nci-cidc-api-modules 1.2.42__py3-none-any.whl → 1.2.44__py3-none-any.whl

cidc_api/__init__.py

@@ -1 +1 @@
-__version__ = "1.2.42"
+__version__ = "1.2.44"

cidc_api/models/data.py

@@ -11,9 +11,9 @@ standard_data_categories = [
 # A class to hold the representation of a trial's dataset all at once
 class Dataset(dict):
     def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
         for data_category in standard_data_categories:
             self[data_category] = []
+        super().__init__(*args, **kwargs)
 
 
 # Maps data categories like "treatment" to their associated pydantic model

cidc_api/models/db/stage1/additional_treatment_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.db.stage1.base_orm import BaseORM
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
     __repr_attrs__ = ["additional_treatment_id", "participant_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "additional_treatment"
 
     additional_treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/adverse_event_orm.py

@@ -20,7 +20,6 @@ from cidc_api.models.types import (
 class AdverseEventORM(BaseORM):
     __tablename__ = "adverse_event"
     __repr_attrs__ = ["adverse_event_id", "participant_id", "event_term"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "adverse_event"
 
     adverse_event_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/baseline_clinical_assessment_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import ECOGScore, KarnofskyScore
 class BaselineClinicalAssessmentORM(BaseORM):
     __tablename__ = "baseline_clinical_assessment"
     __repr_attrs__ = ["baseline_clinical_assessment_id", "participant_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "baseline_clinical_assessment"
 
     baseline_clinical_assessment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/comorbidity_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
 class ComorbidityORM(BaseORM):
     __tablename__ = "comorbidity"
     __repr_attrs__ = ["comorbidity_id", "comorbidity_term"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "comorbidity"
 
     comorbidity_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/consent_group_orm.py

@@ -15,7 +15,6 @@ class ConsentGroupORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage1.trial.trial_id", "stage1.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage1"},
     )
     __data_category__ = "consent_group"
 

cidc_api/models/db/stage1/demographic_orm.py

@@ -23,7 +23,6 @@ from cidc_api.models.types import (
 class DemographicORM(BaseORM):
     __tablename__ = "demographic"
     __repr_attrs__ = ["demographic_id", "participant_id", "age_at_enrollment", "sex"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "demographic"
 
     demographic_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/disease_orm.py

@@ -29,7 +29,6 @@ class DiseaseORM(BaseORM):
         "disease_id",
         "participant_id",
     ]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "disease"
 
     disease_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/exposure_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import YNU, ExposureType
 class ExposureORM(BaseORM):
     __tablename__ = "exposure"
     __repr_attrs__ = ["exposure_id", "exposure_type", "carcinogen_exposure"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "exposure"
 
     exposure_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/gvhd_diagnosis_acute_orm.py

@@ -17,7 +17,6 @@ class GVHDDiagnosisAcuteORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_acute"
     __table_args__ = (
         UniqueConstraint("participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_acute_pre_or_post"),
-        {"schema": "stage1"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
     __data_category__ = "gvhd_diagnosis_acute"

cidc_api/models/db/stage1/gvhd_diagnosis_chronic_orm.py

@@ -19,7 +19,6 @@ class GVHDDiagnosisChronicORM(BaseORM):
         UniqueConstraint(
             "participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_chronic_pre_or_post"
         ),
-        {"schema": "stage1"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
     __data_category__ = "gvhd_diagnosis_chronic"

cidc_api/models/db/stage1/gvhd_organ_acute_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import GVHDOrgan, GVHDOrganAcuteStage
 class GVHDOrganAcuteORM(BaseORM):
     __tablename__ = "gvhd_organ_acute"
     __repr_attrs__ = ["gvhd_organ_acute_id", "organ"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "gvhd_organ_acute"
 
     gvhd_organ_acute_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/gvhd_organ_chronic_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import GVHDOrgan, GVHDOrganChronicScore
 class GVHDOrganChronicORM(BaseORM):
     __tablename__ = "gvhd_organ_chronic"
     __repr_attrs__ = ["gvhd_organ_chronic_id", "organ"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "gvhd_organ_chronic"
 
     gvhd_organ_chronic_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/medical_history_orm.py

@@ -12,7 +12,6 @@ from cidc_api.models.types import TobaccoSmokingStatus
 class MedicalHistoryORM(BaseORM):
     __tablename__ = "medical_history"
     __repr_attrs__ = ["medical_history_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "medical_history"
 
     medical_history_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/other_malignancy_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode,
 class OtherMalignancyORM(BaseORM):
     __tablename__ = "other_malignancy"
     __repr_attrs__ = ["other_malignancy_id", "primary_disease_site"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "other_malignancy"
 
     other_malignancy_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/participant_orm.py

@@ -10,12 +10,11 @@ from cidc_api.models.types import OffStudyReason, YNU
 
 class ParticipantORM(BaseORM):
     __tablename__ = "participant"
-    __repr_attrs__ = ["native_participant_id", "cimac_participant_id"]
+    __repr_attrs__ = ["participant_id", "native_participant_id", "cimac_participant_id"]
     __table_args__ = (
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage1.trial.trial_id", "stage1.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage1"},
     )
     __data_category__ = "participant"
 

cidc_api/models/db/stage1/prior_treatment_orm.py

@@ -13,7 +13,6 @@ from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 class PriorTreatmentORM(BaseORM):
     __tablename__ = "prior_treatment"
     __repr_attrs__ = ["prior_treatment_id", "type"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "prior_treatment"
 
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/radiotherapy_dose_orm.py

@@ -17,7 +17,6 @@ from cidc_api.models.types import (
 class RadiotherapyDoseORM(BaseORM):
     __tablename__ = "radiotherapy_dose"
     __repr_attrs__ = ["radiotherapy_dose_id", "procedure"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "radiotherapy_dose"
 
     radiotherapy_dose_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/response_by_system_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOve
 class ResponseBySystemORM(BaseORM):
     __tablename__ = "response_by_system"
     __repr_attrs__ = ["response_by_system_id", "participant_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "response_by_system"
 
     response_by_system_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/response_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 class ResponseORM(BaseORM):
     __tablename__ = "response"
     __repr_attrs__ = ["response_id", "participant_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "response"
 
     response_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/specimen_orm.py

@@ -33,7 +33,6 @@ from cidc_api.models.types import (
 class SpecimenORM(BaseORM):
     __tablename__ = "specimen"
     __repr_attrs__ = ["specimen_id", "participant_id", "cimac_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "specimen"
 
     specimen_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/stem_cell_transplant_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import StemCellDonorType, AllogeneicDonorType, StemCe
 class StemCellTransplantORM(BaseORM):
     __tablename__ = "stem_cell_transplant"
     __repr_attrs__ = ["stem_cell_transplant_id"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "stem_cell_transplant"
 
     stem_cell_transplant_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/surgery_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
 class SurgeryORM(BaseORM):
     __tablename__ = "surgery"
     __repr_attrs__ = ["surgery_id", "procedure"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "surgery"
 
     surgery_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/therapy_agent_dose_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import TherapyAgentDoseUnits, YNU
 class TherapyAgentDoseORM(BaseORM):
     __tablename__ = "therapy_agent_dose"
     __repr_attrs__ = ["therapy_agent_dose_id", "therapy_agent_name"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "therapy_agent_dose"
 
     therapy_agent_dose_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/treatment_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import YNU, OffTreatmentReason
 class TreatmentORM(BaseORM):
     __tablename__ = "treatment"
     __repr_attrs__ = ["treatment_id", "participant_id", "treatment_description"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "treatment"
 
     treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage1/trial_orm.py

@@ -13,7 +13,6 @@ from cidc_api.models.types import PrimaryPurposeType, AgeGroup
 class TrialORM(BaseORM):
     __tablename__ = "trial"
     __repr_attrs__ = ["trial_id", "version"]
-    __table_args__ = {"schema": "stage1"}
     __data_category__ = "study"
 
     trial_id: Mapped[str] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/additional_treatment_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.db.stage2.base_orm import BaseORM
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
     __repr_attrs__ = ["additional_treatment_id", "participant_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "additional_treatment"
 
     additional_treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/administrative_person_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.db.stage2.base_orm import BaseORM
 class AdministrativePersonORM(BaseORM):
     __tablename__ = "administrative_person"
     __repr_attrs__ = ["first_name", "last_name"]
-    __table_args__ = {"schema": "stage2"}
 
     administrative_person_id: Mapped[int] = mapped_column(primary_key=True)
     institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/administrative_role_assignment_orm.py

@@ -13,7 +13,6 @@ class AdministrativeRoleAssignmentORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     trial_id: Mapped[str] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/adverse_event_orm.py

@@ -20,7 +20,6 @@ from cidc_api.models.types import (
 class AdverseEventORM(BaseORM):
     __tablename__ = "adverse_event"
     __repr_attrs__ = ["adverse_event_id", "participant_id", "event_term"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "adverse_event"
 
     adverse_event_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/arm_orm.py

@@ -12,7 +12,6 @@ class ArmORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     arm_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/baseline_clinical_assessment_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import ECOGScore, KarnofskyScore
 class BaselineClinicalAssessmentORM(BaseORM):
     __tablename__ = "baseline_clinical_assessment"
     __repr_attrs__ = ["baseline_clinical_assessment_id", "participant_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "baseline_clinical_assessment"
 
     baseline_clinical_assessment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/cohort_orm.py

@@ -12,7 +12,6 @@ class CohortORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     cohort_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/comorbidity_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
 class ComorbidityORM(BaseORM):
     __tablename__ = "comorbidity"
     __repr_attrs__ = ["comorbidity_id", "comorbidity_term"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "comorbidity"
 
     comorbidity_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/consent_group_orm.py

@@ -15,7 +15,6 @@ class ConsentGroupORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
     __data_category__ = "consent_group"
 

cidc_api/models/db/stage2/contact_orm.py

@@ -7,7 +7,6 @@ from cidc_api.models.db.stage2.base_orm import BaseORM
 
 class ContactORM(BaseORM):
     __tablename__ = "contact"
-    __table_args__ = {"schema": "stage2"}
 
     contact_id: Mapped[int] = mapped_column(primary_key=True)
     institution_id: Mapped[int] = mapped_column(ForeignKey("stage2.institution.institution_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/demographic_orm.py

@@ -23,7 +23,6 @@ from cidc_api.models.types import (
 class DemographicORM(BaseORM):
     __tablename__ = "demographic"
     __repr_attrs__ = ["demographic_id", "participant_id", "age_at_enrollment", "sex"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "demographic"
 
     demographic_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/disease_orm.py

@@ -29,7 +29,6 @@ class DiseaseORM(BaseORM):
         "disease_id",
         "participant_id",
     ]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "disease"
 
     disease_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/exposure_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import YNU, ExposureType
 class ExposureORM(BaseORM):
     __tablename__ = "exposure"
     __repr_attrs__ = ["exposure_id", "exposure_type", "carcinogen_exposure"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "exposure"
 
     exposure_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/file_orm.py

@@ -14,7 +14,6 @@ class FileORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     file_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/gvhd_diagnosis_acute_orm.py

@@ -17,7 +17,6 @@ class GVHDDiagnosisAcuteORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_acute"
     __table_args__ = (
         UniqueConstraint("participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_acute_pre_or_post"),
-        {"schema": "stage2"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
     __data_category__ = "gvhd_diagnosis_acute"

cidc_api/models/db/stage2/gvhd_diagnosis_chronic_orm.py

@@ -19,7 +19,6 @@ class GVHDDiagnosisChronicORM(BaseORM):
         UniqueConstraint(
             "participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_chronic_pre_or_post"
         ),
-        {"schema": "stage2"},
     )
     __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
     __data_category__ = "gvhd_diagnosis_chronic"

cidc_api/models/db/stage2/gvhd_organ_acute_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import GVHDOrgan, GVHDOrganAcuteStage
 class GVHDOrganAcuteORM(BaseORM):
     __tablename__ = "gvhd_organ_acute"
     __repr_attrs__ = ["gvhd_organ_acute_id", "organ"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "gvhd_organ_acute"
 
     gvhd_organ_acute_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/gvhd_organ_chronic_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import GVHDOrgan, GVHDOrganChronicScore
 class GVHDOrganChronicORM(BaseORM):
     __tablename__ = "gvhd_organ_chronic"
     __repr_attrs__ = ["gvhd_organ_chronic_id", "organ"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "gvhd_organ_chronic"
 
     gvhd_organ_chronic_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/institution_orm.py

@@ -14,7 +14,6 @@ class InstitutionORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     institution_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/medical_history_orm.py

@@ -12,7 +12,6 @@ from cidc_api.models.types import TobaccoSmokingStatus
 class MedicalHistoryORM(BaseORM):
     __tablename__ = "medical_history"
     __repr_attrs__ = ["medical_history_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "medical_history"
 
     medical_history_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/other_clinical_endpoint_orm.py

@@ -9,7 +9,6 @@ from cidc_api.models.types import YNU, ResponseSystem, ResponseSystemVersion
 class OtherClinicalEndpointORM(BaseORM):
     __tablename__ = "other_clinical_endpoint"
     __repr_attrs__ = ["other_clinical_endpoint_id", "name", "event"]
-    __table_args__ = {"schema": "stage2"}
 
     other_clinical_endpoint_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/other_malignancy_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode,
 class OtherMalignancyORM(BaseORM):
     __tablename__ = "other_malignancy"
     __repr_attrs__ = ["other_malignancy_id", "primary_disease_site"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "other_malignancy"
 
     other_malignancy_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/participant_orm.py

@@ -14,7 +14,6 @@ class ParticipantORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
     __data_category__ = "participant"
 

cidc_api/models/db/stage2/prior_treatment_orm.py

@@ -13,7 +13,6 @@ from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 class PriorTreatmentORM(BaseORM):
     __tablename__ = "prior_treatment"
     __repr_attrs__ = ["prior_treatment_id", "type"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "prior_treatment"
 
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/publication_orm.py

@@ -13,7 +13,6 @@ class PublicationORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     publication_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/radiotherapy_dose_orm.py

@@ -17,7 +17,6 @@ from cidc_api.models.types import (
 class RadiotherapyDoseORM(BaseORM):
     __tablename__ = "radiotherapy_dose"
     __repr_attrs__ = ["radiotherapy_dose_id", "procedure"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "radiotherapy_dose"
 
     radiotherapy_dose_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/response_by_system_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOve
 class ResponseBySystemORM(BaseORM):
     __tablename__ = "response_by_system"
     __repr_attrs__ = ["response_by_system_id", "participant_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "response_by_system"
 
     response_by_system_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/response_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath
 class ResponseORM(BaseORM):
     __tablename__ = "response"
     __repr_attrs__ = ["response_id", "participant_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "response"
 
     response_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/shipment_orm.py

@@ -16,7 +16,6 @@ class ShipmentORM(BaseORM):
         ForeignKeyConstraint(
             ["trial_id", "version"], ["stage2.trial.trial_id", "stage2.trial.version"], ondelete="CASCADE"
         ),
-        {"schema": "stage2"},
     )
 
     shipment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/shipment_specimen_orm.py

@@ -10,7 +10,6 @@ from cidc_api.models.db.stage2.base_orm import BaseORM
 class ShipmentSpecimenORM(BaseORM):
     __tablename__ = "shipment_specimen"
     __repr_attrs__ = ["specimen_id", "shipment_id"]
-    __table_args__ = {"schema": "stage2"}
 
     specimen_id: Mapped[int] = mapped_column(
         ForeignKey("stage2.specimen.specimen_id", ondelete="CASCADE"), primary_key=True

cidc_api/models/db/stage2/specimen_orm.py

@@ -33,7 +33,6 @@ from cidc_api.models.types import (
 class SpecimenORM(BaseORM):
     __tablename__ = "specimen"
     __repr_attrs__ = ["specimen_id", "participant_id", "cimac_id"]
-    __table_args__ = {"schema": "stage2"}
 
     specimen_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage2.participant.participant_id", ondelete="CASCADE"))

cidc_api/models/db/stage2/stem_cell_transplant_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import StemCellDonorType, AllogeneicDonorType, StemCe
 class StemCellTransplantORM(BaseORM):
     __tablename__ = "stem_cell_transplant"
     __repr_attrs__ = ["stem_cell_transplant_id"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "stem_cell_transplant"
 
     stem_cell_transplant_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/surgery_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import SurgicalProcedure, UberonAnatomicalTerm, YNU
 class SurgeryORM(BaseORM):
     __tablename__ = "surgery"
     __repr_attrs__ = ["surgery_id", "procedure"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "surgery"
 
     surgery_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/therapy_agent_dose_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import TherapyAgentDoseUnits, YNU
 class TherapyAgentDoseORM(BaseORM):
     __tablename__ = "therapy_agent_dose"
     __repr_attrs__ = ["therapy_agent_dose_id", "therapy_agent_name"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "therapy_agent_dose"
 
     therapy_agent_dose_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/treatment_orm.py

@@ -11,7 +11,6 @@ from cidc_api.models.types import YNU, OffTreatmentReason
 class TreatmentORM(BaseORM):
     __tablename__ = "treatment"
     __repr_attrs__ = ["treatment_id", "participant_id", "treatment_description"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "treatment"
 
     treatment_id: Mapped[int] = mapped_column(primary_key=True)

cidc_api/models/db/stage2/trial_orm.py

@@ -13,7 +13,6 @@ from cidc_api.models.types import AssayType, TrialOrganization, TrialFundingAgen
 class TrialORM(BaseORM):
     __tablename__ = "trial"
     __repr_attrs__ = ["trial_id", "version"]
-    __table_args__ = {"schema": "stage2"}
     __data_category__ = "study"
 
     trial_id: Mapped[str] = mapped_column(primary_key=True)

cidc_api/models/files/facets.py

@@ -376,6 +376,10 @@ assay_facets: Facets = {
         "Channels": FacetConfig(["/maldi_glycan/channels.csv", "Channels csv file for MALDI Glycan run"]),
         "Tiff Zip": FacetConfig(["/maldi_glycan/tiff.zip", "Tiff zip for MALDI Glycan run"]),
     },
+    "TCRseq RNA": {
+        "Alpha Results": FacetConfig(["/tcrseq_rna/alpha.csv"]),
+        "Beta Results": FacetConfig(["/tcrseq_rna/beta.csv"]),
+    },
     "mIHC": {
         "Samples Report": FacetConfig(["/mihc/sample_report.csv"], "Samples report for mIHC run"),
         "Multitiffs": FacetConfig(["/mihc/multitiffs.tar.gz"], "Multi Tiffs file from mIHC run"),

cidc_api/models/models.py

@@ -28,6 +28,7 @@ __all__ = [
     "JobFileCategories",
     "CategoryDataElements",
     "ValidationConfigs",
+    "MASTER_APPENDIX_A",
     "TRIAL_APPENDIX_A",
     "TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER",
     "REQUEST_LETTER",
@@ -3262,6 +3263,7 @@ def upload_manifest_json(
     return manifest_upload.id
 
 
+MASTER_APPENDIX_A = "master_appendix_a"
 TRIAL_APPENDIX_A = "trial_appendix_a"
 REQUEST_LETTER = "request_letter"
 DETAILED_VALIDATION = "detailed_validation"
@@ -3361,6 +3363,16 @@ class PreprocessedFiles(CommonColumns):
         query = cls.add_job_filter(query, job_id)
         return query.all()
 
+    @classmethod
+    @with_default_session
+    def get_latest_current_file(
+        cls, file_category: str, job_id: int = None, session: Session = None
+    ) -> Optional["PreprocessedFiles"]:
+        """Return the latest 'current' file for the given category and job_id. Returns None if no file exists."""
+        query = session.query(cls).filter_by(file_category=file_category, status="current")
+        query = cls.add_job_filter(query, job_id)
+        return query.order_by(cls.version.desc()).first()
+
     @classmethod
     @with_default_session
     def get_file_by_category_and_version(

cidc_api/models/types.py

@@ -113,6 +113,7 @@ AssayType = Literal[
     "snRNA-Seq",
     "Visium",
     "Olink HT",
+    "TCRseq RNA",
 ]
 
 

cidc_api/shared/file_handling.py

@@ -17,14 +17,22 @@ logger = get_logger(__name__)
 
 @trace_()
 def set_current_file(
-    file: FileStorage, file_category: str, gcs_folder: str, session: Session, uploader_email: str, job_id: int = None
+    file: FileStorage,
+    file_category: str,
+    gcs_folder: str,
+    session: Session,
+    uploader_email: str,
+    job_id: int = None,
+    append_timestamp: bool = None,
 ) -> PreprocessedFiles:
     """
     Archives any existing 'current' files for the given category and job,
     then uploads the new file as the latest 'current' version.
     """
     latest_version = PreprocessedFiles.archive_current_files(file_category, job_id=job_id, session=session)
-    latest_file = create_file(file, gcs_folder, file_category, session, uploader_email, job_id, latest_version + 1)
+    latest_file = create_file(
+        file, gcs_folder, file_category, session, uploader_email, job_id, latest_version + 1, append_timestamp
+    )
     return latest_file
 
 
@@ -37,11 +45,12 @@ def create_file(
     uploader_email: str,
     job_id: int = None,
     version: int = None,
+    append_timestamp: bool = None,
 ) -> PreprocessedFiles:
     """Upload file to GCS and create corresponding metadata record in the database."""
     status = "pending" if gcs_folder.endswith("pending/") else "current"
-    # only need timestamp for current/versioned files
-    append_timestamp = status == "current"
+    # only need timestamp for current/versioned files, if not specified otherwise
+    append_timestamp = append_timestamp if append_timestamp is not None else (status == "current")
     # create file in GCS
     gcs_file_path = upload_file_to_gcs(file, GOOGLE_CLINICAL_DATA_BUCKET, gcs_folder, append_timestamp=append_timestamp)
     # create corresponding record in db

cidc_api/shared/gcloud_client.py

@@ -2,6 +2,7 @@
 
 # pylint: disable=logging-fstring-interpolation,too-many-lines, broad-exception-raised
 
+import asyncio
 import base64
 import datetime
 import hashlib
@@ -26,6 +27,8 @@ from typing import (
 )
 
 import googleapiclient.discovery
+from gcloud.aio.storage import Storage
+from pandas.core.frame import DataFrame
 import pandas as pd
 import requests
 from cidc_schemas.prism.constants import ASSAY_TO_FILEPATH
@@ -443,25 +446,50 @@ def upload_xlsx_to_intake_bucket(user_email: str, trial_id: str, upload_type: st
     return f"https://console.cloud.google.com/storage/browser/_details/{bucket_name}/{blob_name}"
 
 
-def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str):
-    """Reads an XLSX or CSV file from Google Cloud Storage into a Pandas DataFrame."""
-    temp_file = get_file_bytes_from_gcs(bucket_name, blob_name)
-
-    # TODO: specify sheet in xlsx file and/or accept tsv and xls files
-    if blob_name[-3:] == "csv":
-        return strip_whitespaces(pd.read_csv(temp_file, dtype=str, keep_default_na=False))
-    elif blob_name[-4:] == "xlsx":
-        return strip_whitespaces(pd.read_excel(temp_file, dtype=str, keep_default_na=False))
+def prepare_dataframe(extension, bytes) -> DataFrame:
+    if extension == "csv":
+        return strip_whitespaces(pd.read_csv(bytes, dtype=str, keep_default_na=False))
+    elif extension == "xlsx":
+        return strip_whitespaces(pd.read_excel(bytes, dtype=str, keep_default_na=False))
     else:
         raise Exception("Can only read csv or xlsx files")
 
 
+def gcs_xlsx_or_csv_file_to_pandas_dataframe(bucket_name: str, blob_name: str) -> DataFrame:
+    """Reads an XLSX or CSV file from Google Cloud Storage into a Pandas DataFrame."""
+    contents = get_file_bytes_from_gcs(bucket_name, blob_name)
+    extension = blob_name.split(".")[-1]
+    return prepare_dataframe(extension, contents)
+
+
 def get_file_bytes_from_gcs(bucket_name: str, blob_name: str) -> io.BytesIO:
     """Reads a file from Google Cloud Storage and returns it as BytesIO."""
     sheet_data = storage.Client().bucket(bucket_name).blob(blob_name).download_as_bytes()
     return io.BytesIO(sheet_data)
 
 
+async def async_gcs_files_to_pandas_dataframes(bucket_name: str, blob_names: List[str]) -> List[DataFrame]:
+    """Async reads a XLSX or CSV files from Google Cloud Storage into a list of Pandas DataFrames."""
+
+    all_contents = await asyncio.gather(
+        *[async_get_file_bytes_from_gcs(bucket_name, blob_name) for blob_name in blob_names]
+    )
+    dataframes = []
+
+    for blob_name, contents in zip(blob_names, all_contents):
+        extension = blob_name.split(".")[-1]
+        dataframes.append(prepare_dataframe(extension, contents))
+    return dataframes
+
+
+async def async_get_file_bytes_from_gcs(bucket_name: str, blob_name: str) -> io.BytesIO:
+    """Async reads a file from Google Cloud Storage and returns it as BytesIO."""
+
+    async with Storage() as client:
+        sheet_data = await client.download(bucket_name, blob_name)
+    return io.BytesIO(sheet_data)
+
+
 def _execute_multiblob_acl_change(
     user_email_list: List[str],
     blob_list: List[storage.Blob],
@@ -907,6 +935,7 @@ def get_signed_url(
     bucket_name: str = GOOGLE_ACL_DATA_BUCKET,
     method: str = "GET",
     expiry_mins: int = 30,
+    use_short_filename: bool = False,
 ) -> str:
     """
     Generate a signed URL for `object_name` to give a client temporary access.
@@ -921,7 +950,11 @@ def get_signed_url(
 
     # Generate the signed URL, allowing a client to use `method` for `expiry_mins` minutes
     expiration = datetime.timedelta(minutes=expiry_mins)
-    full_filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
+    if use_short_filename:
+        filename = os.path.basename(object_name)
+    else:
+        # full filename with path included
+        filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
     other_kwargs = {}
     if os.environ.get("DEV_GOOGLE_STORAGE", None):
         other_kwargs["api_access_endpoint"] = (os.environ.get("DEV_GOOGLE_STORAGE") or "") + (
@@ -931,7 +964,7 @@ def get_signed_url(
         version="v2",
         expiration=expiration,
         method=method,
-        response_disposition=f'attachment; filename="{full_filename}"',
+        response_disposition=f'attachment; filename="{filename}"',
         **other_kwargs,
     )
     logger.info(f"generated signed URL for {object_name}: {url}")

{nci_cidc_api_modules-1.2.42.dist-info → nci_cidc_api_modules-1.2.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.42
+Version: 1.2.44
 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
@@ -13,6 +13,7 @@ Requires-Dist: flask>=3.1.2
 Requires-Dist: flask-migrate>=4.1.0
 Requires-Dist: flask-sqlalchemy>=3.1.1
 Requires-Dist: flask-talisman>=0.7.0
+Requires-Dist: gcloud-aio-storage~=9.6.1
 Requires-Dist: google-auth==2.45.0
 Requires-Dist: google-api-python-client>=2.187.0
 Requires-Dist: google-cloud-bigquery>=3.39.0
@@ -41,7 +42,7 @@ 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==0.28.10
+Requires-Dist: nci-cidc-schemas==0.28.11
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.42.dist-info → nci_cidc_api_modules-1.2.44.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cidc_api/__init__.py,sha256=Ng7mLXI95GEYWOWi3HpHuVabVYSs3igDIcqorkuDZds,23
+cidc_api/__init__.py,sha256=tZ6_k-1uqq2cr3SCnYO9N-chw-LhbafQ_arSm_DOlLs,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
@@ -6,79 +6,79 @@ cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,11
 cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
 cidc_api/config/settings.py,sha256=ttOGvk_6zVMn4dtxIZ2-0w3wF2fpAUVfGpVZbKJ2b6s,4653
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
-cidc_api/models/data.py,sha256=mySTpsG4qEBSh5c7dpQZJ2xTxHiYdFYuXO_a_B2gPXE,1313
+cidc_api/models/data.py,sha256=TyVXk5jJO1NN05CLqejLf5BPp6yLSNNxPmFOgXUnA1M,1313
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
-cidc_api/models/models.py,sha256=h8AvXuxXYuekCwPhiEpYbVGG7jHQog3wnWiEXLIaXdY,153111
+cidc_api/models/models.py,sha256=DTt0eFkFVVxVn23Aqr6TA8CQ7qb2hdqQ0xVJ3RakBBw,153684
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
-cidc_api/models/types.py,sha256=Zv9eUs7XUysJa_lzimbl7jSOEhvNozAkgPGGbvMIafo,30040
+cidc_api/models/types.py,sha256=WVOTEH61FH5aGVwRbEcfNOce8NLjiEnl1ixtPWav2OA,30058
 cidc_api/models/db/stage1/__init__.py,sha256=zsxOSoogzL_xZ8B5OwcwLXvAmm6g2GYx1Zf6LLw8dq8,1917
-cidc_api/models/db/stage1/additional_treatment_orm.py,sha256=aiimE27oj96sE4F9LwZAlkHNLMwH8dNS5GTYA4DnSIU,968
-cidc_api/models/db/stage1/adverse_event_orm.py,sha256=dgFdFQliPMzoYa5yf8TlX0XM1tcyu4zfu9Xq8Hbmzwc,1956
+cidc_api/models/db/stage1/additional_treatment_orm.py,sha256=GCMzsYZl_B-7-TWYDBUXbt_Gri6YDv8XkYRheDLh3pc,926
+cidc_api/models/db/stage1/adverse_event_orm.py,sha256=32Kjpg6fvByp4gEVy6K28MlgMWQryG6GPh3un1F8x64,1914
 cidc_api/models/db/stage1/base_orm.py,sha256=izKizTf2W1fCK2CRUeyuErJbOaxNp6d299n4gqKWHDQ,246
-cidc_api/models/db/stage1/baseline_clinical_assessment_orm.py,sha256=TKI-GquW_jXUxh_cIZntd5G2Soq3n_xwRrsmtd1Jw-c,953
-cidc_api/models/db/stage1/comorbidity_orm.py,sha256=v3a29HA_j7ZTJWQSu17HPutSqACf4m5whgJCVNgoGJs,923
-cidc_api/models/db/stage1/consent_group_orm.py,sha256=4dKIFyFdTog1lUvnhPOfOhe61CvPZYRvRiuVpe9bPlg,1141
-cidc_api/models/db/stage1/demographic_orm.py,sha256=t7fcHya_MGNhdq-0wS0s9MiHEG3W4Xan0fd01uvGGHU,1735
-cidc_api/models/db/stage1/disease_orm.py,sha256=ATghsDBfbOFdA5uvaRKp_-td11ze2QBd8IM7AtI6Gkk,2007
-cidc_api/models/db/stage1/exposure_orm.py,sha256=EAFDF9q3EPEiEscqpfZl2PE5oueMarcde3U3d5d5a5M,853
-cidc_api/models/db/stage1/gvhd_diagnosis_acute_orm.py,sha256=_wV4yy8hZk71Lm9t3Zl1u2OFswzEo1W88Pk0qU9q5Y0,1500
-cidc_api/models/db/stage1/gvhd_diagnosis_chronic_orm.py,sha256=MJAznv516eh0l5pXreIC3ykqS0CPI9B1gvSxActbIHc,1582
-cidc_api/models/db/stage1/gvhd_organ_acute_orm.py,sha256=-6XMobavlAllAUqHc1e-WqjF6APcln1xb31ZChIM17w,880
-cidc_api/models/db/stage1/gvhd_organ_chronic_orm.py,sha256=94eT0sbZT8KF7XVaynKZKlYYZuGrF0TxWiF_yDwtgIk,904
-cidc_api/models/db/stage1/medical_history_orm.py,sha256=RYPEnInuMQIUtod6NWWvlHuJe7cgyTNT3R3Ols4yiAE,1324
-cidc_api/models/db/stage1/other_malignancy_orm.py,sha256=2zQ4r5uXO20vWLbHJtDObpct3tYcL6DD0qT3Bixai58,1345
-cidc_api/models/db/stage1/participant_orm.py,sha256=8-tO3avpih2ntUzyZwewBEYD-wJ3EQkcMwx73ME9dnc,3553
-cidc_api/models/db/stage1/prior_treatment_orm.py,sha256=fcX4KiKVtcn3UzAtwhyvUF-nUD_A58CE1tBlCYDh3RU,1367
-cidc_api/models/db/stage1/radiotherapy_dose_orm.py,sha256=UVEhn5S6JG41oUBpPHfHNpQ8Chk7LfbqTDaYpnkPa-I,1542
-cidc_api/models/db/stage1/response_by_system_orm.py,sha256=Uq99hXlA5Y_KKW19BlGeLpdGXIOOVoPlUV-bbJtsXak,1566
-cidc_api/models/db/stage1/response_orm.py,sha256=2JsI3YwpmVlMrPOwt5ukeWU3fag4fE5CYomJEYIqzNA,1205
-cidc_api/models/db/stage1/specimen_orm.py,sha256=LPKfl0Loa9TdkEJFhV4u6w8KoaiH1bjEXrYJv9yp2BI,1396
-cidc_api/models/db/stage1/stem_cell_transplant_orm.py,sha256=ngKiV5cPbi1hMVp_MTf92XpcvXKk0gyCxsP3BG5wSGY,1139
-cidc_api/models/db/stage1/surgery_orm.py,sha256=ba23DOF9KRpsabq-SaI0Q3WCAeCWJ8czUoy6Xr2PSpg,1060
-cidc_api/models/db/stage1/therapy_agent_dose_orm.py,sha256=rDierfZ3d1JCEL0yMfyImuIgbbfWS3BI_saVVuYqwNs,1348
-cidc_api/models/db/stage1/treatment_orm.py,sha256=77E01T5UI7aR-T_BKY2pDIFqusuz11oeR8SWi0CWO5c,1667
-cidc_api/models/db/stage1/trial_orm.py,sha256=LiYdJUAx7nS_9Whc_KBm4gTBxKokGeWdVPihXlgYUX4,1308
+cidc_api/models/db/stage1/baseline_clinical_assessment_orm.py,sha256=pGanJlwnAm38LPVTu6XF4qP_mw-SqYP8AC3O8w8XPnw,911
+cidc_api/models/db/stage1/comorbidity_orm.py,sha256=C4P3kcpNpnt1ICgU2Xm5S-ou6Xhx6yr690g6F_hBoZ0,881
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