nci-cidc-api-modules 1.2.29__py3-none-any.whl → 1.2.45__py3-none-any.whl

cidc_api/models/db/stage2/comorbidity_orm.py

@@ -1,24 +1,23 @@
-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
 from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
 
 
 class ComorbidityORM(BaseORM):
     __tablename__ = "comorbidity"
     __repr_attrs__ = ["comorbidity_id", "comorbidity_term"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "comorbidity"
 
     comorbidity_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(
         ForeignKey("stage2.medical_history.medical_history_id", ondelete="CASCADE")
     )
 
-    comorbidity_code: Mapped[Optional[ICD10CMCode]]
-    comorbidity_term: Mapped[Optional[ICD10CMTerm]]
-    comorbidity_other: Mapped[Optional[str]]
+    comorbidity_code: Mapped[ICD10CMCode | None]
+    comorbidity_term: Mapped[ICD10CMTerm | None]
+    comorbidity_other: Mapped[str | None]
 
-    medical_history: Mapped["MedicalHistoryORM"] = relationship(back_populates="comorbidities", cascade="all, delete")
+    medical_history: Mapped[MedicalHistoryORM] = relationship(back_populates="comorbidities", cascade="all, delete")

cidc_api/models/db/stage2/consent_group_orm.py

@@ -1,10 +1,11 @@
+from __future__ import annotations
 from typing import List
 
 from pydantic import NonNegativeInt
 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 ConsentGroupORM(BaseORM):
@@ -14,8 +15,8 @@ class ConsentGroupORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
+    __data_category__ = "consent_group"
 
     consent_group_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
@@ -25,7 +26,7 @@ class ConsentGroupORM(BaseORM):
     consent_group_name: Mapped[str]
     consent_group_number: Mapped[NonNegativeInt]
 
-    trial: Mapped["TrialORM"] = relationship(back_populates="consent_groups", cascade="all, delete")
-    participants: Mapped[List["ParticipantORM"]] = relationship(
+    trial: Mapped[TrialORM] = relationship(back_populates="consent_groups", cascade="all, delete")
+    participants: Mapped[List[ParticipantORM]] = relationship(
         back_populates="consent_group", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/db/stage2/contact_orm.py

@@ -1,32 +1,28 @@
-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):
     __tablename__ = "contact"
-    __table_args__ = {"schema": "stage2"}
 
     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

@@ -1,9 +1,12 @@
+from __future__ import annotations
 from pydantic import NonNegativeFloat, PositiveFloat, PositiveInt
+from typing import List
 
 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,
@@ -20,25 +23,25 @@ from cidc_api.models.types import (
 class DemographicORM(BaseORM):
     __tablename__ = "demographic"
     __repr_attrs__ = ["demographic_id", "participant_id", "age_at_enrollment", "sex"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "demographic"
 
     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_older: Mapped[bool]
+    age_90_or_over: Mapped[bool]
     sex: Mapped[Sex]
-    race: Mapped[Race]
+    race: Mapped[List[Race]] = mapped_column(JSON)
     ethnicity: Mapped[Ethnicity]
     height: Mapped[PositiveFloat]
     height_units: Mapped[HeightUnits]
     weight: Mapped[PositiveFloat]
     weight_units: Mapped[WeightUnits]
-    body_mass_index: Mapped[PositiveFloat]
-    body_surface_area: Mapped[PositiveFloat]
-    body_surface_area_units: Mapped[BodySurfaceAreaUnits]
+    body_mass_index: Mapped[PositiveFloat | None]
+    body_surface_area: Mapped[PositiveFloat | None]
+    body_surface_area_units: Mapped[BodySurfaceAreaUnits | None]
     occupation: Mapped[Occupation | None]
     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

@@ -1,13 +1,13 @@
-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 (
-    PrimaryDiagnosisDiseaseGroup,
     TumorGrade,
     CancerStageSystem,
     CancerStageSystemVersion,
@@ -29,25 +29,24 @@ class DiseaseORM(BaseORM):
         "disease_id",
         "participant_id",
     ]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "disease"
 
     disease_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
-    primary_diagnosis_disease_group: Mapped[PrimaryDiagnosisDiseaseGroup]
     primary_disease_site: Mapped[UberonAnatomicalTerm]
-    morphological_code: Mapped[ICDO3MorphologicalCode]
-    morphological_term: Mapped[ICDO3MorphologicalTerm]
+    morphological_code: Mapped[ICDO3MorphologicalCode | None]
+    morphological_term: Mapped[ICDO3MorphologicalTerm | None]
     cancer_type_description: Mapped[str | None]
-    days_since_original_diagnosis: Mapped[NonPositiveInt]
+    days_since_original_diagnosis: Mapped[NonPositiveInt | None]
     tumor_grade: Mapped[TumorGrade | None]
     cancer_stage_system: Mapped[CancerStageSystem]
     cancer_stage_system_version: Mapped[CancerStageSystemVersion | None] = mapped_column(String, nullable=True)
-    cancer_stage: Mapped[CancerStage] = mapped_column(String)
-    t_category: Mapped[TCategory]
-    n_category: Mapped[NCategory]
-    m_category: Mapped[MCategory]
-    metastatic_organ: Mapped[List[UberonAnatomicalTerm]] = mapped_column(JSON, nullable=True)
+    cancer_stage: Mapped[CancerStage | None] = mapped_column(String)
+    t_category: Mapped[TCategory | None]
+    n_category: Mapped[NCategory | None]
+    m_category: Mapped[MCategory | None]
+    metastatic_organ: Mapped[List[UberonAnatomicalTerm] | None] = mapped_column(JSON, nullable=True)
     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

@@ -1,21 +1,22 @@
+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
 
 
 class ExposureORM(BaseORM):
     __tablename__ = "exposure"
     __repr_attrs__ = ["exposure_id", "exposure_type", "carcinogen_exposure"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "exposure"
 
     exposure_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
     carcinogen_exposure: Mapped[YNU]
-    exposure_type: Mapped[ExposureType]
+    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
 
 
@@ -14,17 +14,14 @@ class FileORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     file_id: Mapped[int] = mapped_column(primary_key=True)
     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 +31,5 @@ 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,
@@ -16,9 +17,9 @@ class GVHDDiagnosisAcuteORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_acute"
     __table_args__ = (
         UniqueConstraint("participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_acute_pre_or_post"),
-        {"schema": "stage2"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_acute"
 
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -27,7 +28,7 @@ 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,
@@ -18,9 +19,9 @@ class GVHDDiagnosisChronicORM(BaseORM):
         UniqueConstraint(
             "participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_chronic_pre_or_post"
         ),
-        {"schema": "stage2"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_chronic"
 
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
@@ -29,9 +30,7 @@ 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

@@ -1,14 +1,15 @@
+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
 
 
 class GVHDOrganAcuteORM(BaseORM):
     __tablename__ = "gvhd_organ_acute"
     __repr_attrs__ = ["gvhd_organ_acute_id", "organ"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "gvhd_organ_acute"
 
     gvhd_organ_acute_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(
@@ -17,4 +18,4 @@ 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

@@ -1,14 +1,15 @@
+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
 
 
 class GVHDOrganChronicORM(BaseORM):
     __tablename__ = "gvhd_organ_chronic"
     __repr_attrs__ = ["gvhd_organ_chronic_id", "organ"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "gvhd_organ_chronic"
 
     gvhd_organ_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(
@@ -17,4 +18,4 @@ 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):
@@ -13,7 +14,6 @@ class InstitutionORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     institution_id: Mapped[int] = mapped_column(primary_key=True)
@@ -22,12 +22,12 @@ 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

@@ -1,29 +1,30 @@
-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
 
 
 class MedicalHistoryORM(BaseORM):
     __tablename__ = "medical_history"
     __repr_attrs__ = ["medical_history_id"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "medical_history"
 
     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

@@ -1,28 +1,24 @@
-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
 
 
 class OtherClinicalEndpointORM(BaseORM):
     __tablename__ = "other_clinical_endpoint"
     __repr_attrs__ = ["other_clinical_endpoint_id", "name", "event"]
-    __table_args__ = {"schema": "stage2"}
 
     other_clinical_endpoint_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
     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

@@ -1,30 +1,29 @@
-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
 
 
 class OtherMalignancyORM(BaseORM):
     __tablename__ = "other_malignancy"
     __repr_attrs__ = ["other_malignancy_id", "primary_disease_site"]
-    __table_args__ = {"schema": "stage2"}
+    __data_category__ = "other_malignancy"
 
     other_malignancy_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(
         ForeignKey("stage2.medical_history.medical_history_id", ondelete="CASCADE")
     )
 
-    primary_disease_site: Mapped[UberonAnatomicalTerm]
-    morphological_code: Mapped[Optional[ICDO3MorphologicalCode]]
-    morphological_term: Mapped[Optional[ICDO3MorphologicalTerm]]
-    malignancy_description: Mapped[Optional[str]]
-    days_since_diagnosis: Mapped[Optional[NonPositiveInt]]
-    malignancy_status: Mapped[Optional[MalignancyStatus]]
+    other_malignancy_primary_disease_site: Mapped[UberonAnatomicalTerm]
+    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"
     )