nci-cidc-api-modules 1.2.38__py3-none-any.whl → 1.2.40__py3-none-any.whl

cidc_api/models/db/stage2/contact_orm.py

@@ -1,9 +1,8 @@
-from typing import Optional
-
+from __future__ import annotations
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 
 
 class ContactORM(BaseORM):
@@ -12,21 +11,19 @@ class ContactORM(BaseORM):
 
     contact_id: Mapped[int] = mapped_column(primary_key=True)
     institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))
-    shipment_from_id: Mapped[Optional[int]] = mapped_column(
-        ForeignKey("stage2.shipment.shipment_id", ondelete="CASCADE")
-    )
-    shipment_to_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stage2.shipment.shipment_id", ondelete="CASCADE"))
+    shipment_from_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.shipment.shipment_id", ondelete="CASCADE"))
+    shipment_to_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.shipment.shipment_id", ondelete="CASCADE"))
 
-    name: Mapped[Optional[str]]
-    email: Mapped[Optional[str]]
-    phone: Mapped[Optional[str]]
-    street1: Mapped[Optional[str]]
-    street2: Mapped[Optional[str]]
-    city: Mapped[Optional[str]]
-    state: Mapped[Optional[str]]
-    zip: Mapped[Optional[str]]
-    country: Mapped[Optional[str]]
+    name: Mapped[str | None]
+    email: Mapped[str | None]
+    phone: Mapped[str | None]
+    street1: Mapped[str | None]
+    street2: Mapped[str | None]
+    city: Mapped[str | None]
+    state: Mapped[str | None]
+    zip: Mapped[str | None]
+    country: Mapped[str | None]
 
-    institution: Mapped[Optional["InstitutionORM"]] = relationship(back_populates="contacts", cascade="all, delete")
-    shipment_from: Mapped["ShipmentORM"] = relationship(cascade="all, delete", foreign_keys=[shipment_from_id])
-    shipment_to: Mapped["ShipmentORM"] = relationship(cascade="all, delete", foreign_keys=[shipment_to_id])
+    institution: Mapped[InstitutionORM | None] = relationship(back_populates="contacts", cascade="all, delete")
+    shipment_from: Mapped[ShipmentORM] = relationship(cascade="all, delete", foreign_keys=[shipment_from_id])
+    shipment_to: Mapped[ShipmentORM] = relationship(cascade="all, delete", foreign_keys=[shipment_to_id])

cidc_api/models/db/stage2/demographic_orm.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from pydantic import NonNegativeFloat, PositiveFloat, PositiveInt
 from typing import List
 
@@ -5,7 +6,7 @@ from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import (
     Sex,
     Race,
@@ -44,4 +45,4 @@ class DemographicORM(BaseORM):
     income: Mapped[NonNegativeFloat | None]
     highest_level_of_education: Mapped[Education | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="demographic", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="demographic", cascade="all, delete")

cidc_api/models/db/stage2/disease_orm.py

@@ -1,11 +1,12 @@
-from typing import List, Optional
+from __future__ import annotations
+from typing import List
 
 from pydantic import NonPositiveInt
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import (
     TumorGrade,
     CancerStageSystem,
@@ -49,4 +50,4 @@ class DiseaseORM(BaseORM):
     solely_extramedullary_disease: Mapped[YNU]
     extramedullary_organ: Mapped[List[UberonAnatomicalTerm]] = mapped_column(JSON, nullable=True)
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="diseases", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="diseases", cascade="all, delete")

cidc_api/models/db/stage2/exposure_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from typing import List
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import YNU, ExposureType
 
 
@@ -19,4 +20,4 @@ class ExposureORM(BaseORM):
     carcinogen_exposure: Mapped[YNU]
     exposure_type: Mapped[ExposureType | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="exposures", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="exposures", cascade="all, delete")

cidc_api/models/db/stage2/file_orm.py

@@ -1,10 +1,10 @@
+from __future__ import annotations
 from datetime import datetime
-from typing import Optional
 
 from sqlalchemy import ForeignKeyConstraint, ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import ChecksumType, FileFormat
 
 
@@ -21,10 +21,8 @@ class FileORM(BaseORM):
     trial_id: Mapped[str]
     version: Mapped[str]
 
-    creator_id: Mapped[Optional[int]] = mapped_column(
-        ForeignKey("stage2.institution.institution_id", ondelete="CASCADE")
-    )
-    description: Mapped[Optional[str]]
+    creator_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))
+    description: Mapped[str | None]
     uuid: Mapped[str]
     file_name: Mapped[str]
     object_url: Mapped[str]
@@ -34,5 +32,5 @@ class FileORM(BaseORM):
     checksum_type: Mapped[ChecksumType]
     file_format: Mapped[FileFormat]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="files", cascade="all, delete")
-    creator: Mapped[Optional["InstitutionORM"]] = relationship(back_populates="files", cascade="all, delete")
+    trial: Mapped[TrialORM] = relationship(back_populates="files", cascade="all, delete")
+    creator: Mapped[InstitutionORM | None] = relationship(back_populates="files", cascade="all, delete")

cidc_api/models/db/stage2/gvhd_diagnosis_acute_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from typing import List
 
 from sqlalchemy import ForeignKey, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import (
     GVHDDiagnosisAcuteAssessmentSystem,
     GVHDDiagnosisAcuteAssessmentSystemVersion,
@@ -28,7 +29,7 @@ class GVHDDiagnosisAcuteORM(BaseORM):
     acute_grade: Mapped[GVHDDiagnosisAcuteGrade]
     pre_or_post_enrollment: Mapped[PreOrPostEnrollment]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="gvhd_diagnosis_acutes", cascade="all, delete")
-    organs: Mapped[List["GVHDOrganAcuteORM"]] = relationship(
+    participant: Mapped[ParticipantORM] = relationship(back_populates="gvhd_diagnosis_acutes", cascade="all, delete")
+    organs: Mapped[List[GVHDOrganAcuteORM]] = relationship(
         back_populates="diagnosis", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/db/stage2/gvhd_diagnosis_chronic_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from typing import List
 
 from sqlalchemy import ForeignKey, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import (
     GVHDDiagnosisChronicAssessmentSystem,
     GVHDDiagnosisChronicAssessmentSystemVersion,
@@ -30,9 +31,7 @@ class GVHDDiagnosisChronicORM(BaseORM):
     chronic_global_severity: Mapped[GVHDDiagnosisChronicGlobalSeverity]
     pre_or_post_enrollment: Mapped[PreOrPostEnrollment]
 
-    participant: Mapped["ParticipantORM"] = relationship(
-        back_populates="gvhd_diagnosis_chronics", cascade="all, delete"
-    )
-    organs: Mapped[List["GVHDOrganChronicORM"]] = relationship(
+    participant: Mapped[ParticipantORM] = relationship(back_populates="gvhd_diagnosis_chronics", cascade="all, delete")
+    organs: Mapped[List[GVHDOrganChronicORM]] = relationship(
         back_populates="diagnosis", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/db/stage2/gvhd_organ_acute_orm.py

@@ -1,7 +1,8 @@
+from __future__ import annotations
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganAcuteStage
 
 
@@ -18,4 +19,4 @@ class GVHDOrganAcuteORM(BaseORM):
     organ: Mapped[GVHDOrgan]
     acute_stage: Mapped[GVHDOrganAcuteStage]
 
-    diagnosis: Mapped["GVHDDiagnosisAcuteORM"] = relationship(back_populates="organs", cascade="all, delete")
+    diagnosis: Mapped[GVHDDiagnosisAcuteORM] = relationship(back_populates="organs", cascade="all, delete")

cidc_api/models/db/stage2/gvhd_organ_chronic_orm.py

@@ -1,7 +1,8 @@
+from __future__ import annotations
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganChronicScore
 
 
@@ -18,4 +19,4 @@ class GVHDOrganChronicORM(BaseORM):
     organ: Mapped[GVHDOrgan]
     chronic_score: Mapped[GVHDOrganChronicScore]
 
-    diagnosis: Mapped["GVHDDiagnosisChronicORM"] = relationship(back_populates="organs", cascade="all, delete")
+    diagnosis: Mapped[GVHDDiagnosisChronicORM] = relationship(back_populates="organs", cascade="all, delete")

cidc_api/models/db/stage2/institution_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from typing import List
 
 from sqlalchemy import ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 
 
 class InstitutionORM(BaseORM):
@@ -22,12 +23,12 @@ class InstitutionORM(BaseORM):
 
     name: Mapped[str]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="biobank", cascade="all, delete")
-    administrative_people: Mapped[List["AdministrativePersonORM"]] = relationship(
+    trial: Mapped[TrialORM] = relationship(back_populates="biobank", cascade="all, delete")
+    administrative_people: Mapped[List[AdministrativePersonORM]] = relationship(
         back_populates="institution", cascade="all, delete", passive_deletes=True
     )
-    shipments: Mapped[List["ShipmentORM"]] = relationship(
+    shipments: Mapped[List[ShipmentORM]] = relationship(
         back_populates="institution", cascade="all, delete", passive_deletes=True
     )
-    files: Mapped[List["FileORM"]] = relationship(back_populates="creator", cascade="all, delete", passive_deletes=True)
-    contacts: Mapped[List["ContactORM"]] = relationship(back_populates="institution")
+    files: Mapped[List[FileORM]] = relationship(back_populates="creator", cascade="all, delete", passive_deletes=True)
+    contacts: Mapped[List[ContactORM]] = relationship(back_populates="institution")

cidc_api/models/db/stage2/medical_history_orm.py

@@ -1,10 +1,11 @@
-from typing import Optional, List
+from __future__ import annotations
+from typing import List
 
 from pydantic import NonNegativeInt, PositiveFloat
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import TobaccoSmokingStatus
 
 
@@ -17,14 +18,14 @@ class MedicalHistoryORM(BaseORM):
     medical_history_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
-    tobacco_smoking_status: Mapped[Optional[TobaccoSmokingStatus]]
-    pack_years_smoked: Mapped[Optional[PositiveFloat]]
-    num_prior_systemic_therapies: Mapped[Optional[NonNegativeInt]]
+    tobacco_smoking_status: Mapped[TobaccoSmokingStatus | None]
+    pack_years_smoked: Mapped[PositiveFloat | None]
+    num_prior_systemic_therapies: Mapped[NonNegativeInt | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="medical_history", cascade="all, delete")
-    other_malignancies: Mapped[List["OtherMalignancyORM"]] = relationship(
+    participant: Mapped[ParticipantORM] = relationship(back_populates="medical_history", cascade="all, delete")
+    other_malignancies: Mapped[List[OtherMalignancyORM]] = relationship(
         back_populates="medical_history", cascade="all, delete", passive_deletes=True
     )
-    comorbidities: Mapped[List["ComorbidityORM"]] = relationship(
+    comorbidities: Mapped[List[ComorbidityORM]] = relationship(
         back_populates="medical_history", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/db/stage2/other_clinical_endpoint_orm.py

@@ -1,9 +1,8 @@
-from typing import Optional
-
+from __future__ import annotations
 from sqlalchemy import ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
 
 
@@ -17,12 +16,10 @@ class OtherClinicalEndpointORM(BaseORM):
 
     name: Mapped[str]
     event: Mapped[YNU]
-    days: Mapped[Optional[int]]
-    description: Mapped[Optional[str]]
-    calculation: Mapped[Optional[str]]
-    response_system: Mapped[Optional[ResponseSystem]] = mapped_column(String, nullable=True)
-    response_system_version: Mapped[Optional[ResponseSystemVersion]] = mapped_column(String, nullable=True)
+    days: Mapped[int | None]
+    description: Mapped[str | None]
+    calculation: Mapped[str | None]
+    response_system: Mapped[ResponseSystem | None] = mapped_column(String, nullable=True)
+    response_system_version: Mapped[ResponseSystemVersion | None] = mapped_column(String, nullable=True)
 
-    participant: Mapped["ParticipantORM"] = relationship(
-        back_populates="other_clinical_endpoints", cascade="all, delete"
-    )
+    participant: Mapped[ParticipantORM] = relationship(back_populates="other_clinical_endpoints", cascade="all, delete")

cidc_api/models/db/stage2/other_malignancy_orm.py

@@ -1,10 +1,9 @@
-from typing import Optional
-
+from __future__ import annotations
 from pydantic import NonPositiveInt
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 
@@ -20,12 +19,12 @@ class OtherMalignancyORM(BaseORM):
     )
 
     other_malignancy_primary_disease_site: Mapped[UberonAnatomicalTerm]
-    other_malignancy_morphological_code: Mapped[Optional[ICDO3MorphologicalCode]]
-    other_malignancy_morphological_term: Mapped[Optional[ICDO3MorphologicalTerm]]
-    other_malignancy_description: Mapped[Optional[str]]
-    other_malignancy_days_since_diagnosis: Mapped[Optional[NonPositiveInt]]
-    other_malignancy_status: Mapped[Optional[MalignancyStatus]]
+    other_malignancy_morphological_code: Mapped[ICDO3MorphologicalCode | None]
+    other_malignancy_morphological_term: Mapped[ICDO3MorphologicalTerm | None]
+    other_malignancy_description: Mapped[str | None]
+    other_malignancy_days_since_diagnosis: Mapped[NonPositiveInt | None]
+    other_malignancy_status: Mapped[MalignancyStatus | None]
 
-    medical_history: Mapped["MedicalHistoryORM"] = relationship(
+    medical_history: Mapped[MedicalHistoryORM] = relationship(
         back_populates="other_malignancies", cascade="all, delete"
     )

cidc_api/models/db/stage2/participant_orm.py

@@ -1,9 +1,9 @@
-from typing import List, Optional
-
+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.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import OffStudyReason, YNU
 
 
@@ -24,57 +24,57 @@ class ParticipantORM(BaseORM):
 
     native_participant_id: Mapped[str | None]
     cimac_participant_id: Mapped[str | None]
-    consent_group_id: Mapped[Optional[int]] = mapped_column(
+    consent_group_id: Mapped[int | None] = mapped_column(
         ForeignKey("stage2.consent_group.consent_group_id", ondelete="CASCADE")
     )
     off_study: Mapped[YNU]
-    off_study_reason: Mapped[Optional[OffStudyReason]]
-    off_study_reason_other: Mapped[Optional[str]]
+    off_study_reason: Mapped[OffStudyReason | None]
+    off_study_reason_other: Mapped[str | None]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="participants", cascade="all, delete")
-    demographic: Mapped["DemographicORM"] = relationship(
+    trial: Mapped[TrialORM] = relationship(back_populates="participants", cascade="all, delete")
+    demographic: Mapped[DemographicORM] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    prior_treatments: Mapped[List["PriorTreatmentORM"]] = relationship(
+    prior_treatments: Mapped[List[PriorTreatmentORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    treatments: Mapped[List["TreatmentORM"]] = relationship(
+    treatments: Mapped[List[TreatmentORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    diseases: Mapped[List["DiseaseORM"]] = relationship(
+    diseases: Mapped[List[DiseaseORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    response_by_systems: Mapped[List["ResponseBySystemORM"]] = relationship(
+    response_by_systems: Mapped[List[ResponseBySystemORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    response: Mapped[Optional["ResponseORM"]] = relationship(
+    response: Mapped[ResponseORM | None] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    adverse_events: Mapped[List["AdverseEventORM"]] = relationship(
+    adverse_events: Mapped[List[AdverseEventORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    baseline_clinical_assessment: Mapped[Optional["BaselineClinicalAssessmentORM"]] = relationship(
+    baseline_clinical_assessment: Mapped[BaselineClinicalAssessmentORM | None] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    medical_history: Mapped[Optional["MedicalHistoryORM"]] = relationship(
+    medical_history: Mapped[MedicalHistoryORM | None] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    exposures: Mapped[List["ExposureORM"]] = relationship(
+    exposures: Mapped[List[ExposureORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    gvhd_diagnosis_acutes: Mapped[List["GVHDDiagnosisAcuteORM"]] = relationship(
+    gvhd_diagnosis_acutes: Mapped[List[GVHDDiagnosisAcuteORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    gvhd_diagnosis_chronics: Mapped[List["GVHDDiagnosisChronicORM"]] = relationship(
+    gvhd_diagnosis_chronics: Mapped[List[GVHDDiagnosisChronicORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    specimens: Mapped[List["SpecimenORM"]] = relationship(
+    specimens: Mapped[List[SpecimenORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    other_clinical_endpoints: Mapped[List["OtherClinicalEndpointORM"]] = relationship(
+    other_clinical_endpoints: Mapped[List[OtherClinicalEndpointORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    additional_treatments: Mapped[List["AdditionalTreatmentORM"]] = relationship(
+    additional_treatments: Mapped[List[AdditionalTreatmentORM]] = relationship(
         back_populates="participant", cascade="all, delete", passive_deletes=True
     )
-    consent_group: Mapped["ConsentGroupORM"] = relationship(back_populates="participants", cascade="all, delete")
+    consent_group: Mapped[ConsentGroupORM] = relationship(back_populates="participants", cascade="all, delete")

cidc_api/models/db/stage2/prior_treatment_orm.py

@@ -1,11 +1,12 @@
-from typing import Optional, List
+from __future__ import annotations
+from typing import List
 
 from pydantic import NonPositiveInt, NegativeInt
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
 
 
@@ -18,13 +19,13 @@ class PriorTreatmentORM(BaseORM):
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
-    prior_treatment_days_to_start: Mapped[Optional[NonPositiveInt]]
-    prior_treatment_days_to_end: Mapped[Optional[NonPositiveInt]]
+    prior_treatment_days_to_start: Mapped[NonPositiveInt | None]
+    prior_treatment_days_to_end: Mapped[NonPositiveInt | None]
     prior_treatment_type: Mapped[List[PriorTreatmentType]] = mapped_column(JSON, nullable=False)
-    prior_treatment_description: Mapped[Optional[str]]
-    prior_treatment_best_response: Mapped[Optional[str]]
-    prior_treatment_conditioning_regimen_type: Mapped[Optional[ConditioningRegimenType]]
-    prior_treatment_stem_cell_donor_type: Mapped[Optional[StemCellDonorType]]
-    prior_treatment_days_to_prior_transplant: Mapped[Optional[NegativeInt]]
+    prior_treatment_description: Mapped[str | None]
+    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]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="prior_treatments", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="prior_treatments", cascade="all, delete")

cidc_api/models/db/stage2/publication_orm.py

@@ -1,9 +1,8 @@
-from typing import Optional, List
-
+from __future__ import annotations
 from sqlalchemy import ForeignKeyConstraint, ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
 
 
@@ -22,10 +21,10 @@ class PublicationORM(BaseORM):
     version: Mapped[str]
 
     digital_object_id: Mapped[str]
-    pubmed_id: Mapped[Optional[str]]
-    publication_title: Mapped[Optional[str]]
-    authorship: Mapped[Optional[str]]
-    year_of_publication: Mapped[Optional[str]]
-    journal_citation: Mapped[Optional[str]]
+    pubmed_id: Mapped[str | None]
+    publication_title: Mapped[str | None]
+    authorship: Mapped[str | None]
+    year_of_publication: Mapped[str | None]
+    journal_citation: Mapped[str | None]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="publications", cascade="all, delete")
+    trial: Mapped[TrialORM] = relationship(back_populates="publications", cascade="all, delete")

cidc_api/models/db/stage2/radiotherapy_dose_orm.py

@@ -1,10 +1,10 @@
+from __future__ import annotations
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat
-from typing import Optional
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import (
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
@@ -26,15 +26,15 @@ class RadiotherapyDoseORM(BaseORM):
     days_to_start: Mapped[NonNegativeInt]
     days_to_end: Mapped[NonNegativeInt]
     procedure: Mapped[RadiotherapyProcedure]
-    anatomical_location: Mapped[Optional[UberonAnatomicalTerm]]
+    anatomical_location: Mapped[UberonAnatomicalTerm | None]
     is_total_dose: Mapped[bool]
-    number_of_fractions: Mapped[Optional[NonNegativeInt]]
+    number_of_fractions: Mapped[NonNegativeInt | None]
     received_dose: Mapped[NonNegativeFloat]
     received_dose_units: Mapped[RadiotherapyDoseUnits]
-    planned_dose: Mapped[Optional[PositiveFloat]]
-    planned_dose_units: Mapped[Optional[RadiotherapyDoseUnits]]
+    planned_dose: Mapped[PositiveFloat | None]
+    planned_dose_units: Mapped[RadiotherapyDoseUnits | None]
     dose_changes_delays: Mapped[YNU]
-    changes_delays_description: Mapped[Optional[str]]
+    changes_delays_description: Mapped[str | None]
     radiation_extent: Mapped[RadiationExtent]
 
-    treatment: Mapped["TreatmentORM"] = relationship(back_populates="radiotherapy_doses", cascade="all, delete")
+    treatment: Mapped[TreatmentORM] = relationship(back_populates="radiotherapy_doses", cascade="all, delete")

cidc_api/models/db/stage2/response_by_system_orm.py

@@ -1,8 +1,9 @@
+from __future__ import annotations
 from pydantic import PositiveInt
 from sqlalchemy import ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
 
 
@@ -27,4 +28,4 @@ class ResponseBySystemORM(BaseORM):
     progression_free_survival_event: Mapped[YNUNA]
     progression_free_survival: Mapped[PositiveInt | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="response_by_systems", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="response_by_systems", cascade="all, delete")

cidc_api/models/db/stage2/response_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from pydantic import NonNegativeInt
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 
 
@@ -25,4 +26,4 @@ class ResponseORM(BaseORM):
     evaluable_for_efficacy: Mapped[bool]
     days_to_last_vital_status: Mapped[NonNegativeInt | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="response", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="response", cascade="all, delete")

cidc_api/models/db/stage2/shipment_orm.py

@@ -1,10 +1,11 @@
+from __future__ import annotations
 from datetime import datetime
-from typing import Optional, List
+from typing import List
 
 from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-from cidc_api.models.db.base_orm import BaseORM
+from cidc_api.models.db.stage2.base_orm import BaseORM
 from cidc_api.models.types import AssayPriority, AssayType, Courier, ShipmentCondition, ShipmentQuality
 
 
@@ -24,24 +25,24 @@ class ShipmentORM(BaseORM):
     version: Mapped[str]
 
     manifest_id: Mapped[str]
-    assay_priority: Mapped[Optional[AssayPriority]]
-    assay_type: Mapped[Optional[AssayType]]
-    courier: Mapped[Optional[Courier]]
-    tracking_number: Mapped[Optional[str]]
-    condition: Mapped[Optional[ShipmentCondition]]
-    condition_other: Mapped[Optional[str]]
-    date_shipped: Mapped[Optional[datetime]]
-    date_received: Mapped[Optional[datetime]]
-    quality: Mapped[Optional[ShipmentQuality]]
+    assay_priority: Mapped[AssayPriority | None]
+    assay_type: Mapped[AssayType | None]
+    courier: Mapped[Courier | None]
+    tracking_number: Mapped[str | None]
+    condition: Mapped[ShipmentCondition | None]
+    condition_other: Mapped[str | None]
+    date_shipped: Mapped[datetime | None]
+    date_received: Mapped[datetime | None]
+    quality: Mapped[ShipmentQuality | None]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="shipments", cascade="all, delete")
-    institution: Mapped["InstitutionORM"] = relationship(back_populates="shipments", cascade="all, delete")
-    shipped_from: Mapped["ContactORM"] = relationship(
+    trial: Mapped[TrialORM] = relationship(back_populates="shipments", cascade="all, delete")
+    institution: Mapped[InstitutionORM] = relationship(back_populates="shipments", cascade="all, delete")
+    shipped_from: Mapped[ContactORM] = relationship(
         back_populates="shipment_from", cascade="all, delete", foreign_keys="[ContactORM.shipment_from_id]"
     )
-    shipped_to: Mapped["ContactORM"] = relationship(
+    shipped_to: Mapped[ContactORM] = relationship(
         back_populates="shipment_to", cascade="all, delete", foreign_keys="[ContactORM.shipment_to_id]"
     )
-    shipment_specimens: Mapped[List["ShipmentSpecimenORM"]] = relationship(
+    shipment_specimens: Mapped[List[ShipmentSpecimenORM]] = relationship(
         back_populates="shipment", cascade="all, delete", passive_deletes=True
     )