nci-cidc-api-modules 1.2.47__tar.gz → 1.2.49__tar.gz

{nci_cidc_api_modules-1.2.47/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.49}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.47
+Version: 1.2.49
 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-1.2.49/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.49"

nci_cidc_api_modules-1.2.49/cidc_api/models/errors.py

@@ -0,0 +1,7 @@
+class ValueLocError(ValueError):
+    """A special case of ValueError that allows us to carry along the 'loc' location where a pydantic
+    validation error occured."""
+
+    def __init__(self, *args, loc: str, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.loc = (loc,)  # Make a tuple to match pydantic's loc structure

{nci_cidc_api_modules-1.2.47 → nci_cidc_api_modules-1.2.49}/cidc_api/models/models.py

@@ -3492,6 +3492,7 @@ class IngestionJobs(CommonColumns):
     intake_path = Column(String, nullable=True)
     uploader_email = Column(String, nullable=True)
     is_template_downloaded = Column(Boolean, nullable=True)
+    master_aa_version = Column(Integer, nullable=True)
 
     @staticmethod
     @with_default_session

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/adverse_event.py

@@ -1,9 +1,10 @@
 from typing import Self
 
-from pydantic import NonNegativeInt, model_validator
+from pydantic import Field, NonNegativeInt, model_validator
 
 from cidc_api.models.pydantic.base import Base
 from cidc_api.reference.ctcae import is_ctcae_other_term
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.types import (
     CTCAEEventTerm,
     CTCAEEventCode,
@@ -78,7 +79,10 @@ class AdverseEvent(Base):
     @model_validator(mode="after")
     def validate_term_and_code_cr(self) -> Self:
         if not self.event_term and not self.event_code:
-            raise ValueError("Please provide event_term or event_code or both")
+            raise ValueLocError(
+                "Please provide event_term or event_code or both",
+                loc="event_term",
+            )
         return self
 
     @model_validator(mode="after")
@@ -88,13 +92,28 @@ class AdverseEvent(Base):
             and is_ctcae_other_term(self.event_term)
             and not self.event_other_specify
         ):
-            raise ValueError(
-                'If severity_grade_system is "CTCAE" and the event_code or event_term are of type "Other, specify", please provide event_other_specify'
+            raise ValueLocError(
+                'If severity_grade_system is "CTCAE" and the event_code or event_term are of type '
+                '"Other, specify", please provide event_other_specify',
+                loc="event_other_specify",
             )
         return self
 
     @model_validator(mode="after")
     def validate_system_organ_class_cr(self) -> Self:
         if self.event_other_specify and not self.system_organ_class:
-            raise ValueError("If event_other_specify is provided, please provide system_organ_class.")
+            raise ValueLocError(
+                "If event_other_specify is provided, please provide system_organ_class.",
+                loc="system_organ_class",
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_resolution_of_event_chronology(self) -> Self:
+        if self.days_to_resolution_of_event is not None and self.days_to_onset_of_event is not None:
+            if self.days_to_resolution_of_event < self.days_to_onset_of_event:
+                raise ValueLocError(
+                    'Violate "days_to_onset_of_event" <= "days_to_resolution_of_event"',
+                    loc="days_to_resolution_of_event",
+                )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/comorbidity.py

@@ -1,7 +1,8 @@
-from typing import Self
+from typing import Self, Any
 
-from pydantic import model_validator
+from pydantic import model_validator, field_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
 
@@ -30,7 +31,8 @@ class Comorbidity(Base):
     @model_validator(mode="after")
     def validate_code_or_term_or_other_cr(self) -> Self:
         if not self.comorbidity_code and not self.comorbidity_term and not self.comorbidity_other:
-            raise ValueError(
-                'Please provide at least one of "comorbidity_code", "comorbidity_term" or "comorbidity_other".'
+            raise ValueLocError(
+                'Please provide at least one of "comorbidity_code", "comorbidity_term" or "comorbidity_other".',
+                loc="comorbidity_code",
             )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/demographic.py

@@ -2,6 +2,7 @@ from typing import Self, Annotated, List
 
 from pydantic import PositiveInt, NonNegativeFloat, PositiveFloat, model_validator, field_validator, BeforeValidator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     Sex,
@@ -94,13 +95,15 @@ class Demographic(Base):
     def validate_age_at_enrollment_cr(self) -> Self:
         if self.age_90_or_over:
             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.'
+                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:
             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.'
+                raise ValueLocError(
+                    'If "age_90_or_over" is "No" then "age_at_enrollment" and "age_at_enrollment_units" are required.',
+                    loc="age_at_enrollment_units",
                 )
         return self
 
@@ -111,13 +114,17 @@ class Demographic(Base):
                 self.age_at_enrollment if self.age_at_enrollment_units == "Years" else self.age_at_enrollment / 365.25
             )
             if age_in_years >= 90:
-                raise ValueError('"age_at_enrollment" cannot represent a value greater than 90 years of age.')
+                raise ValueLocError(
+                    '"age_at_enrollment" cannot represent a value greater than 90 years of age.',
+                    loc="age_at_enrollment",
+                )
         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.'
+            raise ValueLocError(
+                'If "body_surface_area" is provided then "body_surface_area_units_other" must also be provided.',
+                loc="body_surface_area_units_other",
             )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/disease.py

@@ -1,6 +1,7 @@
 from pydantic import NonPositiveInt, model_validator, BeforeValidator
 from typing import List, Self, Annotated, get_args
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     TumorGrade,
@@ -95,8 +96,9 @@ class Disease(Base):
     @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".'
+            raise ValueLocError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "cancer_type_description".',
+                loc="morphological_code",
             )
         return self
 
@@ -106,53 +108,67 @@ class Disease(Base):
         if self.cancer_stage_system == "AJCC" and self.cancer_stage_system_version not in get_args(
             CancerStageSystemVersionAJCC
         ):
-            raise ValueError(msg)
+            raise ValueLocError(msg, loc="cancer_stage_system")
         elif self.cancer_stage_system == "RISS" and self.cancer_stage_system_version not in get_args(
             CancerStageSystemVersionRISS
         ):
-            raise ValueError(msg)
+            raise ValueLocError(msg, loc="cancer_stage_system")
         elif self.cancer_stage_system == "FIGO" and self.cancer_stage_system_version not in get_args(
             CancerStageSystemVersionFIGO
         ):
-            raise ValueError(msg)
+            raise ValueLocError(msg, loc="cancer_stage_system")
         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}"'
+            raise ValueLocError(
+                f'Please provide cancer_stage_system_version when cancer_stage_system is "{self.cancer_stage_system}"',
+                loc="cancer_stage_system_version",
             )
         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}"')
+            raise ValueLocError(
+                f'Please provide cancer_stage when cancer_stage_system is "{self.cancer_stage_system}"',
+                loc="cancer_stage",
+            )
         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}"')
+            raise ValueLocError(
+                f'Please provide t_category when cancer_stage_system is "{self.cancer_stage_system}"',
+                loc="t_category",
+            )
         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}"')
+            raise ValueLocError(
+                f'Please provide n_category when cancer_stage_system is "{self.cancer_stage_system}"',
+                loc="n_category",
+            )
         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}"')
+            raise ValueLocError(
+                f'Please provide m_category when cancer_stage_system is "{self.cancer_stage_system}"',
+                loc="m_category",
+            )
         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."
+            raise ValueLocError(
+                "If solely_extramedullary_disease indicates no disease, please leave extramedullary_organ blank.",
+                loc="extramedullary_organ",
             )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/exposure.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, ExposureType
 
@@ -28,5 +29,8 @@ class Exposure(Base):
     @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.")
+            raise ValueLocError(
+                "If carcinogen_exposure indicates non exposure, please leave exposure_type blank.",
+                loc="exposure_type",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/medical_history.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, PositiveFloat, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import TobaccoSmokingStatus
 
@@ -32,5 +33,8 @@ class MedicalHistory(Base):
     @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.")
+            raise ValueLocError(
+                "If tobacco_smoking_status indicates non-smoker, please leave pack_years_smoked blank.",
+                loc="pack_years_smoked",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/other_malignancy.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonPositiveInt, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
@@ -43,7 +44,8 @@ class OtherMalignancy(Base):
             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".'
+            raise ValueLocError(
+                'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".',
+                loc="morphological_code",
             )
         return self

{nci_cidc_api_modules-1.2.47 → nci_cidc_api_modules-1.2.49}/cidc_api/models/pydantic/stage1/participant.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU
 from cidc_api.models.types import OffStudyReason
@@ -41,11 +42,17 @@ class Participant(Base):
     @model_validator(mode="after")
     def off_study_reason_cr(self) -> Self:
         if self.off_study == "Yes" and not self.off_study_reason:
-            raise ValueError('If "off_study" is "Yes" then "off_study_reason" is required.')
+            raise ValueLocError(
+                'If "off_study" is "Yes" then "off_study_reason" is required.',
+                loc="off_study_reason",
+            )
         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.')
+            raise ValueLocError(
+                'If "off_study_reason" is "Other" then "off_study_reason_other" is required.',
+                loc="off_study_reason_other",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/radiotherapy_dose.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import (
     YNU,
@@ -69,11 +70,17 @@ class RadiotherapyDose(Base):
     @model_validator(mode="after")
     def validate_changes_delays_description_cr(self) -> Self:
         if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
-            raise ValueError('If dose_changes_delays is "Yes", please provide changes_delays_description.')
+            raise ValueLocError(
+                'If dose_changes_delays is "Yes", please provide changes_delays_description.',
+                loc="changes_delays_description",
+            )
         return self
 
     @model_validator(mode="after")
     def validate_planned_dose_units_cr(self) -> Self:
         if self.planned_dose and not self.planned_dose_units:
-            raise ValueError("If planned_dose is provided, please provide planned_dose_units.")
+            raise ValueLocError(
+                "If planned_dose is provided, please provide planned_dose_units.",
+                loc="planned_dose_units",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/response.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 
@@ -44,22 +45,31 @@ class Response(Base):
     evaluable_for_efficacy: bool
 
     # Days from enrollment date to the last time the patient's vital status was verified.
-    days_to_last_vital_status: NonNegativeInt | None = None  # TODO: Needs CR check
+    days_to_last_vital_status: NonNegativeInt | None = None
 
     @model_validator(mode="after")
     def validate_cause_of_death_cr(self) -> Self:
         if self.survival_status == "Dead" and not self.cause_of_death:
-            raise ValueError('If survival_status is "Dead" then cause_of_death is required.')
+            raise ValueLocError(
+                'If survival_status is "Dead" then cause_of_death is required.',
+                loc="cause_of_death",
+            )
         return self
 
     @model_validator(mode="after")
     def validate_cause_of_death_cr2(self) -> Self:
         if self.survival_status == "Alive" and self.cause_of_death:
-            raise ValueError('If survival_status is "Alive", please leave cause_of_death blank.')
+            raise ValueLocError(
+                'If survival_status is "Alive", please leave cause_of_death blank.',
+                loc="cause_of_death",
+            )
         return self
 
     @model_validator(mode="after")
     def validate_days_to_death_cr(self) -> Self:
         if self.survival_status in ["Alive", "Unknown"] and self.days_to_death:
-            raise ValueError("If survival_status does not indicate death, please leave days_to_death blank.")
+            raise ValueLocError(
+                "If survival_status does not indicate death, please leave days_to_death blank.",
+                loc="days_to_death",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/response_by_system.py

@@ -2,7 +2,9 @@ from typing import Self
 
 from pydantic import PositiveInt, model_validator, NonNegativeInt
 
+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
 
 
@@ -28,6 +30,9 @@ class ResponseBySystem(Base):
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=12220014%20and%20ver_nr=1
     participant_id: str | None = None
 
+    # The linked parent response for the participant. Used for cross-model validation.
+    response: Response | None = None
+
     # A standardized method used to evaluate and categorize the participant’s clinical response to treatment based on predefined criteria.
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13381490%20and%20ver_nr=1
     response_system: ResponseSystem
@@ -69,44 +74,114 @@ class ResponseBySystem(Base):
     @model_validator(mode="after")
     def validate_response_duration_cr(self) -> Self:
         if self.best_overall_response in negative_response_values and self.response_duration:
-            raise ValueError(
+            raise ValueLocError(
                 "If best_overall_response does not indicate a positive response, "
-                "please leave response_duration blank."
+                "please leave response_duration blank.",
+                loc="response_duration",
             )
         return self
 
     @model_validator(mode="after")
     def validate_days_to_first_response_cr(self) -> Self:
         if self.best_overall_response in negative_response_values and self.days_to_first_response:
-            raise ValueError(
+            raise ValueLocError(
                 "If best_overall_response does not indicate a positive response, "
-                "please leave days_to_first_response blank."
+                "please leave days_to_first_response blank.",
+                loc="days_to_first_response",
             )
         return self
 
     @model_validator(mode="after")
     def validate_days_to_best_response_cr(self) -> Self:
         if self.best_overall_response in negative_response_values and self.days_to_best_response:
-            raise ValueError(
+            raise ValueLocError(
                 "If best_overall_response does not indicate a positive response, \
-                please leave days_to_best_response blank."
+                please leave days_to_best_response blank.",
+                loc="days_to_best_response",
             )
         return self
 
     @model_validator(mode="after")
     def validate_days_to_disease_progression_cr(self) -> Self:
         if self.progression in ["No", "Unknown", "Not Applicable"] and self.days_to_disease_progression:
-            raise ValueError(
+            raise ValueLocError(
                 "If progression does not indicate confirmed progression of the disease, \
-                please leave days_to_disease_progress blank."
+                please leave days_to_disease_progress blank.",
+                loc="days_to_disease_progress",
             )
         return self
 
     @model_validator(mode="after")
     def validate_progression_free_survival_cr(self) -> Self:
         if self.progression_free_survival_event in ["Unknown", "Not Applicable"] and self.progression_free_survival:
-            raise ValueError(
+            raise ValueLocError(
                 "If progression_free_survival_event is not known, \
-                please leave progression_free_survival blank."
+                please leave progression_free_survival blank.",
+                loc="progression_free_survival",
             )
         return self
+
+    @model_validator(mode="after")
+    def validate_days_to_best_response_chronology(self) -> Self:
+        if self.days_to_best_response is not None and self.days_to_first_response is not None:
+            if self.days_to_best_response < self.days_to_first_response:
+                raise ValueLocError(
+                    'Violate "days_to_best_response" >= days_to_first_response"',
+                    loc="days_to_best_response",
+                )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_disease_progression_chronology(self) -> Self:
+        if self.days_to_first_response is not None and self.days_to_disease_progression is not None:
+            if self.days_to_first_response >= self.days_to_disease_progression:
+                raise ValueLocError(
+                    'Violate "days_to_first_response" < "days_to_disease_progression"',
+                    loc="days_to_first_response",
+                )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_best_response_progression_chronology(self) -> Self:
+        if self.days_to_best_response is not None and self.days_to_disease_progression is not None:
+            if self.days_to_best_response >= self.days_to_disease_progression:
+                raise ValueLocError(
+                    'Violate "days_to_best_response" < "days_to_disease_progression"',
+                    loc="days_to_best_response",
+                )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_last_vital_status_chronology(self) -> Self:
+        if not self.response or not self.response.days_to_last_vital_status:
+            return self
+        max_value = max(
+            self.response.days_to_last_vital_status or 0,
+            self.days_to_first_response or 0,
+            self.days_to_best_response or 0,
+            self.days_to_disease_progression or 0,
+        )
+        if (self.response.days_to_last_vital_status or 0) != max_value:
+            raise ValueLocError(
+                '"days_to_last_vital_status" is not the max of all events. Rule: days_to_last_vital_status '
+                ">= max(days_to_first_response,days_to_best_response,days_to_disease_progression)",
+                loc="days_to_last_vital_status,days_to_first_response,days_to_best_response,days_to_disease_progression",
+            )
+        return self
+
+    @model_validator(mode="after")
+    def validate_days_to_death_chronology(self) -> Self:
+        if not self.response or not self.response.days_to_death:
+            return self
+        max_value = max(
+            self.response.days_to_death or 0,
+            self.days_to_first_response or 0,
+            self.days_to_best_response or 0,
+            self.days_to_disease_progression or 0,
+        )
+        if (self.response.days_to_death or 0) != max_value:
+            raise ValueLocError(
+                '"days_to_death" is not the max of all events. Rule: days_to_death'
+                ">= max(days_to_first_response,days_to_best_response,days_to_disease_progression)",
+                loc="days_to_death,days_to_first_response,days_to_best_response,days_to_disease_progression",
+            )

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/surgery.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
 
@@ -45,5 +46,8 @@ class Surgery(Base):
     @model_validator(mode="after")
     def validate_procedure_other_cr(self) -> Self:
         if self.procedure == "Other, specify" and not self.procedure_other:
-            raise ValueError('If procedure is "Other, specify", please provide procedure_other.')
+            raise ValueLocError(
+                'If procedure is "Other, specify", please provide procedure_other.',
+                loc="procedure_other",
+            )
         return self

{nci_cidc_api_modules-1.2.47/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.49/cidc_api/models/pydantic/stage1}/therapy_agent_dose.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat, model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, TherapyAgentDoseUnits
 
@@ -57,11 +58,17 @@ class TherapyAgentDose(Base):
     @model_validator(mode="after")
     def validate_changes_delays_description_cr(self) -> Self:
         if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
-            raise ValueError('If dose_changes_delays is "Yes", please provide changes_delays_description.')
+            raise ValueLocError(
+                'If dose_changes_delays is "Yes", please provide changes_delays_description.',
+                loc="changes_delays_description",
+            )
         return self
 
     @model_validator(mode="after")
     def validate_planned_dose_units_cr(self) -> Self:
         if self.planned_dose and not self.planned_dose_units:
-            raise ValueError("If planned_dose is provided, please provide planned_dose_units.")
+            raise ValueLocError(
+                "If planned_dose is provided, please provide planned_dose_units.",
+                loc="planned_dose_units",
+            )
         return self

{nci_cidc_api_modules-1.2.47 → nci_cidc_api_modules-1.2.49}/cidc_api/models/pydantic/stage1/treatment.py

@@ -2,6 +2,7 @@ from typing import Self
 
 from pydantic import model_validator
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, OffTreatmentReason
 
@@ -40,11 +41,17 @@ class Treatment(Base):
     @model_validator(mode="after")
     def validate_off_treatment_reason_cr(self) -> Self:
         if self.off_treatment == "Yes" and not self.off_treatment_reason:
-            raise ValueError('If off_treatment is "Yes", please provide off_treatment_reason.')
+            raise ValueLocError(
+                'If off_treatment is "Yes", please provide off_treatment_reason.',
+                loc="off_treatment_reason",
+            )
         return self
 
     @model_validator(mode="after")
     def validate_off_treatment_reason_other_cr(self) -> Self:
         if self.off_treatment_reason == "Other" and not self.off_treatment_reason_other:
-            raise ValueError('If off_treatment_reason is "Other", please provide off_treatment_reason_other.')
+            raise ValueLocError(
+                'If off_treatment_reason is "Other", please provide off_treatment_reason_other.',
+                loc="off_treatment_reason_other",
+            )
         return self

{nci_cidc_api_modules-1.2.47 → nci_cidc_api_modules-1.2.49}/cidc_api/shared/file_handling.py

@@ -14,6 +14,8 @@ from ..telemetry import trace_
 
 logger = get_logger(__name__)
 
+MASTER_APPENDIX_A_VERSION_PREFIX = "Master Appendix A Version:"
+
 
 @trace_()
 def set_current_file(