhlakapoor
mekhlakapoor authored Sep 23, 2024
1 parent fc9df3a commit 8f3bee5
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278 changes: 278 additions & 0 deletions src/aind_slims_api/models/ecephys_session.py
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"""Contains a model for an ecephys result stored in SLIMS."""

from datetime import datetime
from typing import Annotated, List, Optional, ClassVar
from pydantic import Field
from aind_slims_api.models.base import SlimsBaseModel
from aind_slims_api.models.utils import UnitSpec


class SlimsStreamsResult(SlimsBaseModel):
"""Model for a SLIMS Result Streams"""

test_label: str = Field(
"Streams", serialization_alias="test_label", validation_alias="test_label"
)
mouse_session: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession_display",
validation_alias="rslt_cf_fk_mouseSession_display",
)
stream_modalities: Optional[List] = Field(
default=None,
serialization_alias="rslt_cf_streamModalities",
validation_alias="rslt_cf_streamModalities",
)
daq_names: Optional[List] = Field(
default=[],
serialization_alias="rslt_cf_daqNames",
validation_alias="rslt_cf_daqNames",
)
camera_names: Optional[List] = Field(
default=None,
serialization_alias="rslt_cf_cameraNames2",
validation_alias="rslt_cf_cameraNames2",
)
# Look up in ReferenceDataRecord table
stream_modules_pk: Optional[List] = Field(
default=None,
serialization_alias="rslt_cf_fk_injectionMaterial2",
validation_alias="rslt_cf_fk_injectionMaterial2",
)
pk: Optional[int] = Field(
None,
serialization_alias="rslt_pk",
validation_alias="rslt_pk",
)
mouse_pk: Optional[int] = Field(
None,
serialization_alias="rslt_fk_content",
validation_alias="rslt_fk_content",
)
mouse_session_pk: Optional[int] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession",
validation_alias="rslt_cf_fk_mouseSession",
)
created_on: Optional[datetime] = Field(
default=None,
serialization_alias="rslt_createdOn",
validation_alias="rslt_createdOn",
)
_slims_table = "Result"
_base_fetch_filters: ClassVar[dict[str, str]] = {
"test_name": "test_ephys_in_vivo_recording_stream",
}


class SlimsStimulusEpochsResult(SlimsBaseModel):
"""Model for a SLIMS Result Stimulus Epochs"""

test_label: str = Field(
"Stimulus Epochs",
serialization_alias="test_label",
validation_alias="test_label",
)
mouse_session: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession_display",
validation_alias="rslt_cf_fk_mouseSession_display",
)
stimulus_device_names: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_stimulusDeviceNames",
validation_alias="rslt_cf_stimulusDeviceNames",
)
stimulus_name: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_stimulusDeviceNames",
validation_alias="rslt_cf_stimulusDeviceNames",
)
stimulus_modalities: Optional[List] = Field(
default=None,
serialization_alias="rslt_cf_stimulusModalities2",
validation_alias="rslt_cf_stimulusModalities2",
)
reward_consumed_during_epoch: Annotated[float | None, UnitSpec("ml")] = Field(
default=None,
serialization_alias="rslt_cf_rewardConsumedDuringEpoch",
validation_alias="rslt_cf_rewardConsumedDuringEpoch",
)
led_name: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_lightEmittingDiodeName",
validation_alias="rslt_cf_lightEmittingDiodeName",
)
led_excitation_power_mw: Annotated[float | None, UnitSpec("mW")] = Field(
default=None,
serialization_alias="rslt_cf_lightEmittingDiodeExcitationPower",
validation_alias="rslt_cf_lightEmittingDiodeExcitationPower",
)
laser_name: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_laserName",
validation_alias="rslt_cf_laserName",
)
laser_wavelength: Annotated[float | None, UnitSpec("nm")] = Field(
default=None,
serialization_alias="rslt_laserWavelength",
validation_alias="rslt_laserWavelength",
)
laser_excitation_power: Annotated[float | None, UnitSpec("mW")] = Field(
default=None,
serialization_alias="rslt_cf_laserExcitationPower",
validation_alias="rslt_cf_laserExcitationPower",
)
speaker_name: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_speakerName",
validation_alias="rslt_cf_speakerName",
)
speaker_volume: Annotated[float | None, UnitSpec("dB")] = Field(
default=None,
serialization_alias="rslt_cf_speakerVolume",
validation_alias="rslt_cf_speakerVolume",
)
pk: Optional[int] = Field(
None,
serialization_alias="rslt_pk",
validation_alias="rslt_pk",
)
mouse_pk: Optional[int] = Field(
None,
serialization_alias="rslt_fk_content",
validation_alias="rslt_fk_content",
)
mouse_session_pk: Optional[int] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession",
validation_alias="rslt_cf_fk_mouseSession",
)
created_on: Optional[datetime] = Field(
default=None,
serialization_alias="rslt_createdOn",
validation_alias="rslt_createdOn",
)
_slims_table = "Result"
_base_fetch_filters: ClassVar[dict[str, str]] = {
"test_name": "test_stimulus_epochs",
}


class SlimsMouseSessionResult(SlimsBaseModel):
"""Model for a SLIMS Result Mouse Session"""

test_label: str = Field(
"Mouse Session", serialization_alias="test_label", validation_alias="test_label"
)
mouse_session_id: str = Field(
...,
serialization_alias="rslt_uniqueIdentifier",
validation_alias="rslt_uniqueIdentifier",
)
mouse_session: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession_display",
validation_alias="rslt_cf_fk_mouseSession_display",
)
weight_prior_g: Annotated[float | None, UnitSpec("g")] = Field(
default=None,
serialization_alias="rslt_cf_animalWeightPrior",
validation_alias="rslt_cf_animalWeightPrior",
)
weight_post_g: Annotated[float | None, UnitSpec("g")] = Field(
default=None,
serialization_alias="rslt_cf_animalWeightPost",
validation_alias="rslt_cf_animalWeightPost",
)
reward_delivery: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_rewardDelivery",
validation_alias="rslt_cf_rewardDelivery",
)
reward_consumed_vol: Annotated[float | None, UnitSpec("ml")] = Field(
default=None,
serialization_alias="rslt_cf_rewardConsumedvolume",
validation_alias="rslt_cf_rewardConsumedvolume",
)
reward_delivery_pk: Optional[int] = Field(
default=None,
serialization_alias="rslt_cf_fk_rewardDelivery",
validation_alias="rslt_cf_fk_rewardDelivery",
)
pk: Optional[int] = Field(
None,
serialization_alias="rslt_pk",
validation_alias="rslt_pk",
)
mouse_pk: Optional[int] = Field(
None,
serialization_alias="rslt_fk_content",
validation_alias="rslt_fk_content",
)
mouse_session_pk: Optional[int] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession",
validation_alias="rslt_cf_fk_mouseSession",
)
created_on: Optional[datetime] = Field(
default=None,
serialization_alias="rslt_createdOn",
validation_alias="rslt_createdOn",
)
_slims_table = "Result"
_base_fetch_filters: ClassVar[dict[str, str]] = {
"test_name": "test_session_information",
}


class SlimsEphysInsertionResult(SlimsBaseModel):
"""Model for a SLIMS Ephys Insertion Result"""

test_label: str = Field(
"EPHYS - Insertion",
serialization_alias="test_label",
validation_alias="test_label",
)
mouse_session: Optional[str] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession_display",
validation_alias="rslt_cf_fk_mouseSession_display",
)
mouse_session_pk: Optional[int] = Field(
default=None,
serialization_alias="rslt_cf_fk_mouseSession",
validation_alias="rslt_cf_fk_mouseSession",
)
dye: Optional[str] = Field(
default=None, serialization_alias="rslt_cf_dye", validation_alias="rslt_cf_dye"
)
manipulator_x: Annotated[float | None, UnitSpec("um")] = Field(
default=None,
serialization_alias="rslt_cf_manipulatorCoordinates",
validation_alias="rslt_cf_manipulatorCoordinates",
)
manipulator_y: Annotated[float | None, UnitSpec("um")] = Field(
default=None,
serialization_alias="rslt_cf_manipulatorY",
validation_alias="rslt_cf_manipulatorY",
)
insertion_fail: Optional[bool] = Field(
default=None,
serialization_alias="rslt_cf_failed",
validation_alias="rslt_cf_failed",
)
mouse_pk: Optional[int] = Field(
None,
serialization_alias="rslt_fk_content",
validation_alias="rslt_fk_content",
)
created_on: Optional[datetime] = Field(
default=None,
serialization_alias="rslt_createdOn",
validation_alias="rslt_createdOn",
)
_slims_table = "Result"
_base_fetch_filters: ClassVar[dict[str, str]] = {
"test_name": "test_ephys_insertion",
}
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