nci-cidc-api-modules 1.2.54__py3-none-any.whl → 1.2.56__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- boot.py +8 -0
- cidc_api/__init__.py +1 -1
- cidc_api/models/dataset.py +80 -0
- cidc_api/models/db/stage1/additional_treatment_orm.py +8 -1
- cidc_api/models/db/stage1/adverse_event_orm.py +8 -1
- cidc_api/models/db/stage1/baseline_clinical_assessment_orm.py +8 -1
- cidc_api/models/db/stage1/comorbidity_orm.py +8 -1
- cidc_api/models/db/stage1/consent_group_orm.py +6 -6
- cidc_api/models/db/stage1/demographic_orm.py +8 -1
- cidc_api/models/db/stage1/disease_orm.py +8 -1
- cidc_api/models/db/stage1/exposure_orm.py +8 -1
- cidc_api/models/db/stage1/gvhd_diagnosis_acute_orm.py +8 -3
- cidc_api/models/db/stage1/gvhd_diagnosis_chronic_orm.py +8 -3
- cidc_api/models/db/stage1/gvhd_organ_acute_orm.py +8 -1
- cidc_api/models/db/stage1/gvhd_organ_chronic_orm.py +8 -1
- cidc_api/models/db/stage1/medical_history_orm.py +8 -1
- cidc_api/models/db/stage1/other_malignancy_orm.py +8 -1
- cidc_api/models/db/stage1/participant_orm.py +4 -5
- cidc_api/models/db/stage1/prior_treatment_orm.py +8 -2
- cidc_api/models/db/stage1/radiotherapy_dose_orm.py +8 -1
- cidc_api/models/db/stage1/response_by_system_orm.py +8 -1
- cidc_api/models/db/stage1/response_orm.py +9 -2
- cidc_api/models/db/stage1/specimen_orm.py +9 -25
- cidc_api/models/db/stage1/stem_cell_transplant_orm.py +8 -1
- cidc_api/models/db/stage1/surgery_orm.py +8 -1
- cidc_api/models/db/stage1/therapy_agent_dose_orm.py +8 -1
- cidc_api/models/db/stage1/treatment_orm.py +8 -1
- cidc_api/models/db/stage1/trial_orm.py +1 -2
- cidc_api/models/db/stage2/additional_treatment_orm.py +8 -1
- cidc_api/models/db/stage2/administrative_person_orm.py +8 -1
- cidc_api/models/db/stage2/administrative_role_assignment_orm.py +1 -0
- cidc_api/models/db/stage2/adverse_event_orm.py +8 -1
- cidc_api/models/db/stage2/arm_orm.py +5 -4
- cidc_api/models/db/stage2/baseline_clinical_assessment_orm.py +8 -1
- cidc_api/models/db/stage2/cohort_orm.py +5 -4
- cidc_api/models/db/stage2/comorbidity_orm.py +8 -1
- cidc_api/models/db/stage2/consent_group_orm.py +5 -5
- cidc_api/models/db/stage2/contact_orm.py +10 -1
- cidc_api/models/db/stage2/demographic_orm.py +8 -1
- cidc_api/models/db/stage2/disease_orm.py +8 -1
- cidc_api/models/db/stage2/exposure_orm.py +8 -1
- cidc_api/models/db/stage2/file_orm.py +4 -4
- cidc_api/models/db/stage2/gvhd_diagnosis_acute_orm.py +8 -3
- cidc_api/models/db/stage2/gvhd_diagnosis_chronic_orm.py +8 -3
- cidc_api/models/db/stage2/gvhd_organ_acute_orm.py +8 -1
- cidc_api/models/db/stage2/gvhd_organ_chronic_orm.py +8 -1
- cidc_api/models/db/stage2/institution_orm.py +4 -4
- cidc_api/models/db/stage2/medical_history_orm.py +8 -1
- cidc_api/models/db/stage2/other_clinical_endpoint_orm.py +9 -1
- cidc_api/models/db/stage2/other_malignancy_orm.py +8 -1
- cidc_api/models/db/stage2/participant_orm.py +6 -6
- cidc_api/models/db/stage2/prior_treatment_orm.py +9 -3
- cidc_api/models/db/stage2/publication_orm.py +5 -4
- cidc_api/models/db/stage2/radiotherapy_dose_orm.py +9 -2
- cidc_api/models/db/stage2/response_by_system_orm.py +8 -1
- cidc_api/models/db/stage2/response_orm.py +9 -2
- cidc_api/models/db/stage2/shipment_orm.py +5 -5
- cidc_api/models/db/stage2/shipment_specimen_orm.py +8 -2
- cidc_api/models/db/stage2/specimen_orm.py +9 -75
- cidc_api/models/db/stage2/stem_cell_transplant_orm.py +8 -1
- cidc_api/models/db/stage2/surgery_orm.py +8 -1
- cidc_api/models/db/stage2/therapy_agent_dose_orm.py +8 -1
- cidc_api/models/db/stage2/treatment_orm.py +8 -1
- cidc_api/models/db/stage2/trial_orm.py +1 -2
- cidc_api/models/pydantic/stage1/response_by_system.py +62 -0
- cidc_api/models/pydantic/stage1/trial.py +1 -1
- cidc_api/models/pydantic/stage2/adverse_event.py +52 -25
- cidc_api/models/pydantic/stage2/comorbidity.py +15 -8
- cidc_api/models/pydantic/stage2/demographic.py +45 -28
- cidc_api/models/pydantic/stage2/disease.py +100 -58
- cidc_api/models/pydantic/stage2/exposure.py +14 -8
- cidc_api/models/pydantic/stage2/medical_history.py +15 -8
- cidc_api/models/pydantic/stage2/other_malignancy.py +17 -11
- cidc_api/models/pydantic/stage2/participant.py +27 -15
- cidc_api/models/pydantic/stage2/prior_treatment.py +2 -0
- cidc_api/models/pydantic/stage2/radiotherapy_dose.py +27 -14
- cidc_api/models/pydantic/stage2/response.py +42 -23
- cidc_api/models/pydantic/stage2/response_by_system.py +138 -30
- cidc_api/models/pydantic/stage2/specimen.py +2 -185
- cidc_api/models/pydantic/stage2/surgery.py +15 -7
- cidc_api/models/pydantic/stage2/therapy_agent_dose.py +27 -14
- cidc_api/models/pydantic/stage2/treatment.py +30 -16
- cidc_api/telemetry.py +13 -13
- {nci_cidc_api_modules-1.2.54.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/METADATA +1 -1
- nci_cidc_api_modules-1.2.56.dist-info/RECORD +163 -0
- cidc_api/models/data.py +0 -28
- nci_cidc_api_modules-1.2.54.dist-info/RECORD +0 -163
- {nci_cidc_api_modules-1.2.54.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/WHEEL +0 -0
- {nci_cidc_api_modules-1.2.54.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_api_modules-1.2.54.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/top_level.txt +0 -0
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from
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from pydantic import NonNegativeInt, model_validator
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from pydantic import NonNegativeInt
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from cidc_api.models.pydantic.base import Base
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from cidc_api.code_systems.ctcae import is_ctcae_other_term
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from cidc_api.models.pydantic.base import forced_validator, forced_validators
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from cidc_api.models.errors import ValueLocError
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from cidc_api.models.types import (
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CTCAEEventTerm,
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CTCAEEventCode,
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SystemOrganClass,
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AttributionCause,
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AttributionLikelihood,
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YNU,
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YN,
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YNU,
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)
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@forced_validators
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class AdverseEvent(Base):
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__data_category__ = "adverse_event"
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__cardinality__ = "many"
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# The individual therapy (therapy agent, radiotherapy, surgery, stem cell transplant) in the treatment that is attributed to the adverse event.
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individual_therapy: str | None = None
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@classmethod
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def validate_term_and_code_cr(cls, data, info) -> None:
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event_code = data.get("event_code", None)
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event_term = data.get("event_term", None)
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if not event_term and not event_code:
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raise ValueLocError(
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"Please provide event_term or event_code or both",
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loc="event_term,event_code",
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)
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@forced_validator
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@classmethod
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def validate_event_other_specify_cr(cls, data, info) -> None:
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event_other_specify = data.get("event_other_specify", None)
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severity_grade_system = data.get("severity_grade_system", None)
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event_term = data.get("event_term", None)
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if severity_grade_system == "CTCAE" and is_ctcae_other_term(event_term) and not event_other_specify:
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raise ValueLocError(
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'If severity_grade_system is "CTCAE" and the event_code or event_term are of type '
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'"Other, specify", please provide event_other_specify',
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loc="event_other_specify",
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@forced_validator
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@classmethod
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def validate_system_organ_class_cr(cls, data, info) -> None:
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event_other_specify = data.get("event_other_specify", None)
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system_organ_class = data.get("system_organ_class", None)
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if event_other_specify and not system_organ_class:
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raise ValueLocError(
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"If event_other_specify is provided, please provide system_organ_class.", loc="system_organ_class"
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@classmethod
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def validate_days_to_resolution_of_event_chronology(cls, data, info) -> None:
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days_to_onset_of_event = data.get("days_to_onset_of_event", None)
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days_to_resolution_of_event = data.get("days_to_resolution_of_event", None)
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if days_to_resolution_of_event is not None and days_to_onset_of_event is not None:
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raise ValueLocError(
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'Violate "days_to_onset_of_event" <= "days_to_resolution_of_event"',
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from typing import Any
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class Comorbidity(Base):
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def validate_code_or_term_or_other_cr(cls, data, info) -> None:
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# CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=2681552%20and%20ver_nr=1
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def validate_age_at_enrollment_cr(cls, data, info) -> None:
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from
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extramedullary_organ: Annotated[List[UberonAnatomicalTerm] | None, BeforeValidator(Base.split_list)] = []
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def validate_code_or_term_or_description_cr(cls, data, info) -> None:
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def validate_cancer_stage_system_version(cls, data, info) -> None:
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CancerStageSystemVersionFIGO
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def validate_cancer_stage_system_version_cr(cls, data, info) -> None:
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f'Please provide cancer_stage_system_version when cancer_stage_system is "{cancer_stage_system}"',
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loc="cancer_stage_system_version",
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)
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def validate_cancer_stage_cr(cls, data, info) -> None:
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|
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raise ValueLocError(
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f'Please provide cancer_stage when cancer_stage_system is "{cancer_stage_system}"',
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loc="cancer_stage",
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)
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@classmethod
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def validate_t_category_cr(cls, data, info) -> None:
|
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|
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+
t_category = data.get("t_category", None)
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+
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|
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raise ValueLocError(
|
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f'Please provide t_category when cancer_stage_system is "{cancer_stage_system}"',
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loc="t_category",
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)
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@
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def
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@
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def
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@
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def validate_extramedullary_organ_cr(
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+
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+
@forced_validator
|
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@classmethod
|
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168
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+
def validate_n_category_cr(cls, data, info) -> None:
|
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+
cancer_stage_system = data.get("cancer_stage_system", None)
|
|
170
|
+
n_category = data.get("n_category", None)
|
|
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|
+
|
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172
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+
if cancer_stage_system == "AJCC" and not n_category:
|
|
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+
raise ValueLocError(
|
|
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|
+
f'Please provide n_category when cancer_stage_system is "{cancer_stage_system}"',
|
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+
loc="n_category",
|
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+
)
|
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+
|
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+
@forced_validator
|
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+
@classmethod
|
|
180
|
+
def validate_m_category_cr(cls, data, info) -> None:
|
|
181
|
+
cancer_stage_system = data.get("cancer_stage_system", None)
|
|
182
|
+
m_category = data.get("m_category", None)
|
|
183
|
+
|
|
184
|
+
if cancer_stage_system == "AJCC" and not m_category:
|
|
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|
+
raise ValueLocError(
|
|
186
|
+
f'Please provide m_category when cancer_stage_system is "{cancer_stage_system}"',
|
|
187
|
+
loc="m_category",
|
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|
+
)
|
|
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|
+
|
|
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|
+
@forced_validator
|
|
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|
+
@classmethod
|
|
192
|
+
def validate_extramedullary_organ_cr(cls, data, info) -> None:
|
|
193
|
+
solely_extramedullary_disease = data.get("solely_extramedullary_disease", None)
|
|
194
|
+
extramedullary_organ = data.get("extramedullary_organ", None)
|
|
195
|
+
|
|
196
|
+
if solely_extramedullary_disease in ["No", "Unknown"] and extramedullary_organ:
|
|
197
|
+
raise ValueLocError(
|
|
198
|
+
"If solely_extramedullary_disease indicates no disease, please leave extramedullary_organ blank.",
|
|
199
|
+
loc="extramedullary_organ",
|
|
157
200
|
)
|
|
158
|
-
return self
|
|
@@ -1,11 +1,11 @@
|
|
|
1
|
-
from
|
|
2
|
-
|
|
3
|
-
from pydantic import model_validator
|
|
1
|
+
from cidc_api.models.pydantic.base import forced_validator, forced_validators
|
|
4
2
|
|
|
3
|
+
from cidc_api.models.errors import ValueLocError
|
|
5
4
|
from cidc_api.models.pydantic.base import Base
|
|
6
5
|
from cidc_api.models.types import YNU, ExposureType
|
|
7
6
|
|
|
8
7
|
|
|
8
|
+
@forced_validators
|
|
9
9
|
class Exposure(Base):
|
|
10
10
|
__data_category__ = "exposure"
|
|
11
11
|
__cardinality__ = "many"
|
|
@@ -25,8 +25,14 @@ class Exposure(Base):
|
|
|
25
25
|
# CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15753203%20and%20ver_nr=1
|
|
26
26
|
exposure_type: ExposureType | None = None
|
|
27
27
|
|
|
28
|
-
@
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
28
|
+
@forced_validator
|
|
29
|
+
@classmethod
|
|
30
|
+
def validate_exposure_type_cr(cls, data, info) -> None:
|
|
31
|
+
carcinogen_exposure = data.get("carcinogen_exposure", None)
|
|
32
|
+
exposure_type = data.get("exposure_type", None)
|
|
33
|
+
|
|
34
|
+
if carcinogen_exposure in ["No", "Unknown"] and exposure_type:
|
|
35
|
+
raise ValueLocError(
|
|
36
|
+
"If carcinogen_exposure indicates non exposure, please leave exposure_type blank.",
|
|
37
|
+
loc="exposure_type",
|
|
38
|
+
)
|
|
@@ -1,11 +1,12 @@
|
|
|
1
|
-
from
|
|
2
|
-
|
|
3
|
-
from pydantic import NonNegativeInt, PositiveFloat, model_validator
|
|
1
|
+
from pydantic import NonNegativeInt, PositiveFloat
|
|
2
|
+
from cidc_api.models.pydantic.base import forced_validator, forced_validators
|
|
4
3
|
|
|
4
|
+
from cidc_api.models.errors import ValueLocError
|
|
5
5
|
from cidc_api.models.pydantic.base import Base
|
|
6
6
|
from cidc_api.models.types import TobaccoSmokingStatus
|
|
7
7
|
|
|
8
8
|
|
|
9
|
+
@forced_validators
|
|
9
10
|
class MedicalHistory(Base):
|
|
10
11
|
__data_category__ = "medical_history"
|
|
11
12
|
__cardinality__ = "one"
|
|
@@ -29,8 +30,14 @@ class MedicalHistory(Base):
|
|
|
29
30
|
# CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=16089302%20and%20ver_nr=1
|
|
30
31
|
num_prior_systemic_therapies: NonNegativeInt | None = None
|
|
31
32
|
|
|
32
|
-
@
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
|
|
33
|
+
@forced_validator
|
|
34
|
+
@classmethod
|
|
35
|
+
def validate_pack_years_smoked_cr(cls, data, info) -> None:
|
|
36
|
+
tobacco_smoking_status = data.get("tobacco_smoking_status", None)
|
|
37
|
+
pack_years_smoked = data.get("pack_years_smoked", None)
|
|
38
|
+
|
|
39
|
+
if tobacco_smoking_status in ["Never Smoker", "Unknown", "Not reported"] and pack_years_smoked:
|
|
40
|
+
raise ValueLocError(
|
|
41
|
+
"If tobacco_smoking_status indicates non-smoker, please leave pack_years_smoked blank.",
|
|
42
|
+
loc="pack_years_smoked",
|
|
43
|
+
)
|
|
@@ -1,11 +1,12 @@
|
|
|
1
|
-
from
|
|
2
|
-
|
|
3
|
-
from pydantic import NonPositiveInt, model_validator
|
|
1
|
+
from pydantic import NonPositiveInt
|
|
2
|
+
from cidc_api.models.pydantic.base import forced_validator, forced_validators
|
|
4
3
|
|
|
4
|
+
from cidc_api.models.errors import ValueLocError
|
|
5
5
|
from cidc_api.models.pydantic.base import Base
|
|
6
6
|
from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
|
|
7
7
|
|
|
8
8
|
|
|
9
|
+
@forced_validators
|
|
9
10
|
class OtherMalignancy(Base):
|
|
10
11
|
__data_category__ = "other_malignancy"
|
|
11
12
|
__cardinality__ = "many"
|
|
@@ -36,14 +37,19 @@ class OtherMalignancy(Base):
|
|
|
36
37
|
# Indicates the participant’s current clinical state regarding the cancer diagnosis.
|
|
37
38
|
other_malignancy_status: MalignancyStatus | None = None
|
|
38
39
|
|
|
39
|
-
@
|
|
40
|
-
|
|
40
|
+
@forced_validator
|
|
41
|
+
@classmethod
|
|
42
|
+
def validate_code_or_term_or_description_cr(cls, data, info) -> None:
|
|
43
|
+
other_malignancy_morphological_term = data.get("other_malignancy_morphological_term", None)
|
|
44
|
+
other_malignancy_description = data.get("other_malignancy_description", None)
|
|
45
|
+
other_malignancy_morphological_code = data.get("other_malignancy_morphological_code", None)
|
|
46
|
+
|
|
41
47
|
if (
|
|
42
|
-
not
|
|
43
|
-
and not
|
|
44
|
-
and not
|
|
48
|
+
not other_malignancy_morphological_code
|
|
49
|
+
and not other_malignancy_morphological_term
|
|
50
|
+
and not other_malignancy_description
|
|
45
51
|
):
|
|
46
|
-
raise
|
|
47
|
-
'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".'
|
|
52
|
+
raise ValueLocError(
|
|
53
|
+
'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".',
|
|
54
|
+
loc="other_malignancy_morphological_code",
|
|
48
55
|
)
|
|
49
|
-
return self
|
|
@@ -1,12 +1,12 @@
|
|
|
1
|
-
from
|
|
2
|
-
|
|
3
|
-
from pydantic import model_validator
|
|
1
|
+
from cidc_api.models.pydantic.base import forced_validator, forced_validators
|
|
4
2
|
|
|
3
|
+
from cidc_api.models.errors import ValueLocError
|
|
5
4
|
from cidc_api.models.pydantic.base import Base
|
|
6
5
|
from cidc_api.models.types import YNU
|
|
7
6
|
from cidc_api.models.types import OffStudyReason
|
|
8
7
|
|
|
9
8
|
|
|
9
|
+
@forced_validators
|
|
10
10
|
class Participant(Base):
|
|
11
11
|
__data_category__ = "participant"
|
|
12
12
|
__cardinality__ = "one"
|
|
@@ -16,7 +16,7 @@ class Participant(Base):
|
|
|
16
16
|
participant_id: str | None = None
|
|
17
17
|
|
|
18
18
|
# The participant identifier assigned by the clinical trial team overseeing the study
|
|
19
|
-
native_participant_id: str
|
|
19
|
+
native_participant_id: str | None = None
|
|
20
20
|
|
|
21
21
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# The globally unique participant identifier assigned by the CIMAC network. e.g. C8P29A7
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cimac_participant_id: str | None = None
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@@ -38,14 +38,26 @@ class Participant(Base):
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38
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# Additional information if "Other" is selected for off_study_reason. e.g. "Transfer to another study"
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off_study_reason_other: str | None = None
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40
40
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41
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-
@
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42
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-
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43
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-
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44
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-
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45
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-
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-
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-
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48
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-
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49
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-
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50
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-
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51
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-
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41
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+
@forced_validator
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42
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+
@classmethod
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43
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+
def off_study_reason_cr(cls, data, info) -> None:
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44
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+
off_study = data.get("off_study", None)
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45
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+
off_study_reason = data.get("off_study_reason", None)
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46
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+
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47
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+
if off_study == "Yes" and not off_study_reason:
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48
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+
raise ValueLocError(
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49
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+
'If "off_study" is "Yes" then "off_study_reason" is required.',
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50
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+
loc="off_study_reason",
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51
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+
)
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52
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+
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53
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+
@forced_validator
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54
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+
@classmethod
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55
|
+
def off_study_reason_other_cr(cls, data, info) -> None:
|
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56
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+
off_study_reason_other = data.get("off_study_reason_other", None)
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57
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+
off_study_reason = data.get("off_study_reason", None)
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|
58
|
+
|
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59
|
+
if off_study_reason == "Other" and not off_study_reason_other:
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60
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+
raise ValueLocError(
|
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61
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+
'If "off_study_reason" is "Other" then "off_study_reason_other" is required.',
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62
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+
loc="off_study_reason_other",
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63
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+
)
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@@ -24,6 +24,8 @@ class PriorTreatment(Base):
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24
24
|
# the treatment modality.
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25
25
|
prior_treatment_days_to_end: NonPositiveInt | None = None
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26
26
|
|
|
27
|
+
# Specifies the category or kind of prior treatment modality a participant received.
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28
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+
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27
29
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# Description of the prior treatment such as its full generic name if it is a type of therapy agent,
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28
30
|
# radiotherapy procedure name and location, or surgical procedure name and location.
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|
29
31
|
prior_treatment_description: str
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