fix!: remove injection (use nonsurgicalinjection)

docs/source/procedures.md

@@ -27,7 +27,7 @@ Description of all procedures performed on a subject, including surgeries, injec
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `subject_name` | `str` | Subject name (Unique name for the subject of data acquisition) |
-| `subject_procedures` | List[[Surgery](components/subject_procedures.md#surgery) or [Injection](components/injection_procedures.md#injection) or [NonSurgicalInjection](components/subject_procedures.md#nonsurgicalinjection) or [TrainingProtocol](components/subject_procedures.md#trainingprotocol) or [WaterRestriction](components/subject_procedures.md#waterrestriction) or [GenericSubjectProcedure](components/subject_procedures.md#genericsubjectprocedure)] | Subject Procedures (Procedures performed on a live subject) |
+| `subject_procedures` | List[[Surgery](components/subject_procedures.md#surgery) or [NonSurgicalInjection](components/subject_procedures.md#nonsurgicalinjection) or [TrainingProtocol](components/subject_procedures.md#trainingprotocol) or [WaterRestriction](components/subject_procedures.md#waterrestriction) or [GenericSubjectProcedure](components/subject_procedures.md#genericsubjectprocedure)] | Subject Procedures (Procedures performed on a live subject) |
 | `specimen_procedures` | List[[SpecimenProcedure](components/specimen_procedures.md#specimenprocedure)] | Specimen Procedures (Procedures performed on tissue extracted after perfusion) |
 | `global_coordinate_system` | Optional[[CoordinateSystem](components/coordinates.md#coordinatesystem)] | Global Coordinate System (Origin and axis definitions for determining the configured position of devices implanted during procedures. Required when coordinates are provided within the Procedures) |
 | `notes` | `Optional[str]` | Notes  |

src/biodata_schema/core/metadata.py

@@ -21,13 +21,14 @@
 
 from biodata_schema.base import DataCoreModel, DraftRequirement
 from biodata_schema.components.identifiers import DatabaseIdentifiers
+from biodata_schema.components.injection_procedures import Injection
 from biodata_schema.components.subject_procedures import TrainingProtocol
 from biodata_schema.components.subjects import CalibrationObject
 from biodata_schema.core.acquisition import Acquisition, DataStream, ExternalDataStream
 from biodata_schema.core.data_description import DataDescription
 from biodata_schema.core.instrument import Instrument
 from biodata_schema.core.model import Model
-from biodata_schema.core.procedures import Injection, Procedures, Surgery
+from biodata_schema.core.procedures import Procedures, Surgery
 from biodata_schema.core.processing import Processing
 from biodata_schema.core.quality_control import QualityControl
 from biodata_schema.core.subject import Subject

src/biodata_schema/core/procedures.py

@@ -6,7 +6,6 @@
 
 from biodata_schema.base import DataCoreModel, DiscriminatedList
 from biodata_schema.components.coordinates import CoordinateSystem
-from biodata_schema.components.injection_procedures import Injection
 from biodata_schema.components.specimen_procedures import SpecimenProcedure
 from biodata_schema.components.subject_procedures import (
     GenericSubjectProcedure,
@@ -32,7 +31,7 @@ class Procedures(DataCoreModel):
         title="Subject name",
     )
     subject_procedures: DiscriminatedList[
-        Surgery | Injection | NonSurgicalInjection | TrainingProtocol | WaterRestriction | GenericSubjectProcedure
+        Surgery | NonSurgicalInjection | TrainingProtocol | WaterRestriction | GenericSubjectProcedure
     ] = Field(default=[], title="Subject Procedures", description="Procedures performed on a live subject")
     specimen_procedures: List[SpecimenProcedure] = Field(
         default=[], title="Specimen Procedures", description="Procedures performed on tissue extracted after perfusion"
@@ -73,18 +72,6 @@ def get_device_names(self) -> List[str]:
 
         return list(device_names)
 
-    @model_validator(mode="after")
-    def reject_injections(self):
-        """Reject bare injections since they must be wrapped
-        in a Surgery or NonSurgicalInjection procedure
-        """
-
-        for procedure in self.subject_procedures:
-            if isinstance(procedure, Injection):
-                raise ValueError("Injection procedures must be wrapped in a Surgery or NonSurgicalInjection procedure.")
-
-        return self
-
     @model_validator(mode="after")
     def validate_subject_specimen_names(self):
         """Validate that the subject_name and specimen_name match"""