nci-cidc-api-modules 1.2.16__py3-none-any.whl → 1.2.25__py3-none-any.whl

cidc_api/models/pydantic/stage2/base.py

@@ -0,0 +1,30 @@
+from pydantic import BaseModel, ConfigDict
+from contextlib import contextmanager
+
+import copy
+
+
+class Base(BaseModel):
+
+    model_config = ConfigDict(validate_assignment=True, from_attributes=True)
+
+    # Validates the new state and updates the object if valid
+    def update(self, **kwargs):
+        self.model_validate(self.__dict__ | kwargs)
+        self.__dict__.update(kwargs)
+
+    # CM that delays validation until all fields are applied.
+    # If validation fails the original fields are restored and the ValidationError is raised.
+    @contextmanager
+    def delay_validation(self):
+        original_dict = copy.deepcopy(self.__dict__)
+        self.model_config["validate_assignment"] = False
+        try:
+            yield
+        finally:
+            self.model_config["validate_assignment"] = True
+        try:
+            self.model_validate(self.__dict__)
+        except:
+            self.__dict__.update(original_dict)
+            raise

cidc_api/models/pydantic/stage2/baseline_clinical_assessment.py

@@ -0,0 +1,23 @@
+from .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: int | 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/stage2/cohort.py

@@ -0,0 +1,16 @@
+from .base import Base
+
+
+class Cohort(Base):
+    # A unique internal identifier for the cohort
+    cohort_id: int | None = None
+
+    # The unique identifier for the associated trial
+    trial_id: str | None = None
+
+    # The version number of the trial dataset
+    version: str | None = None
+
+    # The name of the cohort, e.g. "Cohort A"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7979585%20and%20ver_nr=1
+    name: str

cidc_api/models/pydantic/stage2/comorbidity.py

@@ -0,0 +1,36 @@
+from typing import Self
+
+from pydantic import model_validator
+
+from .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/stage2/consent_group.py

@@ -0,0 +1,30 @@
+from pydantic import NonNegativeInt
+
+from .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: int | 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/stage2/contact.py

@@ -0,0 +1,35 @@
+from .base import Base
+
+
+class Contact(Base):
+    contact_id: int | None = None
+    institution_id: int | None = None
+    shipment_from_id: int | None = None
+    shipment_to_id: int | None = None
+
+    # The name of the contact
+    name: str | None = None
+
+    # The email address of the contact
+    email: str | None = None
+
+    # The phone number of the contact
+    phone: str | None = None
+
+    # Line 1 of the street address of the contact
+    street1: str | None = None
+
+    # Line 2 of the street address of the contact
+    street2: str | None = None
+
+    # The city where the contact is located
+    city: str | None = None
+
+    # The state where the contact is located
+    state: str | None = None
+
+    # The zip code where the contact is located
+    zip: str | None = None
+
+    # The country where the contact is located
+    country: str | None = None

cidc_api/models/pydantic/stage2/demographic.py

@@ -0,0 +1,114 @@
+from typing import Self
+
+from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, model_validator, field_validator
+
+from .base import Base
+from cidc_api.models.types import (
+    Sex,
+    Race,
+    Ethnicity,
+    HeightUnits,
+    WeightUnits,
+    BodySurfaceAreaUnits,
+    Occupation,
+    Education,
+    AgeAtEnrollmentUnits,
+)
+
+
+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: int | 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 older. (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_older: 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: Race
+
+    # 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
+
+    # 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
+
+    # 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
+
+    # 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
+
+    @model_validator(mode="after")
+    def validate_age_at_enrollment_cr(self) -> Self:
+        if self.age_90_or_older:
+            if self.age_at_enrollment or self.age_at_enrollment_units:
+                raise ValueError(
+                    'If "age_90_or_older" is "Yes" then "age_at_enrollment" and "age_at_enrollment_units" must be blank.'
+                )
+        else:
+            if not self.age_at_enrollment or not self.age_at_enrollment_units:
+                raise ValueError(
+                    'If "age_90_or_older" is "No" then "age_at_enrollment" and "age_at_enrollment_units" are required.'
+                )
+        return self
+
+    @model_validator(mode="after")
+    def validate_age_at_enrollment_value(self) -> Self:
+        age_in_years = (
+            self.age_at_enrollment if self.age_at_enrollment_units == "Years" else self.age_at_enrollment / 365.25
+        )
+        if age_in_years >= 90:
+            raise ValueError('"age_at_enrollment" cannot represent a value greater than 90 years of age.')
+        return self

cidc_api/models/pydantic/stage2/disease.py

@@ -0,0 +1,144 @@
+from pydantic import NonPositiveInt, model_validator
+from typing import List, Self
+
+from .base import Base
+from cidc_api.models.types import (
+    PrimaryDiagnosisDiseaseGroup,
+    TumorGrade,
+    CancerStageSystem,
+    CancerStageSystemVersion,
+    CancerStage,
+    TCategory,
+    NCategory,
+    MCategory,
+    UberonAnatomicalTerm,
+    ICDO3MorphologicalCode,
+    ICDO3MorphologicalTerm,
+    YNU,
+)
+
+
+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: int | None = None
+
+    # A term describing the main condition for evaluation and treatment as captured in the Disease or Diagnosis (C2991)
+    # branch of the National Cancer Institute Thesaurus (NCIt) hierarchy tree. e.g. "Melanoma"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14905532%20and%20ver_nr=1
+    primary_diagnosis_disease_group: PrimaryDiagnosisDiseaseGroup
+
+    # 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
+
+    # The ICD-O-3 morphology term that describes the tumor's type. e.g. "Mucinous adenoma"
+    # CDE: TBD
+    morphological_term: ICDO3MorphologicalTerm
+
+    # 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
+
+    # 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
+
+    # 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
+
+    # 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
+
+    # 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
+
+    # The organ site where a tumor develops outside of the bone marrow as specified in the Uberon antatomical term.
+    metastatic_organ: List[UberonAnatomicalTerm] = []
+
+    # Indicates if participant has a hematological malignancy that is only extramedullary. e.g. "Yes"
+    solely_extramedullary_disease: YNU
+
+    extramedullary_organ: List[UberonAnatomicalTerm] = []
+
+    @model_validator(mode="after")
+    def validate_code_or_term_or_description_cr(self) -> Self:
+        if not self.morphological_code and not self.morphological_term and not self.cancer_type_description:
+            raise ValueError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "cancer_type_description".'
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_cancer_stage_system_version_cr(self) -> Self:
+        if self.cancer_stage_system != "Not Applicable" and not self.cancer_stage_system_version:
+            raise ValueError(
+                f'Please provide cancer_stage_system_version when cancer_stage_system is "{self.cancer_stage_system}"'
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_cancer_stage_cr(self) -> Self:
+        if self.cancer_stage_system != "Not Applicable" and not self.cancer_stage:
+            raise ValueError(f'Please provide cancer_stage when cancer_stage_system is "{self.cancer_stage_system}"')
+        return self
+
+    @model_validator(mode="after")
+    def validate_t_category_cr(self) -> Self:
+        if self.cancer_stage_system == "AJCC" and not self.t_category:
+            raise ValueError(f'Please provide t_category when cancer_stage_system is "{self.cancer_stage_system}"')
+        return self
+
+    @model_validator(mode="after")
+    def validate_n_category_cr(self) -> Self:
+        if self.cancer_stage_system == "AJCC" and not self.n_category:
+            raise ValueError(f'Please provide n_category when cancer_stage_system is "{self.cancer_stage_system}"')
+        return self
+
+    @model_validator(mode="after")
+    def validate_m_category_cr(self) -> Self:
+        if self.cancer_stage_system == "AJCC" and not self.m_category:
+            raise ValueError(f'Please provide m_category when cancer_stage_system is "{self.cancer_stage_system}"')
+        return self
+
+    @model_validator(mode="after")
+    def validate_extramedullary_organ_cr(self) -> Self:
+        if self.solely_extramedullary_disease in ["No", "Unknown"] and self.extramedullary_organ:
+            raise ValueError(
+                "If solely_extramedullary_disease indicates no disease, please leave extramedullary_organ blank."
+            )
+        return self

cidc_api/models/pydantic/stage2/exposure.py

@@ -0,0 +1,32 @@
+from typing import Self
+
+from pydantic import model_validator
+
+from .base import Base
+from cidc_api.models.types import YNU, ExposureType
+
+
+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: int | 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
+
+    @model_validator(mode="after")
+    def validate_exposure_type_cr(self) -> Self:
+        if self.carcinogen_exposure in ["No", "Unknown"] and self.exposure_type:
+            raise ValueError("If carcinogen_exposure indicates non exposure, please leave exposure_type blank.")
+        return self

cidc_api/models/pydantic/stage2/file.py

@@ -0,0 +1,44 @@
+from datetime import datetime
+from .base import Base
+from cidc_api.models.types import ChecksumType, FileFormat
+
+
+class File(Base):
+    # The unique internal identifier for this File record
+    file_id: int | None = None
+
+    # The unique identifier for the associated trial
+    trial_id: int | None = None
+
+    # The version number of the trial dataset
+    version: str | None = None
+
+    # The unique internal identifier of the institution that created this file
+    creator_id: int | None = None
+
+    # A description of the file's purpose and contents
+    description: str | None = None
+
+    # A unique UUID to identify the file across systems
+    uuid: str
+
+    # The name of the file
+    file_name: str
+
+    # The url of the file object as found in cloud storage, a bucket, external system, etc.
+    object_url: str
+
+    # The timestamp of when CIDC received the file
+    uploaded_timestamp: datetime
+
+    # The size of the file's contents, in bytes
+    file_size_bytes: int
+
+    # The value of the checksum calculated for the file's contents
+    checksum_value: str
+
+    # The type of the checksum calculated for the file's contents
+    checksum_type: ChecksumType
+
+    # A description or abbreviation of the format of the file's contents, possibly different than the extension
+    file_format: FileFormat

cidc_api/models/pydantic/stage2/gvhd_diagnosis_acute.py

@@ -0,0 +1,33 @@
+from .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: int | 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/stage2/gvhd_diagnosis_chronic.py

@@ -0,0 +1,32 @@
+from .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: int | 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/stage2/gvhd_organ_acute.py

@@ -0,0 +1,22 @@
+from .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/stage2/gvhd_organ_chronic.py

@@ -0,0 +1,23 @@
+from .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/stage2/institution.py

@@ -0,0 +1,10 @@
+from .base import Base
+
+
+class Institution(Base):
+
+    # A unique internal identifier for the Institution
+    institution_id: int | None = None
+
+    # The name by which the institution is known, e.g. "MATCH Central Pathology Lab"
+    name: str