simplify logic for using env vars for values + preventing overrides

Author: jennifer-bowser

src/anyvlm/schemas/vlm.py

@@ -1,10 +1,9 @@
 """Schemas relating to VLM API."""
 
-from collections.abc import Callable
-from typing import Any, ClassVar, Literal, Self
+import os
+from typing import ClassVar, Literal, Self
 
-from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
-from pydantic_settings import BaseSettings, SettingsConfigDict
+from pydantic import BaseModel, ConfigDict, Field, model_validator
 
 from anyvlm.utils.types import Zygosity
 
@@ -13,59 +12,46 @@
 RESULT_ENTITY_TYPE = "genomicVariant"
 
 
-def forbid_env_override(field_name: str) -> Callable[..., Any]:
-    """Returns a Pydantic field validator that forbids explicitly
-    passing a value for `field_name`. The value must come from env.
-    """
+class MissingEnvironmentVariableError(Exception):
+    """Raised when a required environment variable is not set."""
 
-    @field_validator(field_name, mode="before")
-    @classmethod
-    def _forbid_override(cls, value: Any) -> Any:  # noqa: ARG001, ANN401, ANN001
-        if value is not None:
-            raise TypeError(f"{field_name} must be set via environment variable only")
-        return value
 
-    return _forbid_override
+def _get_environment_var(key: str) -> str:
+    value: str | None = os.environ.get(key)
+    if not value:
+        message = f"Missing required environment variable: {key}"
+        raise MissingEnvironmentVariableError(message)
+    return value
 
 
-class HandoverType(BaseSettings):
+class HandoverType(BaseModel):
     """The type of handover the parent `BeaconHandover` represents."""
 
-    id: str = Field(..., description="Node-specific identifier")
-    label: str = Field(..., description="Node-specific label")
-
-    model_config = SettingsConfigDict(env_prefix="HANDOVER_TYPE_", extra="forbid")
-
-    # These validators prevent instantiation of this class with values that would override `id` or `label`
-    _forbid_id_override = forbid_env_override("id")
-    _forbid_label_override = forbid_env_override("label")
+    id: str = Field(
+        _get_environment_var("HANDOVER_TYPE_ID"), description="Node-specific identifier"
+    )
+    label: str = Field(
+        _get_environment_var("HANDOVER_TYPE_LABEL"), description="Node-specific label"
+    )
 
-    # Allows `HandoverType` to be instantiated without providing values for the
-    # any required fields, since both are pulled from environment variables instead
+    # override __init__ to prevent the ability to override attributes that are set via environment variables
     def __init__(self) -> None:
         super().__init__()
 
 
-class BeaconHandover(BaseSettings):
+class BeaconHandover(BaseModel):
     """Describes how users can get more information about the results provided in the parent `VlmResponse`"""
 
     handoverType: HandoverType = Field(default=HandoverType())
     url: str = Field(
-        ...,
+        _get_environment_var("BEACON_HANDOVER_URL"),
         description="""
             A url which directs users to more detailed information about the results tabulated by the API. Must be human-readable.
             Ideally links directly to the variant specified in the query, but can be a generic search page if necessary.
         """,
     )
 
-    model_config = SettingsConfigDict(env_prefix="BEACON_HANDOVER_", extra="forbid")
-
-    # These validators prevent instantiation of this class with values that would override `handoverType` or `url`
-    _forbid_handoverType_override = forbid_env_override("handoverType")
-    _forbid_url_override = forbid_env_override("url")
-
-    # Allows `BeaconHandover` to be instantiated without providing values
-    # for any required fields, since both are generated statically
+    # override __init__ to prevent the ability to override attributes that are set via environment variables
     def __init__(self) -> None:
         super().__init__()
 
@@ -87,16 +73,15 @@ class ReturnedSchema(BaseModel):
     model_config = ConfigDict(populate_by_name=True)
 
 
-class Meta(BaseSettings):
+class Meta(BaseModel):
     """Relevant metadata about the results provided in the parent `VlmResponse`"""
 
     apiVersion: str = Field(
         default="v1.0",
         description="The version of the VLM API that this response conforms to",
     )
     beaconId: str = Field(
-        ...,
-        alias="BEACON_NODE_ID",
+        _get_environment_var("BEACON_NODE_ID"),
         description="""
             The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is,
             in the context of a Beacon network, to disambiguate responses coming from different Beacons. See the beacon documentation
@@ -105,15 +90,7 @@ class Meta(BaseSettings):
     )
     returnedSchemas: list[ReturnedSchema] = [ReturnedSchema()]
 
-    model_config = SettingsConfigDict(
-        env_prefix="", populate_by_name=False, extra="forbid"
-    )
-
-    # This validator prevents instantiation of this class with values that would override `handoverType` or `url`
-    _forbid_beaconId_override = forbid_env_override("beaconId")
-
-    # Allows `Meta` to be instantiated without providing values
-    # for any required fields, since all are generated statically
+    # override __init__ to prevent the ability to override attributes that are set via environment variables
     def __init__(self) -> None:
         super().__init__()
 

tests/conftest.py

@@ -6,14 +6,15 @@
 from ga4gh.vrs import models
 from pydantic import BaseModel
 
+load_dotenv()
 
-@pytest.fixture(scope="session", autouse=True)
-def load_env():
-    """Load `.env` file.
+# @pytest.fixture(scope="session", autouse=True)
+# def load_env():
+#     """Load `.env` file.
 
-    Must set `autouse=True` to run before other fixtures or test cases.
-    """
-    load_dotenv()
+#     Must set `autouse=True` to run before other fixtures or test cases.
+#     """
+#     print("LOADING DOTENV")
 
 
 @pytest.fixture(scope="session")