feature/model update v3

CHANGELOG.md

@@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changes
 
+- upgrade mex-common and mex-model dependencies to metadata model v3
+- apply additional linters in prep for `all` ruff linters
+
 ### Deprecated
 
 ### Removed

mex/backend/constants.py

@@ -0,0 +1 @@
+NUMBER_OF_RULE_TYPES = 3  # Additive, Subtractive and Preventive

mex/backend/exceptions.py

@@ -59,7 +59,7 @@ def handle_uncaught_exception(request: Request, exc: Exception) -> Response:
         content=ErrorResponse(
             message=str(exc),
             debug=DebuggingInfo(
-                errors=[dict(type=type(exc).__name__)],
+                errors=[{"type": type(exc).__name__}],
                 scope=DebuggingScope.model_validate(request.scope),
             ),
         ).model_dump_json(),

mex/backend/graph/connector.py

@@ -92,7 +92,8 @@ def _check_connectivity_and_authentication(self) -> Result:
         query_builder = QueryBuilder.get()
         result = self.commit(query_builder.fetch_database_status())
         if (status := result["currentStatus"]) != "online":
-            raise MExError(f"Database is {status}.") from None
+            msg = f"Database is {status}."
+            raise MExError(msg) from None
         return result
 
     def _seed_constraints(self) -> list[Result]:
@@ -494,7 +495,7 @@ def create_rule_set(
             self._merge_edges(
                 rule,
                 stable_target_id,
-                extra_refs=dict(stableTargetId=stable_target_id),
+                extra_refs={"stableTargetId": stable_target_id},
             )
 
     def ingest(self, models: list[AnyExtractedModel]) -> list[Identifier]:

mex/backend/graph/models.py

@@ -5,6 +5,7 @@
 from neo4j import Result as Neo4jResult
 
 from mex.backend.graph.exceptions import MultipleResultsFoundError, NoResultFoundError
+from mex.backend.logging import LOGGING_LINE_LENGTH
 
 
 class Result:
@@ -31,7 +32,7 @@ def __iter__(self) -> Iterator[dict[str, Any]]:
     def __repr__(self) -> str:
         """Return a human-readable representation of this result object."""
         representation = f"Result({self.all()!r})"
-        if len(representation) > 90:
+        if len(representation) > LOGGING_LINE_LENGTH:
             representation = f"{representation[:40]}... ...{representation[-40:]}"
         return representation
 

mex/backend/graph/query.py

@@ -71,4 +71,4 @@ def __getattr__(self, name: str) -> Callable[..., str]:
 
     def close(self) -> None:
         """Clean up the connector."""
-        pass  # no clean-up needed
+        # no clean-up needed

mex/backend/graph/transform.py

@@ -16,7 +16,7 @@ def expand_references_in_search_result(item: dict[str, Any]) -> None:
     `_SearchResultReference`. Before parsing them into pydantic, we need to inline
     the references back into the `item` dictionary.
     """
-    # XXX if we can use `apoc`, we might do this step directly in the cypher query
+    # TODO(ND): try to re-write directly in the cypher query, if we can use `apoc`
     for ref in cast(list[_SearchResultReference], item.pop("_refs")):
         target_list = item.setdefault(ref["label"], [None])
         length_needed = 1 + ref["position"] - len(target_list)

mex/backend/logging.py

@@ -2,6 +2,7 @@
 
 from mex.common.logging import logger
 
+LOGGING_LINE_LENGTH = 90
 UVICORN_LOGGING_CONFIG = DEFAULT_UVICORN_LOGGING_CONFIG.copy()
 UVICORN_LOGGING_CONFIG["loggers"][logger.name] = {
     "handlers": ["default"],

mex/backend/main.py

@@ -49,7 +49,7 @@ def create_openapi_schema() -> dict[str, Any]:
         summary=app.summary,
         description=app.description,
         routes=app.routes,
-        servers=[dict(url=settings.backend_api_url)],
+        servers=[{"url": settings.backend_api_url}],
     )
     for identifier in chain(EXTRACTED_IDENTIFIER_CLASSES, MERGED_IDENTIFIER_CLASSES):
         name = identifier.__name__
@@ -78,11 +78,11 @@ async def lifespan(_: FastAPI) -> AsyncIterator[None]:
         "The MEx API includes endpoints for multiple use-cases, "
         "e.g. for extractor pipelines, the MEx editor or inter-departmental access."
     ),
-    contact=dict(
-        name="RKI MEx Team",
-        email="[email protected]",
-        url="https://github.com/robert-koch-institut/mex-backend",
-    ),
+    contact={
+        "name": "RKI MEx Team",
+        "email": "[email protected]",
+        "url": "https://github.com/robert-koch-institut/mex-backend",
+    },
     lifespan=lifespan,
     version="v0",
 )

mex/backend/merged/helpers.py

@@ -2,6 +2,7 @@
 
 from pydantic import Field, TypeAdapter, ValidationError
 
+from mex.backend.constants import NUMBER_OF_RULE_TYPES
 from mex.backend.fields import MERGEABLE_FIELDS_BY_CLASS_NAME
 from mex.backend.graph.connector import GraphConnector
 from mex.backend.graph.exceptions import InconsistentGraphError
@@ -109,7 +110,8 @@ def create_merged_item(
     elif extracted_items:
         entity_type = ensure_prefix(extracted_items[0].stemType, "Merged")
     else:
-        raise MExError("One of rule_set or extracted_items is required.")
+        msg = "One of rule_set or extracted_items is required."
+        raise MExError(msg)
     fields = MERGEABLE_FIELDS_BY_CLASS_NAME[entity_type]
     cls = MERGED_MODEL_CLASSES_BY_NAME[entity_type]
 
@@ -178,14 +180,13 @@ def search_merged_items_in_graph(
             for component in item["components"]
             if component["entityType"] in RULE_MODEL_CLASSES_BY_NAME
         ]
-        if len(rules_raw) == 3:
+        if len(rules_raw) == NUMBER_OF_RULE_TYPES:
             rule_set_response = transform_raw_rules_to_rule_set_response(rules_raw)
         elif len(rules_raw) == 0:
             rule_set_response = None
         else:
-            raise MExError(
-                f"Unexpected number of rules found in graph: {len(rules_raw)}"
-            )
+            msg = f"Unexpected number of rules found in graph: {len(rules_raw)}"
+            raise MExError(msg)
 
         items.append(
             create_merged_item(

mex/backend/rules/helpers.py

@@ -1,6 +1,7 @@
 from collections.abc import Mapping
 from typing import Any, Final
 
+from mex.backend.constants import NUMBER_OF_RULE_TYPES
 from mex.backend.graph.connector import GraphConnector
 from mex.common.exceptions import MExError
 from mex.common.models import (
@@ -31,8 +32,9 @@ def transform_raw_rules_to_rule_set_response(
     response: dict[str, Any] = {}
     model: type[AnyRuleModel] | None
 
-    if len(raw_rules) != 3:
-        raise MExError("inconsistent rule item count")
+    if len(raw_rules) != NUMBER_OF_RULE_TYPES:
+        msg = "inconsistent rule item count"
+        raise MExError(msg)
 
     for rule in raw_rules:
         for field_name, model_class_lookup in MODEL_CLASS_LOOKUP_BY_FIELD_NAME.items():
@@ -42,9 +44,11 @@ def transform_raw_rules_to_rule_set_response(
                 stable_target_ids.extend(rule.pop("stableTargetId", []))
 
     if len(set(stem_types)) != 1:
-        raise MExError("inconsistent rule item stem types")
+        msg = "inconsistent rule item stem types"
+        raise MExError(msg)
     if len(set(stable_target_ids)) != 1:
-        raise MExError("inconsistent rule item stableTargetIds")
+        msg = "inconsistent rule item stableTargetIds"
+        raise MExError(msg)
 
     response["stableTargetId"] = stable_target_ids[0]
     response_class_name = ensure_postfix(stem_types[0], "RuleSetResponse")
@@ -102,5 +106,6 @@ def update_and_get_rule_set(
         stable_target_id,
         [rule_set.stemType],
     ):
-        raise MExError("no merged item found for given identifier and type")
+        msg = "no merged item found for given identifier and type"
+        raise MExError(msg)
     return create_and_get_rule_set(rule_set, stable_target_id)

mex/backend/types.py

@@ -56,8 +56,8 @@ 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
+        for value in dct.pop("__names__"):
+            dct[dromedary_to_snake(value).upper()] = value
         return super().__new__(cls, name, bases, dct)
 
 

mex/backend/utils.py

@@ -1,3 +1,4 @@
+import contextlib
 from collections.abc import Callable
 from typing import ParamSpec, TypeVar
 
@@ -21,10 +22,8 @@ def prune_list_in_dict(dict_: dict[str, list[T]], key: str, item: list[T] | T) -
     if not isinstance(item, list):
         item = [item]
     for removable in item:
-        try:
+        with contextlib.suppress(ValueError):
             list_.remove(removable)
-        except ValueError:
-            pass
 
 
 def reraising(

pyproject.toml

@@ -8,13 +8,13 @@ license = { file = "LICENSE" }
 urls = { Repository = "https://github.com/robert-koch-institut/mex-backend" }
 requires-python = ">=3.11,<3.13"
 dependencies = [
-    "fastapi>=0.114.2,<1",
+    "fastapi>=0.115.4,<1",
     "httpx>=0.27.2,<1",
     "jinja2>=3.1.4,<4",
-    "mex-common @ git+https://github.com/robert-koch-institut/mex-common.git@0.38.0",
+    "mex-common @ git+https://github.com/robert-koch-institut/mex-common.git@0.40.0",
     "neo4j>=5.24.0,<6",
     "pydantic>=2.9.1,<3",
-    "starlette>=0.38.5,<1",
+    "starlette>=0.41.2,<1",
     "uvicorn[standard]>=0.30.6,<1",
 ]
 optional-dependencies.dev = [

tests/auxiliary/conftest.py

@@ -6,6 +6,7 @@
 import requests
 from pytest import MonkeyPatch
 from requests import Response
+from starlette import status
 
 from mex.common.wikidata.connector import (
     WikidataAPIConnector,
@@ -15,9 +16,9 @@
 TEST_DATA_DIR = Path(__file__).parent / "test_data"
 
 
-@pytest.fixture()
+@pytest.fixture
 def mocked_wikidata(monkeypatch: MonkeyPatch) -> None:
-    response_query = Mock(spec=Response, status_code=200)
+    response_query = Mock(spec=Response, status_code=status.HTTP_200_OK)
 
     session = MagicMock(spec=requests.Session)
     session.get = MagicMock(side_effect=[response_query])