diff --git a/docs/source/procedures.md b/docs/source/procedures.md index f50e9e95..29e66954 100644 --- a/docs/source/procedures.md +++ b/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 | diff --git a/src/biodata_schema/core/metadata.py b/src/biodata_schema/core/metadata.py index de6fa41e..696b0107 100644 --- a/src/biodata_schema/core/metadata.py +++ b/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 diff --git a/src/biodata_schema/core/procedures.py b/src/biodata_schema/core/procedures.py index 2b8e19ac..69d74670 100644 --- a/src/biodata_schema/core/procedures.py +++ b/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"""