diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8398fbe..3073ec1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,11 +3,11 @@ default_language_version: python: python3.11 repos: - repo: https://github.com/psf/black - rev: 24.3.0 + rev: 24.4.2 hooks: - id: black - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.3.5 + rev: v0.4.6 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] @@ -28,7 +28,7 @@ repos: - id: fix-byte-order-marker name: byte-order - repo: https://github.com/pdm-project/pdm - rev: 2.13.2 + rev: 2.15.3 hooks: - id: pdm-lock-check name: pdm diff --git a/CHANGELOG.md b/CHANGELOG.md index 83b49b8..70aa951 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - updated graph connector for new queries - improved isolation of neo4j dependency - improved documentation and code-readability +- move exception handling middleware to new module +- change `identity_provider` default to `MEMORY` +- add stop-gap code waiting to be resolved by mx-1596 +- migrate to latest `mex-common` ### Deprecated diff --git a/mex/backend/exceptions.py b/mex/backend/exceptions.py new file mode 100644 index 0000000..c75da70 --- /dev/null +++ b/mex/backend/exceptions.py @@ -0,0 +1,55 @@ +from typing import Any + +from fastapi.responses import JSONResponse +from pydantic import BaseModel, ValidationError +from starlette.requests import Request + +from mex.backend.transform import to_primitive +from mex.common.logging import logger + + +class DebuggingScope(BaseModel, extra="ignore"): + """Scope for debugging info of error responses.""" + + http_version: str + method: str + path: str + path_params: dict[str, Any] + query_string: str + scheme: str + + +class DebuggingInfo(BaseModel): + """Debugging information for error responses.""" + + errors: list[dict[str, Any]] + scope: DebuggingScope + + +class ErrorResponse(BaseModel): + """Response model for user and system errors.""" + + message: str + debug: DebuggingInfo + + +def handle_uncaught_exception(request: Request, exc: Exception) -> JSONResponse: + """Handle uncaught errors and provide debugging info.""" + logger.exception("Error %s", exc) + if isinstance(exc, ValidationError): + errors = [dict(error) for error in exc.errors()] + status_code = 400 + else: + errors = [dict(type=type(exc).__name__)] + status_code = 500 + return JSONResponse( + to_primitive( + ErrorResponse( + message=str(exc), + debug=DebuggingInfo( + errors=errors, scope=DebuggingScope.model_validate(request.scope) + ), + ) + ), + status_code, + ) diff --git a/mex/backend/graph/connector.py b/mex/backend/graph/connector.py index 9619e25..89abf48 100644 --- a/mex/backend/graph/connector.py +++ b/mex/backend/graph/connector.py @@ -71,7 +71,7 @@ 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}.") + raise MExError(f"Database is {status}.") from None return result def _seed_constraints(self) -> list[Result]: diff --git a/mex/backend/graph/models.py b/mex/backend/graph/models.py index 73c86de..05d8dca 100644 --- a/mex/backend/graph/models.py +++ b/mex/backend/graph/models.py @@ -61,7 +61,7 @@ def one_or_none(self) -> dict[str, Any] | None: case 0: return None case _: - raise MultipleResultsFoundError + raise MultipleResultsFoundError from None def get_update_counters(self) -> dict[str, int]: """Return a summary of counters for operations the query triggered.""" diff --git a/mex/backend/main.py b/mex/backend/main.py index bd6f2ef..4923ff1 100644 --- a/mex/backend/main.py +++ b/mex/backend/main.py @@ -6,10 +6,9 @@ from fastapi import APIRouter, Depends, FastAPI from fastapi.middleware.cors import CORSMiddleware from fastapi.openapi.utils import get_openapi -from fastapi.responses import JSONResponse -from pydantic import BaseModel, ValidationError -from starlette.requests import Request +from pydantic import BaseModel +from mex.backend.exceptions import handle_uncaught_exception from mex.backend.extracted.main import router as extracted_router from mex.backend.identity.main import router as identity_router from mex.backend.ingest.main import router as ingest_router @@ -17,11 +16,8 @@ from mex.backend.merged.main import router as merged_router from mex.backend.security import has_read_access, has_write_access from mex.backend.settings import BackendSettings -from mex.backend.transform import to_primitive from mex.common.cli import entrypoint -from mex.common.connector import ConnectorContext -from mex.common.exceptions import MExError -from mex.common.logging import logger +from mex.common.connector import CONNECTOR_STORE from mex.common.types import Identifier from mex.common.types.identifier import MEX_ID_PATTERN @@ -61,24 +57,11 @@ def create_openapi_schema() -> dict[str, Any]: return app.openapi_schema -def close_connectors() -> None: - """Try to close all connectors in the current context.""" - context = ConnectorContext.get() - for connector_type, connector in context.items(): - try: - connector.close() - except Exception: - logger.exception("Error closing %s", connector_type) - else: - logger.info("Closed %s", connector_type) - context.clear() - - @asynccontextmanager async def lifespan(_: FastAPI) -> AsyncIterator[None]: """Async context manager to execute setup and teardown of the FastAPI app.""" yield None - close_connectors() + CONNECTOR_STORE.reset() app = FastAPI( @@ -116,20 +99,7 @@ def check_system_status() -> SystemStatus: return SystemStatus(status="ok") -def handle_uncaught_exception(request: Request, exc: Exception) -> JSONResponse: - """Handle uncaught errors and provide some debugging clues.""" - logger.exception("Error %s", exc) - if isinstance(exc, ValidationError): - errors: list[Any] = exc.errors() - else: - errors = [dict(type=type(exc).__name__)] - body = dict(message=str(exc), debug=dict(errors=errors)) - return JSONResponse(to_primitive(body), 500) - - app.include_router(router) -app.add_exception_handler(ValidationError, handle_uncaught_exception) -app.add_exception_handler(MExError, handle_uncaught_exception) app.add_exception_handler(Exception, handle_uncaught_exception) app.add_middleware( CORSMiddleware, diff --git a/mex/backend/security.py b/mex/backend/security.py index 55c839c..280fd33 100644 --- a/mex/backend/security.py +++ b/mex/backend/security.py @@ -12,7 +12,7 @@ X_API_CREDENTIALS = HTTPBasic(auto_error=False) -def __check_header_for_authorization_method( +def _check_header_for_authorization_method( api_key: Annotated[str | None, Depends(X_API_KEY)] = None, credentials: Annotated[ HTTPBasicCredentials | None, Depends(X_API_CREDENTIALS) @@ -71,15 +71,15 @@ def has_write_access( Settings: check credentials in backend_user_database or backend_api_key_database """ - __check_header_for_authorization_method(api_key, credentials, user_agent) + _check_header_for_authorization_method(api_key, credentials, user_agent) settings = BackendSettings.get() can_write = False if api_key: api_key_database = settings.backend_api_key_database - can_write = APIKey(api_key) in api_key_database.write + can_write = APIKey(api_key) in api_key_database["write"] elif credentials: - api_write_user_db = settings.backend_user_database.write + api_write_user_db = settings.backend_user_database["write"] user, pw = credentials.username, credentials.password.encode("utf-8") if api_write_user := api_write_user_db.get(user): can_write = compare_digest( @@ -118,7 +118,7 @@ def has_read_access( Settings: check credentials in backend_user_database or backend_api_key_database """ - __check_header_for_authorization_method(api_key, credentials, user_agent) + _check_header_for_authorization_method(api_key, credentials, user_agent) try: has_write_access(api_key, credentials) # read access implied by write access @@ -130,9 +130,9 @@ def has_read_access( can_read = False if api_key: api_key_database = settings.backend_api_key_database - can_read = APIKey(api_key) in api_key_database.read + can_read = APIKey(api_key) in api_key_database["read"] elif credentials: - api_read_user_db = settings.backend_user_database.read + api_read_user_db = settings.backend_user_database["read"] user, pw = credentials.username, credentials.password.encode("utf-8") if api_read_user := api_read_user_db.get(user): can_read = compare_digest( diff --git a/mex/backend/settings.py b/mex/backend/settings.py index d36d507..e01a54a 100644 --- a/mex/backend/settings.py +++ b/mex/backend/settings.py @@ -71,7 +71,7 @@ class BackendSettings(BaseSettings): validation_alias="MEX_BACKEND_API_USER_DATABASE", ) identity_provider: IdentityProvider | BackendIdentityProvider = Field( - BackendIdentityProvider.GRAPH, + IdentityProvider.MEMORY, description="Provider to assign stableTargetIds to new model instances.", validation_alias="MEX_IDENTITY_PROVIDER", ) # type: ignore[assignment] diff --git a/mex/backend/transform.py b/mex/backend/transform.py index d096cd6..1225d72 100644 --- a/mex/backend/transform.py +++ b/mex/backend/transform.py @@ -8,6 +8,7 @@ JSON_ENCODERS: Final[dict[type, Callable[[Any], str]]] = { Enum: lambda obj: str(obj.value), + Exception: lambda obj: str(obj), Identifier: lambda obj: str(obj), TemporalEntity: lambda obj: str(obj), } diff --git a/mex/backend/types.py b/mex/backend/types.py index abea95b..498424f 100644 --- a/mex/backend/types.py +++ b/mex/backend/types.py @@ -1,10 +1,9 @@ from enum import Enum, EnumMeta, _EnumDict -from typing import Literal +from typing import Literal, cast from pydantic import SecretStr from mex.common.models import ( - BASE_MODEL_CLASSES_BY_NAME, EXTRACTED_MODEL_CLASSES_BY_NAME, MERGED_MODEL_CLASSES_BY_NAME, BaseModel, @@ -39,6 +38,10 @@ class APIKeyDatabase(BaseModel): read: list[APIKey] = [] write: list[APIKey] = [] + def __getitem__(self, key: str) -> list[APIKey]: # stop-gap: MX-1596 + """Return an attribute in indexing syntax.""" + return cast(list[APIKey], getattr(self, key)) + class APIUserDatabase(BaseModel): """Database containing usernames and passwords for backend API.""" @@ -46,6 +49,10 @@ class APIUserDatabase(BaseModel): read: dict[str, APIUserPassword] = {} write: dict[str, APIUserPassword] = {} + def __getitem__(self, key: str) -> dict[str, APIUserPassword]: # stop-gap: MX-1596 + """Return an attribute in indexing syntax.""" + return cast(dict[str, APIUserPassword], getattr(self, key)) + class BackendIdentityProvider(Enum): """Identity providers implemented by mex-backend.""" @@ -68,7 +75,7 @@ def __new__( class UnprefixedType(Enum, metaclass=DynamicStrEnum): """Enumeration of possible types without any prefix.""" - __names__ = list(m.removeprefix("Base") for m in BASE_MODEL_CLASSES_BY_NAME) + __names__ = 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a/pyproject.toml b/pyproject.toml index 7548419..ed8f3dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,9 +10,9 @@ requires-python = "<3.13,>=3.11" dependencies = [ "fastapi==0.111.0", "httpx==0.27.0", - "mex-common@git+https://github.com/robert-koch-institut/mex-common.git@0.22.0", + "mex-common@git+https://github.com/robert-koch-institut/mex-common.git@0.26.1", "neo4j==5.20.0", - "pydantic==2.7.1", + "pydantic==2.7.2", "uvicorn[standard]==0.29.0", ] optional-dependencies.dev = [ @@ -21,8 +21,8 @@ optional-dependencies.dev = [ "mypy==1.10.0", "pytest-cov==5.0.0", "pytest-random-order==1.1.1", - "pytest==8.2.0", - "ruff==0.4.4", + "pytest==8.2.1", + "ruff==0.4.6", "sphinx==7.3.7", "types-pytz==2024.1.0.20240417", ] diff --git a/tests/conftest.py b/tests/conftest.py index 465b28b..678a5a5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -13,7 +13,7 @@ from mex.backend.graph.connector import GraphConnector from mex.backend.main import app from mex.backend.settings import BackendSettings -from mex.backend.types import APIKeyDatabase, APIUserDatabase +from mex.backend.types import APIKeyDatabase, APIUserDatabase, BackendIdentityProvider from mex.common.models import ( MEX_PRIMARY_SOURCE_STABLE_TARGET_ID, AnyExtractedModel, @@ -33,7 +33,6 @@ TextLanguage, Theme, ) -from mex.common.types.identifier import IdentifierT pytest_plugins = ("mex.common.testing.plugin",) @@ -59,7 +58,7 @@ def skip_integration_test_in_ci(is_integration_test: bool) -> None: @pytest.fixture def client() -> TestClient: """Return a fastAPI test client initialized with our app.""" - with TestClient(app) as test_client: + with TestClient(app, raise_server_exceptions=False) as test_client: return test_client @@ -142,18 +141,24 @@ def isolate_identifier_seeds(monkeypatch: MonkeyPatch) -> None: counter = count() original_generate = Identifier.generate - def generate(cls: type[IdentifierT], seed: int | None = None) -> IdentifierT: + def generate(cls: type[Identifier], seed: int | None = None) -> Identifier: return cls(original_generate(seed or next(counter))) monkeypatch.setattr(Identifier, "generate", classmethod(generate)) @pytest.fixture(autouse=True) -def set_identity_provider(is_integration_test: bool) -> None: - """Ensure the identifier provider is set to `MEMORY` in unit tests.""" - if not is_integration_test: - settings = BaseSettings.get() - settings.identity_provider = IdentityProvider.MEMORY +def set_identity_provider(is_integration_test: bool, monkeypatch: MonkeyPatch) -> None: + """Ensure the identifier provider is set correctly for unit and int tests.""" + settings = BaseSettings.get() + if is_integration_test: + # yuck, all this needs cleaning up after MX-1596 + monkeypatch.setitem(settings.model_config, "validate_assignment", False) + monkeypatch.setattr( + settings, "identity_provider", BackendIdentityProvider.GRAPH + ) + else: + monkeypatch.setattr(settings, "identity_provider", IdentityProvider.MEMORY) @pytest.fixture(autouse=True) diff --git a/tests/extracted/test_main.py b/tests/extracted/test_main.py index 701e0b9..087bc41 100644 --- a/tests/extracted/test_main.py +++ b/tests/extracted/test_main.py @@ -76,7 +76,7 @@ def test_search_extracted_items_mocked( "description": [], "documentation": [], "hadPrimarySource": "00000000000000", - "identifier": "00000000000000", + "identifier": "00000000000001", "identifierInPrimarySource": "mex", "locatedAt": [], "stableTargetId": "00000000000000", diff --git a/tests/graph/test_connector.py b/tests/graph/test_connector.py index 7898866..6fff646 100644 --- a/tests/graph/test_connector.py +++ b/tests/graph/test_connector.py @@ -111,12 +111,12 @@ def test_mocked_graph_seed_data(mocked_graph: MockedGraph) -> None: nested_node_labels=[], )""", { - "identifier": ExtractedPrimarySourceIdentifier("00000000000000"), + "identifier": ExtractedPrimarySourceIdentifier("00000000000001"), "stable_target_id": MergedPrimarySourceIdentifier("00000000000000"), "on_match": {"version": None}, "on_create": { "version": None, - "identifier": "00000000000000", + "identifier": "00000000000001", "identifierInPrimarySource": "mex", }, "nested_positions": [], @@ -130,7 +130,7 @@ def test_mocked_graph_seed_data(mocked_graph: MockedGraph) -> None: ref_labels=["hadPrimarySource", "stableTargetId"], )""", { - "identifier": "00000000000000", + "identifier": "00000000000001", "ref_identifiers": ["00000000000000", "00000000000000"], "ref_positions": [0, 0], }, diff --git a/tests/test_exceptions.py b/tests/test_exceptions.py new file mode 100644 index 0000000..499650d --- /dev/null +++ b/tests/test_exceptions.py @@ -0,0 +1,88 @@ +import json +from typing import Any +from unittest.mock import Mock + +import pydantic_core +import pytest +from pydantic import ValidationError + +from mex.backend.exceptions import handle_uncaught_exception +from mex.common.exceptions import MExError + +MOCK_REQUEST_SCOPE = { + "http_version": "1.1", + "method": "GET", + "path": "/test", + "path_params": {}, + "query_string": "", + "scheme": "HTTPS", +} + + +@pytest.mark.parametrize( + ("exception", "expected", "status_code"), + [ + ( + TypeError("foo"), + { + "debug": { + "errors": [{"type": "TypeError"}], + "scope": MOCK_REQUEST_SCOPE, + }, + "message": "foo", + }, + 500, + ), + ( + ValidationError.from_exception_data( + "foo", + [ + { + "type": pydantic_core.PydanticCustomError( + "TestError", "You messed up!" + ), + "loc": ("integerAttribute",), + "input": "mumbo-jumbo", + } + ], + ), + { + "debug": { + "errors": [ + { + "input": "mumbo-jumbo", + "loc": ["integerAttribute"], + "msg": "You messed up!", + "type": "TestError", + } + ], + "scope": MOCK_REQUEST_SCOPE, + }, + "message": "1 validation error for foo\n" + "integerAttribute\n" + " You messed up! [type=TestError, input_value='mumbo-jumbo', " + "input_type=str]", + }, + 400, + ), + ( + MExError("bar"), + { + "message": "MExError: bar ", + "debug": { + "errors": [{"type": "MExError"}], + "scope": MOCK_REQUEST_SCOPE, + }, + }, + 500, + ), + ], + ids=["TypeError", "ValidationError", "MExError"], +) +def test_handle_uncaught_exception( + exception: Exception, expected: dict[str, Any], status_code: int +) -> None: + request = Mock(scope=MOCK_REQUEST_SCOPE) + response = handle_uncaught_exception(request, exception) + assert response.status_code == status_code, response.body + assert json.loads(response.body) == expected diff --git a/tests/test_main.py b/tests/test_main.py index b7f7462..6d217d5 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -1,23 +1,9 @@ -import json -import logging -from typing import Any -from unittest.mock import MagicMock, Mock - -import pydantic_core import pytest from fastapi.testclient import TestClient from neo4j import GraphDatabase -from pydantic import ValidationError -from pytest import LogCaptureFixture -from mex.backend.main import ( - app, - close_connectors, - handle_uncaught_exception, -) +from mex.backend.main import app from mex.backend.settings import BackendSettings -from mex.common.connector import ConnectorContext -from mex.common.exceptions import MExError def test_openapi_schema(client: TestClient) -> None: @@ -44,71 +30,6 @@ def test_health_check(client: TestClient) -> None: assert response.json() == {"status": "ok"} -@pytest.mark.parametrize( - ("exception", "expected"), - [ - ( - TypeError("foo"), - {"debug": {"errors": [{"type": "TypeError"}]}, "message": "foo"}, - ), - ( - ValidationError.from_exception_data( - "foo", - [ - { - "type": pydantic_core.PydanticCustomError( - "TestError", "You messed up!" - ), - "loc": ("integerAttribute",), - "input": "mumbojumbo", - } - ], - ), - { - "debug": { - "errors": [ - { - "input": "mumbojumbo", - "loc": ["integerAttribute"], - "msg": "You messed up!", - "type": "TestError", - } - ] - }, - "message": "1 validation error for foo\n" - "integerAttribute\n" - " You messed up! [type=TestError, input_value='mumbojumbo', " - "input_type=str]", - }, - ), - ( - MExError("bar"), - {"message": "MExError: bar ", "debug": {"errors": [{"type": "MExError"}]}}, - ), - ], - ids=["TypeError", "ValidationError", "MExError"], -) -def test_handle_uncaught_exception( - exception: Exception, expected: dict[str, Any] -) -> None: - response = handle_uncaught_exception(Mock(), exception) - assert response.status_code == 500, response.body - assert json.loads(response.body) == expected - - -def test_close_all_connectors(caplog: LogCaptureFixture) -> None: - context = { - "ConnectorA": Mock(close=MagicMock()), - "ConnectorB": Mock(close=MagicMock(side_effect=Exception())), - } - ConnectorContext.set(context) - - with caplog.at_level(logging.INFO): - close_connectors() - assert "Closed ConnectorA" in caplog.text - assert "Error closing ConnectorB" in caplog.text - - def test_all_endpoints_require_authorization(client: TestClient) -> None: excluded_routes = [ "/openapi.json",