nci-cidc-api-modules 1.2.31__tar.gz → 1.2.39__tar.gz

{nci_cidc_api_modules-1.2.31/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.31
+Version: 1.2.39
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -8,30 +8,39 @@ Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: certifi>=2025.11.12
-Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.5
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.19.0
 Requires-Dist: flask>=3.1.2
 Requires-Dist: flask-migrate>=4.1.0
 Requires-Dist: flask-sqlalchemy>=3.1.1
 Requires-Dist: flask-talisman>=0.7.0
-Requires-Dist: google-auth==2.43.0
-Requires-Dist: google-api-python-client>=2.185.0
-Requires-Dist: google-cloud-bigquery>=3.38.0
-Requires-Dist: google-cloud-pubsub>=2.33.0
-Requires-Dist: google-cloud-secret-manager>=2.25.0
-Requires-Dist: google-cloud-storage>=3.6.0
+Requires-Dist: google-auth==2.45.0
+Requires-Dist: google-api-python-client>=2.187.0
+Requires-Dist: google-cloud-bigquery>=3.39.0
+Requires-Dist: google-cloud-pubsub>=2.34.0
+Requires-Dist: google-cloud-secret-manager>=2.26.0
+Requires-Dist: google-cloud-storage>=3.7.0
 Requires-Dist: jinja2>=3.1.6
-Requires-Dist: marshmallow>=4.1.0
+Requires-Dist: joserfc>=1.6.0
+Requires-Dist: marshmallow>=4.1.2
 Requires-Dist: marshmallow-sqlalchemy>=1.4.2
-Requires-Dist: numpy>=2.3.5
+Requires-Dist: numpy>=2.4.0
 Requires-Dist: packaging>=25.0
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: pyarrow>=22.0.0
-Requires-Dist: pydantic~=2.12.4
+Requires-Dist: pydantic~=2.12.5
 Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
-Requires-Dist: sqlalchemy>=2.0.44
+Requires-Dist: sqlalchemy>=2.0.45
 Requires-Dist: sqlalchemy-mixins~=2.0.5
-Requires-Dist: werkzeug>=3.1.3
+Requires-Dist: werkzeug>=3.1.4
+Requires-Dist: opentelemetry-api>=1.39.1
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc>=1.39.1
+Requires-Dist: opentelemetry-sdk>=1.39.1
+Requires-Dist: opentelemetry-instrumentation-flask>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
+Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
+Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
+Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
 Requires-Dist: nci-cidc-schemas==0.28.10
 Dynamic: description
 Dynamic: description-content-type

nci_cidc_api_modules-1.2.39/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.39"

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/additional_treatment_orm.py

@@ -16,8 +16,8 @@ class AdditionalTreatmentORM(BaseORM):
     additional_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
-    days_to_start: Mapped[Optional[NonNegativeInt]]
-    days_to_end: Mapped[Optional[NonNegativeInt]]
-    description: Mapped[str]
+    additional_treatment_days_to_start: Mapped[Optional[NonNegativeInt]]
+    additional_treatment_days_to_end: Mapped[Optional[NonNegativeInt]]
+    additional_treatment_description: Mapped[str]
 
     participant: Mapped["ParticipantORM"] = relationship(back_populates="additional_treatments", cascade="all, delete")

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/demographic_orm.py

@@ -1,7 +1,9 @@
 from pydantic import NonNegativeFloat, PositiveFloat, PositiveInt
+from typing import List
 
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy.types import JSON
 
 from cidc_api.models.db.base_orm import BaseORM
 from cidc_api.models.types import (
@@ -29,15 +31,15 @@ class DemographicORM(BaseORM):
     age_at_enrollment_units: Mapped[AgeAtEnrollmentUnits | None]
     age_90_or_over: Mapped[bool]
     sex: Mapped[Sex]
-    race: Mapped[Race]
+    race: Mapped[List[Race]] = mapped_column(JSON)
     ethnicity: Mapped[Ethnicity]
     height: Mapped[PositiveFloat]
     height_units: Mapped[HeightUnits]
     weight: Mapped[PositiveFloat]
     weight_units: Mapped[WeightUnits]
-    body_mass_index: Mapped[PositiveFloat]
-    body_surface_area: Mapped[PositiveFloat]
-    body_surface_area_units: Mapped[BodySurfaceAreaUnits]
+    body_mass_index: Mapped[PositiveFloat | None]
+    body_surface_area: Mapped[PositiveFloat | None]
+    body_surface_area_units: Mapped[BodySurfaceAreaUnits | None]
     occupation: Mapped[Occupation | None]
     income: Mapped[NonNegativeFloat | None]
     highest_level_of_education: Mapped[Education | None]

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/other_malignancy_orm.py

@@ -19,12 +19,12 @@ class OtherMalignancyORM(BaseORM):
         ForeignKey("stage2.medical_history.medical_history_id", ondelete="CASCADE")
     )
 
-    primary_disease_site: Mapped[UberonAnatomicalTerm]
-    morphological_code: Mapped[Optional[ICDO3MorphologicalCode]]
-    morphological_term: Mapped[Optional[ICDO3MorphologicalTerm]]
-    malignancy_description: Mapped[Optional[str]]
-    days_since_diagnosis: Mapped[Optional[NonPositiveInt]]
-    malignancy_status: Mapped[Optional[MalignancyStatus]]
+    other_malignancy_primary_disease_site: Mapped[UberonAnatomicalTerm]
+    other_malignancy_morphological_code: Mapped[Optional[ICDO3MorphologicalCode]]
+    other_malignancy_morphological_term: Mapped[Optional[ICDO3MorphologicalTerm]]
+    other_malignancy_description: Mapped[Optional[str]]
+    other_malignancy_days_since_diagnosis: Mapped[Optional[NonPositiveInt]]
+    other_malignancy_status: Mapped[Optional[MalignancyStatus]]
 
     medical_history: Mapped["MedicalHistoryORM"] = relationship(
         back_populates="other_malignancies", cascade="all, delete"

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/prior_treatment_orm.py

@@ -1,8 +1,9 @@
-from typing import Optional
+from typing import Optional, List
 
-from pydantic import NonPositiveInt, NonNegativeInt
+from pydantic import NonPositiveInt, NegativeInt
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy.types import JSON
 
 from cidc_api.models.db.base_orm import BaseORM
 from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
@@ -17,13 +18,13 @@ class PriorTreatmentORM(BaseORM):
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
 
-    days_to_start: Mapped[Optional[NonPositiveInt]]
-    days_to_end: Mapped[Optional[NonPositiveInt]]
-    type: Mapped[PriorTreatmentType]
-    description: Mapped[Optional[str]]
-    best_response: Mapped[Optional[str]]
-    conditioning_regimen_type: Mapped[Optional[ConditioningRegimenType]]
-    stem_cell_donor_type: Mapped[Optional[StemCellDonorType]]
-    days_from_transplant_to_treatment_initiation: Mapped[Optional[NonNegativeInt]]
+    prior_treatment_days_to_start: Mapped[Optional[NonPositiveInt]]
+    prior_treatment_days_to_end: Mapped[Optional[NonPositiveInt]]
+    prior_treatment_type: Mapped[List[PriorTreatmentType]] = mapped_column(JSON, nullable=False)
+    prior_treatment_description: Mapped[Optional[str]]
+    prior_treatment_best_response: Mapped[Optional[str]]
+    prior_treatment_conditioning_regimen_type: Mapped[Optional[ConditioningRegimenType]]
+    prior_treatment_stem_cell_donor_type: Mapped[Optional[StemCellDonorType]]
+    prior_treatment_days_to_prior_transplant: Mapped[Optional[NegativeInt]]
 
     participant: Mapped["ParticipantORM"] = relationship(back_populates="prior_treatments", cascade="all, delete")

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/response_by_system_orm.py

@@ -18,6 +18,7 @@ class ResponseBySystemORM(BaseORM):
     response_system_version: Mapped[ResponseSystemVersion] = mapped_column(String)
     best_overall_response: Mapped[BestOverallResponse] = mapped_column(String)
     response_duration: Mapped[PositiveInt | None]
+    duration_of_stable_disease: Mapped[PositiveInt | None]
     durable_clinical_benefit: Mapped[bool | None]
     days_to_first_response: Mapped[PositiveInt | None]
     days_to_best_response: Mapped[PositiveInt | None]

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/response_orm.py

@@ -16,13 +16,13 @@ class ResponseORM(BaseORM):
     response_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
     survival_status: Mapped[SurvivalStatus]
-    overall_survival: Mapped[NonNegativeInt | None]
+    overall_survival: Mapped[NonNegativeInt]
     abscopal_response: Mapped[YNUNA | None]
     pathological_complete_response: Mapped[YNUNA | None]
     days_to_death: Mapped[NonNegativeInt | None]
     cause_of_death: Mapped[CauseOfDeath | None]
     evaluable_for_toxicity: Mapped[bool]
     evaluable_for_efficacy: Mapped[bool]
-    days_to_last_follow_up: Mapped[NonNegativeInt | None]
+    days_to_last_vital_status: Mapped[NonNegativeInt | None]
 
     participant: Mapped["ParticipantORM"] = relationship(back_populates="response", cascade="all, delete")

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/db/stage2/trial_orm.py

@@ -6,7 +6,7 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
 from cidc_api.models.db.base_orm import BaseORM
-from cidc_api.models.types import AssayType, TrialOrganization, TrialFundingAgency
+from cidc_api.models.types import AssayType, TrialOrganization, TrialFundingAgency, AgeGroup
 
 
 class TrialORM(BaseORM):
@@ -18,23 +18,26 @@ class TrialORM(BaseORM):
     trial_id: Mapped[str] = mapped_column(primary_key=True)
     version: Mapped[str] = mapped_column(primary_key=True)
 
-    nct_id: Mapped[Optional[str]]
-    nci_id: Mapped[Optional[str]]
-    trial_name: Mapped[Optional[str]]
-    trial_type: Mapped[Optional[str]]
-    trial_description: Mapped[Optional[str]]
-    trial_organization: Mapped[Optional[TrialOrganization]]
-    grant_or_affiliated_network: Mapped[Optional[TrialFundingAgency]]
-    biobank_institution_id: Mapped[Optional[int]]
-    justification: Mapped[Optional[str]]
+    primary_endpoint: Mapped[str | None]
+    age_group: Mapped[List[AgeGroup]] = mapped_column(JSON, nullable=True)
+    study_population: Mapped[str | None]
+    nct_id: Mapped[str | None]
+    nci_id: Mapped[str | None]
+    trial_name: Mapped[str | None]
+    trial_type: Mapped[str | None]
+    trial_description: Mapped[str | None]
+    trial_organization: Mapped[TrialOrganization | None]
+    grant_or_affiliated_network: Mapped[TrialFundingAgency | None]
+    biobank_institution_id: Mapped[int | None]
+    justification: Mapped[str | None]
     dates_of_conduct_start: Mapped[datetime]
-    dates_of_conduct_end: Mapped[Optional[datetime]]
-    schema_file_id: Mapped[Optional[int]]
-    biomarker_plan: Mapped[Optional[str]]
-    data_sharing_plan: Mapped[Optional[str]]
-    expected_assays: Mapped[Optional[List[AssayType]]] = mapped_column(JSON, nullable=True)
+    dates_of_conduct_end: Mapped[datetime | None]
+    schema_file_id: Mapped[int | None]
+    biomarker_plan: Mapped[str | None]
+    data_sharing_plan: Mapped[str | None]
+    expected_assays: Mapped[List[AssayType]] = mapped_column(JSON, nullable=True)
     is_liquid_tumor_trial: Mapped[bool]
-    dbgap_study_accession: Mapped[Optional[str]]
+    dbgap_study_accession: Mapped[str | None]
 
     biobank: Mapped["InstitutionORM"] = relationship(back_populates="trial")
     schema: Mapped[Optional["FileORM"]] = relationship(back_populates="trial", viewonly=True)

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/models.py

@@ -35,7 +35,8 @@ __all__ = [
     "ADMIN_FILE_CATEGORIES",
     "FINAL_JOB_STATUS",
     "INGESTION_JOB_STATUSES",
-    "INGESTION_JOB_COLORS",
+    "ASSAY_JOB_COLORS",
+    "CLINICAL_JOB_COLORS",
 ]
 
 import hashlib
@@ -3436,7 +3437,7 @@ INGESTION_JOB_STATUSES = [
 ]
 
 # Business decision to pass hex codes from the backend though that should be done by the front end...
-INGESTION_JOB_COLORS = {
+CLINICAL_JOB_COLORS = {
     "DRAFT": "",
     "INITIAL SUBMISSION": "#ACCAD7",
     "VALIDATION REVIEW": "#DABE90",
@@ -3444,6 +3445,13 @@ INGESTION_JOB_COLORS = {
     "INGESTION": "#8FCEC7",
     "PUBLISHED": "#90D9E6",
 }
+ASSAY_JOB_COLORS = {
+    "INITIAL SUBMISSION": "#43807E",
+    "VALIDATION REVIEW": "#906F3F",
+    "REVISION SUBMISSION": "#95358A",
+    "INGESTION": "#542C88",
+    "PUBLISHED": "#1C81A0",
+}
 # TODO If have "CANCELLED" concept or other final status, add here
 FINAL_JOB_STATUS = ["PUBLISHED"]
 TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER = "Data Category"
@@ -3465,11 +3473,44 @@ class IngestionJobs(CommonColumns):
     pending = Column(Boolean, nullable=False, default=False)
     start_date = Column(DateTime, nullable=True)
     error_status = Column(String, nullable=True)
+    job_type = Column(String, nullable=False, default="clinical")
+    assay_type = Column(String, nullable=True)
+    batch_id = Column(String, nullable=True)
+    submission_id = Column(String, nullable=True)
+    intake_path = Column(String, nullable=True)
+    uploader_email = Column(String, nullable=True)
 
     @staticmethod
     @with_default_session
-    def create(trial_id: str, status: str, version: int, pending: Boolean = False, session: Session = None):
-        new_job = IngestionJobs(trial_id=trial_id, status=status, version=version, pending=pending)
+    def create(
+        trial_id: str,
+        status: str,
+        version: int,
+        error_status: str = None,
+        pending: Boolean = False,
+        job_type: str = "clinical",
+        assay_type: str = None,
+        batch_id: str = None,
+        submission_id: str = None,
+        intake_path: str = None,
+        start_date: datetime = None,
+        uploader_email: str = None,
+        session: Session = None,
+    ):
+        new_job = IngestionJobs(
+            trial_id=trial_id,
+            status=status,
+            error_status=error_status,
+            version=version,
+            pending=pending,
+            job_type=job_type,
+            assay_type=assay_type,
+            batch_id=batch_id,
+            submission_id=submission_id,
+            intake_path=intake_path,
+            start_date=start_date,
+            uploader_email=uploader_email,
+        )
         new_job.insert(session=session)
         return new_job
 
@@ -3494,29 +3535,43 @@ class IngestionJobs(CommonColumns):
 
     @classmethod
     @with_default_session
-    def get_jobs_by_trial(cls, trial_id: str, session: Session = None) -> list["IngestionJobs"]:
-        return session.query(cls).filter(cls.trial_id == trial_id).order_by(cls.version.desc()).all()
+    def get_jobs_by_trial(
+        cls, trial_id: str, job_type: str = "clinical", session: Session = None
+    ) -> list["IngestionJobs"]:
+        return (
+            session.query(cls)
+            .filter(cls.trial_id == trial_id, cls.job_type == job_type)
+            .order_by(cls.version.desc())
+            .all()
+        )
 
     @classmethod
     @with_default_session
-    def get_open_job_by_trial(cls, trial_id: str, session: Session = None) -> Optional["IngestionJobs"]:
+    def get_open_job_by_trial(
+        cls, trial_id: str, job_type: str = "clinical", session: Session = None
+    ) -> Optional["IngestionJobs"]:
         """Return the open job for a given trial if it exists."""
         return (
             session.query(cls)
             .filter(
                 cls.trial_id == trial_id,
+                cls.job_type == job_type,
                 cls.status.notin_(FINAL_JOB_STATUS),
             )
             .order_by(cls._created.desc())
             .first()
         )
 
+    @classmethod
+    def get_jobs_for_user(cls, user: Users, job_type: str = None) -> list["IngestionJobs"]:
+        return cls.get_assay_jobs_for_user(user) if job_type == "assay" else cls.get_clinical_jobs_for_user(user)
+
     @classmethod
     @with_default_session
-    def get_open_jobs_for_user(cls, user: Users, session: Session = None) -> list["IngestionJobs"]:
+    def get_clinical_jobs_for_user(cls, user: Users, session: Session = None) -> list["IngestionJobs"]:
         if user.role not in [CIDCRole.ADMIN.value, CIDCRole.CLINICAL_TRIAL_USER.value]:
             return []
-        job_query = session.query(cls).filter(cls.status.notin_(["DRAFT"]))
+        job_query = session.query(cls).filter(cls.status.notin_(["DRAFT"]), cls.job_type == "clinical")
         if (
             user.role != CIDCRole.ADMIN.value
             and not session.query(Permissions)
@@ -3539,6 +3594,81 @@ class IngestionJobs(CommonColumns):
             job_query = job_query.filter(cls.trial_id.in_(map(lambda x: x.trial_id, authorized_trials)))
         return job_query.order_by(cls._created.desc()).all()
 
+    @classmethod
+    @with_default_session
+    def get_assay_jobs_for_user(cls, user: Users, session: Session = None) -> list["IngestionJobs"]:
+        # TODO allow more than just Admin role and get authorized trials based on permissions
+        if user.role not in [CIDCRole.ADMIN.value]:
+            return []
+        return session.query(cls).filter(cls.job_type == "assay").order_by(cls._created.desc()).all()
+
+    @classmethod
+    @with_default_session
+    def get_unique_assay_job(
+        cls,
+        trial_id: str,
+        assay_type: str,
+        batch_id: str,
+        session: Session = None,
+    ) -> Optional["IngestionJobs"]:
+        """Look for unique assay job with matching trial_id/assay_type/batch_id combination."""
+        return (
+            session.query(cls)
+            .filter(
+                cls.job_type == "assay",
+                cls.trial_id == trial_id,
+                cls.assay_type == assay_type,
+                cls.batch_id == batch_id,
+            )
+            .first()
+        )
+
+    @classmethod
+    @with_default_session
+    def next_assay_submission_id(cls, trial_id: str, assay_type: str, session: Session = None) -> str:
+        """
+        Generate the next CIDC Submission ID for an assay job.
+
+        Format:
+          <trial_id>-<assay_type>-<yyyymmdd>        (first submission of the day)
+          <trial_id>-<assay_type>-<yyyymmdd>-<#>    (subsequent submissions on same day)
+
+        Uses only the most recent matching submission_id to determine the next suffix.
+        """
+        today_str = datetime.now().strftime("%Y%m%d")
+        base_submission_id = f"{trial_id}-{assay_type}-{today_str}"
+
+        # Get the most recent submission_id matching this prefix
+        latest = (
+            session.query(cls.submission_id)
+            .filter(
+                cls.trial_id == trial_id,
+                cls.assay_type == assay_type,
+                cls.submission_id.like(f"{base_submission_id}%"),
+            )
+            .order_by(cls._created.desc())
+            .first()
+        )
+
+        # No existing submission for this prefix -> start at 1
+        if not latest or not latest[0]:
+            return base_submission_id
+
+        last_id = latest[0]
+        # Case 1: the latest is exactly the prefix (i.e., first submission today)
+        if last_id == base_submission_id:
+            return f"{base_submission_id}-2"
+
+        # Case 2: latest already has a suffix
+        try:
+            _, last_suffix = last_id.rsplit("-", 1)
+            n = int(last_suffix)
+            return f"{base_submission_id}-{n + 1}"
+        except Exception as e:
+            # If malformed, restart numbering for safety
+            logger.error("Unexpected error parsing Submission ID in next_assay_submission_id: %s", e)
+            return f"{base_submission_id}-2"
+
 
 class JobFileCategories(CommonColumns):
     __tablename__ = "job_file_categories"
@@ -3613,6 +3743,7 @@ class CategoryDataElements(CommonColumns):
     name = Column(String, nullable=False)
     is_custom = Column(Boolean, nullable=False, default=False, server_default="false")
     element_type = Column(String, nullable=False)
+    data_type = Column(String, nullable=True)
     cardinality = Column(String, nullable=True)
 
     @classmethod

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/additional_treatment.py

@@ -15,11 +15,11 @@ class AdditionalTreatment(Base):
     )
 
     # 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

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/base.py

@@ -6,7 +6,11 @@ import copy
 
 class Base(BaseModel):
 
-    model_config = ConfigDict(validate_assignment=True, from_attributes=True)
+    model_config = ConfigDict(
+        validate_assignment=True,
+        from_attributes=True,
+        # extra="forbid" # TODO: enable me one stage1 models are implemented
+    )
 
     # Validates the new state and updates the object if valid
     def update(self, **kwargs):

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/demographic.py

@@ -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
@@ -113,3 +113,11 @@ class Demographic(Base):
             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

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/other_malignancy.py

@@ -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".'
             )

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/prior_treatment.py

@@ -1,6 +1,6 @@
-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
@@ -18,35 +18,35 @@ class PriorTreatment(Base):
 
     # 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
+    prior_treatment_days_to_end: NonPositiveInt | None = None
 
     # Specifies the category or kind of prior treatment modality a participant received.
-    type: PriorTreatmentType
+    prior_treatment_type: Annotated[List[PriorTreatmentType], BeforeValidator(Base.split_list)]
 
     # 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 | None = None
 
     # 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
+    prior_treatment_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_days_to_prior_transplant: NegativeInt | None = None
 
     @model_validator(mode="after")
     def validate_description_cr(self) -> Self:
-        if self.type == "Other therapy" and not self.description:
+        if "Other therapy" in self.prior_treatment_type and not self.prior_treatment_description:
             raise ValueError('If type is "Other therapy", please provide description.')
         return self

{nci_cidc_api_modules-1.2.31 → nci_cidc_api_modules-1.2.39}/cidc_api/models/pydantic/stage2/response.py

@@ -22,7 +22,7 @@ class Response(Base):
     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
 
     @model_validator(mode="after")
     def validate_cause_of_death_cr(self) -> Self: