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feat 29: ecephys results #31

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merged 6 commits into from
Sep 23, 2024
Merged

feat 29: ecephys results #31

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ce3c8d6
adds models for different ecephys results
mekhlakapoor Sep 20, 2024
57376c8
base filters
mekhlakapoor Sep 20, 2024
ca25aa9
adds unit tests
mekhlakapoor Sep 21, 2024
492d25b
linters
mekhlakapoor Sep 21, 2024
ea898c4
merge main and resolve conflicts
mekhlakapoor Sep 21, 2024
b274207
adds newline to end of metadata.py
mekhlakapoor Sep 21, 2024
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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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