nci-cidc-api-modules 1.2.40__tar.gz → 1.2.42__tar.gz

{nci_cidc_api_modules-1.2.40/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.40
+Version: 1.2.42
 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-1.2.42/cidc_api/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.42"

nci_cidc_api_modules-1.2.42/cidc_api/models/data.py

@@ -0,0 +1,28 @@
+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
+
+standard_data_categories = [
+    model.__data_category__ for model in stage1_all_models if hasattr(model, "__data_category__")
+]
+
+
+# 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] = []
+
+
+# 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__")},
+}

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage1/additional_treatment_orm.py

@@ -9,7 +9,7 @@ from cidc_api.models.db.stage1.base_orm import BaseORM
 
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
-    __repr_attrs__ = ["additional_treatment_id", "participant_id", "description"]
+    __repr_attrs__ = ["additional_treatment_id", "participant_id"]
     __table_args__ = {"schema": "stage1"}
     __data_category__ = "additional_treatment"
 

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage1/prior_treatment_orm.py

@@ -7,7 +7,7 @@ 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.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PriorTreatmentORM(BaseORM):
@@ -21,11 +21,10 @@ class PriorTreatmentORM(BaseORM):
 
     prior_treatment_days_to_start: Mapped[NonPositiveInt | None]
     prior_treatment_days_to_end: Mapped[NonPositiveInt | None]
-    prior_treatment_type: Mapped[List[PriorTreatmentType]] = mapped_column(JSON, nullable=False)
-    prior_treatment_description: Mapped[str | None]
+    prior_treatment_description: Mapped[str]
     prior_treatment_best_response: Mapped[str | None]
     prior_treatment_conditioning_regimen_type: Mapped[ConditioningRegimenType | None]
     prior_treatment_stem_cell_donor_type: Mapped[StemCellDonorType | None]
-    prior_treatment_days_to_prior_transplant: Mapped[NegativeInt | None]
+    prior_treatment_days_from_transplant_to_treatment_initiation: Mapped[NegativeInt | None]
 
     participant: Mapped[ParticipantORM] = relationship(back_populates="prior_treatments", cascade="all, delete")

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage1/specimen_orm.py

@@ -34,6 +34,7 @@ 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)
     participant_id: Mapped[int] = mapped_column(ForeignKey("stage1.participant.participant_id", ondelete="CASCADE"))

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage1/stem_cell_transplant_orm.py

@@ -18,7 +18,7 @@ class StemCellTransplantORM(BaseORM):
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage1.treatment.treatment_id", ondelete="CASCADE"))
 
     stem_cell_donor_type: Mapped[StemCellDonorType]
-    allogeneic_donor_type: Mapped[AllogeneicDonorType]
+    allogeneic_donor_type: Mapped[AllogeneicDonorType | None]
     stem_cell_source: Mapped[StemCellSource]
     days_to_transplant: Mapped[NonNegativeInt]
     conditioning_regimen_type: Mapped[ConditioningRegimenType | None]

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage2/additional_treatment_orm.py

@@ -9,7 +9,7 @@ from cidc_api.models.db.stage2.base_orm import BaseORM
 
 class AdditionalTreatmentORM(BaseORM):
     __tablename__ = "additional_treatment"
-    __repr_attrs__ = ["additional_treatment_id", "participant_id", "description"]
+    __repr_attrs__ = ["additional_treatment_id", "participant_id"]
     __table_args__ = {"schema": "stage2"}
     __data_category__ = "additional_treatment"
 

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage2/prior_treatment_orm.py

@@ -7,7 +7,7 @@ from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.types import JSON
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PriorTreatmentORM(BaseORM):
@@ -21,8 +21,7 @@ class PriorTreatmentORM(BaseORM):
 
     prior_treatment_days_to_start: Mapped[NonPositiveInt | None]
     prior_treatment_days_to_end: Mapped[NonPositiveInt | None]
-    prior_treatment_type: Mapped[List[PriorTreatmentType]] = mapped_column(JSON, nullable=False)
-    prior_treatment_description: Mapped[str | None]
+    prior_treatment_description: Mapped[str]
     prior_treatment_best_response: Mapped[str | None]
     prior_treatment_conditioning_regimen_type: Mapped[ConditioningRegimenType | None]
     prior_treatment_stem_cell_donor_type: Mapped[StemCellDonorType | None]

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage2/publication_orm.py

@@ -3,7 +3,7 @@ from sqlalchemy import ForeignKeyConstraint, ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from cidc_api.models.db.stage2.base_orm import BaseORM
-from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PublicationORM(BaseORM):

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/db/stage2/stem_cell_transplant_orm.py

@@ -18,7 +18,7 @@ class StemCellTransplantORM(BaseORM):
     treatment_id: Mapped[int] = mapped_column(ForeignKey("stage2.treatment.treatment_id", ondelete="CASCADE"))
 
     stem_cell_donor_type: Mapped[StemCellDonorType]
-    allogeneic_donor_type: Mapped[AllogeneicDonorType]
+    allogeneic_donor_type: Mapped[AllogeneicDonorType | None]
     stem_cell_source: Mapped[StemCellSource]
     days_to_transplant: Mapped[NonNegativeInt]
     conditioning_regimen_type: Mapped[ConditioningRegimenType | None]

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/pydantic/base.py

@@ -9,7 +9,7 @@ class Base(BaseModel):
     model_config = ConfigDict(
         validate_assignment=True,
         from_attributes=True,
-        extra="forbid",
+        extra="allow",
     )
 
     # Validates the new state and updates the object if valid

{nci_cidc_api_modules-1.2.40/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.42/cidc_api/models/pydantic/stage1}/participant.py

@@ -16,7 +16,7 @@ class Participant(Base):
     participant_id: str | None = None
 
     # The participant identifier assigned by the clinical trial team overseeing the study
-    native_participant_id: str
+    native_participant_id: str | None = None
 
     # The globally unique participant identifier assigned by the CIMAC network. e.g. C8P29A7
     cimac_participant_id: str | None = None

{nci_cidc_api_modules-1.2.40/cidc_api/models/pydantic/stage2 → nci_cidc_api_modules-1.2.42/cidc_api/models/pydantic/stage1}/prior_treatment.py

@@ -3,7 +3,7 @@ from typing import Self, Annotated, List
 from pydantic import NonPositiveInt, NegativeInt, model_validator, BeforeValidator
 
 from cidc_api.models.pydantic.base import Base
-from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PriorTreatment(Base):
@@ -25,11 +25,10 @@ class PriorTreatment(Base):
     prior_treatment_days_to_end: NonPositiveInt | None = None
 
     # Specifies the category or kind of prior treatment modality a participant received.
-    prior_treatment_type: Annotated[List[PriorTreatmentType], BeforeValidator(Base.split_list)]
 
     # Description of the prior treatment such as its full generic name if it is a type of therapy agent,
     # radiotherapy procedure name and location, or surgical procedure name and location.
-    prior_treatment_description: str | None = None
+    prior_treatment_description: str
 
     # Best response from any response assessment system to the prior treatment if available or applicable.
     prior_treatment_best_response: str | None = None
@@ -44,9 +43,3 @@ class PriorTreatment(Base):
     # If prior treatment is "Stem cell transplant", indicates the number of days from enrollment
     # to the prior transplant. This must be a negative number.
     prior_treatment_days_from_transplant_to_treatment_initiation: NegativeInt | None = None
-
-    @model_validator(mode="after")
-    def validate_description_cr(self) -> Self:
-        if "Other therapy" in self.prior_treatment_type and not self.prior_treatment_description:
-            raise ValueError('If type is "Other therapy", please provide description.')
-        return self

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/pydantic/stage1/specimen.py

@@ -1,32 +1,11 @@
 from datetime import datetime
 
 from cidc_api.models.pydantic.base import Base
-from cidc_api.models.types import (
-    UberonAnatomicalTerm,
-    ICDO3MorphologicalCode,
-    SpecimenType,
-    SpecimenDescription,
-    TumorType,
-    CollectionProcedure,
-    FixationStabilizationType,
-    PrimaryContainerType,
-    VolumeUnits,
-    ProcessedType,
-    ConcentrationUnits,
-    DerivativeType,
-    PBMCRestingPeriodUsed,
-    MaterialUnits,
-    MaterialStorageCondition,
-    QCCondition,
-    ReplacementRequested,
-    ResidualUse,
-    DiagnosisVerification,
-    AssayType,
-)
+from cidc_api.models.types import UberonAnatomicalTerm
 
 
 class Specimen(Base):
-    # __data_category__ = "specimen"
+    __data_category__ = "specimen"
     __cardinality__ = "many"
 
     # The unique internal identifier for the specimen record

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/pydantic/stage1/trial.py

@@ -12,10 +12,10 @@ class Trial(Base):
 
     # The unique identifier for the clinical trial. e.g. "GU16-287","BACCI"
     # CDE: https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5054234%20and%20ver_nr=1
-    trial_id: str
+    trial_id: str | None = None
 
     # The version number of the trial dataset. e.g. "1.0"
-    version: str
+    version: str | None = None
 
     # A broad textual description of the primary endpoint(s) of the trial.
     primary_endpoint: str | None = None

{nci_cidc_api_modules-1.2.40/cidc_api/models/pydantic/stage1 → nci_cidc_api_modules-1.2.42/cidc_api/models/pydantic/stage2}/prior_treatment.py

@@ -3,7 +3,7 @@ from typing import Self, Annotated, List
 from pydantic import NonPositiveInt, NegativeInt, model_validator, BeforeValidator
 
 from cidc_api.models.pydantic.base import Base
-from cidc_api.models.types import PriorTreatmentType, ConditioningRegimenType, StemCellDonorType
+from cidc_api.models.types import ConditioningRegimenType, StemCellDonorType
 
 
 class PriorTreatment(Base):
@@ -24,12 +24,9 @@ class PriorTreatment(Base):
     # the treatment modality.
     prior_treatment_days_to_end: NonPositiveInt | None = None
 
-    # Specifies the category or kind of prior treatment modality a participant received.
-    prior_treatment_type: Annotated[List[PriorTreatmentType], BeforeValidator(Base.split_list)]
-
     # Description of the prior treatment such as its full generic name if it is a type of therapy agent,
     # radiotherapy procedure name and location, or surgical procedure name and location.
-    prior_treatment_description: str | None = None
+    prior_treatment_description: str
 
     # Best response from any response assessment system to the prior treatment if available or applicable.
     prior_treatment_best_response: str | None = None
@@ -44,9 +41,3 @@ class PriorTreatment(Base):
     # If prior treatment is "Stem cell transplant", indicates the number of days from enrollment
     # to the prior transplant. This must be a negative number.
     prior_treatment_days_from_transplant_to_treatment_initiation: NegativeInt | None = None
-
-    @model_validator(mode="after")
-    def validate_description_cr(self) -> Self:
-        if "Other therapy" in self.prior_treatment_type and not self.prior_treatment_description:
-            raise ValueError('If type is "Other therapy", please provide description.')
-        return self

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42}/cidc_api/models/types.py

@@ -1044,21 +1044,6 @@ GVHDDiagnosisChronicGlobalSeverity = Literal["Mild", "Moderate", "Severe"]
 GVHDOrganChronicScore = Literal["0", "1", "2", "3"]
 
 
-PriorTreatmentType = Literal[
-    "Surgery",
-    "Radiotherapy",
-    "Immunotherapy",
-    "Chemotherapy",
-    "Targeted therapy",
-    "Other therapy",
-    "Radiopharmaceutical",
-    "Stem cell transplant",
-    "Immunosuppressive therapy/GVHD prophylaxis for transplant",
-    "Conditioning therapy",
-    "Post-transplant salvage therapy",
-]
-
-
 ConditioningRegimenType = Literal["Myeloablative", "Reduced-intensity", "Non-myeloablative", "Other"]
 
 StemCellDonorType = Literal["Autologous", "Allogeneic"]

{nci_cidc_api_modules-1.2.40 → nci_cidc_api_modules-1.2.42/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.40
+Version: 1.2.42
 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-1.2.40/cidc_api/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.40"

nci_cidc_api_modules-1.2.40/cidc_api/models/data.py

@@ -1,19 +0,0 @@
-from cidc_api.models.pydantic.stage2 import all_models
-from cidc_api.models.db.stage2 import all_models as all_db_models
-
-standard_data_categories = [model.__data_category__ for model in all_models if hasattr(model, "__data_category__")]
-
-
-# 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] = []
-
-
-# Maps data categories like "treatment" to their associated pydantic model
-data_category_to_model = {model.__data_category__: model for model in all_models if hasattr(model, "__data_category__")}
-data_category_to_db_model = {
-    model.__data_category__: model for model in all_db_models if hasattr(model, "__data_category__")
-}