nci-cidc-api-modules 1.2.52__tar.gz → 1.2.54__tar.gz

{nci_cidc_api_modules-1.2.52/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.52
+Version: 1.2.54
 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-1.2.54/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.54"

nci_cidc_api_modules-1.2.54/cidc_api/models/code_systems.py

@@ -0,0 +1,29 @@
+from typing import Optional
+
+from sqlalchemy import MetaData, String
+from sqlalchemy.orm import declarative_base, mapped_column, Mapped
+
+SCHEMA = "code_systems"
+
+metadata_obj = MetaData(schema=SCHEMA)
+Base = declarative_base(metadata=metadata_obj)
+
+
+class Ctcae60(Base):
+    __tablename__ = "ctcae_60"
+
+    code: Mapped[str] = mapped_column(String(8), primary_key=True)
+    term: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+
+    def __repr__(self) -> str:
+        return f"Ctcae60(code={self.code!r}, term={self.term!r})"
+
+
+class Icdo3(Base):
+    __tablename__ = "icdo_3"
+
+    morphological_code: Mapped[str] = mapped_column(String(6), primary_key=True)
+    morphological_term: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+
+    def __repr__(self) -> str:
+        return f"Icdo3(morphological_code={self.morphological_code!r}, morphological_term={self.morphological_term!r})"

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage1/adverse_event_orm.py

@@ -13,6 +13,7 @@ from cidc_api.models.types import (
     SystemOrganClass,
     AttributionCause,
     AttributionLikelihood,
+    YN,
     YNU,
 )
 
@@ -33,7 +34,7 @@ class AdverseEventORM(BaseORM):
     severity_grade: Mapped[SeverityGrade]
     event_other_specify: Mapped[str | None]
     system_organ_class: Mapped[SystemOrganClass | None]
-    discontinuation_due_to_event: Mapped[bool]
+    discontinuation_due_to_event: Mapped[YN]
     days_to_onset_of_event: Mapped[NonNegativeInt]
     days_to_resolution_of_event: Mapped[NonNegativeInt | None]
     serious_adverse_event: Mapped[YNU]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage1/demographic_orm.py

@@ -17,6 +17,7 @@ from cidc_api.models.types import (
     Occupation,
     Education,
     AgeAtEnrollmentUnits,
+    YN,
 )
 
 
@@ -29,7 +30,7 @@ class DemographicORM(BaseORM):
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))
     age_at_enrollment: Mapped[PositiveInt | None]
     age_at_enrollment_units: Mapped[AgeAtEnrollmentUnits | None]
-    age_90_or_over: Mapped[bool]
+    age_90_or_over: Mapped[YN]
     sex: Mapped[Sex]
     race: Mapped[List[Race]] = mapped_column(JSON)
     ethnicity: Mapped[Ethnicity]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage1/radiotherapy_dose_orm.py

@@ -9,8 +9,9 @@ from cidc_api.models.types import (
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
     RadiotherapyDoseUnits,
-    YNU,
     RadiationExtent,
+    YN,
+    YNU,
 )
 
 
@@ -26,7 +27,7 @@ class RadiotherapyDoseORM(BaseORM):
     days_to_end: Mapped[NonNegativeInt]
     procedure: Mapped[RadiotherapyProcedure]
     anatomical_location: Mapped[UberonAnatomicalTerm | None]
-    is_total_dose: Mapped[bool]
+    is_total_dose: Mapped[YN]
     number_of_fractions: Mapped[NonNegativeInt | None]
     received_dose: Mapped[NonNegativeFloat]
     received_dose_units: Mapped[RadiotherapyDoseUnits]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage1/response_by_system_orm.py

@@ -4,7 +4,7 @@ from sqlalchemy import ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
-from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
 class ResponseBySystemORM(BaseORM):
@@ -19,7 +19,7 @@ class ResponseBySystemORM(BaseORM):
     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]
+    durable_clinical_benefit: Mapped[YN | None]
     days_to_first_response: Mapped[PositiveInt | None]
     days_to_best_response: Mapped[PositiveInt | None]
     progression: Mapped[YNUNA]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage1/response_orm.py

@@ -5,7 +5,7 @@ from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath, YN
 
 
 class ResponseORM(BaseORM):
@@ -21,8 +21,8 @@ class ResponseORM(BaseORM):
     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]
+    evaluable_for_toxicity: Mapped[YN]
+    evaluable_for_efficacy: Mapped[YN]
     days_to_last_vital_status: Mapped[NonNegativeInt | None]
 
     participant: Mapped[ParticipantORM] = relationship(back_populates="response", cascade="all, delete")

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage2/adverse_event_orm.py

@@ -13,6 +13,7 @@ from cidc_api.models.types import (
     SystemOrganClass,
     AttributionCause,
     AttributionLikelihood,
+    YN,
     YNU,
 )
 
@@ -33,7 +34,7 @@ class AdverseEventORM(BaseORM):
     severity_grade: Mapped[SeverityGrade]
     event_other_specify: Mapped[str | None]
     system_organ_class: Mapped[SystemOrganClass | None]
-    discontinuation_due_to_event: Mapped[bool]
+    discontinuation_due_to_event: Mapped[YN]
     days_to_onset_of_event: Mapped[NonNegativeInt]
     days_to_resolution_of_event: Mapped[NonNegativeInt | None]
     serious_adverse_event: Mapped[YNU]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage2/demographic_orm.py

@@ -17,6 +17,7 @@ from cidc_api.models.types import (
     Occupation,
     Education,
     AgeAtEnrollmentUnits,
+    YN,
 )
 
 
@@ -29,7 +30,7 @@ class DemographicORM(BaseORM):
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))
     age_at_enrollment: Mapped[PositiveInt | None]
     age_at_enrollment_units: Mapped[AgeAtEnrollmentUnits | None]
-    age_90_or_over: Mapped[bool]
+    age_90_or_over: Mapped[YN]
     sex: Mapped[Sex]
     race: Mapped[List[Race]] = mapped_column(JSON)
     ethnicity: Mapped[Ethnicity]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage2/radiotherapy_dose_orm.py

@@ -9,6 +9,7 @@ from cidc_api.models.types import (
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
     RadiotherapyDoseUnits,
+    YN,
     YNU,
     RadiationExtent,
 )
@@ -26,7 +27,7 @@ class RadiotherapyDoseORM(BaseORM):
     days_to_end: Mapped[NonNegativeInt]
     procedure: Mapped[RadiotherapyProcedure]
     anatomical_location: Mapped[UberonAnatomicalTerm | None]
-    is_total_dose: Mapped[bool]
+    is_total_dose: Mapped[YN]
     number_of_fractions: Mapped[NonNegativeInt | None]
     received_dose: Mapped[NonNegativeFloat]
     received_dose_units: Mapped[RadiotherapyDoseUnits]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage2/response_by_system_orm.py

@@ -4,7 +4,7 @@ from sqlalchemy import ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
 class ResponseBySystemORM(BaseORM):
@@ -19,7 +19,7 @@ class ResponseBySystemORM(BaseORM):
     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]
+    durable_clinical_benefit: Mapped[YN | None]
     days_to_first_response: Mapped[PositiveInt | None]
     days_to_best_response: Mapped[PositiveInt | None]
     progression: Mapped[YNUNA]

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/db/stage2/response_orm.py

@@ -5,7 +5,7 @@ from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+from cidc_api.models.types import SurvivalStatus, YNUNA, YN, CauseOfDeath
 
 
 class ResponseORM(BaseORM):
@@ -21,8 +21,8 @@ class ResponseORM(BaseORM):
     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]
+    evaluable_for_toxicity: Mapped[YN]
+    evaluable_for_efficacy: Mapped[YN]
     days_to_last_vital_status: Mapped[NonNegativeInt | None]
 
     participant: Mapped[ParticipantORM] = relationship(back_populates="response", cascade="all, delete")

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage1/adverse_event.py

@@ -1,7 +1,7 @@
 from pydantic import NonNegativeInt
 
 from cidc_api.models.pydantic.base import Base
-from cidc_api.reference.ctcae import is_ctcae_other_term
+from cidc_api.code_systems.ctcae import is_ctcae_other_term
 from cidc_api.models.pydantic.base import forced_validator, forced_validators
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.types import (
@@ -13,6 +13,7 @@ from cidc_api.models.types import (
     SystemOrganClass,
     AttributionCause,
     AttributionLikelihood,
+    YN,
     YNU,
 )
 
@@ -53,7 +54,7 @@ class AdverseEvent(Base):
     system_organ_class: SystemOrganClass | None = None
 
     # Indicator to identify whether a participant exited the study prematurely due to the adverse event being described.
-    discontinuation_due_to_event: bool
+    discontinuation_due_to_event: YN
 
     # Days from enrollment date to date of onset of the adverse event.
     days_to_onset_of_event: NonNegativeInt

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage1/demographic.py

@@ -15,6 +15,7 @@ from cidc_api.models.types import (
     Occupation,
     Education,
     AgeAtEnrollmentUnits,
+    YN,
 )
 
 
@@ -39,7 +40,7 @@ class Demographic(Base):
 
     # Indicates whether the participant is 90 years old or over. (for PHI purposes)
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15354920%20and%20ver_nr=1
-    age_90_or_over: bool
+    age_90_or_over: YN
 
     # A textual description of a person's sex at birth. e.g. "Male"
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7572817%20and%20ver_nr=3
@@ -100,13 +101,13 @@ class Demographic(Base):
         age_90_or_over = data.get("age_90_or_over", None)
         age_at_enrollment = int(data.get("age_at_enrollment", None) or 0)
 
-        if age_90_or_over:
+        if age_90_or_over == "Yes":
             if age_at_enrollment or age_at_enrollment_units:
                 raise ValueLocError(
                     'If "age_90_or_over" is "Yes" then "age_at_enrollment" and "age_at_enrollment_units" must be blank.',
                     loc="age_at_enrollment",
                 )
-        else:
+        elif age_90_or_over == "No":
             if not age_at_enrollment or not age_at_enrollment_units:
                 raise ValueLocError(
                     'If "age_90_or_over" is "No" then "age_at_enrollment" and "age_at_enrollment_units" are required.',
@@ -120,7 +121,7 @@ class Demographic(Base):
         age_90_or_over = data.get("age_90_or_over", None)
         age_at_enrollment = int(data.get("age_at_enrollment", None) or 0)
 
-        if not age_90_or_over:
+        if age_90_or_over == "No":
             age_in_years = age_at_enrollment if age_at_enrollment_units == "Years" else age_at_enrollment / 365.25
             if age_in_years >= 90:
                 raise ValueLocError(

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage1/radiotherapy_dose.py

@@ -4,6 +4,7 @@ from cidc_api.models.pydantic.base import forced_validator, forced_validators
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
+    YN,
     YNU,
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
@@ -38,7 +39,7 @@ class RadiotherapyDose(Base):
 
     # 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
+    is_total_dose: YN
 
     # The number of fractions a participant received to deliver the radiation dose.
     number_of_fractions: NonNegativeInt | None = None

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage1/response.py

@@ -3,7 +3,7 @@ from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
+from cidc_api.models.types import SurvivalStatus, YNUNA, YN, CauseOfDeath
 
 
 @forced_validators
@@ -39,10 +39,10 @@ class Response(Base):
     cause_of_death: CauseOfDeath | None = None
 
     # Indicates whether participant was evaluable for toxicity (adverse events, DLT, etc.) overall.
-    evaluable_for_toxicity: bool
+    evaluable_for_toxicity: YN
 
     # Indicates whether participant was evaluable for efficacy (for example, response, PFS, OS, etc.) overall.
-    evaluable_for_efficacy: bool
+    evaluable_for_efficacy: YN
 
     # Days from enrollment date to the last time the patient's vital status was verified.
     days_to_last_vital_status: NonNegativeInt | None = None

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage1/response_by_system.py

@@ -6,7 +6,7 @@ from cidc_api.models.pydantic.base import forced_validator, forced_validators
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.pydantic.stage1.response import Response
-from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
 negative_response_values = [
@@ -52,7 +52,7 @@ class ResponseBySystem(Base):
     duration_of_stable_disease: NonNegativeInt | None = None
 
     # Indicates whether a patient achieved a durable clinical benefit.
-    durable_clinical_benefit: bool | None = None
+    durable_clinical_benefit: YN | None = None
 
     # Number of days between enrollment date and the date of first response to trial treatment.
     days_to_first_response: PositiveInt | None = None

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage2/adverse_event.py

@@ -3,7 +3,7 @@ from typing import Self
 from pydantic import NonNegativeInt, model_validator
 
 from cidc_api.models.pydantic.base import Base
-from cidc_api.reference.ctcae import is_ctcae_other_term
+from cidc_api.code_systems.ctcae import is_ctcae_other_term
 from cidc_api.models.types import (
     CTCAEEventTerm,
     CTCAEEventCode,
@@ -14,6 +14,7 @@ from cidc_api.models.types import (
     AttributionCause,
     AttributionLikelihood,
     YNU,
+    YN,
 )
 
 
@@ -52,7 +53,7 @@ class AdverseEvent(Base):
     system_organ_class: SystemOrganClass | None = None
 
     # Indicator to identify whether a participant exited the study prematurely due to the adverse event being described.
-    discontinuation_due_to_event: bool
+    discontinuation_due_to_event: YN
 
     # Days from enrollment date to date of onset of the adverse event.
     days_to_onset_of_event: NonNegativeInt

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage2/demographic.py

@@ -13,6 +13,7 @@ from cidc_api.models.types import (
     Occupation,
     Education,
     AgeAtEnrollmentUnits,
+    YN,
 )
 
 
@@ -36,7 +37,7 @@ class Demographic(Base):
 
     # Indicates whether the participant is 90 years old or over. (for PHI purposes)
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15354920%20and%20ver_nr=1
-    age_90_or_over: bool
+    age_90_or_over: YN
 
     # A textual description of a person's sex at birth. e.g. "Male"
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7572817%20and%20ver_nr=3
@@ -92,12 +93,12 @@ class Demographic(Base):
 
     @model_validator(mode="after")
     def validate_age_at_enrollment_cr(self) -> Self:
-        if self.age_90_or_over:
+        if self.age_90_or_over == "Yes":
             if self.age_at_enrollment or self.age_at_enrollment_units:
                 raise ValueError(
                     'If "age_90_or_over" is "Yes" then "age_at_enrollment" and "age_at_enrollment_units" must be blank.'
                 )
-        else:
+        elif self.age_90_or_over == "No":
             if not self.age_at_enrollment or not self.age_at_enrollment_units:
                 raise ValueError(
                     'If "age_90_or_over" is "No" then "age_at_enrollment" and "age_at_enrollment_units" are required.'
@@ -106,7 +107,7 @@ class Demographic(Base):
 
     @model_validator(mode="after")
     def validate_age_at_enrollment_value(self) -> Self:
-        if not self.age_90_or_over:
+        if self.age_90_or_over == "No":
             age_in_years = (
                 self.age_at_enrollment if self.age_at_enrollment_units == "Years" else self.age_at_enrollment / 365.25
             )

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage2/radiotherapy_dose.py

@@ -4,6 +4,7 @@ from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
 
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
+    YN,
     YNU,
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
@@ -37,7 +38,7 @@ class RadiotherapyDose(Base):
 
     # 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
+    is_total_dose: YN
 
     # The number of fractions a participant received to deliver the radiation dose.
     number_of_fractions: NonNegativeInt | None = None

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage2/response.py

@@ -3,7 +3,7 @@ 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
+from cidc_api.models.types import SurvivalStatus, YN, YNUNA, CauseOfDeath
 
 
 class Response(Base):
@@ -38,10 +38,10 @@ class Response(Base):
     cause_of_death: CauseOfDeath | None = None
 
     # Indicates whether participant was evaluable for toxicity (adverse events, DLT, etc.) overall.
-    evaluable_for_toxicity: bool
+    evaluable_for_toxicity: YN
 
     # Indicates whether participant was evaluable for efficacy (for example, response, PFS, OS, etc.) overall.
-    evaluable_for_efficacy: bool
+    evaluable_for_efficacy: YN
 
     # 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

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/pydantic/stage2/response_by_system.py

@@ -3,7 +3,7 @@ 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
+from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
 negative_response_values = [
@@ -45,7 +45,7 @@ class ResponseBySystem(Base):
     duration_of_stable_disease: NonNegativeInt | None = None
 
     # Indicates whether a patient achieved a durable clinical benefit.
-    durable_clinical_benefit: bool | None = None
+    durable_clinical_benefit: YN | None = None
 
     # Number of days between enrollment date and the date of first response to trial treatment.
     days_to_first_response: PositiveInt | None = None

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/cidc_api/models/types.py

@@ -3,19 +3,19 @@ from typing import Annotated, Literal
 from pydantic import AfterValidator
 from sqlalchemy.types import TypeDecorator, Unicode
 
-from cidc_api.reference.icdo3 import is_ICDO3_code, is_ICDO3_term
-from cidc_api.reference.uberon import is_uberon_term
-from cidc_api.reference.ctcae import (
+from cidc_api.code_systems.icdo3 import is_ICDO3_code, is_ICDO3_term
+from cidc_api.code_systems.uberon import is_uberon_term
+from cidc_api.code_systems.ctcae import (
     is_ctcae_event_term,
     is_ctcae_event_code,
     is_ctcae_severity_grade,
     is_ctcae_system_organ_class,
 )
-from cidc_api.reference.icd10cm import (
+from cidc_api.code_systems.icd10cm import (
     is_ICD10CM_code,
     is_ICD10CM_term,
 )
-from cidc_api.reference.gvhd import is_gvhd_organ
+from cidc_api.code_systems.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
 
@@ -468,6 +468,12 @@ MCategory = Literal[
 ]
 
 
+YN = Literal[
+    "Yes",
+    "No",
+]
+
+
 YNU = Literal[
     "Yes",
     "No",

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.52
+Version: 1.2.54
 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-1.2.52 → nci_cidc_api_modules-1.2.54}/nci_cidc_api_modules.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ cidc_api/config/logging.py
 cidc_api/config/secrets.py
 cidc_api/config/settings.py
 cidc_api/models/__init__.py
+cidc_api/models/code_systems.py
 cidc_api/models/data.py
 cidc_api/models/errors.py
 cidc_api/models/migrations.py
@@ -151,11 +152,6 @@ cidc_api/models/pydantic/stage2/surgery.py
 cidc_api/models/pydantic/stage2/therapy_agent_dose.py
 cidc_api/models/pydantic/stage2/treatment.py
 cidc_api/models/pydantic/stage2/trial.py
-cidc_api/reference/ctcae.py
-cidc_api/reference/gvhd.py
-cidc_api/reference/icd10cm.py
-cidc_api/reference/icdo3.py
-cidc_api/reference/uberon.py
 cidc_api/shared/__init__.py
 cidc_api/shared/assay_handling.py
 cidc_api/shared/auth.py

{nci_cidc_api_modules-1.2.52 → nci_cidc_api_modules-1.2.54}/setup.py

@@ -13,7 +13,6 @@ from cidc_api import __version__
 packages = [
     "cidc_api.config",
     "cidc_api.models",
-    "cidc_api.reference",
     "cidc_api.shared",
 ]
 packages += find_namespace_packages(include=["cidc_api.models.*"])

nci_cidc_api_modules-1.2.52/cidc_api/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.52"

nci_cidc_api_modules-1.2.52/cidc_api/reference/ctcae.py

@@ -1,34 +0,0 @@
-# Stubbed to accept any string
-def is_ctcae_event_term(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Stubbed to accept any string
-def is_ctcae_event_code(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Stubbed to accept any string
-def is_ctcae_severity_grade(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Stubbed to accept any string
-def is_ctcae_system_organ_class(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Determines if the CTCAE term is one of the "Other, specify" types of terms for which we include
-# additional data about the AE.
-def is_ctcae_other_term(v):
-    if isinstance(v, str):
-        return "Other, specify" in v
-    return False

nci_cidc_api_modules-1.2.52/cidc_api/reference/gvhd.py

@@ -1,6 +0,0 @@
-# Stubbed to accept any string
-# Should support MAGIC and Modified Glucksberg
-def is_gvhd_organ(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v

nci_cidc_api_modules-1.2.52/cidc_api/reference/icd10cm.py

@@ -1,12 +0,0 @@
-# Stubbed to accept any string
-def is_ICD10CM_code(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Stubbed to accept any string
-def is_ICD10CM_term(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v

nci_cidc_api_modules-1.2.52/cidc_api/reference/icdo3.py

@@ -1,12 +0,0 @@
-# Stubbed to accept any string
-def is_ICDO3_code(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v
-
-
-# Stubbed to accept any string
-def is_ICDO3_term(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v

nci_cidc_api_modules-1.2.52/cidc_api/reference/uberon.py

@@ -1,5 +0,0 @@
-# Stubbed to accept any string
-def is_uberon_term(v):
-    if not isinstance(v, str):
-        raise TypeError("Value must be a string")
-    return v