moves logic to pull info from env vars out of 'VlmResponse' classes and into 'build_vlm_response_from_caf_data'

Author: jennifer-bowser

src/anyvlm/functions/build_vlm_response.py

@@ -1,12 +1,36 @@
 """Craft a VlmResponse object from a list of CohortAlleleFrequencyStudyResults"""
 
+import os
+
 from ga4gh.va_spec.base.core import CohortAlleleFrequencyStudyResult
 
 from anyvlm.schemas.vlm import (
+    BeaconHandover,
+    HandoverType,
+    ResponseField,
+    ResponseSummary,
     VlmResponse,
 )
 
 
+class MissingEnvironmentVariableError(Exception):
+    """Raised when a required environment variable is not set."""
+
+
+def _get_environment_var(key: str) -> str:
+    """Retrieves an environment variable, raising an error if it is not set.
+
+    :param key: The key for the environment variable
+    :returns: The value for the environment variable of the provided `key`
+    :raises: MissingEnvironmentVariableError if environment variable is not found.
+    """
+    value: str | None = os.environ.get(key)
+    if not value:
+        message = f"Missing required environment variable: {key}"
+        raise MissingEnvironmentVariableError(message)
+    return value
+
+
 def build_vlm_response_from_caf_data(
     caf_data: list[CohortAlleleFrequencyStudyResult],
 ) -> VlmResponse:
@@ -15,4 +39,31 @@ def build_vlm_response_from_caf_data(
     :param caf_data: A list of `CohortAlleleFrequencyStudyResult` objects that will be used to build the VlmResponse
     :return: A `VlmResponse` object.
     """
-    raise NotImplementedError  # TODO: Implement this during/after Issue #16
+    raise NotImplementedError  # TODO: Remove this and finish implementing this function in Issue #35
+
+    # TODO - create `handover_type` and `beacon_handovers` dynamically,
+    # instead of pulling from environment variables. See Issue #37.
+    handover_type = HandoverType(
+        id=_get_environment_var("HANDOVER_TYPE_ID"),
+        label=_get_environment_var("HANDOVER_TYPE_LABEL"),
+    )
+
+    beacon_handovers: list[BeaconHandover] = [
+        BeaconHandover(
+            handoverType=handover_type, url=_get_environment_var("BEACON_HANDOVER_URL")
+        )
+    ]
+
+    num_results = len(caf_data)
+    response_summary = ResponseSummary(
+        exists=num_results > 0, numTotalResults=num_results
+    )
+
+    # TODO - create this field in Issue #35
+    response_field = ResponseField()
+
+    return VlmResponse(
+        beaconHandovers=beacon_handovers,
+        responseSummary=response_summary,
+        response=response_field,
+    )

src/anyvlm/schemas/vlm.py

@@ -12,65 +12,21 @@
 RESULT_ENTITY_TYPE = "genomicVariant"
 
 
-class HandoverSettings(BaseSettings):
-    """Settings for 'HandoverType' class"""
-
-    id: str
-    label: str
-
-    model_config = SettingsConfigDict(
-        env_prefix="HANDOVER_TYPE_",
-        extra="ignore",
-    )
-
-
-handover_type_settings = HandoverSettings()  # type: ignore
-
-
 class HandoverType(BaseModel):
     """The type of handover the parent `BeaconHandover` represents."""
 
-    id: str = Field(
-        "",
-        description="Node-specific identifier",
-        frozen=True,
-    )
+    id: str = Field(default="gregor", description="Node-specific identifier")
     label: str = Field(
-        "",
-        description="Node-specific label",
-        frozen=True,
-    )
-
-    model_config = ConfigDict(
-        extra="forbid",
-    )
-
-    # custom __init__ to prevent overriding attributes that are static/set via environment variables
-    def __init__(self) -> None:
-        super().__init__(
-            id=handover_type_settings.id,
-            label=handover_type_settings.label,
-        )
-
-
-class BeaconHandoverSettings(BaseSettings):
-    """Settings for 'BeaconHandover' class"""
-
-    url: str
-
-    model_config = SettingsConfigDict(
-        env_prefix="BEACON_HANDOVER_",
-        extra="ignore",
+        description="Node-specific identifier",
     )
 
 
-beacon_handover_settings = BeaconHandoverSettings()  # type: ignore
-
-
 class BeaconHandover(BaseModel):
     """Describes how users can get more information about the results provided in the parent `VlmResponse`"""
 
-    handoverType: HandoverType = Field(default=HandoverType())
+    handoverType: HandoverType = Field(
+        ..., description="The type of handover this represents"
+    )
     url: str = Field(
         "",
         description="""
@@ -79,10 +35,6 @@ class BeaconHandover(BaseModel):
         """,
     )
 
-    # custom __init__ to prevent overriding attributes that are static/set via environment variables
-    def __init__(self) -> None:
-        super().__init__(url=beacon_handover_settings.url)
-
 
 class ReturnedSchema(BaseModel):
     """Fixed [Beacon Schema](https://github.com/ga4gh-beacon/beacon-v2/blob/c6558bf2e6494df3905f7b2df66e903dfe509500/framework/json/common/beaconCommonComponents.json#L241)"""
@@ -190,7 +142,7 @@ class ResponseField(BaseModel):
 class VlmResponse(BaseModel):
     """Define response structure for the variant_counts endpoint."""
 
-    beaconHandovers: list[BeaconHandover] = [BeaconHandover()]
+    beaconHandovers: list[BeaconHandover]
     meta: Meta = Meta()
     responseSummary: ResponseSummary
     response: ResponseField