hexkit 3.5.0__tar.gz → 3.6.0__tar.gz

{hexkit-3.5.0/src/hexkit.egg-info → hexkit-3.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hexkit
-Version: 3.5.0
+Version: 3.6.0
 Summary: A Toolkit for Building Microservices using the Hexagonal Architecture
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0

{hexkit-3.5.0 → hexkit-3.6.0}/pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "hexkit"
-version = "3.5.0"
+version = "3.6.0"
 description = "A Toolkit for Building Microservices using the Hexagonal Architecture"
 dependencies = [
     "pydantic >=2, <3",

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/config.py

@@ -143,7 +143,7 @@ def config_from_yaml(
                 model_config = SettingsConfigDict(frozen=True, env_prefix=f"{prefix}_")
 
                 @classmethod
-                def settings_customise_sources(  # noqa: PLR0913
+                def settings_customise_sources(
                     cls,
                     settings_cls: type[BaseSettings],
                     init_settings: PydanticBaseSettingsSource,

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/protocols/dao.py

@@ -21,6 +21,7 @@ with the database.
 # ruff: noqa: PLR0913
 
 import typing
+import warnings
 from abc import ABC, abstractmethod
 from collections.abc import AsyncGenerator, AsyncIterator, Collection, Mapping
 from contextlib import AbstractAsyncContextManager
@@ -29,6 +30,7 @@ from typing import Any, Optional, TypeVar, Union, overload
 from uuid import uuid4
 
 from pydantic import BaseModel
+from typing_extensions import deprecated
 
 from hexkit.utils import FieldNotInModelError, validate_fields_in_model
 
@@ -259,6 +261,9 @@ class DaoNaturalId(DaoCommons[Dto], typing.Protocol[Dto]):
         ...
 
 
+@deprecated(
+    "uuid4_id_generator is deprecated as of v3.6 and will be removed in hexkit v4."
+)
 async def uuid4_id_generator() -> AsyncGenerator[str, None]:
     """Generates a new ID using the UUID4 algorithm.
     This is an AsyncGenerator to be compliant with the id_generator requirements of the
@@ -441,6 +446,15 @@ class DaoFactoryProtocol(DaoFactoryBase, ABC):
             # instantiate the default ID generator:
             id_generator = uuid4_id_generator()
 
+        if dto_creation_model is not None:
+            dep_msg = (
+                "The DAO API (and existing providers) are deprecated as of v3.6."
+                + " They will be simplified in hexkit v4."
+                + " Please plan to provide IDs during resource creation. The same model"
+                + " should be used for both creation and retrieval."
+            )
+            warnings.warn(dep_msg, category=DeprecationWarning, stacklevel=2)
+
         return await self._get_dao(
             name=name,
             dto_model=dto_model,

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/providers/mongodb/provider.py

@@ -22,6 +22,7 @@ Utilities for testing are located in `./testutils.py`.
 # ruff: noqa: PLR0913
 
 import json
+import warnings
 from abc import ABC
 from collections.abc import AsyncGenerator, AsyncIterator, Collection, Mapping
 from contextlib import AbstractAsyncContextManager
@@ -163,6 +164,17 @@ class MongoDbDaoBase(ABC, Generic[Dto]):
         self._document_to_dto = document_to_dto
         self._dto_to_document = dto_to_document
 
+        warnings.warn(
+            "The MongoDbDaoBase class and subclasses are deprecated as of v3.6 and will"
+            + " be replaced in hexkit v4 with the new MongoDbDao class. To replace the"
+            + " MongoDbDaoNaturalId: just use the new class. To replace the"
+            + " MongoDbDaoSurrogateId: use the new class, remove the creation model and"
+            + " id_generator parameters, and make sure the supplied DTO model includes"
+            + " the ID field with a default factory for generating new IDs.",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+
     async def get_by_id(self, id_: str) -> Dto:
         """Get a resource by providing its ID.
 

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/providers/mongokafka/provider.py

@@ -255,7 +255,14 @@ class MongoKafkaDaoPublisher(Generic[Dto]):
         document = self._dao._dto_to_document(dto)
         document.setdefault("__metadata__", {})["correlation_id"] = correlation_id
         result = await self._collection.replace_one(
-            {"_id": document["_id"], "__metadata__.deleted": False}, document
+            {
+                "_id": document["_id"],
+                "$or": [
+                    {"__metadata__": {"$exists": False}},
+                    {"__metadata__.deleted": False},
+                ],
+            },
+            document,
         )
         if result.matched_count == 0:
             raise ResourceNotFoundError(id_=document["_id"])
@@ -282,7 +289,14 @@ class MongoKafkaDaoPublisher(Generic[Dto]):
             },
         }
         result = await self._collection.replace_one(
-            {"_id": document["_id"], "__metadata__.deleted": False}, document
+            {
+                "_id": document["_id"],
+                "$or": [
+                    {"__metadata__": {"$exists": False}},
+                    {"__metadata__.deleted": False},
+                ],
+            },
+            document,
         )
         if result.matched_count == 0:
             raise ResourceNotFoundError(id_=id_)

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/providers/s3/testutils/__init__.py

@@ -20,18 +20,27 @@ from ._fixtures import (
     MEBIBYTE,
     TEST_FILE_DIR,
     TEST_FILE_PATHS,
+    FederatedS3Fixture,
     FileObject,
     S3ContainerFixture,
     S3Fixture,
+    S3MultiContainerFixture,
     calc_md5,
+    clean_federated_s3_fixture,
     clean_s3_fixture,
+    federated_s3_fixture,
+    get_clean_federated_s3_fixture,
     get_clean_s3_fixture,
+    get_persistent_federated_s3_fixture,
     get_persistent_s3_fixture,
     get_s3_container_fixture,
+    get_s3_multi_container_fixture,
+    persistent_federated_s3_fixture,
     persistent_s3_fixture,
     populate_storage,
     s3_container_fixture,
     s3_fixture,
+    s3_multi_container_fixture,
     temp_file_object,
     tmp_file,
     upload_file,
@@ -73,4 +82,13 @@ __all__ = [
     "upload_part",
     "upload_part_of_size",
     "upload_part_via_url",
+    "FederatedS3Fixture",
+    "S3MultiContainerFixture",
+    "clean_federated_s3_fixture",
+    "federated_s3_fixture",
+    "get_clean_federated_s3_fixture",
+    "get_s3_multi_container_fixture",
+    "get_persistent_federated_s3_fixture",
+    "s3_multi_container_fixture",
+    "persistent_federated_s3_fixture",
 ]

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/providers/s3/testutils/_fixtures.py

@@ -344,3 +344,151 @@ def tmp_file() -> Generator[FileObject, None, None]:
     """A fixture that provides a temporary file."""
     with temp_file_object() as temp_file:
         yield temp_file
+
+
+class FederatedS3Fixture:
+    """Fixture containing multiple S3 fixtures to simulate federated storage."""
+
+    def __init__(self, storages: dict[str, S3Fixture]):
+        self.storages = storages
+
+    def get_configs_by_alias(self) -> dict[str, S3Config]:
+        """Get the S3Config instance for each object storage in the fixture."""
+        return {alias: self.storages[alias].config for alias in self.storages}
+
+    async def populate_dummy_items(self, alias: str, contents: dict[str, list[str]]):
+        """Convenience function to populate a specific S3Fixture.
+
+        Args:
+        - `alias`: The alias of the S3Fixture to populate.
+        - `contents`: A dictionary with bucket names as keys and lists of object names
+        as values. The buckets can be empty, and the objects are created with a size of
+        1 byte.
+        """
+        if alias not in self.storages:
+            # This would indicate some kind of mismatch between config and fixture
+            raise RuntimeError(f"Alias '{alias}' not found in the federated S3 fixture")
+        storage = self.storages[alias]
+
+        # Populate the buckets so even empty buckets are established
+        await storage.populate_buckets([bucket for bucket in contents])
+
+        # Add the dummy items
+        for bucket, objects in contents.items():
+            for object in objects:
+                with temp_file_object(bucket, object, 1) as file:
+                    await storage.populate_file_objects([file])
+
+
+class S3MultiContainerFixture:
+    """Fixture for managing multiple running S3 test containers in order to mimic
+    multiple object storages.
+
+    Without this fixture, separate S3Fixture instances would access the same
+    underlying storage resources.
+    """
+
+    def __init__(self, s3_containers: dict[str, S3ContainerFixture]):
+        self.s3_containers = s3_containers
+
+    def __enter__(self):
+        """Enter the context manager and start the S3 containers."""
+        for container in self.s3_containers.values():
+            container.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Exit the context manager and clean up the S3 containers."""
+        for container in self.s3_containers.values():
+            container.__exit__(exc_type, exc_val, exc_tb)
+
+
+def _s3_multi_container_fixture(
+    request,
+) -> Generator[S3MultiContainerFixture, None, None]:
+    """Fixture function for getting multiple running S3 test containers."""
+    try:
+        storage_aliases = request.getfixturevalue("storage_aliases")
+    except pytest.FixtureLookupError as err:
+        raise NotImplementedError(
+            "You must provide a 'storage_aliases' fixture in your test setup."
+            + " It must have the same scope as 's3_multi_container'"
+            + " and it must return a list of the storage aliases to be used."
+        ) from err
+
+    if not storage_aliases:
+        raise RuntimeError("The 'storage_aliases' list must not be empty.")
+    s3_containers = {
+        alias: S3ContainerFixture(name=f"{alias}_s3_container")
+        for alias in storage_aliases
+    }
+    with S3MultiContainerFixture(s3_containers) as s3_multi_container:
+        yield s3_multi_container
+
+
+def get_s3_multi_container_fixture(
+    scope: PytestScope = "session", name: str = "s3_multi_container"
+):
+    """Get a fixture containing multiple LocalStack test containers.
+
+    By default, the session scope is used for LocalStack test containers.
+    Requires that a 'storage_aliases' fixture is provided in the test setup.
+    """
+    return pytest.fixture(_s3_multi_container_fixture, scope=scope, name=name)
+
+
+s3_multi_container_fixture = get_s3_multi_container_fixture()
+
+
+def _persistent_federated_s3_fixture(
+    s3_multi_container: S3MultiContainerFixture,
+) -> Generator[FederatedS3Fixture, None, None]:
+    """Fixture function that creates a persistent FederatedS3Fixture.
+
+    The state of each S3 storage in the fixture is not cleaned up.
+    """
+    s3_fixtures = {}
+    for alias, container in s3_multi_container.s3_containers.items():
+        config = container.s3_config
+        storage = S3ObjectStorage(config=config)
+        s3_fixtures[alias] = S3Fixture(config=config, storage=storage)
+    yield FederatedS3Fixture(s3_fixtures)
+
+
+def get_persistent_federated_s3_fixture(
+    scope: PytestScope = "function", name: str = "federated_s3"
+):
+    """Get a federated S3 storage fixture with desired scope.
+
+    The state of the S3 storage is not cleaned up by the fixture.
+    """
+    return pytest.fixture(_persistent_federated_s3_fixture, scope=scope, name=name)
+
+
+persistent_federated_s3_fixture = get_persistent_federated_s3_fixture()
+
+
+async def _clean_federated_s3_fixture(
+    s3_multi_container: S3MultiContainerFixture,
+) -> AsyncGenerator[FederatedS3Fixture, None]:
+    """Fixture function that creates a clean FederatedS3Fixture instance.
+
+    The state of each S3 storage is cleaned up before yielding the fixture.
+    """
+    for federated_s3_fixture in _persistent_federated_s3_fixture(s3_multi_container):
+        for s3_fixture in federated_s3_fixture.storages.values():
+            await s3_fixture.delete_buckets()
+        yield federated_s3_fixture
+
+
+def get_clean_federated_s3_fixture(
+    scope: PytestScope = "function", name: str = "federated_s3"
+):
+    """Get a federated S3 storage fixture with desired scope.
+
+    The state of the S3 storage is not cleaned up by the fixture.
+    """
+    return pytest_asyncio.fixture(_clean_federated_s3_fixture, scope=scope, name=name)
+
+
+federated_s3_fixture = clean_federated_s3_fixture = get_clean_federated_s3_fixture()

{hexkit-3.5.0 → hexkit-3.6.0}/src/hexkit/providers/s3/testutils/_utils.py

@@ -44,7 +44,7 @@ class FileObject(BaseModel):
     bucket_id: str
     object_id: str
 
-    @computed_field  # type: ignore [misc]
+    @computed_field  # type: ignore [prop-decorator]
     @property
     def content(self) -> bytes:
         """Extract the content from the file at the provided path"""
@@ -53,7 +53,7 @@ class FileObject(BaseModel):
         with open(self.file_path, "rb") as file:
             return file.read()
 
-    @computed_field  # type: ignore [misc]
+    @computed_field  # type: ignore [prop-decorator]
     @property
     def md5(self) -> str:
         """Calculate the md5 hash of the content"""

{hexkit-3.5.0 → hexkit-3.6.0/src/hexkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hexkit
-Version: 3.5.0
+Version: 3.6.0
 Summary: A Toolkit for Building Microservices using the Hexagonal Architecture
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0