nci-cidc-api-modules 1.2.42__tar.gz → 1.2.44__tar.gz

{nci_cidc_api_modules-1.2.42/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.44}/PKG-INFO

@@ -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-1.2.44/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.44"

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"
 

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"
 

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"))

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"
 

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"))

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"))

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"
 

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"))

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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)

{nci_cidc_api_modules-1.2.42 → nci_cidc_api_modules-1.2.44}/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"),