nci-cidc-api-modules 1.2.39__py3-none-any.whl → 1.2.40__py3-none-any.whl

cidc_api/models/db/stage2/shipment_specimen_orm.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
 from datetime import datetime
 
 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 ShipmentSpecimenORM(BaseORM):
@@ -20,5 +21,5 @@ class ShipmentSpecimenORM(BaseORM):
     box_number: Mapped[str]
     sample_location: Mapped[str]
 
-    specimen: Mapped["SpecimenORM"] = relationship(back_populates="shipment_specimen", cascade="all, delete")
-    shipment: Mapped["ShipmentORM"] = relationship(back_populates="shipment_specimens", cascade="all, delete")
+    specimen: Mapped[SpecimenORM] = relationship(back_populates="shipment_specimen", cascade="all, delete")
+    shipment: Mapped[ShipmentORM] = relationship(back_populates="shipment_specimens", cascade="all, delete")

cidc_api/models/db/stage2/specimen_orm.py

@@ -1,10 +1,11 @@
+from __future__ import annotations
 from datetime import datetime
 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 (
     UberonAnatomicalTerm,
     ICDO3MorphologicalCode,
@@ -45,7 +46,7 @@ class SpecimenORM(BaseORM):
     organ_site_of_collection: Mapped[UberonAnatomicalTerm | None]
     histology_behavior: Mapped[ICDO3MorphologicalCode | None]
     histology_behavior_description: Mapped[str | None]
-    collection_event_name: Mapped[str | None]
+    collection_event_name: Mapped[str]
     specimen_type: Mapped[SpecimenType | None]
     specimen_type_other: Mapped[str | None]
     specimen_description: Mapped[SpecimenDescription | None]
@@ -92,9 +93,10 @@ class SpecimenORM(BaseORM):
     diagnosis_verification: Mapped[DiagnosisVerification | None]
     intended_assay: Mapped[AssayType | None]
     date_ingested: Mapped[datetime | None]
-    days_to_specimen_collection: Mapped[int | None]
+    days_to_specimen_collection: Mapped[int]
+    organ_site_of_collection: Mapped[UberonAnatomicalTerm]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="specimens", cascade="all, delete")
-    shipment_specimen: Mapped["ShipmentSpecimenORM"] = relationship(
+    participant: Mapped[ParticipantORM] = relationship(back_populates="specimens", cascade="all, delete")
+    shipment_specimen: Mapped[ShipmentSpecimenORM] = relationship(
         back_populates="specimen", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/db/stage2/stem_cell_transplant_orm.py

@@ -1,10 +1,10 @@
+from __future__ import annotations
 from pydantic import NonNegativeInt
-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 StemCellDonorType, AllogeneicDonorType, StemCellSource, ConditioningRegimenType
 
 
@@ -19,8 +19,8 @@ class StemCellTransplantORM(BaseORM):
 
     stem_cell_donor_type: Mapped[StemCellDonorType]
     allogeneic_donor_type: Mapped[AllogeneicDonorType]
-    stem_cells_source: Mapped[StemCellSource]
+    stem_cell_source: Mapped[StemCellSource]
     days_to_transplant: Mapped[NonNegativeInt]
-    conditioning_regimen_type: Mapped[Optional[ConditioningRegimenType]]
+    conditioning_regimen_type: Mapped[ConditioningRegimenType | None]
 
-    treatment: Mapped["TreatmentORM"] = relationship(back_populates="stem_cell_transplants", cascade="all, delete")
+    treatment: Mapped[TreatmentORM] = relationship(back_populates="stem_cell_transplants", cascade="all, delete")

cidc_api/models/db/stage2/surgery_orm.py

@@ -1,10 +1,10 @@
+from __future__ import annotations
 from pydantic import NonNegativeInt
-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 SurgicalProcedure, UberonAnatomicalTerm, YNU
 
 
@@ -18,11 +18,11 @@ class SurgeryORM(BaseORM):
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))
 
     procedure: Mapped[SurgicalProcedure]
-    procedure_other: Mapped[Optional[str]]
+    procedure_other: Mapped[str | None]
     days_to_procedure: Mapped[NonNegativeInt]
     anatomical_location: Mapped[UberonAnatomicalTerm]
     therapeutic: Mapped[YNU]
-    findings: Mapped[Optional[str]]
-    extent_of_residual_disease: Mapped[Optional[str]]
+    findings: Mapped[str | None]
+    extent_of_residual_disease: Mapped[str | None]
 
-    treatment: Mapped["TreatmentORM"] = relationship(back_populates="surgeries", cascade="all, delete")
+    treatment: Mapped[TreatmentORM] = relationship(back_populates="surgeries", cascade="all, delete")

cidc_api/models/db/stage2/therapy_agent_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 TherapyAgentDoseUnits, YNU
 
 
@@ -17,16 +17,16 @@ class TherapyAgentDoseORM(BaseORM):
     therapy_agent_dose_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))
 
-    course_number: Mapped[Optional[str]]
+    course_number: Mapped[str | None]
     therapy_agent_name: Mapped[str]
     days_to_start: Mapped[NonNegativeInt]
     days_to_end: Mapped[NonNegativeInt]
     number_of_doses: Mapped[NonNegativeInt]
     received_dose: Mapped[NonNegativeFloat]
     received_dose_units: Mapped[TherapyAgentDoseUnits]
-    planned_dose: Mapped[Optional[PositiveFloat]]
-    planned_dose_units: Mapped[Optional[TherapyAgentDoseUnits]]
+    planned_dose: Mapped[PositiveFloat | None]
+    planned_dose_units: Mapped[TherapyAgentDoseUnits | None]
     dose_changes_delays: Mapped[YNU]
-    changes_delays_description: Mapped[Optional[str]]
+    changes_delays_description: Mapped[str | None]
 
-    treatment: Mapped["TreatmentORM"] = relationship(back_populates="therapy_agent_doses", cascade="all, delete")
+    treatment: Mapped[TreatmentORM] = relationship(back_populates="therapy_agent_doses", cascade="all, delete")

cidc_api/models/db/stage2/treatment_orm.py

@@ -1,9 +1,10 @@
-from typing import List, Optional
+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, OffTreatmentReason
 
 
@@ -15,26 +16,26 @@ class TreatmentORM(BaseORM):
 
     treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
-    arm_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stage2.arm.arm_id", ondelete="CASCADE"))
-    cohort_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stage2.cohort.cohort_id", ondelete="CASCADE"))
+    arm_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.arm.arm_id", ondelete="CASCADE"))
+    cohort_id: Mapped[int | None] = mapped_column(ForeignKey("stage2.cohort.cohort_id", ondelete="CASCADE"))
 
     treatment_description: Mapped[str]
     off_treatment: Mapped[YNU]
-    off_treatment_reason: Mapped[Optional[OffTreatmentReason]]
-    off_treatment_reason_other: Mapped[Optional[str]]
+    off_treatment_reason: Mapped[OffTreatmentReason | None]
+    off_treatment_reason_other: Mapped[str | None]
 
-    participant: Mapped["ParticipantORM"] = relationship(back_populates="treatments", cascade="all, delete")
-    arm: Mapped[Optional["ArmORM"]] = relationship(cascade="all, delete")
-    cohort: Mapped[Optional["CohortORM"]] = relationship(cascade="all, delete")
-    adverse_events: Mapped[List["AdverseEventORM"]] = relationship(back_populates="treatment", cascade="all, delete")
+    participant: Mapped[ParticipantORM] = relationship(back_populates="treatments", cascade="all, delete")
+    arm: Mapped[ArmORM | None] = relationship(cascade="all, delete")
+    cohort: Mapped[CohortORM | None] = relationship(cascade="all, delete")
+    adverse_events: Mapped[List[AdverseEventORM]] = relationship(back_populates="treatment", cascade="all, delete")
 
-    therapy_agent_doses: Mapped[List["TherapyAgentDoseORM"]] = relationship(
+    therapy_agent_doses: Mapped[List[TherapyAgentDoseORM]] = relationship(
         back_populates="treatment", cascade="all, delete"
     )
-    radiotherapy_doses: Mapped[List["RadiotherapyDoseORM"]] = relationship(
+    radiotherapy_doses: Mapped[List[RadiotherapyDoseORM]] = relationship(
         back_populates="treatment", cascade="all, delete"
     )
-    surgeries: Mapped[List["SurgeryORM"]] = relationship(back_populates="treatment", cascade="all, delete")
-    stem_cell_transplants: Mapped[List["StemCellTransplantORM"]] = relationship(
+    surgeries: Mapped[List[SurgeryORM]] = relationship(back_populates="treatment", cascade="all, delete")
+    stem_cell_transplants: Mapped[List[StemCellTransplantORM]] = relationship(
         back_populates="treatment", cascade="all, delete"
     )

cidc_api/models/db/stage2/trial_orm.py

@@ -1,12 +1,13 @@
+from __future__ import annotations
 from datetime import datetime
-from typing import List, Optional
+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.types import AssayType, TrialOrganization, TrialFundingAgency, AgeGroup
+from cidc_api.models.db.stage2.base_orm import BaseORM
+from cidc_api.models.types import AssayType, TrialOrganization, TrialFundingAgency, AgeGroup, PrimaryPurposeType
 
 
 class TrialORM(BaseORM):
@@ -36,28 +37,26 @@ class TrialORM(BaseORM):
     biomarker_plan: Mapped[str | None]
     data_sharing_plan: Mapped[str | None]
     expected_assays: Mapped[List[AssayType]] = mapped_column(JSON, nullable=True)
-    is_liquid_tumor_trial: Mapped[bool]
+    primary_purpose_type: Mapped[PrimaryPurposeType]
     dbgap_study_accession: Mapped[str | None]
 
-    biobank: Mapped["InstitutionORM"] = relationship(back_populates="trial")
-    schema: Mapped[Optional["FileORM"]] = relationship(back_populates="trial", viewonly=True)
-    administrative_role_assignments: Mapped[List["AdministrativeRoleAssignmentORM"]] = relationship(
+    biobank: Mapped[InstitutionORM] = relationship(back_populates="trial")
+    schema: Mapped[FileORM | None] = relationship(back_populates="trial", viewonly=True)
+    administrative_role_assignments: Mapped[List[AdministrativeRoleAssignmentORM]] = relationship(
         back_populates="trial", cascade="all, delete", passive_deletes=True
     )
-    arms: Mapped[List["ArmORM"]] = relationship(back_populates="trial", cascade="all, delete", passive_deletes=True)
-    cohorts: Mapped[List["CohortORM"]] = relationship(
+    arms: Mapped[List[ArmORM]] = relationship(back_populates="trial", cascade="all, delete", passive_deletes=True)
+    cohorts: Mapped[List[CohortORM]] = relationship(back_populates="trial", cascade="all, delete", passive_deletes=True)
+    participants: Mapped[List[ParticipantORM]] = relationship(
         back_populates="trial", cascade="all, delete", passive_deletes=True
     )
-    participants: Mapped[List["ParticipantORM"]] = relationship(
+    shipments: Mapped[List[ShipmentORM]] = relationship(
         back_populates="trial", cascade="all, delete", passive_deletes=True
     )
-    shipments: Mapped[List["ShipmentORM"]] = relationship(
+    files: Mapped[List[FileORM]] = relationship(back_populates="trial", cascade="all, delete", passive_deletes=True)
+    publications: Mapped[List[PublicationORM]] = relationship(
         back_populates="trial", cascade="all, delete", passive_deletes=True
     )
-    files: Mapped[List["FileORM"]] = relationship(back_populates="trial", cascade="all, delete", passive_deletes=True)
-    publications: Mapped[List["PublicationORM"]] = relationship(
-        back_populates="trial", cascade="all, delete", passive_deletes=True
-    )
-    consent_groups: Mapped[List["ConsentGroupORM"]] = relationship(
+    consent_groups: Mapped[List[ConsentGroupORM]] = relationship(
         back_populates="trial", cascade="all, delete", passive_deletes=True
     )

cidc_api/models/models.py

@@ -3479,6 +3479,7 @@ class IngestionJobs(CommonColumns):
     submission_id = Column(String, nullable=True)
     intake_path = Column(String, nullable=True)
     uploader_email = Column(String, nullable=True)
+    is_template_downloaded = Column(Boolean, nullable=True)
 
     @staticmethod
     @with_default_session

cidc_api/models/pydantic/{stage2/base.py → base.py}

@@ -9,7 +9,7 @@ class Base(BaseModel):
     model_config = ConfigDict(
         validate_assignment=True,
         from_attributes=True,
-        # extra="forbid" # TODO: enable me one stage1 models are implemented
+        extra="forbid",
     )
 
     # Validates the new state and updates the object if valid

cidc_api/models/pydantic/stage1/__init__.py

@@ -0,0 +1,56 @@
+from .additional_treatment import AdditionalTreatment
+from .adverse_event import AdverseEvent
+from .baseline_clinical_assessment import BaselineClinicalAssessment
+from .comorbidity import Comorbidity
+from .consent_group import ConsentGroup
+from .demographic import Demographic
+from .disease import Disease
+from .exposure import Exposure
+from .gvhd_diagnosis_acute import GVHDDiagnosisAcute
+from .gvhd_diagnosis_chronic import GVHDDiagnosisChronic
+from .gvhd_organ_acute import GVHDOrganAcute
+from .gvhd_organ_chronic import GVHDOrganChronic
+from .medical_history import MedicalHistory
+from .other_malignancy import OtherMalignancy
+from .participant import Participant
+from .prior_treatment import PriorTreatment
+from .radiotherapy_dose import RadiotherapyDose
+from .response import Response
+from .response_by_system import ResponseBySystem
+from .specimen import Specimen
+from .stem_cell_transplant import StemCellTransplant
+from .surgery import Surgery
+from .therapy_agent_dose import TherapyAgentDose
+from .treatment import Treatment
+from .trial import Trial
+
+
+__all__ = [
+    "AdditionalTreatment",
+    "AdverseEvent",
+    "BaselineClinicalAssessment",
+    "Comorbidity",
+    "ConsentGroup",
+    "Demographic",
+    "Disease",
+    "Exposure",
+    "GVHDDiagnosisAcute",
+    "GVHDOrganAcute",
+    "GVHDDiagnosisChronic",
+    "GVHDOrganChronic",
+    "MedicalHistory",
+    "OtherMalignancy",
+    "Participant",
+    "PriorTreatment",
+    "RadiotherapyDose",
+    "Response",
+    "ResponseBySystem",
+    "Specimen",
+    "StemCellTransplant",
+    "Surgery",
+    "TherapyAgentDose",
+    "Treatment",
+    "Trial",
+]
+
+all_models = [globals()[cls_name] for cls_name in __all__]

cidc_api/models/pydantic/stage1/additional_treatment.py

@@ -0,0 +1,23 @@
+from pydantic import NonNegativeInt
+from cidc_api.models.pydantic.base import Base
+
+
+class AdditionalTreatment(Base):
+    __data_category__ = "additional_treatment"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the AdditionalTreatment record
+    additional_treatment_id: int | None = None
+
+    # The unique internal identifier for the associated Participant record
+    participant_id: str | None = None
+
+    # Number of days from the enrollment date to the first recorded administration or occurrence of the treatment modality.
+    additional_treatment_days_to_start: NonNegativeInt | None = None
+
+    # Number of days from the enrollment date to the last recorded administration or occurrence of the treatment modality.
+    additional_treatment_days_to_end: NonNegativeInt | None = None
+
+    # Description of the prior treatment such as its full generic name if it is a type of therapy agent, radiotherapy procedure
+    # name and location, or surgical procedure name and location.
+    additional_treatment_description: str

cidc_api/models/pydantic/stage1/adverse_event.py

@@ -0,0 +1,100 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.reference.ctcae import is_ctcae_other_term
+from cidc_api.models.types import (
+    CTCAEEventTerm,
+    CTCAEEventCode,
+    SeverityGradeSystem,
+    SeverityGradeSystemVersion,
+    SeverityGrade,
+    SystemOrganClass,
+    AttributionCause,
+    AttributionLikelihood,
+    YNU,
+)
+
+
+class AdverseEvent(Base):
+    __data_category__ = "adverse_event"
+    __cardinality__ = "many"
+
+    # The unique internal identifier of the adverse event
+    adverse_event_id: int | None = None
+
+    # The unique internal identifier of the associated participant
+    participant_id: str | None = None
+
+    # The unique internal identifier of the attributed treatment, if any
+    treatment_id: int | None = None
+
+    # Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.
+    event_term: CTCAEEventTerm | None = None
+
+    # A MedDRA code mapped to a CTCAE low level name for an adverse event.
+    event_code: CTCAEEventCode | None = None
+
+    # System used to define and report adverse event severity grade.
+    severity_grade_system: SeverityGradeSystem
+
+    # The version of the adverse event grading system.
+    severity_grade_system_version: SeverityGradeSystemVersion
+
+    # Numerical grade indicating the severity of an adverse event.
+    severity_grade: SeverityGrade
+
+    # A brief description that sufficiently details the event.
+    event_other_specify: str | None = None
+
+    # The highest level of the MedDRA hierarchy, distinguished by anatomical or physiological system, etiology (disease origin) or purpose.
+    system_organ_class: SystemOrganClass | None = None
+
+    # Indicator to identify whether a participant exited the study prematurely due to the adverse event being described.
+    discontinuation_due_to_event: bool
+
+    # Days from enrollment date to date of onset of the adverse event.
+    days_to_onset_of_event: NonNegativeInt
+
+    # Days from enrollment date to date of resolution of the adverse event.
+    days_to_resolution_of_event: NonNegativeInt | None = None
+
+    # Indicates whether the adverse event was a serious adverse event (SAE).
+    serious_adverse_event: YNU
+
+    # Indicates whether the adverse event was a dose-limiting toxicity (DLT).
+    dose_limiting_toxicity: YNU
+
+    # Indicates if the adverse was attributable to the protocol as a whole or to an individual treatment.
+    attribution_cause: AttributionCause
+
+    # The code that indicates whether the adverse event is related to the treatment/intervention.
+    attribution_likelihood: AttributionLikelihood
+
+    # The individual therapy (therapy agent, radiotherapy, surgery, stem cell transplant) in the treatment that is attributed to the adverse event.
+    individual_therapy: str | None = None
+
+    @model_validator(mode="after")
+    def validate_term_and_code_cr(self) -> Self:
+        if not self.event_term and not self.event_code:
+            raise ValueError("Please provide event_term or event_code or both")
+        return self
+
+    @model_validator(mode="after")
+    def validate_event_other_specify_cr(self) -> Self:
+        if (
+            self.severity_grade_system == "CTCAE"
+            and is_ctcae_other_term(self.event_term)
+            and not self.event_other_specify
+        ):
+            raise ValueError(
+                'If severity_grade_system is "CTCAE" and the event_code or event_term are of type "Other, specify", please provide event_other_specify'
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_system_organ_class_cr(self) -> Self:
+        if self.event_other_specify and not self.system_organ_class:
+            raise ValueError("If event_other_specify is provided, please provide system_organ_class.")
+        return self

cidc_api/models/pydantic/stage1/baseline_clinical_assessment.py

@@ -0,0 +1,23 @@
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import ECOGScore, KarnofskyScore
+
+
+class BaselineClinicalAssessment(Base):
+    __data_category__ = "baseline_clinical_assessment"
+    __cardinality__ = "one"
+
+    # A unique internal identifier for the baseline clinical assessment
+    baseline_clinical_assessment_id: int | None = None
+
+    # The unique identifier for the associated participant
+    participant_id: str | None = None
+
+    # The numerical score that represents the functional capabilities of a participant at the
+    # enrollment date using the Eastern Cooperative Oncology Group Performance Status assessment.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=88%20and%20ver_nr=5.1
+    ecog_score: ECOGScore | None = None
+
+    # Score from the Karnofsky Performance status scale, representing the functional capabilities of a participant
+    # at the enrollment date.
+    # CDE: 	https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2003853%20and%20ver_nr=4.2
+    karnofsky_score: KarnofskyScore | None = None

cidc_api/models/pydantic/stage1/comorbidity.py

@@ -0,0 +1,36 @@
+from typing import Self
+
+from pydantic import model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
+
+
+class Comorbidity(Base):
+    __data_category__ = "comorbidity"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the comorbidity record
+    comorbidity_id: int | None = None
+
+    # The unique internal identifier for the associated MedicalHistory record
+    medical_history_id: int | None = None
+
+    # The diagnosis, in humans, as captured in the tenth version of the
+    # International Classification of Disease (ICD-10-CM, the disease code subset of ICD-10).
+    comorbidity_code: ICD10CMCode | None = None
+
+    # The words from the tenth version of the International Classification of Disease (ICD-10-CM,
+    # the disease subset of ICD-10) used to identify the diagnosis in humans.
+    comorbidity_term: ICD10CMTerm | None = None
+
+    # A descriptive string that names or briefly describes the comorbidity.
+    comorbidity_other: str | None = None
+
+    @model_validator(mode="after")
+    def validate_code_or_term_or_other_cr(self) -> Self:
+        if not self.comorbidity_code and not self.comorbidity_term and not self.comorbidity_other:
+            raise ValueError(
+                'Please provide at least one of "comorbidity_code", "comorbidity_term" or "comorbidity_other".'
+            )
+        return self

cidc_api/models/pydantic/stage1/consent_group.py

@@ -0,0 +1,30 @@
+from pydantic import NonNegativeInt
+
+from cidc_api.models.pydantic.base import Base
+
+
+class ConsentGroup(Base):
+    __data_category__ = "consent_group"
+    __cardinality__ = "one"
+
+    # The unique internal identifier for the consent group record
+    consent_group_id: int | None = None
+
+    # The unique internal identifier for the associated Trial record
+    trial_id: str | None = None
+
+    # The version number of the trial dataset
+    version: str | None = None
+
+    # An abbreviated name for the consent group
+    consent_group_short_name: str
+
+    # The words or acronym which describe a set of study participants
+    # who have signed the same consent agreement and that will be included in the dbGaP repository.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14534329%20and%20ver_nr=1.00
+    consent_group_name: str
+
+    # A numeral or string of numerals used to identify the set of study participants who have signed the same consent
+    # agreement and that will be included in the dbGaP repository.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14534330%20and%20ver_nr=1.00
+    consent_group_number: NonNegativeInt