nci-cidc-api-modules 1.2.30__tar.gz → 1.2.32__tar.gz

{nci_cidc_api_modules-1.2.30/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.30
+Version: 1.2.32
 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

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/db/stage2/demographic_orm.py

@@ -35,9 +35,9 @@ class DemographicORM(BaseORM):
     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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/db/stage2/participant_orm.py

@@ -23,7 +23,7 @@ class ParticipantORM(BaseORM):
     version: Mapped[str]
 
     native_participant_id: Mapped[str | None]
-    cimac_participant_id: Mapped[str] = mapped_column(unique=True)
+    cimac_participant_id: Mapped[str | None]
     consent_group_id: Mapped[Optional[int]] = mapped_column(
         ForeignKey("stage2.consent_group.consent_group_id", ondelete="CASCADE")
     )

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/pydantic/stage2/base.py

@@ -6,7 +6,7 @@ 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")
 
     # Validates the new state and updates the object if valid
     def update(self, **kwargs):
@@ -38,5 +38,7 @@ class Base(BaseModel):
             if not val:
                 return []
             return val.split("|")
+        elif val == None:
+            return []
         else:
             raise ValueError("Field value must be string or list")

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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-1.2.30 → nci_cidc_api_modules-1.2.32}/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:

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/pydantic/stage2/response_by_system.py

@@ -1,6 +1,6 @@
 from typing import Self
 
-from pydantic import PositiveInt, model_validator
+from pydantic import PositiveInt, model_validator, NonNegativeInt
 
 from .base import Base
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
@@ -41,6 +41,9 @@ class ResponseBySystem(Base):
     # 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
 

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/pydantic/stage2/trial.py

@@ -1,8 +1,9 @@
 from datetime import datetime
-from typing import List
+from pydantic import BeforeValidator
+from typing import List, Annotated
 
 from .base import Base
-from cidc_api.models.types import TrialOrganization, TrialFundingAgency, AssayType
+from cidc_api.models.types import TrialOrganization, TrialFundingAgency, AssayType, AgeGroup
 
 
 class Trial(Base):
@@ -16,6 +17,15 @@ class Trial(Base):
     # 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
+
     # ClinicalTrials.gov identifier. e.g. "NCT03731260"
     # TODO need cde from janice, they will make one
     nct_id: str | None = None

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/cidc_api/models/types.py

@@ -20,6 +20,12 @@ from cidc_api.reference.gvhd import is_gvhd_organ
 # As python Enums are rather cumbersome when we only want a list of permissible values for a string, use Literal instead
 
 
+AgeGroup = Literal[
+    "Adolescent and Young Adult",
+    "Adult",
+    "Pediatric",
+]
+
 TrialOrganization = Literal[
     "ECOG-ACRIN",
     "SWOG",

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.30
+Version: 1.2.32
 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

{nci_cidc_api_modules-1.2.30 → nci_cidc_api_modules-1.2.32}/pyproject.toml

@@ -13,3 +13,6 @@ line-length = 120
 minversion = "6.0"
 # configure a webdriver for testing Dash dashboards
 # addopts = "--webdriver Chrome --headless"
+filterwarnings = [
+    "ignore::DeprecationWarning:dash.*:"
+]