nci-cidc-api-modules 1.2.50__py3-none-any.whl → 1.2.52__py3-none-any.whl

cidc_api/models/pydantic/stage1/other_malignancy.py

@@ -1,12 +1,12 @@
-from typing import Self
-
-from pydantic import NonPositiveInt, model_validator
+from pydantic import NonPositiveInt
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 
+@forced_validators
 class OtherMalignancy(Base):
     __data_category__ = "other_malignancy"
     __cardinality__ = "many"
@@ -37,15 +37,19 @@ class OtherMalignancy(Base):
     # Indicates the participant’s current clinical state regarding the cancer diagnosis.
     other_malignancy_status: MalignancyStatus | None = None
 
-    @model_validator(mode="after")
-    def validate_code_or_term_or_description_cr(self) -> Self:
+    @forced_validator
+    @classmethod
+    def validate_code_or_term_or_description_cr(cls, data, info) -> None:
+        other_malignancy_morphological_term = data.get("other_malignancy_morphological_term", None)
+        other_malignancy_description = data.get("other_malignancy_description", None)
+        other_malignancy_morphological_code = data.get("other_malignancy_morphological_code", None)
+
         if (
-            not self.other_malignancy_morphological_code
-            and not self.other_malignancy_morphological_term
-            and not self.other_malignancy_description
+            not other_malignancy_morphological_code
+            and not other_malignancy_morphological_term
+            and not other_malignancy_description
         ):
             raise ValueLocError(
                 'Please provide at least one of "morphological_code", "morphological_term" or "malignancy_description".',
-                loc="morphological_code",
+                loc="other_malignancy_morphological_code",
             )
-        return self

cidc_api/models/pydantic/stage1/participant.py

@@ -1,6 +1,4 @@
-from typing import Self
-
-from pydantic import model_validator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
@@ -8,6 +6,7 @@ from cidc_api.models.types import YNU
 from cidc_api.models.types import OffStudyReason
 
 
+@forced_validators
 class Participant(Base):
     __data_category__ = "participant"
     __cardinality__ = "one"
@@ -39,20 +38,26 @@ class Participant(Base):
     # Additional information if "Other" is selected for off_study_reason. e.g. "Transfer to another study"
     off_study_reason_other: str | None = None
 
-    @model_validator(mode="after")
-    def off_study_reason_cr(self) -> Self:
-        if self.off_study == "Yes" and not self.off_study_reason:
+    @forced_validator
+    @classmethod
+    def off_study_reason_cr(cls, data, info) -> None:
+        off_study = data.get("off_study", None)
+        off_study_reason = data.get("off_study_reason", None)
+
+        if off_study == "Yes" and not off_study_reason:
             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:
+    @forced_validator
+    @classmethod
+    def off_study_reason_other_cr(cls, data, info) -> None:
+        off_study_reason_other = data.get("off_study_reason_other", None)
+        off_study_reason = data.get("off_study_reason", None)
+
+        if off_study_reason == "Other" and not off_study_reason_other:
             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

@@ -1,6 +1,5 @@
-from typing import Self
-
-from pydantic import NonNegativeInt, NonNegativeFloat, model_validator
+from pydantic import NonNegativeInt, NonNegativeFloat
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
@@ -13,6 +12,7 @@ from cidc_api.models.types import (
 )
 
 
+@forced_validators
 class RadiotherapyDose(Base):
     __data_category__ = "radiotherapy_dose"
     __cardinality__ = "many"
@@ -67,20 +67,26 @@ class RadiotherapyDose(Base):
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=7063755%20and%20ver_nr=1
     radiation_extent: RadiationExtent
 
-    @model_validator(mode="after")
-    def validate_changes_delays_description_cr(self) -> Self:
-        if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
+    @forced_validator
+    @classmethod
+    def validate_changes_delays_description_cr(cls, data, info) -> None:
+        dose_changes_delays = data.get("dose_changes_delays", None)
+        changes_delays_description = data.get("changes_delays_description", None)
+
+        if dose_changes_delays == "Yes" and not 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:
+    @forced_validator
+    @classmethod
+    def validate_planned_dose_units_cr(cls, data, info) -> None:
+        planned_dose = data.get("planned_dose", None)
+        planned_dose_units = data.get("planned_dose_units", None)
+
+        if planned_dose and not 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

@@ -1,12 +1,12 @@
-from typing import Self
-
-from pydantic import NonNegativeInt, model_validator
+from pydantic import NonNegativeInt
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 
 
+@forced_validators
 class Response(Base):
     __data_category__ = "response"
     __cardinality__ = "one"
@@ -47,29 +47,38 @@ class Response(Base):
     # Days from enrollment date to the last time the patient's vital status was verified.
     days_to_last_vital_status: NonNegativeInt | None = None
 
-    @model_validator(mode="after")
-    def validate_cause_of_death_cr(self) -> Self:
-        if self.survival_status == "Dead" and not self.cause_of_death:
+    @forced_validator
+    @classmethod
+    def validate_cause_of_death_cr(cls, data, info) -> None:
+        survival_status = data.get("survival_status", None)
+        cause_of_death = data.get("cause_of_death", None)
+
+        if survival_status == "Dead" and not cause_of_death:
             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:
+    @forced_validator
+    @classmethod
+    def validate_cause_of_death_cr2(cls, data, info) -> None:
+        survival_status = data.get("survival_status", None)
+        cause_of_death = data.get("cause_of_death", None)
+
+        if survival_status == "Alive" and cause_of_death:
             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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_death_cr(cls, data, info) -> None:
+        survival_status = data.get("survival_status", None)
+        days_to_death = data.get("days_to_death", None)
+
+        if survival_status in ["Alive", "Unknown"] and days_to_death:
             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

@@ -1,6 +1,7 @@
 from typing import Self
 
-from pydantic import PositiveInt, model_validator, NonNegativeInt
+from pydantic import PositiveInt, NonNegativeInt, model_validator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
@@ -19,6 +20,7 @@ negative_response_values = [
 ]
 
 
+@forced_validators
 class ResponseBySystem(Base):
     __data_category__ = "response_by_system"
     __cardinality__ = "many"
@@ -71,90 +73,117 @@ class ResponseBySystem(Base):
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5143957%20and%20ver_nr=1
     progression_free_survival: PositiveInt | None = None
 
-    @model_validator(mode="after")
-    def validate_response_duration_cr(self) -> Self:
-        if self.best_overall_response in negative_response_values and self.response_duration:
+    @forced_validator
+    @classmethod
+    def validate_response_duration_cr(cls, data, info) -> None:
+        best_overall_response = data.get("best_overall_response", None)
+        response_duration = data.get("response_duration", None)
+
+        if best_overall_response in negative_response_values and response_duration:
             raise ValueLocError(
                 "If best_overall_response does not indicate a positive response, "
                 "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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_first_response_cr(cls, data, info) -> None:
+        best_overall_response = data.get("best_overall_response", None)
+        days_to_first_response = data.get("days_to_first_response", None)
+
+        if best_overall_response in negative_response_values and days_to_first_response:
             raise ValueLocError(
                 "If best_overall_response does not indicate a positive response, "
                 "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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_best_response_cr(cls, data, info) -> None:
+        best_overall_response = data.get("best_overall_response", None)
+        days_to_best_response = data.get("days_to_best_response", None)
+
+        if best_overall_response in negative_response_values and days_to_best_response:
             raise ValueLocError(
-                "If best_overall_response does not indicate a positive response, \
-                please leave days_to_best_response blank.",
+                "If best_overall_response does not indicate a positive response, "
+                "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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_disease_progression_cr(cls, data, info) -> None:
+        progression = data.get("progression", None)
+        days_to_disease_progression = data.get("days_to_disease_progression", None)
+
+        if progression in ["No", "Unknown", "Not Applicable"] and days_to_disease_progression:
             raise ValueLocError(
-                "If progression does not indicate confirmed progression of the disease, \
-                please leave days_to_disease_progress blank.",
-                loc="days_to_disease_progress",
+                "If progression does not indicate confirmed progression of the disease, "
+                "please leave days_to_disease_progression blank.",
+                loc="days_to_disease_progression",
             )
-        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:
+    @forced_validator
+    @classmethod
+    def validate_progression_free_survival_cr(cls, data, info) -> None:
+        progression_free_survival_event = data.get("progression_free_survival_event", None)
+        progression_free_survival = data.get("progression_free_survival", None)
+
+        if progression_free_survival_event in ["Unknown", "Not Applicable"] and progression_free_survival:
             raise ValueLocError(
-                "If progression_free_survival_event is not known, \
-                please leave progression_free_survival blank.",
+                "If progression_free_survival_event is not known, " "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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_best_response_chronology(cls, data, info) -> None:
+        days_to_first_response = data.get("days_to_first_response", None)
+        days_to_best_response = data.get("days_to_best_response", None)
+
+        if days_to_best_response is not None and days_to_first_response is not None:
+            if int(days_to_best_response) < int(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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_disease_progression_chronology(cls, data, info) -> None:
+        days_to_disease_progression = data.get("days_to_disease_progression", None)
+        days_to_first_response = data.get("days_to_first_response", None)
+
+        if days_to_first_response is not None and days_to_disease_progression is not None:
+            if int(days_to_first_response) >= int(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:
+    @forced_validator
+    @classmethod
+    def validate_days_to_best_response_progression_chronology(cls, data, info) -> None:
+        days_to_disease_progression = data.get("days_to_disease_progression", None)
+        days_to_best_response = data.get("days_to_best_response", None)
+
+        if days_to_best_response is not None and days_to_disease_progression is not None:
+            if int(days_to_best_response) >= int(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:
+        if not self.response:
+            return self
+
+        if 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,
@@ -171,8 +200,11 @@ class ResponseBySystem(Base):
 
     @model_validator(mode="after")
     def validate_days_to_death_chronology(self) -> Self:
-        if not self.response or not self.response.days_to_death:
+        if not self.response:
             return self
+        if 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,
@@ -185,3 +217,4 @@ class ResponseBySystem(Base):
                 ">= 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",
             )
+        return self

cidc_api/models/pydantic/stage1/surgery.py

@@ -1,12 +1,13 @@
-from typing import Self
+from pydantic import NonNegativeInt
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
-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
 
 
+@forced_validators
 class Surgery(Base):
     __data_category__ = "surgery"
     __cardinality__ = "many"
@@ -43,11 +44,14 @@ class Surgery(Base):
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=13362284%20and%20ver_nr=1
     extent_of_residual_disease: str | None = None
 
-    @model_validator(mode="after")
-    def validate_procedure_other_cr(self) -> Self:
-        if self.procedure == "Other, specify" and not self.procedure_other:
+    @forced_validator
+    @classmethod
+    def validate_procedure_other_cr(cls, data, info) -> None:
+        procedure = data.get("procedure", None)
+        procedure_other = data.get("procedure_other", None)
+
+        if procedure == "Other, specify" and not 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

@@ -1,12 +1,12 @@
-from typing import Self
-
-from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat, model_validator
+from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, TherapyAgentDoseUnits
 
 
+@forced_validators
 class TherapyAgentDose(Base):
     __data_category__ = "therapy_agent_dose"
     __cardinality__ = "many"
@@ -55,20 +55,26 @@ class TherapyAgentDose(Base):
     # Description of the dose changes, misses, or delays.
     changes_delays_description: str | None = None
 
-    @model_validator(mode="after")
-    def validate_changes_delays_description_cr(self) -> Self:
-        if self.dose_changes_delays == "Yes" and not self.changes_delays_description:
+    @forced_validator
+    @classmethod
+    def validate_changes_delays_description_cr(cls, data, info) -> None:
+        dose_changes_delays = data.get("dose_changes_delays", None)
+        changes_delays_description = data.get("changes_delays_description", None)
+
+        if dose_changes_delays == "Yes" and not 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:
+    @forced_validator
+    @classmethod
+    def validate_planned_dose_units_cr(cls, data, info) -> None:
+        planned_dose = data.get("planned_dose", None)
+        planned_dose_units = data.get("planned_dose_units", None)
+
+        if planned_dose and not 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

@@ -1,12 +1,11 @@
-from typing import Self
-
-from pydantic import model_validator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
 from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, OffTreatmentReason
 
 
+@forced_validators
 class Treatment(Base):
     __data_category__ = "treatment"
     __cardinality__ = "many"
@@ -38,20 +37,28 @@ class Treatment(Base):
     # If "Other" is selected for "off_treatment_reason", provide a description of the reason.
     off_treatment_reason_other: str | None = None
 
-    @model_validator(mode="after")
-    def validate_off_treatment_reason_cr(self) -> Self:
-        if self.off_treatment == "Yes" and not self.off_treatment_reason:
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_cr(cls, data, info) -> None:
+        off_treatment = data.get("off_treatment", None)
+        off_treatment_reason = data.get("off_treatment_reason", None)
+
+        if off_treatment == "Yes" and not off_treatment_reason:
             raise ValueLocError(
                 'If off_treatment is "Yes", please provide off_treatment_reason.',
                 loc="off_treatment_reason",
             )
-        return self
+        return off_treatment_reason
+
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_other_cr(cls, data, info) -> None:
+        off_treatment_reason = data.get("off_treatment_reason", None)
+        off_treatment_reason_other = data.get("off_treatment_reason_other", None)
 
-    @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:
+        if off_treatment_reason == "Other" and not 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
+        return off_treatment_reason_other

cidc_api/shared/gcloud_client.py

@@ -61,6 +61,7 @@ from ..config.settings import (
     GOOGLE_HL_CLINICAL_VALIDATION_TOPIC,
     GOOGLE_DL_CLINICAL_VALIDATION_TOPIC,
     GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC,
+    GOOGLE_CLINICAL_DATA_INGESTION_PROCESSING_TOPIC,
     TESTING,
     ENV,
     IS_EMAIL_ON,
@@ -1067,6 +1068,12 @@ def publish_assay_metadata_validation(job_id: int) -> None:
     _report = _encode_and_publish(str(job_id), GOOGLE_ASSAY_METADATA_VALIDATION_TOPIC)
 
 
+def publish_clinical_data_ingestion(job_id: int) -> None:
+    """Start ingestion of clinical data job"""
+    # Start asynchronously
+    _report = _encode_and_publish(str(job_id), GOOGLE_CLINICAL_DATA_INGESTION_PROCESSING_TOPIC)
+
+
 def send_email(to_emails: List[str], subject: str, html_content: str, **kw) -> None:
     """
     Publish an email-to-send to the emails topic.

{nci_cidc_api_modules-1.2.50.dist-info → nci_cidc_api_modules-1.2.52.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.50
+Version: 1.2.52
 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
@@ -43,7 +43,7 @@ Requires-Dist: opentelemetry-instrumentation-requests>=0.59b0
 Requires-Dist: opentelemetry-instrumentation-sqlalchemy>=0.59b0
 Requires-Dist: opentelemetry-exporter-gcp-trace>=1.11.0
 Requires-Dist: opentelemetry-propagator-gcp>=1.11.0
-Requires-Dist: nci-cidc-schemas==0.28.11
+Requires-Dist: nci-cidc-schemas==0.28.12
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page