nci-cidc-api-modules 1.2.53__py3-none-any.whl → 1.2.55__py3-none-any.whl

cidc_api/models/db/stage2/gvhd_diagnosis_chronic_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from typing import List
 
-from sqlalchemy import ForeignKey, UniqueConstraint
+from sqlalchemy import ForeignKey, UniqueConstraint, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import (
     GVHDDiagnosisChronicAssessmentSystem,
     GVHDDiagnosisChronicAssessmentSystemVersion,
@@ -15,13 +16,17 @@ from cidc_api.models.types import (
 
 class GVHDDiagnosisChronicORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_chronic"
+    __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_chronic"
     __table_args__ = (
         UniqueConstraint(
             "participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_chronic_pre_or_post"
         ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
-    __data_category__ = "gvhd_diagnosis_chronic"
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/gvhd_organ_acute_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganAcuteStage
 
 
@@ -10,6 +11,12 @@ class GVHDOrganAcuteORM(BaseORM):
     __tablename__ = "gvhd_organ_acute"
     __repr_attrs__ = ["gvhd_organ_acute_id", "organ"]
     __data_category__ = "gvhd_organ_acute"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_organ_acute_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(

cidc_api/models/db/stage2/gvhd_organ_chronic_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganChronicScore
 
 
@@ -10,6 +11,12 @@ class GVHDOrganChronicORM(BaseORM):
     __tablename__ = "gvhd_organ_chronic"
     __repr_attrs__ = ["gvhd_organ_chronic_id", "organ"]
     __data_category__ = "gvhd_organ_chronic"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_organ_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(

cidc_api/models/db/stage2/institution_orm.py

@@ -5,21 +5,21 @@ from sqlalchemy import ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 
 
 class InstitutionORM(BaseORM):
     __tablename__ = "institution"
     __repr_attrs__ = ["name"]
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
 
-    institution_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    institution_id: Mapped[int] = mapped_column(primary_key=True)
+
     name: Mapped[str]
 
     trial: Mapped[TrialORM] = relationship(back_populates="biobank", cascade="all, delete")

cidc_api/models/db/stage2/medical_history_orm.py

@@ -2,10 +2,11 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonNegativeInt, PositiveFloat
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import TobaccoSmokingStatus
 
 
@@ -13,6 +14,12 @@ class MedicalHistoryORM(BaseORM):
     __tablename__ = "medical_history"
     __repr_attrs__ = ["medical_history_id"]
     __data_category__ = "medical_history"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     medical_history_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/other_clinical_endpoint_orm.py

@@ -1,14 +1,22 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey, String
+from sqlalchemy import String, ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
 
 
 class OtherClinicalEndpointORM(BaseORM):
     __tablename__ = "other_clinical_endpoint"
     __repr_attrs__ = ["other_clinical_endpoint_id", "name", "event"]
+    __data_category__ = "other_clinical_endpoint"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     other_clinical_endpoint_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/other_malignancy_orm.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 from pydantic import NonPositiveInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 
@@ -11,6 +12,12 @@ class OtherMalignancyORM(BaseORM):
     __tablename__ = "other_malignancy"
     __repr_attrs__ = ["other_malignancy_id", "primary_disease_site"]
     __data_category__ = "other_malignancy"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     other_malignancy_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(

cidc_api/models/db/stage2/participant_orm.py

@@ -1,26 +1,26 @@
 from __future__ import annotations
 from typing import List
+
 from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import OffStudyReason, YNU
 
 
 class ParticipantORM(BaseORM):
     __tablename__ = "participant"
-    __repr_attrs__ = ["native_participant_id", "cimac_participant_id"]
+    __repr_attrs__ = ["participant_id", "native_participant_id", "cimac_participant_id"]
+    __data_category__ = "participant"
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __data_category__ = "participant"
 
-    participant_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    participant_id: Mapped[int] = mapped_column(primary_key=True)
     native_participant_id: Mapped[str | None]
     cimac_participant_id: Mapped[str | None]
     consent_group_id: Mapped[int | None] = mapped_column(

cidc_api/models/db/stage2/prior_treatment_orm.py

@@ -2,11 +2,11 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonPositiveInt, NegativeInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
@@ -14,6 +14,12 @@ class PriorTreatmentORM(BaseORM):
     __tablename__ = "prior_treatment"
     __repr_attrs__ = ["prior_treatment_id", "type"]
     __data_category__ = "prior_treatment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -24,6 +30,6 @@ class PriorTreatmentORM(BaseORM):
     prior_treatment_best_response: Mapped[str | None]
     prior_treatment_conditioning_regimen_type: Mapped[ConditioningRegimenType | None]
     prior_treatment_stem_cell_donor_type: Mapped[StemCellDonorType | None]
-    prior_treatment_days_to_prior_transplant: Mapped[NegativeInt | None]
+    prior_treatment_days_from_transplant_to_treatment_initiation: Mapped[NegativeInt | None]
 
     participant: Mapped[ParticipantORM] = relationship(back_populates="prior_treatments", cascade="all, delete")

cidc_api/models/db/stage2/publication_orm.py

@@ -3,22 +3,23 @@ from sqlalchemy import ForeignKeyConstraint, ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PublicationORM(BaseORM):
     __tablename__ = "publication"
     __repr_attrs__ = ["publication_id", "publication_title"]
+    __data_category__ = "publication"
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
 
-    publication_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    publication_id: Mapped[int] = mapped_column(primary_key=True)
+
     digital_object_id: Mapped[str]
     pubmed_id: Mapped[str | None]
     publication_title: Mapped[str | None]

cidc_api/models/db/stage2/radiotherapy_dose_orm.py

@@ -1,16 +1,18 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import (
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
     RadiotherapyDoseUnits,
-    YNU,
     RadiationExtent,
+    YN,
+    YNU,
 )
 
 
@@ -18,6 +20,12 @@ class RadiotherapyDoseORM(BaseORM):
     __tablename__ = "radiotherapy_dose"
     __repr_attrs__ = ["radiotherapy_dose_id", "procedure"]
     __data_category__ = "radiotherapy_dose"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     radiotherapy_dose_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))
@@ -26,7 +34,7 @@ class RadiotherapyDoseORM(BaseORM):
     days_to_end: Mapped[NonNegativeInt]
     procedure: Mapped[RadiotherapyProcedure]
     anatomical_location: Mapped[UberonAnatomicalTerm | None]
-    is_total_dose: Mapped[bool]
+    is_total_dose: Mapped[YN]
     number_of_fractions: Mapped[NonNegativeInt | None]
     received_dose: Mapped[NonNegativeFloat]
     received_dose_units: Mapped[RadiotherapyDoseUnits]

cidc_api/models/db/stage2/response_by_system_orm.py

@@ -1,16 +1,23 @@
 from __future__ import annotations
 from pydantic import PositiveInt
-from sqlalchemy import ForeignKey, String
+from sqlalchemy import String, ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+from cidc_api.models.db.stage2.trial_orm import TrialORM
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
 class ResponseBySystemORM(BaseORM):
     __tablename__ = "response_by_system"
     __repr_attrs__ = ["response_by_system_id", "participant_id"]
     __data_category__ = "response_by_system"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     response_by_system_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -19,7 +26,7 @@ class ResponseBySystemORM(BaseORM):
     best_overall_response: Mapped[BestOverallResponse] = mapped_column(String)
     response_duration: Mapped[PositiveInt | None]
     duration_of_stable_disease: Mapped[PositiveInt | None]
-    durable_clinical_benefit: Mapped[bool | None]
+    durable_clinical_benefit: Mapped[YN | None]
     days_to_first_response: Mapped[PositiveInt | None]
     days_to_best_response: Mapped[PositiveInt | None]
     progression: Mapped[YNUNA]

cidc_api/models/db/stage2/response_orm.py

@@ -1,17 +1,24 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+from cidc_api.models.db.stage2.trial_orm import TrialORM
+from cidc_api.models.types import SurvivalStatus, CauseOfDeath, YNUNA, YN
 
 
 class ResponseORM(BaseORM):
     __tablename__ = "response"
     __repr_attrs__ = ["response_id", "participant_id"]
     __data_category__ = "response"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     response_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -21,8 +28,8 @@ class ResponseORM(BaseORM):
     pathological_complete_response: Mapped[YNUNA | None]
     days_to_death: Mapped[NonNegativeInt | None]
     cause_of_death: Mapped[CauseOfDeath | None]
-    evaluable_for_toxicity: Mapped[bool]
-    evaluable_for_efficacy: Mapped[bool]
+    evaluable_for_toxicity: Mapped[YN]
+    evaluable_for_efficacy: Mapped[YN]
     days_to_last_vital_status: Mapped[NonNegativeInt | None]
 
     participant: Mapped[ParticipantORM] = relationship(back_populates="response", cascade="all, delete")

cidc_api/models/db/stage2/shipment_orm.py

@@ -6,6 +6,7 @@ from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import AssayPriority, AssayType, Courier, ShipmentCondition, ShipmentQuality
 
 
@@ -13,16 +14,15 @@ class ShipmentORM(BaseORM):
     __tablename__ = "shipment"
     __repr_attrs__ = ["shipment_id", "institution_id", "trial_id"]
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
 
-    shipment_id: Mapped[int] = mapped_column(primary_key=True)
-    institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    shipment_id: Mapped[int] = mapped_column(primary_key=True)
+    institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))
+
     manifest_id: Mapped[str]
     assay_priority: Mapped[AssayPriority | None]
     assay_type: Mapped[AssayType | None]

cidc_api/models/db/stage2/shipment_specimen_orm.py

@@ -1,15 +1,21 @@
 from __future__ import annotations
-from datetime import datetime
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 
 
 class ShipmentSpecimenORM(BaseORM):
     __tablename__ = "shipment_specimen"
     __repr_attrs__ = ["specimen_id", "shipment_id"]
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     specimen_id: Mapped[int] = mapped_column(
         ForeignKey("stage2.specimen.specimen_id", ondelete="CASCADE"), primary_key=True

cidc_api/models/db/stage2/specimen_orm.py

@@ -1,97 +1,31 @@
 from __future__ import annotations
-from datetime import datetime
-from typing import List
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import (
     UberonAnatomicalTerm,
-    ICDO3MorphologicalCode,
-    SpecimenType,
-    SpecimenDescription,
-    TumorType,
-    CollectionProcedure,
-    FixationStabilizationType,
-    PrimaryContainerType,
-    VolumeUnits,
-    ProcessedType,
-    ConcentrationUnits,
-    DerivativeType,
-    PBMCRestingPeriodUsed,
-    MaterialUnits,
-    MaterialStorageCondition,
-    QCCondition,
-    ReplacementRequested,
-    ResidualUse,
-    DiagnosisVerification,
-    AssayType,
 )
 
 
 class SpecimenORM(BaseORM):
     __tablename__ = "specimen"
     __repr_attrs__ = ["specimen_id", "participant_id", "cimac_id"]
+    __data_category__ = "specimen"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     specimen_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
     cimac_id: Mapped[str]
-    surgical_pathology_report_id: Mapped[str | None]
-    clinical_report_id: Mapped[str | None]
-    parent_specimen_id: Mapped[str | None]
-    processed_specimen_id: Mapped[str | None]
-    organ_site_of_collection: Mapped[UberonAnatomicalTerm | None]
-    histology_behavior: Mapped[ICDO3MorphologicalCode | None]
-    histology_behavior_description: Mapped[str | None]
     collection_event_name: Mapped[str]
-    specimen_type: Mapped[SpecimenType | None]
-    specimen_type_other: Mapped[str | None]
-    specimen_description: Mapped[SpecimenDescription | None]
-    tumor_type: Mapped[TumorType | None]
-    collection_procedure: Mapped[CollectionProcedure | None]
-    collection_procedure_other: Mapped[str | None]
-    core_number: Mapped[str | None]
-    fixation_stabilization_type: Mapped[FixationStabilizationType | None]
-    primary_container_type: Mapped[PrimaryContainerType | None]
-    primary_container_type_other: Mapped[str | None]
-    volume: Mapped[float | None]
-    volume_units: Mapped[VolumeUnits | None]
-    processed_type: Mapped[ProcessedType | None]
-    processed_volume: Mapped[float | None]
-    processed_volume_units: Mapped[VolumeUnits | None]
-    processed_concentration: Mapped[float | None]
-    processed_concentration_units: Mapped[ConcentrationUnits | None]
-    processed_quantity: Mapped[float | None]
-    derivative_type: Mapped[DerivativeType | None]
-    derivative_volume: Mapped[float | None]
-    derivative_volume_units: Mapped[VolumeUnits | None]
-    derivative_concentration: Mapped[float | None]
-    derivative_concentration_units: Mapped[ConcentrationUnits | None]
-    tumor_tissue_total_area_percentage: Mapped[float | None]
-    viable_tumor_area_percentage: Mapped[float | None]
-    viable_stroma_area_percentage: Mapped[float | None]
-    necrosis_area_percentage: Mapped[float | None]
-    fibrosis_area_percentage: Mapped[float | None]
-    din: Mapped[float | None]
-    a260_a280: Mapped[float | None]
-    a260_a230: Mapped[float | None]
-    pbmc_viability: Mapped[float | None]
-    pbmc_recovery: Mapped[float | None]
-    pbmc_resting_period_used: Mapped[PBMCRestingPeriodUsed | None]
-    material_used: Mapped[float | None]
-    material_used_units: Mapped[MaterialUnits | None]
-    material_remaining: Mapped[float | None]
-    material_remaining_units: Mapped[MaterialUnits | None]
-    material_storage_condition: Mapped[MaterialStorageCondition | None]
-    qc_condition: Mapped[QCCondition | None]
-    replacement_requested: Mapped[ReplacementRequested | None]
-    residual_use: Mapped[ResidualUse | None]
-    comments: Mapped[str | None]
-    diagnosis_verification: Mapped[DiagnosisVerification | None]
-    intended_assay: Mapped[AssayType | None]
-    date_ingested: Mapped[datetime | None]
     days_to_specimen_collection: Mapped[int]
     organ_site_of_collection: Mapped[UberonAnatomicalTerm]
 

cidc_api/models/db/stage2/stem_cell_transplant_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import StemCellDonorType, AllogeneicDonorType, StemCellSource, ConditioningRegimenType
 
 
@@ -12,6 +13,12 @@ class StemCellTransplantORM(BaseORM):
     __tablename__ = "stem_cell_transplant"
     __repr_attrs__ = ["stem_cell_transplant_id"]
     __data_category__ = "stem_cell_transplant"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     stem_cell_transplant_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/surgery_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
 
 
@@ -12,6 +13,12 @@ class SurgeryORM(BaseORM):
     __tablename__ = "surgery"
     __repr_attrs__ = ["surgery_id", "procedure"]
     __data_category__ = "surgery"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     surgery_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/therapy_agent_dose_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import TherapyAgentDoseUnits, YNU
 
 
@@ -12,6 +13,12 @@ class TherapyAgentDoseORM(BaseORM):
     __tablename__ = "therapy_agent_dose"
     __repr_attrs__ = ["therapy_agent_dose_id", "therapy_agent_name"]
     __data_category__ = "therapy_agent_dose"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     therapy_agent_dose_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/treatment_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from typing import List
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.db.stage2.trial_orm import TrialORM
 from cidc_api.models.types import YNU, OffTreatmentReason
 
 
@@ -12,6 +13,12 @@ class TreatmentORM(BaseORM):
     __tablename__ = "treatment"
     __repr_attrs__ = ["treatment_id", "participant_id", "treatment_description"]
     __data_category__ = "treatment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))