nci-cidc-api-modules 1.2.48__py3-none-any.whl → 1.2.49__py3-none-any.whl

cidc_api/__init__.py

@@ -1 +1 @@
-__version__ = "1.2.48"
+__version__ = "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

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

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

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

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

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

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

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

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

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

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

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

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",
+            )

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

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

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

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(

cidc_api/shared/gcloud_client.py

@@ -479,7 +479,10 @@ async def async_gcs_files_to_pandas_dataframes(bucket_name: str, blob_names: Lis
 
     for blob_name, contents in zip(blob_names, all_contents):
         extension = blob_name.split(".")[-1]
-        dataframes.append(prepare_dataframe(extension, contents))
+        try:
+            dataframes.append(prepare_dataframe(extension, contents))
+        except pd.errors.EmptyDataError:
+            logger.warning(f"The dataframe retrieved from {blob_name} was empty!")
     return dataframes
 
 

{nci_cidc_api_modules-1.2.48.dist-info → nci_cidc_api_modules-1.2.49.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.48
+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-1.2.48.dist-info → nci_cidc_api_modules-1.2.49.dist-info}/RECORD

@@ -1,5 +1,5 @@
 boot.py,sha256=oS_16OgU34iDxyFNpJl5rb5KbfbsCXroUCNLwVPxPNg,416
-cidc_api/__init__.py,sha256=Zm4hDkoG9GX2KfPn6Wt1kdPl888Wv-de5OuQhdWNP9E,23
+cidc_api/__init__.py,sha256=qkDVgmmc_W7WSA8UFQzKzULlTX27bnHrBTAlSeTYqYs,23
 cidc_api/telemetry.py,sha256=LuZWkG8CKCn23O41RTNxEOQwMmfpp-fQ6zSInZhVJg8,3333
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
 cidc_api/config/db.py,sha256=mEz8ugjvRNGylCqDYHaaMqaZfDh7sbd76BowmfBvq5c,2428
@@ -8,8 +8,9 @@ cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,14
 cidc_api/config/settings.py,sha256=loern8cejUrOJJAog4z0iW9EQaa0nlN0rFrFOdZ-cLE,4483
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/data.py,sha256=TyVXk5jJO1NN05CLqejLf5BPp6yLSNNxPmFOgXUnA1M,1313
+cidc_api/models/errors.py,sha256=UncRrh-4v0CR5mpLO0erWD1y9ctus3Nk6XOSvrTjfco,338
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
-cidc_api/models/models.py,sha256=DTt0eFkFVVxVn23Aqr6TA8CQ7qb2hdqQ0xVJ3RakBBw,153684
+cidc_api/models/models.py,sha256=3O0Oc_MgovrMS1qz-r3zOnPd5_41p7sXc30Qj03QJ6s,153739
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 cidc_api/models/types.py,sha256=WVOTEH61FH5aGVwRbEcfNOce8NLjiEnl1ixtPWav2OA,30058
 cidc_api/models/db/stage1/__init__.py,sha256=zsxOSoogzL_xZ8B5OwcwLXvAmm6g2GYx1Zf6LLw8dq8,1917
@@ -83,29 +84,29 @@ cidc_api/models/files/facets.py,sha256=vieZ3z_tYB29NqtvNzvKqajVwxM5ZLLZKeyQTq5lh
 cidc_api/models/pydantic/base.py,sha256=6Lsf4fekIS1E-DwZmgCXlfm3Qq9_23dA_v3iz1w2JoA,1427
 cidc_api/models/pydantic/stage1/__init__.py,sha256=H-NDjCd8isHTgZ7sqz-MIbzC-PpW1kEtR-x-Dyc8r6Q,1667
 cidc_api/models/pydantic/stage1/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
-cidc_api/models/pydantic/stage1/adverse_event.py,sha256=zPy02xoRQeyaXBSmqDdQt4BaRTD6OHBjycVHVtBaAow,3880
+cidc_api/models/pydantic/stage1/adverse_event.py,sha256=YzH8YbgxvjrrcJENtbctYCziR_io4fKPtSiHxO0GV9A,4652
 cidc_api/models/pydantic/stage1/baseline_clinical_assessment.py,sha256=5FYvtOVf_nIK1h3xTs3vQgJe2ivQSVHt_wfrTSDgVxU,1119
-cidc_api/models/pydantic/stage1/comorbidity.py,sha256=dk4SJnkaaju-boexf2SW_rNNGXl-Os2LR5lnIxCb-dA,1413
+cidc_api/models/pydantic/stage1/comorbidity.py,sha256=K9MyK4XsSGr-3TjrDH_GJN1rG3uWqkyECbwGGuqkbzc,1528
 cidc_api/models/pydantic/stage1/consent_group.py,sha256=aP_nd0GKK6K7VH-6IZRSDDX2RxFM_j9B36FIRGwysOU,1216
-cidc_api/models/pydantic/stage1/demographic.py,sha256=X0YoFdK7S8JQ9p_Jm3l-R5HgEl9sZnZVFXrECA2i_zw,6007
-cidc_api/models/pydantic/stage1/disease.py,sha256=fwK1FSxTm33BzViGTNsb6AahoDc2BTTXMitCGY3KyDk,7650
-cidc_api/models/pydantic/stage1/exposure.py,sha256=ERoVQLuNWynw2zugh5bVdUT0NzNbJ6fIUmKhPSCQfqk,1306
+cidc_api/models/pydantic/stage1/demographic.py,sha256=V5Fymdl2ge6eGcnCnP7ekCJuzfR7XeCgwclBKCMeolE,6304
+cidc_api/models/pydantic/stage1/disease.py,sha256=e-BT6Z_QMyDJhtzJcYbMdqABkuVsX4OWw5HGnNuLzZM,8212
+cidc_api/models/pydantic/stage1/exposure.py,sha256=XtnLxXSBrvuvOgrdg2A-x_FclQvT8zJkGeXIB50ZJs0,1426
 cidc_api/models/pydantic/stage1/gvhd_diagnosis_acute.py,sha256=jVMoWuLfspOZtOpC7rg1EzdvEAg8qEabcTaS6RRobZ8,1395
 cidc_api/models/pydantic/stage1/gvhd_diagnosis_chronic.py,sha256=SRwkAL07YyIZM4bYCqm01aKqSvj3yRmpsqFKxAZEZoM,1382
 cidc_api/models/pydantic/stage1/gvhd_organ_acute.py,sha256=VxlNGRJYjm9tW2lyLll8pD0t9JZs18gicnH-Ci_nR2I,771
 cidc_api/models/pydantic/stage1/gvhd_organ_chronic.py,sha256=Fnp1Qm-ZDDtDLrgOAnEOUnQVNWI9WrTSomiFPStGmjc,810
-cidc_api/models/pydantic/stage1/medical_history.py,sha256=IXtEvXrrLhTt6JEsj2MpDiZtLAkmrrsUS4aoe7sxans,1697
-cidc_api/models/pydantic/stage1/other_malignancy.py,sha256=V-Jru6uukipocKs7lDbmkGyJsHBxlM3A3NJoTShjJ9I,2188
-cidc_api/models/pydantic/stage1/participant.py,sha256=iDQrwYYtJY_XrkdbhsRNZuL44ighvW8JHCGxH-qo8jk,2199
+cidc_api/models/pydantic/stage1/medical_history.py,sha256=5QU01b5-lKIWiz7GoIwZmZ_meFJ70ku7tvd3To1OpIA,1821
+cidc_api/models/pydantic/stage1/other_malignancy.py,sha256=wIiYa3EffLYA4hu8JJORCZwG2GRbRdl2y47VJN4OffI,2283
+cidc_api/models/pydantic/stage1/participant.py,sha256=QQVi0jhqSot1TiopongU_VnJHvk2RLKUpKtR15a_A1M,2402
 cidc_api/models/pydantic/stage1/prior_treatment.py,sha256=axhyPHwYCoIvcIonjyPJ95HUyaAXqIuOd6hhoDM3LJU,2101
-cidc_api/models/pydantic/stage1/radiotherapy_dose.py,sha256=c5q0TxPOrYHX9KTd9he5B01zirKgcCxMnvW_7adzCrI,3327
-cidc_api/models/pydantic/stage1/response.py,sha256=rPqfYZhaZRcA1E7dkGOaHe9f2_YIcIg9-KtIPSTh1s8,2886
-cidc_api/models/pydantic/stage1/response_by_system.py,sha256=f8ZnLfNXGJLCfFL1X2jxlSUJPGvJKnOCf6PYbJVMXW8,4909
+cidc_api/models/pydantic/stage1/radiotherapy_dose.py,sha256=eGCkqfK2jIu3Lh0G51hXs4oqP9CRAxJrSbApdNjANb8,3536
+cidc_api/models/pydantic/stage1/response.py,sha256=3Cuhu0DBew96e-k0sSN4vvPJ1xSoejXJdjpXw9HPtjo,3126
+cidc_api/models/pydantic/stage1/response_by_system.py,sha256=3Om1R2vJd6C7UDQAIh-suDnwrZGquFf9SpirPJDKFUs,8590
 cidc_api/models/pydantic/stage1/specimen.py,sha256=scDekZ-RtXOQTTLburhqT3RF4KM34iY9NAV1wYi_HSg,1281
 cidc_api/models/pydantic/stage1/stem_cell_transplant.py,sha256=XsDVUksqbIprPxHwLlwHGyji4jsIFNMcIk-S0H4rDnQ,1228
-cidc_api/models/pydantic/stage1/surgery.py,sha256=53NrET_kNOlXXPP-mH5ecIPrNqDpDQt5s9WfsjPDM-s,2149
-cidc_api/models/pydantic/stage1/therapy_agent_dose.py,sha256=Y2L0vAqkfA5eI2qg7iQrqzCORwbkjyVEsthc6f5HKas,3021
-cidc_api/models/pydantic/stage1/treatment.py,sha256=1TeBaDJ352IfB10AtJH2iREdex3SZgDRXNUkhT0FZMo,2033
+cidc_api/models/pydantic/stage1/surgery.py,sha256=IPBhgyPHuPrPpy0Qs9j2rHO7ig7J8ixBVNp_1l5TvzU,2271
+cidc_api/models/pydantic/stage1/therapy_agent_dose.py,sha256=ZIsImguwBuAFGogla1rBN6N_FNUzhoC3OkconsJ-33k,3230
+cidc_api/models/pydantic/stage1/treatment.py,sha256=C2xQ_fU0ZxGgBzes7hyHOHvicAzSjyva3Z5F78tor30,2244
 cidc_api/models/pydantic/stage1/trial.py,sha256=EFsMVMxxHbPeaBb6JG9JpX1qjtoho2t-GZnaI0gsYrY,1859
 cidc_api/models/pydantic/stage2/__init__.py,sha256=OQRG5wFkNsyAU_0KI1W5PDn8pBDe1EJDcgKZ19shh_g,2331
 cidc_api/models/pydantic/stage2/additional_treatment.py,sha256=TFVzjd1NPLSfH9UnL2W3aZhpZSzDsg97j9IK8t882YA,1050
@@ -154,13 +155,13 @@ cidc_api/shared/assay_handling.py,sha256=zzWSqQ-ddLVzX5IuHvsaSib2H1lnjXpo9Lbxaoq
 cidc_api/shared/auth.py,sha256=EIP9AKokLNrI79Fkpv3P7WdzaddJIsuGGICc1W494X0,9110
 cidc_api/shared/email_layout.html,sha256=pBoTNw3ACHH-ncZFaNvcy5bXMqPwizR78usb0uCYtIc,7670
 cidc_api/shared/emails.py,sha256=8kNFEaSnKpY-GX_iE59QUhSp3c4_uzy3SpHYt2QjuqI,6121
-cidc_api/shared/file_handling.py,sha256=ObsLvBrkwHo6Nv48GvFXDKElNNl4inGpxv--001H_xc,5843
-cidc_api/shared/gcloud_client.py,sha256=0B13MRF_CUMbzaKtKVDd9fxErNdNGBpxfkknQ5deu7w,39972
+cidc_api/shared/file_handling.py,sha256=9MZXx5RfXO3A_pXf8Ulb7DQEuyp9j12eO9ad-PcTBXo,5908
+cidc_api/shared/gcloud_client.py,sha256=7q6CWpAZdqSJoAkMpm9Rw7yFwNLIk6D9WZGJeTOwo54,40113
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
 cidc_api/shared/utils.py,sha256=-gLnzxCR9E6h0plt2xrNisUG5_Y6GhhVwz3DgDIzpvs,367
-nci_cidc_api_modules-1.2.48.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.48.dist-info/METADATA,sha256=nsHP8cxYPyO_ut25JYyLy3TDef7eeuorTsJFFSqMc-w,40301
-nci_cidc_api_modules-1.2.48.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.48.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
-nci_cidc_api_modules-1.2.48.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.49.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.49.dist-info/METADATA,sha256=vy1hCgQ0v8NmAfY8w71VOrXET5k9u95FmpAUJb-vxHQ,40301
+nci_cidc_api_modules-1.2.49.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+nci_cidc_api_modules-1.2.49.dist-info/top_level.txt,sha256=BSJqF6ura8-bWCKZvarvQEKvidMM05lH0bLQsNOrI0o,14
+nci_cidc_api_modules-1.2.49.dist-info/RECORD,,

{nci_cidc_api_modules-1.2.48.dist-info → nci_cidc_api_modules-1.2.49.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.1)
 Root-Is-Purelib: true
 Tag: py3-none-any