refactor: remove the Meta in Metadata

src/aind_data_schema/__init__.py

@@ -1,4 +1,4 @@
-""" imports for MetadataModel subclasses
+""" imports for DataModel subclasses
 """
 
 __version__ = "2.0.0"

src/aind_data_schema/base.py

@@ -94,7 +94,7 @@ def validate_fieldnames(self):
 GenericModelType = TypeVar("GenericModelType", bound=GenericModel)
 
 
-class MetadataModel(BaseModel, Generic[GenericModelType]):
+class DataModel(BaseModel, Generic[GenericModelType]):
     """BaseModel that disallows extra fields
 
     Also performs validation checks / coercion / upgrades where necessary
@@ -130,7 +130,7 @@ def unit_validator(cls, values):
         return values
 
 
-class MetadataCoreModel(MetadataModel):
+class DataCoreModel(DataModel):
     """Generic base class to hold common fields/validators/etc for all basic AIND schema"""
 
     _FILE_EXTENSION = PrivateAttr(default=".json")
@@ -155,7 +155,7 @@ def default_filename(cls):
         Returns standard filename in snakecase
         """
         parent_classes = [
-            base_class for base_class in cls.__bases__ if base_class.__name__ != MetadataCoreModel.__name__
+            base_class for base_class in cls.__bases__ if base_class.__name__ != DataCoreModel.__name__
         ]
 
         name = cls.__name__

src/aind_data_schema/components/coordinates.py

@@ -8,7 +8,7 @@
 from pydantic import Field
 from typing_extensions import Annotated
 
-from aind_data_schema.base import MetadataModel
+from aind_data_schema.base import DataModel
 
 
 class CcfVersion(str, Enum):
@@ -45,7 +45,7 @@ class AnatomicalDirection(str, Enum):
     OTHER = "Other"
 
 
-class CoordinateTransform(MetadataModel):
+class CoordinateTransform(DataModel):
     """Generic base class for coordinate transform subtypes"""
 
     type: str = Field(..., title="transformation type")
@@ -83,15 +83,15 @@ class Affine3dTransform(CoordinateTransform):
     )
 
 
-class Size2d(MetadataModel):
+class Size2d(DataModel):
     """2D size of an object"""
 
     width: int = Field(..., title="Width")
     height: int = Field(..., title="Height")
     unit: SizeUnit = Field(SizeUnit.PX, title="Size unit")
 
 
-class Size3d(MetadataModel):
+class Size3d(DataModel):
     """3D size of an object"""
 
     width: int = Field(..., title="Width")
@@ -100,7 +100,7 @@ class Size3d(MetadataModel):
     unit: SizeUnit = Field(SizeUnit.M, title="Size unit")
 
 
-class Orientation3d(MetadataModel):
+class Orientation3d(DataModel):
     """3D orientation of an object"""
 
     pitch: Decimal = Field(..., title="Angle pitch", ge=0, le=360)
@@ -109,15 +109,15 @@ class Orientation3d(MetadataModel):
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class ModuleOrientation2d(MetadataModel):
+class ModuleOrientation2d(DataModel):
     """2D module orientation of an object"""
 
     arc_angle: Decimal = Field(..., title="Arc angle")
     module_angle: Decimal = Field(..., title="Module angle")
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class ModuleOrientation3d(MetadataModel):
+class ModuleOrientation3d(DataModel):
     """3D module orientation of an object"""
 
     arc_angle: Decimal = Field(..., title="Arc angle")
@@ -126,7 +126,7 @@ class ModuleOrientation3d(MetadataModel):
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class Coordinates3d(MetadataModel):
+class Coordinates3d(DataModel):
     """Coordinates in a 3D grid"""
 
     x: Decimal = Field(..., title="Position X")
@@ -135,7 +135,7 @@ class Coordinates3d(MetadataModel):
     unit: SizeUnit = Field(SizeUnit.UM, title="Position unit")
 
 
-class CcfCoords(MetadataModel):
+class CcfCoords(DataModel):
     """Coordinates in CCF template space"""
 
     ml: Decimal = Field(..., title="ML")
@@ -145,7 +145,7 @@ class CcfCoords(MetadataModel):
     ccf_version: CcfVersion = Field(CcfVersion.CCFv3, title="CCF version")
 
 
-class Axis(MetadataModel):
+class Axis(DataModel):
     """Description of an axis"""
 
     name: AxisName = Field(..., title="Axis")
@@ -168,7 +168,7 @@ class ImageAxis(Axis):
     unit: SizeUnit = Field(SizeUnit.UM, title="Axis physical units")
 
 
-class RelativePosition(MetadataModel):
+class RelativePosition(DataModel):
     """Position and rotation of a device in a rig or instrument"""
 
     device_position_transformations: List[

src/aind_data_schema/components/devices.py

@@ -19,7 +19,7 @@
 from pydantic import Field, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated
 
-from aind_data_schema.base import GenericModel, GenericModelType, MetadataModel, AwareDatetimeWithDefault
+from aind_data_schema.base import GenericModel, GenericModelType, DataModel, AwareDatetimeWithDefault
 from aind_data_schema.components.coordinates import RelativePosition, Size3d
 from aind_data_schema.components.reagent import Reagent
 
@@ -261,7 +261,7 @@ class MyomatrixArrayType(str, Enum):
     SUTURED = "Sutured"
 
 
-class Device(MetadataModel):
+class Device(DataModel):
     """Generic device"""
 
     device_type: str = Field(..., title="Device type")  # Needs to be set by child classes that inherits
@@ -277,7 +277,7 @@ class Device(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class Software(MetadataModel):
+class Software(DataModel):
     """Description of generic software"""
 
     name: str = Field(..., title="Software name")
@@ -286,7 +286,7 @@ class Software(MetadataModel):
     parameters: GenericModelType = Field(GenericModel(), title="Software parameters")
 
 
-class Calibration(MetadataModel):
+class Calibration(DataModel):
     """Generic calibration class"""
 
     calibration_date: AwareDatetimeWithDefault = Field(..., title="Date and time of calibration")
@@ -297,7 +297,7 @@ class Calibration(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class Maintenance(MetadataModel):
+class Maintenance(DataModel):
     """Generic maintenance class"""
 
     maintenance_date: AwareDatetimeWithDefault = Field(..., title="Date and time of maintenance")
@@ -444,7 +444,7 @@ def validate_other(cls, value: Optional[str], info: ValidationInfo) -> Optional[
         return value
 
 
-class CameraAssembly(MetadataModel):
+class CameraAssembly(DataModel):
     """Named assembly of a camera and lens (and optionally a filter)"""
 
     # required fields
@@ -458,7 +458,7 @@ class CameraAssembly(MetadataModel):
     position: Optional[RelativePosition] = Field(default=None, title="Relative position of this assembly")
 
 
-class DAQChannel(MetadataModel):
+class DAQChannel(DataModel):
     """Named input or output channel on a DAQ device"""
 
     # required fields
@@ -560,7 +560,7 @@ class Lamp(Device):
     temperature_unit: Optional[TemperatureUnit] = Field(default=None, title="Temperature unit")
 
 
-class ProbePort(MetadataModel):
+class ProbePort(DataModel):
     """Port for a probe connection"""
 
     index: int = Field(..., title="One-based port index")
@@ -610,7 +610,7 @@ class Patch(Device):
     photobleaching_date: Optional[date] = Field(default=None, title="Photobleaching date")
 
 
-class LaserAssembly(MetadataModel):
+class LaserAssembly(DataModel):
     """Assembly for optogenetic stimulation"""
 
     name: str = Field(..., title="Laser assembly name")
@@ -638,7 +638,7 @@ class EphysProbe(Device):
     headstage: Optional[Headstage] = Field(default=None, title="Headstage for this probe")
 
 
-class EphysAssembly(MetadataModel):
+class EphysAssembly(DataModel):
     """Module for electrophysiological recording"""
 
     name: str = Field(..., title="Ephys assembly name")
@@ -659,7 +659,7 @@ class FiberProbe(Device):
     length_unit: SizeUnit = Field(default=SizeUnit.MM, title="Length unit")
 
 
-class FiberAssembly(MetadataModel):
+class FiberAssembly(DataModel):
     """Module for inserted fiber photometry recording"""
 
     name: str = Field(..., title="Fiber assembly name")
@@ -839,7 +839,7 @@ def validate_other(self):
         return self
 
 
-class RewardDelivery(MetadataModel):
+class RewardDelivery(DataModel):
     """Description of reward delivery system"""
 
     device_type: Literal["Reward delivery"] = "Reward delivery"
@@ -862,7 +862,7 @@ class ChannelType(Enum):
     CARRIER = "Carrier"
 
 
-class OlfactometerChannel(MetadataModel):
+class OlfactometerChannel(DataModel):
     """description of a Olfactometer channel"""
 
     channel_index: int = Field(..., title="Channel index")

src/aind_data_schema/components/reagent.py

@@ -7,10 +7,10 @@
 from aind_data_schema_models.pid_names import PIDName
 from pydantic import Field
 
-from aind_data_schema.base import MetadataModel
+from aind_data_schema.base import DataModel
 
 
-class Reagent(MetadataModel):
+class Reagent(DataModel):
     """Description of reagent used in procedure"""
 
     name: str = Field(..., title="Name")

src/aind_data_schema/components/stimulus.py

@@ -7,7 +7,7 @@
 from aind_data_schema_models.units import ConcentrationUnit, FrequencyUnit, PowerUnit, TimeUnit
 from pydantic import Field, model_validator
 
-from aind_data_schema.base import GenericModel, GenericModelType, MetadataModel
+from aind_data_schema.base import GenericModel, GenericModelType, DataModel
 
 
 class PulseShape(str, Enum):
@@ -25,7 +25,7 @@ class FilterType(str, Enum):
     OTHER = "Other"
 
 
-class OptoStimulation(MetadataModel):
+class OptoStimulation(DataModel):
     """Description of opto stimulation parameters"""
 
     stimulus_type: Literal["Opto Stimulation"] = "Opto Stimulation"
@@ -53,7 +53,7 @@ class OptoStimulation(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class VisualStimulation(MetadataModel):
+class VisualStimulation(DataModel):
     """Description of visual stimulus parameters. Provides a high level description of stimulus."""
 
     stimulus_type: Literal["Visual Stimulation"] = "Visual Stimulation"
@@ -71,7 +71,7 @@ class VisualStimulation(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class PhotoStimulationGroup(MetadataModel):
+class PhotoStimulationGroup(DataModel):
     """Description of a photostimulation group"""
 
     group_index: int = Field(..., title="Group index")
@@ -88,7 +88,7 @@ class PhotoStimulationGroup(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class PhotoStimulation(MetadataModel):
+class PhotoStimulation(DataModel):
     """Description of a photostimulation session"""
 
     stimulus_type: Literal["Photo Stimulation"] = "Photo Stimulation"
@@ -101,7 +101,7 @@ class PhotoStimulation(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class OlfactometerChannelConfig(MetadataModel):
+class OlfactometerChannelConfig(DataModel):
     """Description of olfactometer channel configurations"""
 
     channel_index: int = Field(..., title="Channel index")
@@ -111,7 +111,7 @@ class OlfactometerChannelConfig(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class OlfactoryStimulation(MetadataModel):
+class OlfactoryStimulation(DataModel):
     """Description of a olfactory stimulus"""
 
     stimulus_type: Literal["Olfactory Stimulation"] = "Olfactory Stimulation"
@@ -120,7 +120,7 @@ class OlfactoryStimulation(MetadataModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class AuditoryStimulation(MetadataModel):
+class AuditoryStimulation(DataModel):
     """Description of an auditory stimulus"""
 
     stimulus_type: Literal["Auditory Stimulation"] = "Auditory Stimulation"

src/aind_data_schema/components/tile.py

@@ -6,7 +6,7 @@
 from pydantic import Field
 from typing_extensions import Annotated
 
-from aind_data_schema.base import MetadataModel, AwareDatetimeWithDefault
+from aind_data_schema.base import DataModel, AwareDatetimeWithDefault
 from aind_data_schema.components.coordinates import (
     Affine3dTransform,
     Rotation3dTransform,
@@ -15,7 +15,7 @@
 )
 
 
-class Channel(MetadataModel):
+class Channel(DataModel):
     """Description of a channel"""
 
     channel_name: str = Field(..., title="Channel")
@@ -36,7 +36,7 @@ class Channel(MetadataModel):
     description: Optional[str] = Field(default=None, title="Description")
 
 
-class Tile(MetadataModel):
+class Tile(DataModel):
     """Description of an image tile"""
 
     coordinate_transformations: List[

src/aind_data_schema/core/acquisition.py

@@ -6,20 +6,20 @@
 from aind_data_schema_models.process_names import ProcessName
 from pydantic import Field, SkipValidation, field_validator
 
-from aind_data_schema.base import MetadataCoreModel, MetadataModel, AwareDatetimeWithDefault
+from aind_data_schema.base import DataCoreModel, DataModel, AwareDatetimeWithDefault
 from aind_data_schema.components.coordinates import AnatomicalDirection, AxisName, ImageAxis
 from aind_data_schema.components.devices import Calibration, ImmersionMedium, Maintenance, Software
 from aind_data_schema.components.tile import AcquisitionTile
 
 
-class Immersion(MetadataModel):
+class Immersion(DataModel):
     """Description of immersion medium"""
 
     medium: ImmersionMedium = Field(..., title="Immersion medium")
     refractive_index: Decimal = Field(..., title="Index of refraction")
 
 
-class ProcessingSteps(MetadataModel):
+class ProcessingSteps(DataModel):
     """Description of downstream processing steps"""
 
     channel_name: str = Field(..., title="Channel name")
@@ -40,10 +40,10 @@ class ProcessingSteps(MetadataModel):
     ] = Field(...)
 
 
-class Acquisition(MetadataCoreModel):
+class Acquisition(DataCoreModel):
     """Description of an imaging acquisition session"""
 
-    _DESCRIBED_BY_URL = MetadataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/acquisition.py"
+    _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/acquisition.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
     schema_version: SkipValidation[Literal["1.0.4"]] = Field(default="1.0.4")
     protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")