nci-cidc-api-modules 1.2.54__tar.gz → 1.2.56__tar.gz

{nci_cidc_api_modules-1.2.54/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.56}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.54
+Version: 1.2.56
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/boot.py

@@ -1,9 +1,17 @@
 from os import mkdir, path
 import shutil
+from flask_migrate import upgrade
 
 TEMPLATES_DIR = path.join("/tmp", "templates")
 
 
+def apply_migrations():
+    from cidc_api.app import app
+
+    with app.app_context():
+        upgrade(app.config["MIGRATIONS_PATH"])
+
+
 # set up the directories for holding generated templates
 def set_up_templates_directories():
     if path.exists(TEMPLATES_DIR):

nci_cidc_api_modules-1.2.56/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.56"

nci_cidc_api_modules-1.2.56/cidc_api/models/dataset.py

@@ -0,0 +1,80 @@
+from enum import StrEnum
+from typing import Any
+
+from sqlalchemy import and_
+from sqlalchemy.orm.session import Session
+
+from cidc_api.models.pydantic.stage1 import all_models as stage1_all_models
+from cidc_api.models.pydantic.stage2 import all_models as stage2_all_models
+from cidc_api.models.db.stage1 import all_models as stage1_all_db_models
+from cidc_api.models.db.stage2 import all_models as stage2_all_db_models
+from cidc_api.models.db.stage1 import TrialORM as s1TrialORM
+from cidc_api.models.db.stage2 import TrialORM as s2TrialORM
+
+
+standard_data_categories = [
+    model.__data_category__ for model in stage1_all_models if hasattr(model, "__data_category__")
+]
+
+
+# Maps data categories like "treatment" to their associated pydantic model
+data_category_to_model = {
+    "stage1": {model.__data_category__: model for model in stage1_all_models if hasattr(model, "__data_category__")},
+    "stage2": {model.__data_category__: model for model in stage2_all_models if hasattr(model, "__data_category__")},
+}
+
+
+data_category_to_db_model = {
+    "stage1": {model.__data_category__: model for model in stage1_all_db_models if hasattr(model, "__data_category__")},
+    "stage2": {model.__data_category__: model for model in stage2_all_db_models if hasattr(model, "__data_category__")},
+}
+
+
+class Stages(StrEnum):
+    STAGE1 = "stage1"
+    STAGE2 = "stage2"
+    STAGE3 = "stage3"
+
+    @classmethod
+    def members(cls):
+        return list(v.value for v in cls.__members__.values())
+
+
+def trial_exists(trial_id: str, version: str, stage: str, session: Session) -> bool:
+    if stage not in Stages:
+        raise ValueError(f"value for 'stage' must be in {Stages.members()}")
+
+    if stage == Stages.STAGE1:
+        TrialORM = s1TrialORM
+    elif stage == Stages.STAGE2:
+        TrialORM = s2TrialORM
+    elif stage == Stages.STAGE3:
+        pass  # stub
+
+    trials = session.query(TrialORM).filter(and_(TrialORM.trial_id == trial_id, TrialORM.version == version)).all()
+    return len(trials) == 1
+
+
+# A class to hold the entire model representation of a trial's dataset
+class Dataset(dict):
+    def __init__(self, *args, **kwargs):
+        for data_category in standard_data_categories:
+            self[data_category] = []
+        super().__init__(*args, **kwargs)
+
+    def load(self, trial_id: str, version: str, stage: str, session: Session):
+        if stage not in Stages:
+            raise ValueError(f"value for 'stage' must be in {Stages.members()}")
+
+        for data_category, _ in self.items():
+            db_model_cls = data_category_to_db_model[stage][data_category]
+            db_models = self.load_db_models(trial_id, version, db_model_cls, session)
+            self[data_category] = db_models
+
+    def load_db_models(self, trial_id: str, version: str, db_model_cls: Any, session: Session):
+        db_models = (
+            session.query(db_model_cls)
+            .filter(and_(db_model_cls.trial_id == trial_id, db_model_cls.version == version))
+            .all()
+        )
+        return db_models

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/additional_treatment_orm.py

@@ -1,16 +1,23 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 
 
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
     __repr_attrs__ = ["additional_treatment_id", "participant_id"]
     __data_category__ = "additional_treatment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     additional_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/adverse_event_orm.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     CTCAEEventTerm,
     CTCAEEventCode,
@@ -22,6 +23,12 @@ class AdverseEventORM(BaseORM):
     __tablename__ = "adverse_event"
     __repr_attrs__ = ["adverse_event_id", "participant_id", "event_term"]
     __data_category__ = "adverse_event"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     adverse_event_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/baseline_clinical_assessment_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import ECOGScore, KarnofskyScore
 
 
@@ -10,6 +11,12 @@ class BaselineClinicalAssessmentORM(BaseORM):
     __tablename__ = "baseline_clinical_assessment"
     __repr_attrs__ = ["baseline_clinical_assessment_id", "participant_id"]
     __data_category__ = "baseline_clinical_assessment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     baseline_clinical_assessment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/comorbidity_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import ICD10CMCode, ICD10CMTerm
 
 
@@ -10,6 +11,12 @@ class ComorbidityORM(BaseORM):
     __tablename__ = "comorbidity"
     __repr_attrs__ = ["comorbidity_id", "comorbidity_term"]
     __data_category__ = "comorbidity"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     comorbidity_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/consent_group_orm.py

@@ -2,26 +2,26 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonNegativeInt
-from sqlalchemy import ForeignKeyConstraint
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 
 
 class ConsentGroupORM(BaseORM):
     __tablename__ = "consent_group"
     __repr_attrs__ = ["consent_group_id", "consent_group_name"]
+    __data_category__ = "consent_group"
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage1.trial.trial_id", "stage1.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __data_category__ = "consent_group"
 
-    consent_group_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    consent_group_id: Mapped[int] = mapped_column(primary_key=True)
+
     consent_group_short_name: Mapped[str]
     consent_group_name: Mapped[str]
     consent_group_number: Mapped[NonNegativeInt]

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/demographic_orm.py

@@ -2,11 +2,12 @@ from __future__ import annotations
 from pydantic import NonNegativeFloat, PositiveFloat, PositiveInt
 from typing import List
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     Sex,
     Race,
@@ -25,6 +26,12 @@ class DemographicORM(BaseORM):
     __tablename__ = "demographic"
     __repr_attrs__ = ["demographic_id", "participant_id", "age_at_enrollment", "sex"]
     __data_category__ = "demographic"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     demographic_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/disease_orm.py

@@ -2,11 +2,12 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonPositiveInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     TumorGrade,
     CancerStageSystem,
@@ -30,6 +31,12 @@ class DiseaseORM(BaseORM):
         "participant_id",
     ]
     __data_category__ = "disease"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     disease_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/exposure_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from typing import List
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import YNU, ExposureType
 
 
@@ -12,6 +13,12 @@ class ExposureORM(BaseORM):
     __tablename__ = "exposure"
     __repr_attrs__ = ["exposure_id", "exposure_type", "carcinogen_exposure"]
     __data_category__ = "exposure"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     exposure_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/gvhd_diagnosis_acute_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from typing import List
 
-from sqlalchemy import ForeignKey, UniqueConstraint
+from sqlalchemy import ForeignKey, UniqueConstraint, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     GVHDDiagnosisAcuteAssessmentSystem,
     GVHDDiagnosisAcuteAssessmentSystemVersion,
@@ -15,11 +16,15 @@ from cidc_api.models.types import (
 
 class GVHDDiagnosisAcuteORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_acute"
+    __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_acute"
     __table_args__ = (
         UniqueConstraint("participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_acute_pre_or_post"),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __repr_attrs__ = ["gvhd_diagnosis_acute_id", "pre_or_post_enrollment"]
-    __data_category__ = "gvhd_diagnosis_acute"
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/gvhd_diagnosis_chronic_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from typing import List
 
-from sqlalchemy import ForeignKey, UniqueConstraint
+from sqlalchemy import ForeignKey, ForeignKeyConstraint, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     GVHDDiagnosisChronicAssessmentSystem,
     GVHDDiagnosisChronicAssessmentSystemVersion,
@@ -15,13 +16,17 @@ from cidc_api.models.types import (
 
 class GVHDDiagnosisChronicORM(BaseORM):
     __tablename__ = "gvhd_diagnosis_chronic"
+    __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
+    __data_category__ = "gvhd_diagnosis_chronic"
     __table_args__ = (
         UniqueConstraint(
             "participant_id", "pre_or_post_enrollment", name="unique_ix_gvhd_diagnosis_chronic_pre_or_post"
         ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __repr_attrs__ = ["gvhd_diagnosis_chronic_id", "pre_or_post_enrollment"]
-    __data_category__ = "gvhd_diagnosis_chronic"
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/gvhd_organ_acute_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganAcuteStage
 
 
@@ -10,6 +11,12 @@ class GVHDOrganAcuteORM(BaseORM):
     __tablename__ = "gvhd_organ_acute"
     __repr_attrs__ = ["gvhd_organ_acute_id", "organ"]
     __data_category__ = "gvhd_organ_acute"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_organ_acute_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_acute_id: Mapped[int] = mapped_column(

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/gvhd_organ_chronic_orm.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import GVHDOrgan, GVHDOrganChronicScore
 
 
@@ -10,6 +11,12 @@ class GVHDOrganChronicORM(BaseORM):
     __tablename__ = "gvhd_organ_chronic"
     __repr_attrs__ = ["gvhd_organ_chronic_id", "organ"]
     __data_category__ = "gvhd_organ_chronic"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     gvhd_organ_chronic_id: Mapped[int] = mapped_column(primary_key=True)
     gvhd_diagnosis_chronic_id: Mapped[int] = mapped_column(

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/medical_history_orm.py

@@ -2,10 +2,11 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonNegativeInt, PositiveFloat
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import TobaccoSmokingStatus
 
 
@@ -13,6 +14,12 @@ class MedicalHistoryORM(BaseORM):
     __tablename__ = "medical_history"
     __repr_attrs__ = ["medical_history_id"]
     __data_category__ = "medical_history"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     medical_history_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/other_malignancy_orm.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 from pydantic import NonPositiveInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import UberonAnatomicalTerm, ICDO3MorphologicalCode, ICDO3MorphologicalTerm, MalignancyStatus
 
 
@@ -11,6 +12,12 @@ class OtherMalignancyORM(BaseORM):
     __tablename__ = "other_malignancy"
     __repr_attrs__ = ["other_malignancy_id", "primary_disease_site"]
     __data_category__ = "other_malignancy"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     other_malignancy_id: Mapped[int] = mapped_column(primary_key=True)
     medical_history_id: Mapped[int] = mapped_column(

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/participant_orm.py

@@ -5,23 +5,22 @@ from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import OffStudyReason, YNU
 
 
 class ParticipantORM(BaseORM):
     __tablename__ = "participant"
     __repr_attrs__ = ["participant_id", "native_participant_id", "cimac_participant_id"]
+    __data_category__ = "participant"
     __table_args__ = (
-        ForeignKeyConstraint(
-            ["trial_id", "version"], ["stage1.trial.trial_id", "stage1.trial.version"], ondelete="CASCADE"
-        ),
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
     )
-    __data_category__ = "participant"
 
-    participant_id: Mapped[int] = mapped_column(primary_key=True)
     trial_id: Mapped[str]
     version: Mapped[str]
 
+    participant_id: Mapped[int] = mapped_column(primary_key=True)
     native_participant_id: Mapped[str | None]
     cimac_participant_id: Mapped[str | None]
     consent_group_id: Mapped[int | None] = mapped_column(

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/prior_treatment_orm.py

@@ -2,11 +2,11 @@ from __future__ import annotations
 from typing import List
 
 from pydantic import NonPositiveInt, NegativeInt
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
@@ -14,6 +14,12 @@ class PriorTreatmentORM(BaseORM):
     __tablename__ = "prior_treatment"
     __repr_attrs__ = ["prior_treatment_id", "type"]
     __data_category__ = "prior_treatment"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     prior_treatment_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/radiotherapy_dose_orm.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt, NonNegativeFloat, PositiveFloat
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import (
     RadiotherapyProcedure,
     UberonAnatomicalTerm,
@@ -19,6 +20,12 @@ class RadiotherapyDoseORM(BaseORM):
     __tablename__ = "radiotherapy_dose"
     __repr_attrs__ = ["radiotherapy_dose_id", "procedure"]
     __data_category__ = "radiotherapy_dose"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     radiotherapy_dose_id: Mapped[int] = mapped_column(primary_key=True)
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage1.treatment.treatment_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/response_by_system_orm.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 from pydantic import PositiveInt
-from sqlalchemy import ForeignKey, String
+from sqlalchemy import String, ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
+from cidc_api.models.db.stage1.trial_orm import TrialORM
 from cidc_api.models.types import ResponseSystem, ResponseSystemVersion, BestOverallResponse, YNUNA, YN
 
 
@@ -11,6 +12,12 @@ class ResponseBySystemORM(BaseORM):
     __tablename__ = "response_by_system"
     __repr_attrs__ = ["response_by_system_id", "participant_id"]
     __data_category__ = "response_by_system"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     response_by_system_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.54 → nci_cidc_api_modules-1.2.56}/cidc_api/models/db/stage1/response_orm.py

@@ -1,17 +1,24 @@
 from __future__ import annotations
 from pydantic import NonNegativeInt
 
-from sqlalchemy import ForeignKey
+from sqlalchemy import ForeignKey, ForeignKeyConstraint
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage1.base_orm import BaseORM
-from cidc_api.models.types import SurvivalStatus, YNUNA, CauseOfDeath, YN
+from cidc_api.models.db.stage1.trial_orm import TrialORM
+from cidc_api.models.types import SurvivalStatus, CauseOfDeath, YNUNA, YN
 
 
 class ResponseORM(BaseORM):
     __tablename__ = "response"
     __repr_attrs__ = ["response_id", "participant_id"]
     __data_category__ = "response"
+    __table_args__ = (
+        ForeignKeyConstraint(["trial_id", "version"], [TrialORM.trial_id, TrialORM.version], ondelete="CASCADE"),
+    )
+
+    trial_id: Mapped[str]
+    version: Mapped[str]
 
     response_id: Mapped[int] = mapped_column(primary_key=True)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))