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

cidc_api/models/db/stage1/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.stage1.base_orm import BaseORM
-from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+from cidc_api.models.db.stage1.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("stage1.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/stage1/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.stage1.base_orm import BaseORM
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+from cidc_api.models.db.stage1.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("stage1.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/stage1/specimen_orm.py

@@ -1,39 +1,23 @@
 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.stage1.base_orm import BaseORM
-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,
-)
+from cidc_api.models.db.stage1.trial_orm import TrialORM
+from cidc_api.models.types import UberonAnatomicalTerm
 
 
 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("stage1.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage1/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.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.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("stage1.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage1/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.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.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("stage1.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage1/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.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.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("stage1.treatment.treatment_id", ondelete="CASCADE"))

cidc_api/models/db/stage1/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.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.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("stage1.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage1/trial_orm.py

@@ -2,12 +2,11 @@ from __future__ import annotations
 from typing import List
 from datetime import datetime
 
-from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
-from cidc_api.models.types import PrimaryPurposeType, AgeGroup
+from cidc_api.models.types import AssayType, TrialOrganization, TrialFundingAgency, AgeGroup, PrimaryPurposeType
 
 
 class TrialORM(BaseORM):

cidc_api/models/db/stage2/additional_treatment_orm.py

@@ -1,16 +1,23 @@
 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
 
 
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
     __repr_attrs__ = ["additional_treatment_id", "participant_id"]
     __data_category__ = "additional_treatment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     additional_treatment_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/administrative_person_orm.py

@@ -1,15 +1,22 @@
 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
 
 
 class AdministrativePersonORM(BaseORM):
     __tablename__ = "administrative_person"
     __repr_attrs__ = ["first_name", "last_name"]
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     administrative_person_id: Mapped[int] = mapped_column(primary_key=True)
     institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/administrative_role_assignment_orm.py

@@ -17,6 +17,7 @@ class AdministrativeRoleAssignmentORM(BaseORM):
 
     trial_id: Mapped[str] = mapped_column(primary_key=True)
     version: Mapped[str] = mapped_column(primary_key=True)
+
     administrative_person_id: Mapped[int] = mapped_column(
         ForeignKey("stage2.administrative_person.administrative_person_id", ondelete="CASCADE"), primary_key=True
     )

cidc_api/models/db/stage2/adverse_event_orm.py

@@ -1,9 +1,10 @@
 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 (
     CTCAEEventTerm,
     CTCAEEventCode,
@@ -13,6 +14,7 @@ from cidc_api.models.types import (
     SystemOrganClass,
     AttributionCause,
     AttributionLikelihood,
+    YN,
     YNU,
 )
 
@@ -21,6 +23,12 @@ class AdverseEventORM(BaseORM):
     __tablename__ = "adverse_event"
     __repr_attrs__ = ["adverse_event_id", "participant_id", "event_term"]
     __data_category__ = "adverse_event"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     adverse_event_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -33,7 +41,7 @@ class AdverseEventORM(BaseORM):
     severity_grade: Mapped[SeverityGrade]
     event_other_specify: Mapped[str | None]
     system_organ_class: Mapped[SystemOrganClass | None]
-    discontinuation_due_to_event: Mapped[bool]
+    discontinuation_due_to_event: Mapped[YN]
     days_to_onset_of_event: Mapped[NonNegativeInt]
     days_to_resolution_of_event: Mapped[NonNegativeInt | None]
     serious_adverse_event: Mapped[YNU]

cidc_api/models/db/stage2/arm_orm.py

@@ -3,21 +3,22 @@ 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 ArmORM(BaseORM):
     __tablename__ = "arm"
     __repr_attrs__ = ["trial_id", "arm_name"]
+    __data_category__ = "arm"
     __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"),
     )
 
-    arm_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    arm_id: Mapped[int] = mapped_column(primary_key=True)
+
     name: Mapped[str]
 
     trial: Mapped[TrialORM] = relationship(back_populates="arms", cascade="all, delete")

cidc_api/models/db/stage2/baseline_clinical_assessment_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 ECOGScore, KarnofskyScore
 
 
@@ -10,6 +11,12 @@ class BaselineClinicalAssessmentORM(BaseORM):
     __tablename__ = "baseline_clinical_assessment"
     __repr_attrs__ = ["baseline_clinical_assessment_id", "participant_id"]
     __data_category__ = "baseline_clinical_assessment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     baseline_clinical_assessment_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/cohort_orm.py

@@ -3,21 +3,22 @@ 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 CohortORM(BaseORM):
     __tablename__ = "cohort"
     __repr_attrs__ = ["trial_id", "cohort_name"]
+    __data_category__ = "cohort"
     __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"),
     )
 
-    cohort_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    cohort_id: Mapped[int] = mapped_column(primary_key=True)
+
     name: Mapped[str]
 
     trial: Mapped[TrialORM] = relationship(back_populates="cohorts", cascade="all, delete")

cidc_api/models/db/stage2/comorbidity_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 ICD10CMCode, ICD10CMTerm
 
 
@@ -10,6 +11,12 @@ class ComorbidityORM(BaseORM):
     __tablename__ = "comorbidity"
     __repr_attrs__ = ["comorbidity_id", "comorbidity_term"]
     __data_category__ = "comorbidity"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     comorbidity_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(

cidc_api/models/db/stage2/consent_group_orm.py

@@ -6,22 +6,22 @@ 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 ConsentGroupORM(BaseORM):
     __tablename__ = "consent_group"
     __repr_attrs__ = ["consent_group_id", "consent_group_name"]
+    __data_category__ = "consent_group"
     __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__ = "consent_group"
 
-    consent_group_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    consent_group_id: Mapped[int] = mapped_column(primary_key=True)
+
     consent_group_short_name: Mapped[str]
     consent_group_name: Mapped[str]
     consent_group_number: Mapped[NonNegativeInt]

cidc_api/models/db/stage2/contact_orm.py

@@ -1,12 +1,21 @@
 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
 
 
 class ContactORM(BaseORM):
     __tablename__ = "contact"
+    __repr_attrs__ = ["contact_id", "name"]
+    __data_category__ = "demographic"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     contact_id: Mapped[int] = mapped_column(primary_key=True)
     institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/demographic_orm.py

@@ -2,11 +2,12 @@ from __future__ import annotations
 from pydantic import NonNegativeFloat, PositiveFloat, PositiveInt
 from typing import List
 
-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 (
     Sex,
     Race,
@@ -17,6 +18,7 @@ from cidc_api.models.types import (
     Occupation,
     Education,
     AgeAtEnrollmentUnits,
+    YN,
 )
 
 
@@ -24,12 +26,18 @@ class DemographicORM(BaseORM):
     __tablename__ = "demographic"
     __repr_attrs__ = ["demographic_id", "participant_id", "age_at_enrollment", "sex"]
     __data_category__ = "demographic"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     demographic_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
     age_at_enrollment: Mapped[PositiveInt | None]
     age_at_enrollment_units: Mapped[AgeAtEnrollmentUnits | None]
-    age_90_or_over: Mapped[bool]
+    age_90_or_over: Mapped[YN]
     sex: Mapped[Sex]
     race: Mapped[List[Race]] = mapped_column(JSON)
     ethnicity: Mapped[Ethnicity]

cidc_api/models/db/stage2/disease_orm.py

@@ -2,11 +2,12 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonPositiveInt
-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 (
     TumorGrade,
     CancerStageSystem,
@@ -30,6 +31,12 @@ class DiseaseORM(BaseORM):
         "participant_id",
     ]
     __data_category__ = "disease"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     disease_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/exposure_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, ExposureType
 
 
@@ -12,6 +13,12 @@ class ExposureORM(BaseORM):
     __tablename__ = "exposure"
     __repr_attrs__ = ["exposure_id", "exposure_type", "carcinogen_exposure"]
     __data_category__ = "exposure"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     exposure_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/file_orm.py

@@ -5,21 +5,21 @@ 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 ChecksumType, FileFormat
 
 
 class FileORM(BaseORM):
     __tablename__ = "file"
     __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"),
     )
 
-    file_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    file_id: Mapped[int] = mapped_column(primary_key=True)
+
     creator_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))
     description: Mapped[str | None]
     uuid: Mapped[str]

cidc_api/models/db/stage2/gvhd_diagnosis_acute_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 (
     GVHDDiagnosisAcuteAssessmentSystem,
     GVHDDiagnosisAcuteAssessmentSystemVersion,
@@ -15,11 +16,15 @@ from cidc_api.models.types import (
 
 class GVHDDiagnosisAcuteORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_acute"
+    __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_acute"
     __table_args__ = (
         UniqueConstraint("participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_acute_pre_or_post"),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
-    __data_category__ = "gvhd_diagnosis_acute"
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))