nci-cidc-api-modules 1.2.34__py3-none-any.whl → 1.2.53__py3-none-any.whl

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

cidc_api/models/pydantic/stage1/demographic.py

@@ -0,0 +1,140 @@
+from typing import Annotated, List
+
+from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, BeforeValidator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
+
+from cidc_api.models.errors import ValueLocError
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    Sex,
+    Race,
+    Ethnicity,
+    HeightUnits,
+    WeightUnits,
+    BodySurfaceAreaUnits,
+    Occupation,
+    Education,
+    AgeAtEnrollmentUnits,
+)
+
+
+@forced_validators
+class Demographic(Base):
+    __data_category__ = "demographic"
+    __cardinality__ = "one"
+
+    # The unique internal identifier for this demographic record
+    demographic_id: int | None = None
+
+    # The unique internal identifier for the associated participant
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12220014%20and%20ver_nr=1
+    participant_id: str | None = None
+
+    # The age of the subject when the subject enrolled in the study.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15742605%20and%20ver_nr=1
+    age_at_enrollment: PositiveInt | None = None
+
+    # Unit of measurement for the age of the participant. e.g. "Years"
+    age_at_enrollment_units: AgeAtEnrollmentUnits | None = None
+
+    # Indicates whether the participant is 90 years old or over. (for PHI purposes)
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15354920%20and%20ver_nr=1
+    age_90_or_over: bool
+
+    # A textual description of a person's sex at birth. e.g. "Male"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7572817%20and%20ver_nr=3
+    sex: Sex
+
+    # The race of the participant. e.g. "White"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2192199%20and%20ver_nr=1
+    race: Annotated[List[Race], BeforeValidator(Base.split_list)]
+
+    # The ethnicity of the participant. e.g. "Hispanic or Latino"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2192217%20and%20ver_nr=2
+    ethnicity: Ethnicity
+
+    # The number that describes the vertical distance of the participant at enrollment date.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2179643%20and%20ver_nr=4
+    height: PositiveFloat
+
+    # Unit of measurement for the height of the participant at the enrollment date. e.g. "in"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2538920%20and%20ver_nr=1
+    height_units: HeightUnits
+
+    # The mass of the participant's entire body at the enrollment date.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2179689%20and%20ver_nr=4
+    weight: PositiveFloat
+
+    # Unit of measurement for the weight of the participant at the enrollment date. e.g. "kg"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2630200%20and%20ver_nr=1
+    weight_units: WeightUnits
+
+    # The body mass index of the participant at the enrollment date.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2006410%20and%20ver_nr=3
+    body_mass_index: PositiveFloat | None = None
+
+    # A decimal number that represents the measure of the 2-dimensional extent of the body surface (i.e., the skin) of the participant at the enrollment date.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6606197%20and%20ver_nr=1
+    body_surface_area: PositiveFloat | None = None
+
+    # Unit of measurement for body surface area of the participant at the enrollment date. e.g. "m2"
+    # https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15114329%20and%20ver_nr=1
+    body_surface_area_units: BodySurfaceAreaUnits | None = None
+
+    # The occupation/job category of the participant. e.g. "Manager"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6617540%20and%20ver_nr=1
+    occupation: Occupation | None = None
+
+    # The amount of earnings in USD made by the participant's family in a year.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14834966%20and%20ver_nr=1
+    income: NonNegativeFloat | None = None
+
+    # The highest level of education attained by the participant. e.g. "Bachelor's Degree"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2681552%20and%20ver_nr=1
+    highest_level_of_education: Education | None = None
+
+    @forced_validator
+    @classmethod
+    def validate_age_at_enrollment_cr(cls, data, info) -> None:
+        age_at_enrollment_units = data.get("age_at_enrollment_units", None)
+        age_90_or_over = data.get("age_90_or_over", None)
+        age_at_enrollment = int(data.get("age_at_enrollment", None) or 0)
+
+        if age_90_or_over == True or age_90_or_over == "Yes":
+            if age_at_enrollment or age_at_enrollment_units:
+                raise ValueLocError(
+                    'If "age_90_or_over" is "Yes" then "age_at_enrollment" and "age_at_enrollment_units" must be blank.',
+                    loc="age_at_enrollment",
+                )
+        elif age_90_or_over == False or age_90_or_over == "No":
+            if not age_at_enrollment or not age_at_enrollment_units:
+                raise ValueLocError(
+                    'If "age_90_or_over" is "No" then "age_at_enrollment" and "age_at_enrollment_units" are required.',
+                    loc="age_at_enrollment",
+                )
+
+    @forced_validator
+    @classmethod
+    def validate_age_at_enrollment_value(cls, data, info) -> None:
+        age_at_enrollment_units = data.get("age_at_enrollment_units", None)
+        age_90_or_over = data.get("age_90_or_over", None)
+        age_at_enrollment = int(data.get("age_at_enrollment", None) or 0)
+
+        if not age_90_or_over == True or age_90_or_over == "Yes":
+            age_in_years = age_at_enrollment if age_at_enrollment_units == "Years" else age_at_enrollment / 365.25
+            if age_in_years >= 90:
+                raise ValueLocError(
+                    '"age_at_enrollment" cannot represent a value greater than 90 years of age.',
+                    loc="age_at_enrollment",
+                )
+
+    @forced_validator
+    @classmethod
+    def validate_body_surface_area_units_cr(cls, data, info) -> None:
+        body_surface_area = data.get("body_surface_area", None)
+        body_surface_area_units = data.get("body_surface_area_units", None)
+
+        if body_surface_area and not body_surface_area_units:
+            raise ValueLocError(
+                'If "body_surface_area" is provided then "body_surface_area_units" must also be provided.'
+            )

cidc_api/models/pydantic/stage1/disease.py

@@ -0,0 +1,200 @@
+from pydantic import NonPositiveInt, BeforeValidator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
+
+from typing import List, Self, Annotated, get_args, Any
+
+from cidc_api.models.errors import ValueLocError
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    TumorGrade,
+    CancerStageSystem,
+    CancerStageSystemVersion,
+    CancerStageSystemVersionAJCC,
+    CancerStageSystemVersionRISS,
+    CancerStageSystemVersionFIGO,
+    CancerStage,
+    TCategory,
+    NCategory,
+    MCategory,
+    UberonAnatomicalTerm,
+    ICDO3MorphologicalCode,
+    ICDO3MorphologicalTerm,
+    YNU,
+)
+
+
+@forced_validators
+class Disease(Base):
+    __data_category__ = "disease"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for this disease record
+    disease_id: int | None = None
+
+    # The unique internal identifier for the associated participant
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12220014%20and%20ver_nr=1
+    participant_id: str | None = None
+
+    # The location within the body from where the disease of interest originated as captured in the Uberon identifier. e.g. "lung"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14883047%20and%20ver_nr=1
+    primary_disease_site: UberonAnatomicalTerm
+
+    # The ICD-O-3 morphology code that describes the tumor's histology, behavior, and grade-differentiation. e.g. "8480/6"
+    # CDE: TBD
+    morphological_code: ICDO3MorphologicalCode | None
+
+    # The ICD-O-3 morphology term that describes the tumor's type. e.g. "Mucinous adenoma"
+    # CDE: TBD
+    morphological_term: ICDO3MorphologicalTerm | None
+
+    # Words that broadly describe the cancer's characteristics and type. e.g. "Inflitrating Ductal Carcinoma"
+    # CDE: TBD
+    cancer_type_description: str | None = None
+
+    # The number of days elapsed since the participant was first diagnosed with this condition.
+    days_since_original_diagnosis: NonPositiveInt | None
+
+    # Words that express the degree of abnormality of cancer cells as a measure of differentiation and aggressiveness. e.g. "G1 Low Grade"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=11325685%20and%20ver_nr=2
+    tumor_grade: TumorGrade | None = None
+
+    # The name of the staging system used in the evaluation of the disease. e.g. "AJCC"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7429602%20and%20ver_nr=1
+    cancer_stage_system: CancerStageSystem
+
+    # Release version of the staging system used in the evaluation of the disease. e.g. "8" (for AJCC)
+    cancer_stage_system_version: CancerStageSystemVersion | None = None
+
+    # Stage of the cancer at enrollment date as determined by the specific staging system. e.g. "Stage 0" (for AJCC)
+    # CDE(AJCC): https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440332%20and%20ver_nr=1
+    # CDE(FIGO): TBD
+    # CDE(RISS): TBD
+    cancer_stage: CancerStage | None = None
+
+    # Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. e.g. "T0"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440328%20and%20ver_nr=1
+    # TODO: Verify this CDE
+    t_category: TCategory | None = None
+
+    # Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters
+    # determined prior to treatment. e.g. "N0"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3440330%20and%20ver_nr=1
+    # TODO: Verify this CDE
+    n_category: NCategory | None = None
+
+    # Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined
+    # prior to treatment. e.g. "M0"
+    # CDE: https://teams.microsoft.com/l/message/19:1c292b63-5df1-4f29-b177-86aed53f393d_f224ae83-209b-4cd9-a7ef-83d9d2120a27@unq.gbl.spaces/1758827414202?context=%7B%22contextType%22%3A%22chat%22%7D
+    # TODO: Verify this CDE
+    m_category: MCategory | None = None
+
+    # The organ site where a tumor develops outside of the bone marrow as specified in the Uberon antatomical term.
+    metastatic_organ: Annotated[List[UberonAnatomicalTerm] | None, BeforeValidator(Base.split_list)] = []
+
+    # Indicates if participant has a hematological malignancy that is only extramedullary. e.g. "Yes"
+    solely_extramedullary_disease: YNU
+
+    extramedullary_organ: Annotated[List[UberonAnatomicalTerm] | None, BeforeValidator(Base.split_list)] = []
+
+    @forced_validator
+    @classmethod
+    def validate_code_or_term_or_description_cr(cls, data, info) -> None:
+        morphological_term = data.get("morphological_term", None)
+        cancer_type_description = data.get("cancer_type_description", None)
+        morphological_code = data.get("morphological_code", None)
+
+        if not morphological_code and not morphological_term and not cancer_type_description:
+            raise ValueLocError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "cancer_type_description".',
+                loc="morphological_code",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_cancer_stage_system_version(cls, data, info) -> None:
+        cancer_stage_system_version = data.get("cancer_stage_system_version", None)
+        cancer_stage_system = data.get("cancer_stage_system", None)
+
+        msg = f"{cancer_stage_system_version} is not applicable to {cancer_stage_system}"
+        if cancer_stage_system == "AJCC" and cancer_stage_system_version not in get_args(CancerStageSystemVersionAJCC):
+            raise ValueLocError(msg, loc="cancer_stage_system")
+        elif cancer_stage_system == "RISS" and cancer_stage_system_version not in get_args(
+            CancerStageSystemVersionRISS
+        ):
+            raise ValueLocError(msg, loc="cancer_stage_system")
+        elif cancer_stage_system == "FIGO" and cancer_stage_system_version not in get_args(
+            CancerStageSystemVersionFIGO
+        ):
+            raise ValueLocError(msg, loc="cancer_stage_system")
+
+    @forced_validator
+    @classmethod
+    def validate_cancer_stage_system_version_cr(cls, data, info) -> None:
+        cancer_stage_system = data.get("cancer_stage_system", None)
+        cancer_stage_system_version = data.get("cancer_stage_system_version", None)
+
+        if cancer_stage_system != "Not Applicable" and not cancer_stage_system_version:
+            raise ValueLocError(
+                f'Please provide cancer_stage_system_version when cancer_stage_system is "{cancer_stage_system}"',
+                loc="cancer_stage_system_version",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_cancer_stage_cr(cls, data, info) -> None:
+        cancer_stage_system = data.get("cancer_stage_system", None)
+        cancer_stage = data.get("cancer_stage", None)
+
+        if cancer_stage_system != "Not Applicable" and not cancer_stage:
+            raise ValueLocError(
+                f'Please provide cancer_stage when cancer_stage_system is "{cancer_stage_system}"',
+                loc="cancer_stage",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_t_category_cr(cls, data, info) -> None:
+        cancer_stage_system = data.get("cancer_stage_system", None)
+        t_category = data.get("t_category", None)
+
+        if cancer_stage_system == "AJCC" and not t_category:
+            raise ValueLocError(
+                f'Please provide t_category when cancer_stage_system is "{cancer_stage_system}"',
+                loc="t_category",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_n_category_cr(cls, data, info) -> None:
+        cancer_stage_system = data.get("cancer_stage_system", None)
+        n_category = data.get("n_category", None)
+
+        if cancer_stage_system == "AJCC" and not n_category:
+            raise ValueLocError(
+                f'Please provide n_category when cancer_stage_system is "{cancer_stage_system}"',
+                loc="n_category",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_m_category_cr(cls, data, info) -> None:
+        cancer_stage_system = data.get("cancer_stage_system", None)
+        m_category = data.get("m_category", None)
+
+        if cancer_stage_system == "AJCC" and not m_category:
+            raise ValueLocError(
+                f'Please provide m_category when cancer_stage_system is "{cancer_stage_system}"',
+                loc="m_category",
+            )
+
+    @forced_validator
+    @classmethod
+    def validate_extramedullary_organ_cr(cls, data, info) -> None:
+        solely_extramedullary_disease = data.get("solely_extramedullary_disease", None)
+        extramedullary_organ = data.get("extramedullary_organ", None)
+
+        if solely_extramedullary_disease in ["No", "Unknown"] and extramedullary_organ:
+            raise ValueLocError(
+                "If solely_extramedullary_disease indicates no disease, please leave extramedullary_organ blank.",
+                loc="extramedullary_organ",
+            )

cidc_api/models/pydantic/stage1/exposure.py

@@ -0,0 +1,38 @@
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
+
+from cidc_api.models.errors import ValueLocError
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import YNU, ExposureType
+
+
+@forced_validators
+class Exposure(Base):
+    __data_category__ = "exposure"
+    __cardinality__ = "many"
+
+    # A unique internal identifier for the exposure
+    exposure_id: int | None = None
+
+    # The unique identifier for the associated participant
+    participant_id: str | None = None
+
+    # An indication of whether the subject was exposed to any chemical, biological or physical agents
+    # that increase the risk of neoplasms in humans or animals.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5205578%20and%20ver_nr=3
+    carcinogen_exposure: YNU
+
+    # The type of potentially harmful environmental agents to which an individual was exposed.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15753203%20and%20ver_nr=1
+    exposure_type: ExposureType | None = None
+
+    @forced_validator
+    @classmethod
+    def validate_exposure_type_cr(cls, data, info) -> None:
+        carcinogen_exposure = data.get("carcinogen_exposure", None)
+        exposure_type = data.get("exposure_type", None)
+
+        if carcinogen_exposure in ["No", "Unknown"] and exposure_type:
+            raise ValueLocError(
+                "If carcinogen_exposure indicates non exposure, please leave exposure_type blank.",
+                loc="exposure_type",
+            )

cidc_api/models/pydantic/stage1/gvhd_diagnosis_acute.py

@@ -0,0 +1,33 @@
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    GVHDDiagnosisAcuteAssessmentSystem,
+    GVHDDiagnosisAcuteAssessmentSystemVersion,
+    GVHDDiagnosisAcuteGrade,
+    PreOrPostEnrollment,
+)
+
+
+class GVHDDiagnosisAcute(Base):
+    __data_category__ = "gvhd_diagnosis_acute"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the GVHD Diagnosis Acute Record
+    gvhd_diagnosis_acute_id: int | None = None
+
+    # The unique internal identifier for the associated participant
+    participant_id: str | None = None
+
+    # The clinical grading system used to stage involvement of affected organs (skin, liver, GI tract)
+    # in acute GVHD and assign an overall severity grade (I–IV) based on predefined criteria.
+    acute_assessment_system: GVHDDiagnosisAcuteAssessmentSystem
+
+    # Release version of the clinical grading system used in the evaluation of acute GVHD.
+    system_version: GVHDDiagnosisAcuteAssessmentSystemVersion
+
+    # The overall severity grade (I–IV) assigned to a patient with acute GVHD based on the extent of
+    # involvement in affected organs (skin, liver, and GI tract), determined using a standardized
+    # assessment system.
+    acute_grade: GVHDDiagnosisAcuteGrade
+
+    # Indicator for whether the acute GVHD diagnosis was made before or after trial enrollment.
+    pre_or_post_enrollment: PreOrPostEnrollment

cidc_api/models/pydantic/stage1/gvhd_diagnosis_chronic.py

@@ -0,0 +1,32 @@
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    GVHDDiagnosisChronicAssessmentSystem,
+    GVHDDiagnosisChronicAssessmentSystemVersion,
+    GVHDDiagnosisChronicGlobalSeverity,
+    PreOrPostEnrollment,
+)
+
+
+class GVHDDiagnosisChronic(Base):
+    __data_category__ = "gvhd_diagnosis_chronic"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the GVHD chronic diagnosis
+    gvhd_diagnosis_chronic_id: int | None = None
+
+    # The unique internal identifier for the associated participant
+    participant_id: str | None = None
+
+    # The standardized clinical system used to evaluate and grade the extent and severity
+    # of organ involvement in chronic GVHD, resulting in an overall disease severity score.
+    chronic_assessment_system: GVHDDiagnosisChronicAssessmentSystem
+
+    # Release version of the clinical grading system used in the evaluation of chronic GVHD.
+    system_version: GVHDDiagnosisChronicAssessmentSystemVersion
+
+    # An overall score reflecting the combined severity of chronic graft-versus-host disease
+    # across all affected organs, summarizing the participant’s total disease burden.
+    chronic_global_severity: GVHDDiagnosisChronicGlobalSeverity
+
+    # Indicator for whether the chronic GVHD diagnosis was made before or after trial enrollment.
+    pre_or_post_enrollment: PreOrPostEnrollment

cidc_api/models/pydantic/stage1/gvhd_organ_acute.py

@@ -0,0 +1,22 @@
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    GVHDOrgan,
+    GVHDOrganAcuteStage,
+)
+
+
+class GVHDOrganAcute(Base):
+    __data_category__ = "gvhd_organ_acute"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the GVHD Organ Acute Record
+    gvhd_organ_acute_id: int | None = None
+
+    # The unique internal identifier for the associated GVHD Diagnosis Acute record
+    gvhd_diagnosis_acute_id: int | None = None
+
+    # An organ affected by acute GVHD for which the stage is assessed as part of the overall acute GVHD evaluation.
+    organ: GVHDOrgan
+
+    # The severity level of an individual organ’s involvement in acute GVHD, usually scored from 0 (none) to 4 (severe).
+    acute_stage: GVHDOrganAcuteStage

cidc_api/models/pydantic/stage1/gvhd_organ_chronic.py

@@ -0,0 +1,23 @@
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    GVHDOrgan,
+    GVHDOrganChronicScore,
+)
+
+
+class GVHDOrganChronic(Base):
+    __data_category__ = "gvhd_organ_chronic"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the GVHD Organ Chronic Record
+    gvhd_organ_chronic_id: int | None = None
+
+    # The unique internal identifier for the associated GVHD Diagnosis Chronic record
+    gvhd_diagnosis_chronic_id: int | None = None
+
+    # An organ affected by chronic GVHD identified by its Uberon ontology ID
+    # and evaluated for severity as part of the overall chronic GVHD assessment.
+    organ: GVHDOrgan
+
+    # The severity score for an individual organ affected by chronic GVHD based on clinical criteria.
+    chronic_score: GVHDOrganChronicScore

cidc_api/models/pydantic/stage1/medical_history.py

@@ -0,0 +1,43 @@
+from pydantic import NonNegativeInt, PositiveFloat
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
+
+from cidc_api.models.errors import ValueLocError
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import TobaccoSmokingStatus
+
+
+@forced_validators
+class MedicalHistory(Base):
+    __data_category__ = "medical_history"
+    __cardinality__ = "one"
+
+    # A unique internal identifier for the medical history
+    medical_history_id: int | None = None
+
+    # The unique identifier for the associated participant
+    participant_id: str | None = None
+
+    # Text representation of a person's status relative to smoking tobacco in the form of cigarettes,
+    # based on questions about current and former use of cigarettes.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16333929%20and%20ver_nr=1
+    tobacco_smoking_status: TobaccoSmokingStatus | None = None
+
+    # Average number of packs of cigarettes smoked per day multiplied by number of years the participant has smoked.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6841869%20and%20ver_nr=1
+    pack_years_smoked: PositiveFloat | None = None
+
+    # Number of prior systemic therapies.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16089302%20and%20ver_nr=1
+    num_prior_systemic_therapies: NonNegativeInt | None = None
+
+    @forced_validator
+    @classmethod
+    def validate_pack_years_smoked_cr(cls, data, info) -> None:
+        tobacco_smoking_status = data.get("tobacco_smoking_status", None)
+        pack_years_smoked = data.get("pack_years_smoked", None)
+
+        if tobacco_smoking_status in ["Never Smoker", "Unknown", "Not reported"] and pack_years_smoked:
+            raise ValueLocError(
+                "If tobacco_smoking_status indicates non-smoker, please leave pack_years_smoked blank.",
+                loc="pack_years_smoked",
+            )

cidc_api/models/pydantic/stage1/other_malignancy.py

@@ -0,0 +1,55 @@
+from pydantic import NonPositiveInt
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
+
+from cidc_api.models.errors import ValueLocError
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
+
+
+@forced_validators
+class OtherMalignancy(Base):
+    __data_category__ = "other_malignancy"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the OtherMalignancy record
+    other_malignancy_id: int | None = None
+
+    # The unique internal identifier for the associated MedicalHistory record
+    medical_history_id: int | None = None
+
+    # The location within the body from where the prior malignancy originated as captured in the Uberon anatomical term.
+    other_malignancy_primary_disease_site: UberonAnatomicalTerm
+
+    # The ICD-O-3 code which identifies the specific appearance of cells and tissues (normal and abnormal) used
+    # to define the presence and nature of disease.
+    other_malignancy_morphological_code: ICDO3MorphologicalCode | None = None
+
+    # The ICD-O-3 textual label which identifies the specific appearance of cells and tissues (normal and abnormal) used
+    # to define the presence and nature of disease.
+    other_malignancy_morphological_term: ICDO3MorphologicalTerm | None = None
+
+    # Description of the cancer type as recorded in the trial.
+    other_malignancy_description: str | None = None
+
+    # Number of days since original diagnosis from the enrollment date. This may be a negative number.
+    other_malignancy_days_since_diagnosis: NonPositiveInt | None = None
+
+    # Indicates the participant’s current clinical state regarding the cancer diagnosis.
+    other_malignancy_status: MalignancyStatus | None = None
+
+    @forced_validator
+    @classmethod
+    def validate_code_or_term_or_description_cr(cls, data, info) -> None:
+        other_malignancy_morphological_term = data.get("other_malignancy_morphological_term", None)
+        other_malignancy_description = data.get("other_malignancy_description", None)
+        other_malignancy_morphological_code = data.get("other_malignancy_morphological_code", None)
+
+        if (
+            not other_malignancy_morphological_code
+            and not other_malignancy_morphological_term
+            and not other_malignancy_description
+        ):
+            raise ValueLocError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".',
+                loc="other_malignancy_morphological_code",
+            )