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

cidc_api/models/pydantic/stage2/consent_group.py

@@ -1,6 +1,6 @@
 from pydantic import NonNegativeInt
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class ConsentGroup(Base):
@@ -11,7 +11,7 @@ class ConsentGroup(Base):
     consent_group_id: int | None = None
 
     # The unique internal identifier for the associated Trial record
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/contact.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Contact(Base):

cidc_api/models/pydantic/stage2/demographic.py

@@ -1,8 +1,8 @@
-from typing import Self
+from typing import Self, Annotated, List
 
-from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, model_validator, field_validator
+from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, model_validator, field_validator, BeforeValidator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     Sex,
     Race,
@@ -25,7 +25,7 @@ class Demographic(Base):
 
     # 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
+    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
@@ -34,9 +34,9 @@ class Demographic(Base):
     # 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)
+    # 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_older: bool
+    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
@@ -44,7 +44,7 @@ class Demographic(Base):
 
     # 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
+    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
@@ -68,15 +68,15 @@ class Demographic(Base):
 
     # 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
+    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
+    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
+    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
@@ -92,23 +92,32 @@ class Demographic(Base):
 
     @model_validator(mode="after")
     def validate_age_at_enrollment_cr(self) -> Self:
-        if self.age_90_or_older:
+        if self.age_90_or_over:
             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.'
+                    'If "age_90_or_over" 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.'
+                    'If "age_90_or_over" 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.')
+        if not self.age_90_or_over:
+            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
+
+    @model_validator(mode="after")
+    def validate_body_surface_area_units_cr(self) -> Self:
+        if self.body_surface_area and not self.body_surface_area_units:
+            raise ValueError(
+                'If "body_surface_area" is provided then "body_surface_area_units_other" must also be provided.'
+            )
         return self

cidc_api/models/pydantic/stage2/disease.py

@@ -1,12 +1,14 @@
-from pydantic import NonPositiveInt, model_validator
-from typing import List, Self
+from pydantic import NonPositiveInt, model_validator, BeforeValidator
+from typing import List, Self, Annotated, get_args
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
-    PrimaryDiagnosisDiseaseGroup,
     TumorGrade,
     CancerStageSystem,
     CancerStageSystemVersion,
+    CancerStageSystemVersionAJCC,
+    CancerStageSystemVersionRISS,
+    CancerStageSystemVersionFIGO,
     CancerStage,
     TCategory,
     NCategory,
@@ -27,12 +29,7 @@ class Disease(Base):
 
     # 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
+    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
@@ -40,18 +37,18 @@ class Disease(Base):
 
     # 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
+    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
+    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
+    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
@@ -68,32 +65,32 @@ class Disease(Base):
     # 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
+    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
+    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
+    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
+    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: List[UberonAnatomicalTerm] = []
+    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: List[UberonAnatomicalTerm] = []
+    extramedullary_organ: Annotated[List[UberonAnatomicalTerm] | None, BeforeValidator(Base.split_list)] = []
 
     @model_validator(mode="after")
     def validate_code_or_term_or_description_cr(self) -> Self:
@@ -103,6 +100,23 @@ class Disease(Base):
             )
         return self
 
+    @model_validator(mode="after")
+    def validate_cancer_stage_system_version(self) -> Self:
+        msg = f"{self.cancer_stage_system_version} is not applicable to {self.cancer_stage_system}"
+        if self.cancer_stage_system == "AJCC" and self.cancer_stage_system_version not in get_args(
+            CancerStageSystemVersionAJCC
+        ):
+            raise ValueError(msg)
+        elif self.cancer_stage_system == "RISS" and self.cancer_stage_system_version not in get_args(
+            CancerStageSystemVersionRISS
+        ):
+            raise ValueError(msg)
+        elif self.cancer_stage_system == "FIGO" and self.cancer_stage_system_version not in get_args(
+            CancerStageSystemVersionFIGO
+        ):
+            raise ValueError(msg)
+        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:

cidc_api/models/pydantic/stage2/exposure.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, ExposureType
 
 
@@ -14,7 +14,7 @@ class Exposure(Base):
     exposure_id: int | None = None
 
     # The unique identifier for the associated participant
-    participant_id: int | None = None
+    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.
@@ -23,7 +23,7 @@ class Exposure(Base):
 
     # 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
+    exposure_type: ExposureType | None = None
 
     @model_validator(mode="after")
     def validate_exposure_type_cr(self) -> Self:

cidc_api/models/pydantic/stage2/file.py

@@ -1,5 +1,5 @@
 from datetime import datetime
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import ChecksumType, FileFormat
 
 
@@ -8,7 +8,7 @@ class File(Base):
     file_id: int | None = None
 
     # The unique identifier for the associated trial
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/gvhd_diagnosis_acute.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDDiagnosisAcuteAssessmentSystem,
     GVHDDiagnosisAcuteAssessmentSystemVersion,
@@ -15,7 +15,7 @@ class GVHDDiagnosisAcute(Base):
     gvhd_diagnosis_acute_id: int | None = None
 
     # The unique internal identifier for the associated participant
-    participant_id: int | None = None
+    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.

cidc_api/models/pydantic/stage2/gvhd_diagnosis_chronic.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDDiagnosisChronicAssessmentSystem,
     GVHDDiagnosisChronicAssessmentSystemVersion,
@@ -15,7 +15,7 @@ class GVHDDiagnosisChronic(Base):
     gvhd_diagnosis_chronic_id: int | None = None
 
     # The unique internal identifier for the associated participant
-    participant_id: int | None = None
+    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.

cidc_api/models/pydantic/stage2/gvhd_organ_acute.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDOrgan,
     GVHDOrganAcuteStage,

cidc_api/models/pydantic/stage2/gvhd_organ_chronic.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     GVHDOrgan,
     GVHDOrganChronicScore,

cidc_api/models/pydantic/stage2/institution.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Institution(Base):

cidc_api/models/pydantic/stage2/medical_history.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, PositiveFloat, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import TobaccoSmokingStatus
 
 
@@ -14,7 +14,7 @@ class MedicalHistory(Base):
     medical_history_id: int | None = None
 
     # The unique identifier for the associated participant
-    participant_id: int | None = None
+    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.

cidc_api/models/pydantic/stage2/other_clinical_endpoint.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
 
 

cidc_api/models/pydantic/stage2/other_malignancy.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonPositiveInt, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 
@@ -17,28 +17,32 @@ class OtherMalignancy(Base):
     medical_history_id: int | None = None
 
     # The location within the body from where the prior malignancy originated as captured in the Uberon anatomical term.
-    primary_disease_site: UberonAnatomicalTerm
+    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.
-    morphological_code: ICDO3MorphologicalCode | None = None
+    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.
-    morphological_term: ICDO3MorphologicalTerm | None = None
+    other_malignancy_morphological_term: ICDO3MorphologicalTerm | None = None
 
     # Description of the cancer type as recorded in the trial.
-    malignancy_description: str | None = None
+    other_malignancy_description: str | None = None
 
     # Number of days since original diagnosis from the enrollment date. This may be a negative number.
-    days_since_diagnosis: NonPositiveInt | None = None
+    other_malignancy_days_since_diagnosis: NonPositiveInt | None = None
 
     # Indicates the participant’s current clinical state regarding the cancer diagnosis.
-    malignancy_status: MalignancyStatus | None = None
+    other_malignancy_status: MalignancyStatus | None = None
 
     @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.malignancy_description:
+        if (
+            not self.other_malignancy_morphological_code
+            and not self.other_malignancy_morphological_term
+            and not self.other_malignancy_description
+        ):
             raise ValueError(
                 'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".'
             )

cidc_api/models/pydantic/stage2/participant.py

@@ -2,7 +2,8 @@ from typing import Self
 
 from pydantic import model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import YNU
 from cidc_api.models.types import OffStudyReason
 
 
@@ -12,20 +13,23 @@ class Participant(Base):
 
     # The unique internal identifier for the 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
+    participant_id: str | None = None
 
     # The participant identifier assigned by the clinical trial team overseeing the study
     native_participant_id: str
 
     # The globally unique participant identifier assigned by the CIMAC network. e.g. C8P29A7
-    cimac_participant_id: str
+    cimac_participant_id: str | None = None
 
     # The unique identifier for the associated trial that the participant is participating in
-    trial_id: int | None = None
+    trial_id: str | None = None
+
+    # The version number of the trial dataset. e.g. "1.0"
+    version: str | None = None
 
     # Indicates if the individual is no longer actively participating in the clinical trial.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14834973%20and%20ver_nr=1
-    off_study: bool
+    off_study: YNU
 
     # An explanation describing why an individual is no longer participating in the clinical trial.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13362265%20and%20ver_nr=1
@@ -36,7 +40,7 @@ class Participant(Base):
 
     @model_validator(mode="after")
     def off_study_reason_cr(self) -> Self:
-        if self.off_study and not self.off_study_reason:
+        if self.off_study == "Yes" and not self.off_study_reason:
             raise ValueError('If "off_study" is "Yes" then "off_study_reason" is required.')
         return self
 

cidc_api/models/pydantic/stage2/prior_treatment.py

@@ -1,9 +1,9 @@
-from typing import Self
+from typing import Self, Annotated, List
 
-from pydantic import NonPositiveInt, NonNegativeInt, model_validator
+from pydantic import NonPositiveInt, NegativeInt, model_validator, BeforeValidator
 
-from .base import Base
-from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PriorTreatment(Base):
@@ -14,39 +14,30 @@ class PriorTreatment(Base):
     prior_treatment_id: int | None = None
 
     # A unique internal identifier for the associated participant record
-    participant_id: int | None = None
+    participant_id: str | None = None
 
     # Number of days from the enrollment date to the first recorded administration or occurrence of
     # the treatment modality.
-    days_to_start: NonPositiveInt | None = None
+    prior_treatment_days_to_start: NonPositiveInt | None = None
 
     # Number of days from the enrollment date to the last recorded administration or occurrence of
     # the treatment modality.
-    days_to_end: NonPositiveInt | None = None
-
-    # Specifies the category or kind of prior treatment modality a participant received.
-    type: PriorTreatmentType
+    prior_treatment_days_to_end: NonPositiveInt | 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.
-    description: str | None = None
+    prior_treatment_description: str
 
     # Best response from any response assessment system to the prior treatment if available or applicable.
-    best_response: str | None = None
+    prior_treatment_best_response: str | None = None
 
     # If the prior treatment is "Conditioning therapy" received before a stem cell transplant, specifies what
     # type of conditioning regimen used.
-    conditioning_regimen_type: ConditioningRegimenType | None = None
+    prior_treatment_conditioning_regimen_type: ConditioningRegimenType | None = None
 
     # If prior treatment is "Stem cell transplant", indicates what stem cell donor type used.
-    stem_cell_donor_type: StemCellDonorType | None = None
-
-    # If prior treatment is "Stem cell transplant", indicates the number of days from the transplant
-    # date to the start of the current treatment.
-    days_from_transplant_to_treatment_initiation: NonNegativeInt | None = None
+    prior_treatment_stem_cell_donor_type: StemCellDonorType | None = None
 
-    @model_validator(mode="after")
-    def validate_description_cr(self) -> Self:
-        if self.type == "Other therapy" and not self.description:
-            raise ValueError('If type is "Other therapy", please provide description.')
-        return self
+    # If prior treatment is "Stem cell transplant", indicates the number of days from enrollment
+    # to the prior transplant. This must be a negative number.
+    prior_treatment_days_from_transplant_to_treatment_initiation: NegativeInt | None = None

cidc_api/models/pydantic/stage2/publication.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Publication(Base):
@@ -6,7 +6,7 @@ class Publication(Base):
     publication_id: int | None = None
 
     # The unique internal identifier for the associated Trial record
-    trial_id: int | None = None
+    trial_id: str | None = None
 
     # The version number of the trial dataset
     version: str | None = None

cidc_api/models/pydantic/stage2/radiotherapy_dose.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     YNU,
     RadiotherapyProcedure,
@@ -17,7 +17,7 @@ class RadiotherapyDose(Base):
     __cardinality__ = "many"
 
     # The unique internal identifier for the radiotherapy dose record
-    therapy_agent_dose_id: int | None = None
+    radiotherapy_dose_id: int | None = None
 
     # The unique internal identifier for the associated treatment record
     treatment_id: int | None = None

cidc_api/models/pydantic/stage2/response.py

@@ -2,7 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, model_validator
 
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 
 
@@ -15,14 +15,14 @@ class Response(Base):
 
     # 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
+    participant_id: str | None = None
 
     # The response to a question that describes a participant's survival status.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2847330%20and%20ver_nr=1
     survival_status: SurvivalStatus
 
     # Number of days from enrollment date to death date.
-    overall_survival: NonNegativeInt | None = None
+    overall_survival: NonNegativeInt
 
     # Indicator for whether there was an abscopal effect on disease after local therapy.
     abscopal_response: YNUNA | None = None
@@ -43,14 +43,8 @@ class Response(Base):
     # Indicates whether participant was evaluable for efficacy (for example, response, PFS, OS, etc.) overall.
     evaluable_for_efficacy: bool
 
-    # Days from enrollment date to the last time patient had follow-up.
-    days_to_last_follow_up: NonNegativeInt | None = None
-
-    @model_validator(mode="after")
-    def validate_overall_survival_cr(self) -> Self:
-        if self.survival_status != "Unknown" and not self.overall_survival:
-            raise ValueError('If survival_status is not "Unknown" then overall_survival is required.')
-        return self
+    # Days from enrollment date to the last time the patient's vital status was verified.
+    days_to_last_vital_status: NonNegativeInt | None = None  # TODO: Needs CR check
 
     @model_validator(mode="after")
     def validate_cause_of_death_cr(self) -> Self: