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

cidc_api/models/pydantic/stage1/radiotherapy_dose.py

@@ -0,0 +1,79 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    YNU,
+    RadiotherapyProcedure,
+    UberonAnatomicalTerm,
+    RadiotherapyDoseUnits,
+    RadiationExtent,
+)
+
+
+class RadiotherapyDose(Base):
+    __data_category__ = "radiotherapy_dose"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the radiotherapy dose record
+    radiotherapy_dose_id: int | None = None
+
+    # The unique internal identifier for the associated treatment record
+    treatment_id: int | None = None
+
+    # Number of days from enrollment date to the start of the radiotherapy dose.
+    days_to_start: NonNegativeInt
+
+    # Number of days from enrollment date to the end of the radiotherapy dose.
+    days_to_end: NonNegativeInt
+
+    # The term that describes the kind of radiotherapy procedure administered.
+    procedure: RadiotherapyProcedure
+
+    # The Uberon anatomical term for the site of surgery.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14461856%20and%20ver_nr=1
+    anatomical_location: UberonAnatomicalTerm | None = None
+
+    # Indicates whether the record represents the total dose for a radiotherapy treatment course (which may be either
+    # a multi-fractionated or a single-fraction dose).
+    is_total_dose: bool
+
+    # The number of fractions a participant received to deliver the radiation dose.
+    number_of_fractions: NonNegativeInt | None = None
+
+    # The dose amount received by the participant.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13433490%20and%20ver_nr=1
+    received_dose: NonNegativeFloat
+
+    # Unit of measure for the dose of the radiotherapy to be received by the participant.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13383458%20and%20ver_nr=1
+    received_dose_units: RadiotherapyDoseUnits
+
+    # The planned dose amount for the participant.
+    planned_dose: NonNegativeFloat | None = None
+
+    # Unit of measure for the planned total dose of the radiotherapy to be received by the participant.
+    planned_dose_units: RadiotherapyDoseUnits | None = None
+
+    # Indicates if the radiotherapy dose was changed, missed, or delayed.
+    dose_changes_delays: YNU
+
+    # Description of the radiotherapy dose changes, misses, or delays.
+    changes_delays_description: str | None = None
+
+    # The extent of radiation exposure administered to the patient's body during radiation therapy.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7063755%20and%20ver_nr=1
+    radiation_extent: RadiationExtent
+
+    @model_validator(mode="after")
+    def validate_changes_delays_description_cr(self) -> Self:
+        if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
+            raise ValueError('If dose_changes_delays is "Yes", please provide changes_delays_description.')
+        return self
+
+    @model_validator(mode="after")
+    def validate_planned_dose_units_cr(self) -> Self:
+        if self.planned_dose and not self.planned_dose_units:
+            raise ValueError("If planned_dose is provided, please provide planned_dose_units.")
+        return self

cidc_api/models/pydantic/stage1/response.py

@@ -0,0 +1,65 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+
+
+class Response(Base):
+    __data_category__ = "response"
+    __cardinality__ = "one"
+
+    # The unique internal identifier for the response record
+    response_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 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
+
+    # Indicator for whether there was an abscopal effect on disease after local therapy.
+    abscopal_response: YNUNA | None = None
+
+    # Indicates if pathological complete response (pCR) occurred.
+    pathological_complete_response: YNUNA | None = None
+
+    # Number of days between enrollment date and date of death, if applicable.
+    days_to_death: NonNegativeInt | None = None
+
+    # The circumstance or condition of greatest rank or importance that results in the death of the participant
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=4783274%20and%20ver_nr=1
+    cause_of_death: CauseOfDeath | None = None
+
+    # Indicates whether participant was evaluable for toxicity (adverse events, DLT, etc.) overall.
+    evaluable_for_toxicity: bool
+
+    # 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 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:
+        if self.survival_status == "Dead" and not self.cause_of_death:
+            raise ValueError('If survival_status is "Dead" then cause_of_death is required.')
+        return self
+
+    @model_validator(mode="after")
+    def validate_cause_of_death_cr2(self) -> Self:
+        if self.survival_status == "Alive" and self.cause_of_death:
+            raise ValueError('If survival_status is "Alive", please leave cause_of_death blank.')
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_death_cr(self) -> Self:
+        if self.survival_status in ["Alive", "Unknown"] and self.days_to_death:
+            raise ValueError("If survival_status does not indicate death, please leave days_to_death blank.")
+        return self

cidc_api/models/pydantic/stage1/response_by_system.py

@@ -0,0 +1,112 @@
+from typing import Self
+
+from pydantic import PositiveInt, model_validator, NonNegativeInt
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+
+
+negative_response_values = [
+    "Progressive Disease",
+    "Stable Disease",
+    "immune Unconfirmed Progressive Disease",
+    "immune Confirmed Progressive Disease",
+    "immune Stable Disease",
+    "Not available",
+    "Not assessed",
+]
+
+
+class ResponseBySystem(Base):
+    __data_category__ = "response_by_system"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for this ResponseBySystem record
+    response_by_system_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
+
+    # A standardized method used to evaluate and categorize the participant’s clinical response to treatment based on predefined criteria.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13381490%20and%20ver_nr=1
+    response_system: ResponseSystem
+
+    # The release version of the clinical assessment system used to evaluate a participant’s response to treatment.
+    response_system_version: ResponseSystemVersion
+
+    # Confirmed best overall response to study treatment by the corresponding response system.
+    best_overall_response: BestOverallResponse
+
+    # Days from first response to progression.
+    response_duration: PositiveInt | None = None
+
+    # The number of days from the start of the treatment to the first signs of disease progression.
+    duration_of_stable_disease: NonNegativeInt | None = None
+
+    # Indicates whether a patient achieved a durable clinical benefit.
+    durable_clinical_benefit: bool | None = None
+
+    # Number of days between enrollment date and the date of first response to trial treatment.
+    days_to_first_response: PositiveInt | None = None
+
+    # Number of days between enrollment date and the date of the best response to trial treatment.
+    days_to_best_response: PositiveInt | None = None
+
+    # Indicates whether a participant's disease progressed.
+    progression: YNUNA
+
+    # Number of days between enrollment date and date of disease progression.
+    days_to_disease_progression: PositiveInt | None = None
+
+    # Indicator to identify whether a patient had a Progression-Free Survival (PFS) event.
+    progression_free_survival_event: YNUNA
+
+    # The number of days from the date the patient was enrolled in the study to the date the patient was last verified to be free of progression.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5143957%20and%20ver_nr=1
+    progression_free_survival: PositiveInt | None = None
+
+    @model_validator(mode="after")
+    def validate_response_duration_cr(self) -> Self:
+        if self.best_overall_response in negative_response_values and self.response_duration:
+            raise ValueError(
+                "If best_overall_response does not indicate a positive response, "
+                "please leave response_duration blank."
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_first_response_cr(self) -> Self:
+        if self.best_overall_response in negative_response_values and self.days_to_first_response:
+            raise ValueError(
+                "If best_overall_response does not indicate a positive response, "
+                "please leave days_to_first_response blank."
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_best_response_cr(self) -> Self:
+        if self.best_overall_response in negative_response_values and self.days_to_best_response:
+            raise ValueError(
+                "If best_overall_response does not indicate a positive response, \
+                please leave days_to_best_response blank."
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_disease_progression_cr(self) -> Self:
+        if self.progression in ["No", "Unknown", "Not Applicable"] and self.days_to_disease_progression:
+            raise ValueError(
+                "If progression does not indicate confirmed progression of the disease, \
+                please leave days_to_disease_progress blank."
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_progression_free_survival_cr(self) -> Self:
+        if self.progression_free_survival_event in ["Unknown", "Not Applicable"] and self.progression_free_survival:
+            raise ValueError(
+                "If progression_free_survival_event is not known, \
+                please leave progression_free_survival blank."
+            )
+        return self

cidc_api/models/pydantic/stage1/specimen.py

@@ -0,0 +1,31 @@
+from datetime import datetime
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import UberonAnatomicalTerm
+
+
+class Specimen(Base):
+    __data_category__ = "specimen"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the specimen record
+    specimen_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 unique specimen identifier assigned by the CIMAC-CIDC Network.
+    # Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
+    cimac_id: str
+
+    # Categorical description of timepoint at which the sample was taken.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5899851%20and%20ver_nr=1
+    # Note: CIDC doesn't conform to this CDE's PVs
+    collection_event_name: str
+
+    # Days from enrollment date to date specimen was collected.
+    days_to_specimen_collection: int
+
+    # The location within the body from which a specimen was originally obtained as captured in the Uberon anatomical term.
+    organ_site_of_collection: UberonAnatomicalTerm

cidc_api/models/pydantic/stage1/stem_cell_transplant.py

@@ -0,0 +1,35 @@
+from pydantic import NonNegativeInt
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import (
+    StemCellDonorType,
+    AllogeneicDonorType,
+    StemCellSource,
+    ConditioningRegimenType,
+)
+
+
+class StemCellTransplant(Base):
+    __data_category__ = "stem_cell_transplant"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the stem cell transplant record
+    stem_cell_transplant_id: int | None = None
+
+    # The unique internal identifier for the associated Treatment record
+    treatment_id: int | None = None
+
+    # Indicates the stem cell donor type.
+    stem_cell_donor_type: StemCellDonorType
+
+    # If "stem_cell_donor_type" is "Allogeneic", specifies the relationship and
+    # compatibility of the donor relative to the receipient
+    allogeneic_donor_type: AllogeneicDonorType | None = None
+
+    # Source of the stem cells used for transplant.
+    stem_cell_source: StemCellSource
+
+    # Days from the enrollment date to the date of the stem cell transplant.
+    days_to_transplant: NonNegativeInt
+
+    # Specifies what type of conditioning regimen was used for the stem cell transplant if applicable.
+    conditioning_regimen_type: ConditioningRegimenType | None = None

cidc_api/models/pydantic/stage1/surgery.py

@@ -0,0 +1,49 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
+
+
+class Surgery(Base):
+    __data_category__ = "surgery"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the surgery record
+    surgery_id: int | None = None
+
+    # The unique internal identifier for the associated treatment record
+    treatment_id: int | None = None
+
+    # The term that describes the kind of surgical procedure administered.
+    procedure: SurgicalProcedure
+
+    # The name of surgical procedure if the value provided for procedure is "Other, specify".
+    procedure_other: str | None = None
+
+    # Number of days from enrollment date to surgical procedure date.
+    days_to_procedure: NonNegativeInt
+
+    # The Uberon identifier for the location within the body targeted by a procedure that
+    # is intended to alter or stop a pathologic process.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14980609%20and%20ver_nr=1
+    anatomical_location: UberonAnatomicalTerm
+
+    # An indication as to whether the surgical procedure in question was performed with therapeutic intent.
+    therapeutic: YNU
+
+    # A narrative description of any significant findings observed during the surgical procedure in question.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14918773%20and%20ver_nr=1
+    findings: str | None = None
+
+    # A textual description of evidence for remaining tumor following primary treatment that is only
+    # apparent using highly sensitive techniques.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13362284%20and%20ver_nr=1
+    extent_of_residual_disease: str | None = None
+
+    @model_validator(mode="after")
+    def validate_procedure_other_cr(self) -> Self:
+        if self.procedure == "Other, specify" and not self.procedure_other:
+            raise ValueError('If procedure is "Other, specify", please provide procedure_other.')
+        return self

cidc_api/models/pydantic/stage1/therapy_agent_dose.py

@@ -0,0 +1,67 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat, model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import YNU, TherapyAgentDoseUnits
+
+
+class TherapyAgentDose(Base):
+    __data_category__ = "therapy_agent_dose"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the therapy agent dose record
+    therapy_agent_dose_id: int | None = None
+
+    # The unique internal identifier for the associated treatment record
+    treatment_id: int | None = None
+
+    # A numeric identifier used to indicate a specific course or cycle of treatment.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16391085%20and%20ver_nr=1
+    course_number: str | None = None
+
+    # The full generic name of the therapeutic agent, if available, as captured in the Pharmacological
+    # Substance (C1909) branch of the National Cancer Institute Thesaurus (NCIt).
+    therapy_agent_name: str
+
+    # Number of days from the enrollment date to the start date of the therapy dose.
+    days_to_start: NonNegativeInt
+
+    # Number of days from enrollment date to the end date of the therapy dose.
+    days_to_end: NonNegativeInt
+
+    # Number of individual doses the patient received of the therapy agent.
+    number_of_doses: NonNegativeInt
+
+    # The amount that represents the dose of the therapy agent received by the participant.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2182728%20and%20ver_nr=3
+    received_dose: NonNegativeFloat
+
+    # Unit of measure for the dose of the agent received by the participant.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2321160%20and%20ver_nr=4
+    received_dose_units: TherapyAgentDoseUnits
+
+    # The amount that represents the planned dose of the therapy agent to be received by the participant.
+    planned_dose: PositiveFloat | None = None
+
+    # Unit of measure for the planned dose of the agent to be received by the participant.
+    # TODO: This CDE will probably be 2321160 but needs to be finalized with Janice
+    planned_dose_units: TherapyAgentDoseUnits | None = None
+
+    # Indicates if the therapy agent dose was changed, missed, or delayed.
+    dose_changes_delays: YNU
+
+    # Description of the dose changes, misses, or delays.
+    changes_delays_description: str | None = None
+
+    @model_validator(mode="after")
+    def validate_changes_delays_description_cr(self) -> Self:
+        if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
+            raise ValueError('If dose_changes_delays is "Yes", please provide changes_delays_description.')
+        return self
+
+    @model_validator(mode="after")
+    def validate_planned_dose_units_cr(self) -> Self:
+        if self.planned_dose and not self.planned_dose_units:
+            raise ValueError("If planned_dose is provided, please provide planned_dose_units.")
+        return self

cidc_api/models/pydantic/stage1/treatment.py

@@ -0,0 +1,50 @@
+from typing import Self
+
+from pydantic import model_validator
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import YNU, OffTreatmentReason
+
+
+class Treatment(Base):
+    __data_category__ = "treatment"
+    __cardinality__ = "many"
+
+    # The unique internal identifier for the Treatment record
+    treatment_id: int | None = None
+
+    # The unique internal identifier for the associated Participant record
+    participant_id: str | None = None
+
+    # The unique internal identifier for the associated Arm record
+    arm: str | None = None
+
+    # The unique internal identifier for the associated Cohort record
+    cohort: str | None = None
+
+    # A unique identifier used to describe a distinct, specific intervention or
+    # treatment that a group or subgroup of participants in a clinical trial receives.
+    treatment_description: str
+
+    # Indicates if the participant has stopped receiving this particular treatment at
+    # the time of data submission.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16391087%20and%20ver_nr=1
+    off_treatment: YNU
+
+    # An explanation describing why an individual is no longer receiving this particular treatment.
+    off_treatment_reason: OffTreatmentReason | None = None
+
+    # If "Other" is selected for "off_treatment_reason", provide a description of the reason.
+    off_treatment_reason_other: str | None = None
+
+    @model_validator(mode="after")
+    def validate_off_treatment_reason_cr(self) -> Self:
+        if self.off_treatment == "Yes" and not self.off_treatment_reason:
+            raise ValueError('If off_treatment is "Yes", please provide off_treatment_reason.')
+        return self
+
+    @model_validator(mode="after")
+    def validate_off_treatment_reason_other_cr(self) -> Self:
+        if self.off_treatment_reason == "Other" and not self.off_treatment_reason_other:
+            raise ValueError('If off_treatment_reason is "Other", please provide off_treatment_reason_other.')
+        return self

cidc_api/models/pydantic/stage1/trial.py

@@ -0,0 +1,45 @@
+from datetime import datetime
+from pydantic import BeforeValidator
+from typing import List, Annotated
+
+from cidc_api.models.pydantic.base import Base
+from cidc_api.models.types import PrimaryPurposeType, AgeGroup
+
+
+class Trial(Base):
+    __data_category__ = "study"
+    __cardinality__ = None
+
+    # The unique identifier for the clinical trial. e.g. "GU16-287","BACCI"
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5054234%20and%20ver_nr=1
+    trial_id: str | None = None
+
+    # The version number of the trial dataset. e.g. "1.0"
+    version: str | None = None
+
+    # A broad textual description of the primary endpoint(s) of the trial.
+    primary_endpoint: str | None = None
+
+    # The identifiable class of the study participant based upon their age.
+    age_group: Annotated[List[AgeGroup], BeforeValidator(Base.split_list)]
+
+    # Clinical and/or molecular characteristics of the cancer(s) in the study population.
+    study_population: str | None = None
+
+    # The type of clinical trial conducted
+    trial_type: str | None = None
+
+    # The official day that study activity began
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16333702%20and%20ver_nr=1
+    dates_of_conduct_start: datetime
+
+    # The official day that study activity ended
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16333703%20and%20ver_nr=1
+    dates_of_conduct_end: datetime | None = None
+
+    # A classification of the study based upon the primary intent of the study's activities.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=11160683%20and%20ver_nr=1
+    primary_purpose_type: PrimaryPurposeType
+
+    # The dbgap study accession number associated with the trial.
+    dbgap_study_accession: str

cidc_api/models/pydantic/stage2/additional_treatment.py

@@ -1,5 +1,5 @@
 from pydantic import NonNegativeInt
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class AdditionalTreatment(Base):
@@ -10,14 +10,14 @@ class AdditionalTreatment(Base):
     additional_treatment_id: int | None = None
 
     # The 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: NonNegativeInt | None = None
+    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.
-    days_to_end: NonNegativeInt | None = None
+    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.
-    description: str
+    additional_treatment_description: str

cidc_api/models/pydantic/stage2/administrative_person.py

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

cidc_api/models/pydantic/stage2/administrative_role_assignment.py

@@ -1,10 +1,10 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import AdministrativeRole
 
 
 class AdministrativeRoleAssignment(Base):
     # 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/adverse_event.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.reference.ctcae import is_ctcae_other_term
 from cidc_api.models.types import (
     CTCAEEventTerm,
@@ -25,7 +25,7 @@ class AdverseEvent(Base):
     adverse_event_id: int | None = None
 
     # The unique internal identifier of the associated participant
-    participant_id: int | None = None
+    participant_id: str | None = None
 
     # The unique internal identifier of the attributed treatment, if any
     treatment_id: int | None = None

cidc_api/models/pydantic/stage2/arm.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 
 
 class Arm(Base):
@@ -6,7 +6,7 @@ class Arm(Base):
     arm_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/baseline_clinical_assessment.py

@@ -1,4 +1,4 @@
-from .base import Base
+from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import ECOGScore, KarnofskyScore
 
 
@@ -10,7 +10,7 @@ class BaselineClinicalAssessment(Base):
     baseline_clinical_assessment_id: int | None = None
 
     # The unique identifier for the associated participant
-    participant_id: int | None = None
+    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.

cidc_api/models/pydantic/stage2/cohort.py

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

cidc_api/models/pydantic/stage2/comorbidity.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 ICD10CMCode, ICD10CMTerm