nci-cidc-api-modules 1.2.54__py3-none-any.whl → 1.2.56__py3-none-any.whl

cidc_api/models/pydantic/stage2/treatment.py

@@ -1,11 +1,11 @@
-from typing import Self
-
-from pydantic import model_validator
+from cidc_api.models.pydantic.base import forced_validator, forced_validators
 
+from cidc_api.models.errors import ValueLocError
 from cidc_api.models.pydantic.base import Base
 from cidc_api.models.types import YNU, OffTreatmentReason
 
 
+@forced_validators
 class Treatment(Base):
     __data_category__ = "treatment"
     __cardinality__ = "many"
@@ -17,10 +17,10 @@ class Treatment(Base):
     participant_id: str | None = None
 
     # The unique internal identifier for the associated Arm record
-    arm_id: int | None = None
+    arm: str | None = None
 
     # The unique internal identifier for the associated Cohort record
-    cohort_id: int | None = None
+    cohort: str | None = None
 
     # A unique identifier used to describe a distinct, specific intervention or
     # treatment that a group or subgroup of participants in a clinical trial receives.
@@ -37,14 +37,28 @@ class Treatment(Base):
     # If "Other" is selected for "off_treatment_reason", provide a description of the reason.
     off_treatment_reason_other: str | None = None
 
-    @model_validator(mode="after")
-    def validate_off_treatment_reason_cr(self) -> Self:
-        if self.off_treatment == "Yes" and not self.off_treatment_reason:
-            raise ValueError('If off_treatment is "Yes", please provide off_treatment_reason.')
-        return self
-
-    @model_validator(mode="after")
-    def validate_off_treatment_reason_other_cr(self) -> Self:
-        if self.off_treatment_reason == "Other" and not self.off_treatment_reason_other:
-            raise ValueError('If off_treatment_reason is "Other", please provide off_treatment_reason_other.')
-        return self
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_cr(cls, data, info) -> None:
+        off_treatment = data.get("off_treatment", None)
+        off_treatment_reason = data.get("off_treatment_reason", None)
+
+        if off_treatment == "Yes" and not off_treatment_reason:
+            raise ValueLocError(
+                'If off_treatment is "Yes", please provide off_treatment_reason.',
+                loc="off_treatment_reason",
+            )
+        return off_treatment_reason
+
+    @forced_validator
+    @classmethod
+    def validate_off_treatment_reason_other_cr(cls, data, info) -> None:
+        off_treatment_reason = data.get("off_treatment_reason", None)
+        off_treatment_reason_other = data.get("off_treatment_reason_other", None)
+
+        if off_treatment_reason == "Other" and not off_treatment_reason_other:
+            raise ValueLocError(
+                'If off_treatment_reason is "Other", please provide off_treatment_reason_other.',
+                loc="off_treatment_reason_other",
+            )
+        return off_treatment_reason_other

cidc_api/telemetry.py

@@ -43,19 +43,19 @@ resource = Resource(attributes={"service.name": f"CIDC-{ENV}"})
 provider = TracerProvider(resource=resource)
 
 
-if ENV == "dev" and not TESTING:
-    from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter
-
-    COLLECTOR_ENDPOINT = "127.0.0.1"
-    COLLECTOR_GRPC_PORT = 6004
-
-    # send spans to local exporter
-    # 1. download latest version from https://github.com/open-telemetry/opentelemetry-collector-releases/releases (otelcol-contrib_0.140.1_darwin_arm64)
-    # 2. start exporter from otel folder with `./otelcol-contrib --config=config.yaml`
-    # 3. download and start Jeager (all-in-one image)  - https://www.jaegertracing.io/download/
-    exporter = OTLPSpanExporter(endpoint=f"http://{COLLECTOR_ENDPOINT}:{COLLECTOR_GRPC_PORT}", insecure=True)
-    processor = BatchSpanProcessor(exporter)
-    provider.add_span_processor(processor)
+# if ENV == "dev" and not TESTING:
+#     from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter
+
+#     COLLECTOR_ENDPOINT = "127.0.0.1"
+#     COLLECTOR_GRPC_PORT = 6004
+
+#     # send spans to local exporter
+#     # 1. download latest version from https://github.com/open-telemetry/opentelemetry-collector-releases/releases (otelcol-contrib_0.140.1_darwin_arm64)
+#     # 2. start exporter from otel folder with `./otelcol-contrib --config=config.yaml`
+#     # 3. download and start Jeager (all-in-one image)  - https://www.jaegertracing.io/download/
+#     exporter = OTLPSpanExporter(endpoint=f"http://{COLLECTOR_ENDPOINT}:{COLLECTOR_GRPC_PORT}", insecure=True)
+#     processor = BatchSpanProcessor(exporter)
+#     provider.add_span_processor(processor)
 
 if ENV == "dev-int":
     from opentelemetry.exporter.cloud_trace import CloudTraceSpanExporter

{nci_cidc_api_modules-1.2.54.dist-info → nci_cidc_api_modules-1.2.56.dist-info}/METADATA

@@ -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-1.2.56.dist-info/RECORD

@@ -0,0 +1,163 @@
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+nci_cidc_api_modules-1.2.56.dist-info/RECORD,,

cidc_api/models/data.py

@@ -1,28 +0,0 @@
-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):
-        for data_category in standard_data_categories:
-            self[data_category] = []
-        super().__init__(*args, **kwargs)
-
-
-# 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-1.2.54.dist-info/RECORD

@@ -1,163 +0,0 @@
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