add FluorescentReagent (#1860)

* add FluorescentReagent

* update docs

* whitespace

* update docs

* specimen procedures

* update docs

* lint

---------

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

Author: saskiad

docs/source/components/reagent.md

@@ -2,9 +2,27 @@
 
 ## Model definitions
 
+### FluorescentReagent
+
+Description of an inherently fluorescent marker. Note this class will change name in v3.0
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `stain_type` | [StainType](../aind_data_schema_models/reagent.md#staintype) |   |
+| `excitation_wavelength` | `int` | Excitation wavelength (nm)  |
+| `emission_wavelength` | `int` | Emission wavelength (nm)  |
+| `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Excitation wavelength unit  |
+| `name` | `str` | Name  |
+| `source` | [Organization](../aind_data_schema_models/organizations.md#organization) | Source  |
+| `rrid` | Optional[[PIDName](../aind_data_schema_models/pid_names.md#pidname)] | Research Resource ID  |
+| `lot_number` | `Optional[str]` | Lot number  |
+| `expiration_date` | `Optional[datetime.date]` | Lot expiration date  |
+
+
 ### FluorescentStain
 
-Description of a fluorescent stain
+Description of a fluorescent stain consisting of a probe associated with a fluorophore.
+Note this class will change names in v3.0
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|

docs/source/components/specimen_procedures.md

@@ -107,7 +107,7 @@ Description of surgical or other procedure performed on a specimen
 | `end_date` | `datetime.date` | End date  |
 | `experimenters` | `List[str]` | experimenter(s)  |
 | `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.) |
+| `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentReagent](reagent.md#fluorescentreagent) 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) |
 

src/aind_data_schema/components/reagent.py

@@ -83,9 +83,19 @@ class ProbeReagent(Reagent):
 
 
 class FluorescentStain(Reagent):
-    """Description of a fluorescent stain"""
+    """Description of a fluorescent stain consisting of a probe associated with a fluorophore.
+    Note this class will change names in v3.0"""
 
     probe: Discriminated[GeneProbe | ProteinProbe | SmallMoleculeProbe] = Field(..., title="Target of the stain")
     stain_type: StainType = Field(..., title="Stain type")
     fluorophore: Fluorophore = Field(..., title="Fluorophore used in the stain")
     initiator_name: Optional[str] = Field(default=None, title="Initiator for HCR probes")
+
+
+class FluorescentReagent(Reagent):
+    """Description of an inherently fluorescent marker. Note this class will change name in v3.0"""
+
+    stain_type: StainType = Field(..., type="Stain type")
+    excitation_wavelength: int = Field(..., title="Excitation wavelength (nm)")
+    emission_wavelength: int = Field(..., title="Emission wavelength (nm)")
+    wavelength_unit: SizeUnit = Field(default=SizeUnit.NM, title="Excitation wavelength unit")

src/aind_data_schema/components/specimen_procedures.py

@@ -14,7 +14,14 @@
 from aind_data_schema.base import AwareDatetimeWithDefault, DataModel, DiscriminatedList
 from aind_data_schema.components.coordinates import Atlas, CoordinateSystem, Translation
 from aind_data_schema.components.identifiers import ProtocolListMixin
-from aind_data_schema.components.reagent import FluorescentStain, GeneProbeSet, ProbeReagent, Reagent, Solution
+from aind_data_schema.components.reagent import (
+    FluorescentReagent,
+    FluorescentStain,
+    GeneProbeSet,
+    ProbeReagent,
+    Reagent,
+    Solution,
+)
 from aind_data_schema.utils.exceptions import OneOfError
 
 
@@ -178,7 +185,15 @@ class SpecimenProcedure(ProtocolListMixin, DataModel):
     )
 
     procedure_details: DiscriminatedList[
-        HCRSeries | FluorescentStain | Sectioning | PlanarSectioning | ProbeReagent | Reagent | GeneProbeSet | Solution
+        HCRSeries
+        | FluorescentReagent
+        | FluorescentStain
+        | Sectioning
+        | PlanarSectioning
+        | ProbeReagent
+        | Reagent
+        | GeneProbeSet
+        | Solution
     ] = Field(
         default=[],
         title="Procedure details",
@@ -193,6 +208,7 @@ def validate_procedure_type(self):
 
         has_hcr_series = any(isinstance(detail, HCRSeries) for detail in self.procedure_details)
         has_fluorescent_stain = any(isinstance(detail, FluorescentStain) for detail in self.procedure_details)
+        has_fluorescent_reagent = any(isinstance(detail, FluorescentReagent) for detail in self.procedure_details)
         has_protein_probe = any(isinstance(detail, ProbeReagent) for detail in self.procedure_details)
         has_sectioning = any(
             (isinstance(detail, PlanarSectioning) or isinstance(detail, Sectioning))
@@ -210,7 +226,7 @@ def validate_procedure_type(self):
         elif self.procedure_type == SpecimenProcedureType.HYBRIDIZATION_CHAIN_REACTION and not has_hcr_series:
             raise AssertionError("HCRSeries required if procedure_type is HCR.")
         elif self.procedure_type == SpecimenProcedureType.IMMUNOLABELING and not (
-            has_fluorescent_stain or has_protein_probe
+            has_fluorescent_stain or has_protein_probe or has_fluorescent_reagent
         ):
             raise AssertionError("FluorescentStain or ProbeReagent required if procedure_type is Immunolabeling.")
         elif self.procedure_type == SpecimenProcedureType.SECTIONING and not has_sectioning: