nci-cidc-api-modules 1.2.22__py3-none-any.whl → 1.2.24__py3-none-any.whl

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

cidc_api/models/pydantic/stage2/medical_history.py

@@ -0,0 +1,36 @@
+from typing import Self
+
+from pydantic import NonNegativeInt, PositiveFloat, model_validator
+
+from .base import Base
+from cidc_api.models.types import TobaccoSmokingStatus
+
+
+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: int | 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
+
+    @model_validator(mode="after")
+    def validate_pack_years_smoked_cr(self) -> Self:
+        if self.tobacco_smoking_status in ["Never Smoker", "Unknown", "Not reported"] and self.pack_years_smoked:
+            raise ValueError("If tobacco_smoking_status indicates non-smoker, please leave pack_years_smoked blank.")
+        return self

cidc_api/models/pydantic/stage2/other_clinical_endpoint.py

@@ -0,0 +1,32 @@
+from .base import Base
+from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
+
+
+class OtherClinicalEndpoint(Base):
+
+    # The unique internal identifier for the other clinical endpoint
+    other_clinical_endpoint_id: int | None = None
+
+    # The unique internal identifier for the associated participant
+    participant_id: int | None = None
+
+    # The name of the clinical endpoint. e.g. "iPFS"
+    name: str
+
+    # Whether the event that defines the clinical endpoint occurred
+    event: YNU
+
+    # The number of days to the occurrence of the event
+    days: int | None = None
+
+    # A description of this clinical endpoint
+    description: str | None = None
+
+    # The formula used to calculate the clinical endpoint criteria
+    calculation: str | None = None
+
+    # The response system used to define the clinical endpoint criteria. e.g. "RECIST"
+    response_system: ResponseSystem | None = None
+
+    # The version of the system used to define the clinical endpoint criteria.
+    response_system_version: ResponseSystemVersion | None = None

cidc_api/models/pydantic/stage2/other_malignancy.py

@@ -0,0 +1,45 @@
+from typing import Self
+
+from pydantic import NonPositiveInt, model_validator
+
+from .base import Base
+from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
+
+
+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.
+    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
+
+    # 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
+
+    # Description of the cancer type as recorded in the trial.
+    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
+
+    # Indicates the participant’s current clinical state regarding the cancer diagnosis.
+    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:
+            raise ValueError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".'
+            )
+        return self

cidc_api/models/pydantic/stage2/participant.py

@@ -0,0 +1,47 @@
+from typing import Self
+
+from pydantic import model_validator
+
+from .base import Base
+from cidc_api.models.types import OffStudyReason
+
+
+class Participant(Base):
+    __data_category__ = "participant"
+    __cardinality__ = "one"
+
+    # 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
+
+    # 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
+
+    # The unique identifier for the associated trial that the participant is participating in
+    trial_id: int | 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
+
+    # 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
+    off_study_reason: OffStudyReason | None = None
+
+    # Additional information if "Other" is selected for off_study_reason. e.g. "Transfer to another study"
+    off_study_reason_other: str | None = None
+
+    @model_validator(mode="after")
+    def off_study_reason_cr(self) -> Self:
+        if self.off_study and not self.off_study_reason:
+            raise ValueError('If "off_study" is "Yes" then "off_study_reason" is required.')
+        return self
+
+    @model_validator(mode="after")
+    def off_study_reason_other_cr(self) -> Self:
+        if self.off_study_reason == "Other" and not self.off_study_reason_other:
+            raise ValueError('If "off_study_reason" is "Other" then "off_study_reason_other" is required.')
+        return self

cidc_api/models/pydantic/stage2/prior_treatment.py

@@ -0,0 +1,52 @@
+from typing import Self
+
+from pydantic import NonPositiveInt, NonNegativeInt, model_validator
+
+from .base import Base
+from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+
+
+class PriorTreatment(Base):
+    __data_category__ = "prior_treatment"
+    __cardinality__ = "many"
+
+    # A unique internal identifier for the prior treatment record
+    prior_treatment_id: int | None = None
+
+    # A unique internal identifier for the associated participant record
+    participant_id: int | 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
+
+    # 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
+
+    # 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
+
+    # Best response from any response assessment system to the prior treatment if available or applicable.
+    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
+
+    # 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
+
+    @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

cidc_api/models/pydantic/stage2/publication.py

@@ -0,0 +1,37 @@
+from .base import Base
+
+
+class Publication(Base):
+    # The unique internal identifier for the Publication record
+    publication_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
+
+    # The digital object identifier string. www.doi.org. e.g. 10.47366/sabia.v5n1a3
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15915370%20and%20ver_nr=1
+    digital_object_id: str
+
+    # The pubmed identifier string. pubmed.ncbi.nlm.nih.gov. e.g. 41135560
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15915377%20and%20ver_nr=1
+    pubmed_id: str | None = None
+
+    # The full title of the publication stated exactly as it appears on the published work.
+    # https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16078531%20and%20ver_nr=1
+    publication_title: str | None = None
+
+    # A list of authors for the cited work.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16081468%20and%20ver_nr=1
+    authorship: str | None = None
+
+    # The year in which the cited work was published.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16081475%20and%20ver_nr=1
+    year_of_publication: str | None = None
+
+    # The name of the journal in which the cited work was published, inclusive of the citation itself in terms of
+    # journal volume number, part number where applicable, and page numbers.
+    # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16081476%20and%20ver_nr=1
+    journal_citation: str | None = None