Clean up enum, add tests, bump versions

mex/backend/extracted/main.py

@@ -25,7 +25,7 @@ def search_extracted_items(
     query_results = graph.query_nodes(
         q,
         stableTargetId,
-        [t.value for t in entityType or ExtractedType],
+        [str(t.value) for t in entityType or ExtractedType],
         skip,
         limit,
     )

mex/backend/extracted/models.py

@@ -1,31 +1,21 @@
-from enum import Enum, EnumMeta, _EnumDict
+from enum import Enum
 from typing import TYPE_CHECKING, Union
 
 from pydantic import Field
 
+from mex.backend.types import DynamicStrEnum
 from mex.common.models import (
     EXTRACTED_MODEL_CLASSES_BY_NAME,
     BaseExtractedData,
     BaseModel,
 )
-from mex.common.transform import dromedary_to_snake
 
 
-class ExtractedTypeMeta(EnumMeta):
-    """Meta class to dynamically populate the entity type enumeration."""
-
-    def __new__(
-        cls: type["ExtractedTypeMeta"], name: str, bases: tuple[type], dct: _EnumDict
-    ) -> "ExtractedTypeMeta":
-        """Create a new entity type enum by adding an entry for each model."""
-        for entity_type in EXTRACTED_MODEL_CLASSES_BY_NAME:
-            dct[dromedary_to_snake(entity_type).upper()] = entity_type
-        return super().__new__(cls, name, bases, dct)
-
-
-class ExtractedType(Enum, metaclass=ExtractedTypeMeta):
+class ExtractedType(Enum, metaclass=DynamicStrEnum):
     """Enumeration of possible types for extracted items."""
 
+    __names__ = list(EXTRACTED_MODEL_CLASSES_BY_NAME)
+
 
 if TYPE_CHECKING:  # pragma: no cover
     AnyExtractedModel = BaseExtractedData

mex/backend/graph/connector.py

@@ -26,14 +26,13 @@
 from mex.common.logging import logger
 from mex.common.models import (
     EXTRACTED_MODEL_CLASSES_BY_NAME,
+    MEX_PRIMARY_SOURCE_IDENTIFIER,
     MEX_PRIMARY_SOURCE_IDENTIFIER_IN_PRIMARY_SOURCE,
     MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
     ExtractedPrimarySource,
 )
 from mex.common.types import Identifier
 
-MEX_PRIMARY_SOURCE_IDENTIFIER = Identifier("00000000000000")
-
 
 class GraphConnector(BaseConnector):
     """Connector to handle authentication and transactions with the graph database."""

mex/backend/identity/provider.py

@@ -4,10 +4,6 @@
 from mex.backend.graph.transform import transform_identity_result_to_identity
 from mex.common.exceptions import MExError
 from mex.common.identity import BaseProvider, Identity
-from mex.common.models import (
-    MEX_PRIMARY_SOURCE_IDENTIFIER_IN_PRIMARY_SOURCE,
-    MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
-)
 from mex.common.types import Identifier, PrimarySourceID
 
 
@@ -29,20 +25,6 @@ def assign(
             raise MExError("found multiple identities indicating graph inconsistency")
         if len(graph_result.data) == 1:
             return transform_identity_result_to_identity(graph_result.data[0])
-        if (
-            identifier_in_primary_source
-            == MEX_PRIMARY_SOURCE_IDENTIFIER_IN_PRIMARY_SOURCE
-            and had_primary_source == MEX_PRIMARY_SOURCE_STABLE_TARGET_ID
-        ):
-            # This is to deal with the edge case where primary source is the parent of
-            # all primary sources and has no parents for itself,
-            # this will add itself as its parent.
-            return Identity(
-                hadPrimarySource=had_primary_source,
-                identifier=MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
-                identifierInPrimarySource=identifier_in_primary_source,
-                stableTargetId=MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
-            )
         return Identity(
             hadPrimarySource=had_primary_source,
             identifier=Identifier.generate(),

mex/backend/main.py

@@ -77,7 +77,7 @@ def close_connectors() -> None:
 
 
 @asynccontextmanager
-async def lifespan(app: FastAPI) -> AsyncIterator[None]:
+async def lifespan(_: FastAPI) -> AsyncIterator[None]:
     """Async context manager to execute setup and teardown of the FastAPI app."""
     yield None
     close_connectors()

mex/backend/merged/main.py

@@ -3,7 +3,11 @@
 from fastapi import APIRouter, Query
 
 from mex.backend.graph.connector import GraphConnector
-from mex.backend.merged.models import MergedItemSearchResponse, MergedType
+from mex.backend.merged.models import (
+    MergedItemSearchResponse,
+    MergedType,
+    UnprefixedType,
+)
 from mex.backend.merged.transform import (
     transform_graph_results_to_merged_item_search_response_facade,
 )
@@ -16,7 +20,7 @@
 def search_merged_items_facade(
     q: str = Query("", max_length=1000),
     stableTargetId: Identifier | None = Query(None),  # noqa: N803
-    entityType: Sequence[MergedType] = Query([]),  # noqa: N803
+    entityType: Sequence[MergedType | UnprefixedType] = Query([]),  # noqa: N803
     skip: int = Query(0, ge=0, le=10e10),
     limit: int = Query(10, ge=1, le=100),
 ) -> MergedItemSearchResponse:
@@ -27,7 +31,12 @@ def search_merged_items_facade(
     query_results = graph.query_nodes(
         q,
         stableTargetId,
-        [t.value.replace("Merged", "Extracted") for t in entityType or MergedType],
+        [
+            # Allow 'MergedPerson' as well as 'Person' as an entityType for this
+            # endpoint to keep compatibility with previous API clients.
+            f"Extracted{t.value.removeprefix('Merged')}"
+            for t in entityType or MergedType
+        ],
         skip,
         limit,
     )

mex/backend/merged/models.py

@@ -1,28 +1,24 @@
-from enum import Enum, EnumMeta, _EnumDict
+from enum import Enum
 from typing import TYPE_CHECKING, Union
 
 from pydantic import Field
 
+from mex.backend.types import DynamicStrEnum
 from mex.common.models import MERGED_MODEL_CLASSES_BY_NAME, MergedItem
 from mex.common.models.base import BaseModel
-from mex.common.transform import dromedary_to_snake
 
 
-class MergedTypeMeta(EnumMeta):
-    """Meta class to dynamically populate the entity type enumeration."""
+class UnprefixedType(Enum, metaclass=DynamicStrEnum):
+    """Enumeration of possible unprefixed types for merged items."""
 
-    def __new__(
-        cls: type["MergedTypeMeta"], name: str, bases: tuple[type], dct: _EnumDict
-    ) -> "MergedTypeMeta":
-        """Create a new entity type enum by adding an entry for each model."""
-        for entity_type in MERGED_MODEL_CLASSES_BY_NAME:
-            dct[dromedary_to_snake(entity_type).upper()] = entity_type
-        return super().__new__(cls, name, bases, dct)
+    __names__ = list(m.removeprefix("Merged") for m in MERGED_MODEL_CLASSES_BY_NAME)
 
 
-class MergedType(Enum, metaclass=MergedTypeMeta):
+class MergedType(Enum, metaclass=DynamicStrEnum):
     """Enumeration of possible types for merged items."""
 
+    __names__ = list(MERGED_MODEL_CLASSES_BY_NAME)
+
 
 if TYPE_CHECKING:  # pragma: no cover
     AnyMergedModel = MergedItem

mex/backend/types.py

@@ -1,8 +1,9 @@
-from enum import Enum
+from enum import Enum, EnumMeta, _EnumDict
 
 from pydantic import SecretStr
 
 from mex.common.models import BaseModel
+from mex.common.transform import dromedary_to_snake
 
 
 class AccessLevel(Enum):
@@ -42,3 +43,15 @@ class BackendIdentityProvider(Enum):
     """Identity providers implemented by mex-backend."""
 
     GRAPH = "graph"
+
+
+class DynamicStrEnum(EnumMeta):
+    """Meta class to dynamically populate the an enumeration from a list of strings."""
+
+    def __new__(
+        cls: type["DynamicStrEnum"], name: str, bases: tuple[type], dct: _EnumDict
+    ) -> "DynamicStrEnum":
+        """Create a new enum by adding an entry for each name in the source."""
+        for name in dct.pop("__names__"):
+            dct[dromedary_to_snake(name).upper()] = name
+        return super().__new__(cls, name, bases, dct)

pyproject.toml

@@ -12,7 +12,7 @@ packages = [{ include = "mex" }]
 python = "^3.11"
 fastapi = "^0.108.0"
 httpx = "^0.26.0"
-mex-common = { git = "https://github.com/robert-koch-institut/mex-common.git", rev = "0.19.0" }
+mex-common = { git = "https://github.com/robert-koch-institut/mex-common.git", rev = "feature/mx-1533-prep-graph-id-provider" }
 neo4j = "^5.16.0"
 pydantic = "^2.5.3"
 uvicorn = { version = "^0.25.0", extras = ["standard"] }

tests/identity/test_main.py

@@ -5,6 +5,7 @@
 from fastapi.testclient import TestClient
 
 from mex.common.models import (
+    MEX_PRIMARY_SOURCE_IDENTIFIER,
     MEX_PRIMARY_SOURCE_IDENTIFIER_IN_PRIMARY_SOURCE,
     MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
 )
@@ -142,7 +143,7 @@ def test_fetch_identity_invalid_query_params_mocked(
             },
             {
                 "hadPrimarySource": MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
-                "identifier": MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
+                "identifier": MEX_PRIMARY_SOURCE_IDENTIFIER,
                 "identifierInPrimarySource": MEX_PRIMARY_SOURCE_IDENTIFIER_IN_PRIMARY_SOURCE,
                 "stableTargetId": MEX_PRIMARY_SOURCE_STABLE_TARGET_ID,
             },