feat: add Solution object, in-house reagents (#1825)

* add solution

* update docs

---------

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

Author: saskiad

docs/source/aind_data_schema_models/harp_types.md

@@ -18,6 +18,7 @@ Harp device types
 | `CURRENTDRIVER` | `CurrentDriver` | `1282` |
 | `CUTTLEFISH` | `cuTTLefish` | `1403` |
 | `CUTTLEFISHFIP` | `cuTTLefishFip` | `1407` |
+| `DELUXDRIVER` | `deLuxDriver` | `1410` |
 | `DRIVER12VOLTS` | `Driver12Volts` | `1072` |
 | `ENVIRONMENTSENSOR` | `EnvironmentSensor` | `1405` |
 | `FLYPAD` | `FlyPad` | `1200` |

docs/source/aind_data_schema_models/organizations.md

@@ -47,6 +47,7 @@ Organization
 | `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `EMORY` | `Emory` | `Emory University` | `Research Organization Registry (ROR)` | `03czfpz43` |
 | `EURESYS` | `None` | `Euresys` | `None` | `None` |
+| `EXCELITAS_TECHNOLOGIES` | `None` | `Excelitas Technologies` | `Research Organization Registry (ROR)` | `01tpbbf75` |
 | `FILTER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `FLIR` | `FLIR` | `Teledyne FLIR` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `FUJINON` | `None` | `Fujinon` | `None` | `None` |

docs/source/aind_data_schema_models/process_names.md

@@ -17,6 +17,7 @@ Process names
 | `EPHYS_VISUALIZATION` | `Ephys visualization` |
 | `FIDUCIAL_SEGMENTATION` | `Fiducial segmentation` |
 | `FILE_FORMAT_CONVERSION` | `File format conversion` |
+| `FIX_COLOR_RANGE` | `Fix color range` |
 | `FLUORESCENCE_EVENT_DETECTION` | `Fluorescence event detection` |
 | `IMAGE_ATLAS_ALIGNMENT` | `Image atlas alignment` |
 | `IMAGE_BACKGROUND_SUBTRACTION` | `Image background subtraction` |
@@ -28,6 +29,7 @@ Process names
 | `IMAGE_FLAT_FIELD_CORRECTION` | `Image flat-field correction` |
 | `IMAGE_IMPORTING` | `Image importing` |
 | `IMAGE_MIP_VISUALIZATION` | `Image mip visualization` |
+| `IMAGE_MULTISCALING` | `Image multiscaling` |
 | `IMAGE_RADIAL_CORRECTION` | `Image radial correction` |
 | `IMAGE_SPOT_DETECTION` | `Image spot detection` |
 | `IMAGE_SPOT_SPECTRAL_UNMIXING` | `Image spot spectral unmixing` |

docs/source/aind_data_schema_models/specimen_procedure_types.md

@@ -25,6 +25,5 @@ Specimen procedures
 | `SOAK` | `Soak` |
 | `STORAGE` | `Storage` |
 | `STRIPPING` | `Stripping` |
-| `TAMOXIFEN_INDUCTION` | `Tamoxifen induction` |
 
 

docs/source/components/reagent.md

@@ -115,3 +115,13 @@ Description of a small molecule probe
 | `mass_unit` | [MassUnit](../aind_data_schema_models/units.md#massunit) | Mass unit  |
 
 
+### Solution
+
+Description of a solution made in house. Should match a solution named in protocol.
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `name` | `str` | Name  |
+| `lot_number` | `Optional[str]` | Lot number  |
+
+

docs/source/components/specimen_procedures.md

@@ -108,7 +108,7 @@ Description of surgical or other procedure performed on a specimen
 | `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)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
+| `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  |
 
 

src/aind_data_schema/components/reagent.py

@@ -31,6 +31,13 @@ class Reagent(DataModel):
     expiration_date: Optional[date] = Field(default=None, title="Lot expiration date")
 
 
+class Solution(DataModel):
+    """Description of a solution made in house. Should match a solution named in protocol."""
+
+    name: str = Field(..., title="Name")
+    lot_number: Optional[str] = Field(default=None, title="Lot number")
+
+
 class OligoProbe(DataModel):
     """Description of an oligonucleotide probe"""
 

src/aind_data_schema/components/specimen_procedures.py

@@ -13,7 +13,7 @@
 
 from aind_data_schema.base import AwareDatetimeWithDefault, DataModel, DiscriminatedList
 from aind_data_schema.components.coordinates import Atlas, CoordinateSystem, Translation
-from aind_data_schema.components.reagent import FluorescentStain, GeneProbeSet, ProbeReagent, Reagent
+from aind_data_schema.components.reagent import FluorescentStain, GeneProbeSet, ProbeReagent, Reagent, Solution
 from aind_data_schema.utils.exceptions import OneOfError
 
 
@@ -178,7 +178,7 @@ class SpecimenProcedure(DataModel):
     )
 
     procedure_details: DiscriminatedList[
-        HCRSeries | FluorescentStain | Sectioning | PlanarSectioning | ProbeReagent | Reagent | GeneProbeSet
+        HCRSeries | FluorescentStain | Sectioning | PlanarSectioning | ProbeReagent | Reagent | GeneProbeSet | Solution
     ] = Field(
         default=[],
         title="Procedure details",