Merge branch 'dev' into 1794-isi-instrumentjson

Author: dbirman

docs/source/acquisition.md

@@ -83,7 +83,6 @@ while the StimulusEpoch represents all stimuli being presented.
 | `acquisition_start_tz` | `int or pydantic_extra_types.timezone_name.TimeZoneName or NoneType` | Acquisition start timezone (Automatically populated by a validator based on acquisition_start_time. Will be a TimeZoneName (IANA name) when the datetime uses a ZoneInfo timezone, or an integer UTC offset in hours for fixed-offset timezones. Use ZoneInfo (from the zoneinfo standard library) to preserve the named timezone.) |
 | `acquisition_end_time` | `datetime (timezone-aware)` | Acquisition end time  |
 | `experimenters` | `List[str]` | experimenter(s)  |
-| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 | `ethics_review_id` | `Optional[List[str]]` | Ethics review ID  |
 | `instrument_id` | `Optional[str]` | Instrument ID (Should match the Instrument.instrument_id. Required when instrument metadata is available.) |
 | `acquisition_type` | `str` | Acquisition type (Descriptive string detailing the type of acquisition, should be consistent across similar acquisitions for the same experiment.) |
@@ -95,6 +94,7 @@ while the StimulusEpoch represents all stimuli being presented.
 | `stimulus_epochs` | List[[StimulusEpoch](acquisition.md#stimulusepoch)] | Stimulus (A stimulus epoch captures all stimuli being presented during an acquisition. Epochs should be split when the purpose of the stimulus changes.) |
 | `manipulations` | List[[Manipulation](acquisition.md#manipulation)] | Manipulations (Procedures performed during the acquisition.) |
 | `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | Subject details (Required for in vivo acquisitions.) |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ## Model definitions
@@ -151,9 +151,10 @@ Description of procedures performed during an acquisition.
 |-------|------|-------------|
 | `start_time` | `datetime (timezone-aware)` | Manipulation start time (Must be between the acquisition start and end times) |
 | `end_time` | `datetime (timezone-aware)` | Manipulation end time (Must be between the acquisition start and end times) |
-| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection)]] | Procedures (Procedures performed during the manipulation) |
+| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection) or [Reagent](components/reagent.md#reagent)]] | Procedures (Procedures performed during the manipulation) |
 | `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ### PerformanceMetrics

docs/source/components/injection_procedures.md

@@ -12,7 +12,7 @@ Description of an injection procedure
 | `targeted_structure` | Optional[[MouseAnatomyModel](../aind_data_schema_models/external.md#mouseanatomymodel)] | Injection target (Use InjectionTargets) |
 | `relative_position` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Relative position  |
 | `dynamics` | List[[InjectionDynamics](#injectiondynamics)] | Injection dynamics (List of injection events, one per location/depth) |
-| <del>`protocol_id`</del> | `Optional[str]` | **[DEPRECATED]** Use protocol_id in Surgery or NonSurgicalInjection instead. Protocol ID (DOI for protocols.io) |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### InjectionDynamics

docs/source/components/measurements.md

@@ -10,7 +10,6 @@ Generic calibration class
 |-------|------|-------------|
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
 | `description` | `str` | Description (Brief description of what is being calibrated) |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `input` | `List[float or str]` | Inputs (Calibration input) |
 | `input_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) or {TorqueUnit} | Input unit  |
@@ -19,6 +18,7 @@ Generic calibration class
 | `output_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) or {TorqueUnit} | Output unit  |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -51,9 +51,9 @@ Generic maintenance class
 |-------|------|-------------|
 | `maintenance_date` | `datetime (timezone-aware)` | Date and time of maintenance  |
 | `description` | `str` | Description (Description on maintenance procedure) |
-| `protocol_id` | `Optional[str]` | Protocol ID  |
 | `reagents` | Optional[List[[Reagent](reagent.md#reagent)]] | Reagents  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -69,11 +69,11 @@ Calibration of a device that outputs power based on input strength
 | `output_unit` | [PowerUnit](../aind_data_schema_models/units.md#powerunit) | Output unit  |
 | `description` | `"Power measured for various power or percentage input strengths"` |   |
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `repeats` | `Optional[int]` | Number of repeats (If each input was repeated multiple times, provide the number of repeats) |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -90,10 +90,10 @@ Calibration of a liquid delivery device based on solenoid/valve opening times
 | `output_unit` | [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) | Output unit  |
 | `description` | `"Volume measured for various solenoid opening times"` |   |
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 

docs/source/components/specimen_procedures.md

@@ -106,9 +106,9 @@ Description of surgical or other procedure performed on a specimen
 | `start_date` | `datetime.date` | Start date  |
 | `end_date` | `datetime.date` | End date  |
 | `experimenters` | `List[str]` | experimenter(s)  |
-| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 | `protocol_parameters` | `Optional[Dict[str, str]]` | Protocol parameters (Parameters defined in the protocol and their value during this procedure) |
 | `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [Sectioning](#sectioning) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset) or [Solution](reagent.md#solution)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 

docs/source/components/subject_procedures.md

@@ -11,9 +11,9 @@ Description of a non-surgical procedure performed on a subject
 | `start_date` | `datetime.date` | Start date  |
 | `experimenters` | `Optional[List[str]]` | experimenter(s)  |
 | `ethics_review_id` | `str` | Ethics review ID  |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `description` | `str` | Description  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### NonSurgicalInjection
@@ -36,7 +36,6 @@ Description of subject procedures performed at one time
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `start_date` | `datetime.date` | Start date  |
 | `experimenters` | `Optional[List[str]]` | experimenter(s)  |
 | `ethics_review_id` | `Optional[str]` | Ethics review ID  |
@@ -49,6 +48,7 @@ Description of subject procedures performed at one time
 | `measured_coordinates` | Optional[Dict[[Origin](../aind_data_schema_models/coordinates.md#origin), [Translation](coordinates.md#translation)]] | Measured coordinates (Coordinates measured during the procedure, for example Bregma and Lambda) |
 | `procedures` | List[[CatheterImplant](surgery_procedures.md#catheterimplant) or [Craniotomy](surgery_procedures.md#craniotomy) or [ProbeImplant](surgery_procedures.md#probeimplant) or [Headframe](surgery_procedures.md#headframe) or [BrainInjection](surgery_procedures.md#braininjection) or [Injection](injection_procedures.md#injection) or [MyomatrixInsertion](surgery_procedures.md#myomatrixinsertion) or [GenericSurgeryProcedure](surgery_procedures.md#genericsurgeryprocedure) or [Perfusion](surgery_procedures.md#perfusion) or [SampleCollection](surgery_procedures.md#samplecollection)] | Procedures  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### TrainingProtocol

docs/source/components/surgery_procedures.md

@@ -26,7 +26,7 @@ Description of an injection procedure into a brain
 | `injection_materials` | List[[ViralMaterial](injection_procedures.md#viralmaterial) or [NonViralMaterial](injection_procedures.md#nonviralmaterial)] | Injection material  |
 | `relative_position` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Relative position  |
 | `dynamics` | List[[InjectionDynamics](injection_procedures.md#injectiondynamics)] | Injection dynamics (List of injection events, one per location/depth) |
-| <del>`protocol_id`</del> | `Optional[str]` | **[DEPRECATED]** Use protocol_id in Surgery or NonSurgicalInjection instead. Protocol ID (DOI for protocols.io) |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### CatheterImplant
@@ -46,7 +46,6 @@ Description of craniotomy procedure
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `craniotomy_type` | [CraniotomyType](#craniotomytype) | Craniotomy type  |
 | `coordinate_system_name` | `Optional[str]` | Coordinate system name  |
 | `position` | [Translation](coordinates.md#translation) or List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)] or NoneType | Craniotomy position  |
@@ -55,6 +54,7 @@ Description of craniotomy procedure
 | `protective_material` | Optional[[ProtectiveMaterial](#protectivematerial)] | Protective material  |
 | `implant_part_number` | `Optional[str]` | Implant part number  |
 | `dura_removed` | `Optional[bool]` | Dura removed  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### CraniotomyType
@@ -76,9 +76,9 @@ Description of a surgery procedure performed on a subject
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `description` | `str` | Description  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### GroundWireImplant
@@ -110,12 +110,12 @@ Description of headframe procedure
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `headframe_type` | `str` | Headframe type  |
 | `headframe_part_number` | `Optional[str]` | Headframe part number  |
 | `headframe_material` | Optional[[HeadframeMaterial](#headframematerial)] | Headframe material  |
 | `well_part_number` | `Optional[str]` | Well part number  |
 | `well_type` | `Optional[str]` | Well type  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### HeadframeMaterial
@@ -135,9 +135,9 @@ Description of a Myomatrix array insertion for EMG
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `ground_electrode` | [GroundWireImplant](#groundwireimplant) | Ground electrode  |
 | `implanted_device` | [MyomatrixArray](devices.md#myomatrixarray) | Implanted device  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### Perfusion
@@ -146,8 +146,8 @@ Description of a perfusion procedure that creates a specimen
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `output_specimen_ids` | `List[str]` | Specimen ID (IDs of specimens resulting from this procedure. Whole brains can use the {subject_id}, partial sections should always include a suffix {subject_id}_###) |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### ProbeImplant
@@ -156,9 +156,9 @@ Description of a probe (fiber, ephys) implant procedure
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `implanted_device` | [EphysProbe](devices.md#ephysprobe) or [FiberProbe](devices.md#fiberprobe) | Implanted device  |
 | `device_config` | [ProbeConfig](configs.md#probeconfig) | Device configuration  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### ProtectiveMaterial

src/aind_data_schema/base.py

@@ -201,7 +201,11 @@ def default_filename(cls):
         """
         Returns standard filename in snakecase
         """
-        parent_classes = [base_class for base_class in cls.__bases__ if base_class.__name__ != DataCoreModel.__name__]
+        parent_classes = [
+            base_class
+            for base_class in cls.__bases__
+            if base_class.__name__ != DataCoreModel.__name__ and issubclass(base_class, DataModel)
+        ]
 
         name = cls.__name__
 

src/aind_data_schema/components/identifiers.py

@@ -5,7 +5,7 @@
 from typing import Dict, List, Optional
 
 from aind_data_schema_models.registries import Registry
-from pydantic import Field, model_validator
+from pydantic import Field, BaseModel, model_validator
 import warnings
 
 from typing import Annotated
@@ -53,6 +53,18 @@ class Person(DataModel):
     registry_identifier: Optional[str] = Field(default=None, title="ORCID ID")
 
 
+class ProtocolMixin(BaseModel):
+    """Mixin that adds a protocol_id field (single DOI string)"""
+
+    protocol_id: Optional[str] = Field(default=None, title="Protocol ID", description="DOI for protocols.io")
+
+
+class ProtocolListMixin(BaseModel):
+    """Mixin that adds a protocol_id field (list of DOI strings)"""
+
+    protocol_id: Optional[List[str]] = Field(default=None, title="Protocol ID", description="DOI for protocols.io")
+
+
 class Software(DataModel):
     """Software package identifier"""
 

src/aind_data_schema/components/injection_procedures.py

@@ -11,6 +11,7 @@
 from pydantic import Field, model_validator
 
 from aind_data_schema.base import DataModel, DiscriminatedList
+from aind_data_schema.components.identifiers import ProtocolMixin
 from aind_data_schema.components.reagent import Reagent
 
 
@@ -102,7 +103,7 @@ def check_volume_or_current(self):
         return self
 
 
-class Injection(DataModel):
+class Injection(ProtocolMixin, DataModel):
     """Description of an injection procedure"""
 
     injection_materials: DiscriminatedList[ViralMaterial | NonViralMaterial] = Field(
@@ -116,9 +117,3 @@ class Injection(DataModel):
     dynamics: List[InjectionDynamics] = Field(
         ..., title="Injection dynamics", description="List of injection events, one per location/depth"
     )
-    protocol_id: Optional[str] = Field(
-        default=None,
-        title="Protocol ID",
-        description="DOI for protocols.io",
-        deprecated="Use protocol_id in Surgery or NonSurgicalInjection instead",
-    )