fix: add Reagent as an option for Acquisition.manipulations (#1797)

* fix: add SpecimenProcedure as an option for Acquisition.manipulations

* update docs [skip actions]

* chore: delete unmaintained CHANGELOG.md

* update docs [skip actions]

* Revert "chore: delete unmaintained CHANGELOG.md"

This reverts commit 28d430e.

* refactor: turn protocol_id fields into a Mixin class

* feat: add Reagent as an option for Manipulation

* update docs

* update docs

* chore: lint

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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/aind_data_schema_models/organizations.md

@@ -22,6 +22,7 @@ Organization
 | `ASUS` | `None` | `ASUS` | `Research Organization Registry (ROR)` | `00bxkz165` |
 | `BASLER` | `None` | `Basler` | `None` | `None` |
 | `BCM` | `BCM` | `Baylor College of Medicine` | `Research Organization Registry (ROR)` | `02pttbw34` |
+| `BROADCOM` | `None` | `Broadcom` | `Research Organization Registry (ROR)` | `035gt5s03` |
 | `BRUKER` | `None` | `Bruker` | `Research Organization Registry (ROR)` | `04r739x86` |
 | `BU` | `BU` | `Boston University` | `Research Organization Registry (ROR)` | `05qwgg493` |
 | `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Research Organization Registry (ROR)` | `05pdc0q70` |
@@ -67,6 +68,7 @@ Organization
 | `JENOPTIK` | `None` | `Jenoptik` | `Research Organization Registry (ROR)` | `05g7t5c49` |
 | `JHU` | `JHU` | `Johns Hopkins University` | `Research Organization Registry (ROR)` | `00za53h95` |
 | `JULABO` | `None` | `Julabo` | `None` | `None` |
+| `KENT_SCIENTIFIC_CORPORATION` | `None` | `Kent Scientific Corporation` | `Research Organization Registry (ROR)` | `03xkj6a08` |
 | `KOWA` | `None` | `Kowa` | `Research Organization Registry (ROR)` | `03zbwg482` |
 | `LASER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LASOS` | `LASOS` | `LASOS Lasertechnik` | `None` | `None` |
@@ -105,6 +107,7 @@ Organization
 | `OLYMPUS` | `None` | `Olympus` | `Research Organization Registry (ROR)` | `02vcdte90` |
 | `OPTOTUNE` | `None` | `Optotune` | `None` | `None` |
 | `OTHER` | `None` | `Other` | `None` | `None` |
+| `OXFORD_INSTRUMENTS` | `None` | `Oxford Instruments` | `Research Organization Registry (ROR)` | `01age2z78` |
 | `OXXIUS` | `None` | `Oxxius` | `None` | `None` |
 | `PLACID_INDUSTRIES` | `None` | `Placid Industries` | `None` | `None` |
 | `PRIZMATIX` | `None` | `Prizmatix` | `None` | `None` |
@@ -113,6 +116,7 @@ Organization
 | `RESEARCH_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `SAME_SKY` | `None` | `Same Sky` | `None` | `None` |
 | `SCHNEIDER_KREUZNACH` | `None` | `Schneider-Kreuznach` | `None` | `None` |
+| `SCIENTIFICA` | `None` | `Scientifica` | `Research Organization Registry (ROR)` | `00z72df47` |
 | `SECOND_ORDER_EFFECTS` | `None` | `Second Order Effects` | `None` | `None` |
 | `SEMROCK` | `None` | `Semrock` | `None` | `None` |
 | `SICGEN` | `None` | `SICGEN` | `None` | `None` |
@@ -138,5 +142,6 @@ Organization
 | `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |
+| `WPI` | `WPI` | `World Precision Intstruments` | `Research Organization Registry (ROR)` | `03st5df34` |
 
 

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__