hexkit 4.1.1__tar.gz → 4.3.0__tar.gz

{hexkit-4.1.1 → hexkit-4.3.0}/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
    for the German Human Genome-Phenome Archive (GHGA)
 
    Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1/src/hexkit.egg-info → hexkit-4.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: hexkit
-Version: 4.1.1
+Version: 4.3.0
 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
@@ -11,6 +11,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
 Classifier: Topic :: Software Development :: Libraries
@@ -18,30 +19,32 @@ Classifier: Intended Audience :: Developers
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pydantic<3,>=2
-Requires-Dist: pydantic_settings<3,>=2
+Requires-Dist: opentelemetry-api<2,>=1.31.1
+Requires-Dist: pydantic<3,>=2.10
+Requires-Dist: pydantic_settings<3,>=2.8
 Requires-Dist: PyYAML<7,>=6
 Provides-Extra: akafka
 Requires-Dist: aiokafka~=0.12.0; extra == "akafka"
 Requires-Dist: jsonschema<5,>=4.23; extra == "akafka"
 Provides-Extra: s3
-Requires-Dist: boto3<2,>=1.35.80; extra == "s3"
-Requires-Dist: botocore<2,>=1.35.80; extra == "s3"
+Requires-Dist: boto3<2,>=1.37; extra == "s3"
+Requires-Dist: botocore<2,>=1.37; extra == "s3"
 Provides-Extra: mongodb
-Requires-Dist: motor<4,>=3.5.0; extra == "mongodb"
+Requires-Dist: motor<4,>=3.7; extra == "mongodb"
 Provides-Extra: test-akafka
 Requires-Dist: hexkit[akafka]; extra == "test-akafka"
-Requires-Dist: testcontainers[kafka]<5,>=4.9.0; extra == "test-akafka"
+Requires-Dist: testcontainers[kafka]<5,>=4.9; extra == "test-akafka"
 Provides-Extra: test-s3
 Requires-Dist: hexkit[s3]; extra == "test-s3"
-Requires-Dist: testcontainers<5,>=4.9.0; extra == "test-s3"
+Requires-Dist: testcontainers<5,>=4.9; extra == "test-s3"
 Provides-Extra: test-mongodb
 Requires-Dist: hexkit[mongodb]; extra == "test-mongodb"
-Requires-Dist: testcontainers[mongo]<5,>=4.9.0; extra == "test-mongodb"
+Requires-Dist: testcontainers[mongo]<5,>=4.9; extra == "test-mongodb"
 Provides-Extra: test
 Requires-Dist: hexkit[test-akafka,test-mongodb,test-s3]; extra == "test"
 Provides-Extra: all
 Requires-Dist: hexkit[test]; extra == "all"
+Dynamic: license-file
 
 ![tests](https://github.com/ghga-de/hexkit/actions/workflows/tests.yaml/badge.svg)
 [![PyPI version shields.io](https://img.shields.io/pypi/v/hexkit.svg)](https://pypi.python.org/pypi/hexkit/)
@@ -49,7 +52,7 @@ Requires-Dist: hexkit[test]; extra == "all"
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/hexkit/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/hexkit?branch=main)
 
 # hexkit
-A chassis library for building domain-focused, infrastructure-agnostic and event-driven
+A chassis library for building domain-focused, infrastructure-agnostic, and event-driven
 microservices in Python.
 
 ## In a Nutshell
@@ -76,8 +79,8 @@ for an individual service is to implement service-specific translators between t
 service's ports and the general-purpose protocols (in addition to implementing the
 domain functionality of the service, of course).
 
-Hexkit is designed as a general-purpose library. However, currently, it only contains a
-very limited collection of protocol-provider pairs that are of immediate interest to the
+Hexkit is designed as a general-purpose library. However, it currently contains only
+a limited collection of protocol-provider pairs that are of immediate interest to the
 authors. We like to add support for more protocols and technologies over time.
 
 The following protocols and providers are currently available:
@@ -94,9 +97,9 @@ for the rest. For example, you could use hexkit for simplifying the exchange of
 between microservices but use a classical web framework such as FastAPI for designing
 REST API and an ORM like SQLAlchemy for interacting with databases.
 
-Please also feel free to develop hexagonal components yourself (using the base classes of
-hexkit or not). Not every protocol or provider has to be general-purpose,
-however, if they are, please consider contributing them to hexkit.
+Feel free to develop hexagonal components yourself, whether or not you use the base
+classes of hexkit. Not every protocol or provider has to be general-purpose, however,
+if they are, please consider contributing them to hexkit.
 
 ## Getting started
 
@@ -132,25 +135,26 @@ The following extras are available:
 For setting up the development environment, we rely on the
 [devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode.
 
-To use it, you have to have Docker as well as vscode with its "Remote - Containers" extension (`ms-vscode-remote.remote-containers`) extension installed.
+To use it, you need Docker and VS Code with the "Remote - Containers" extension
+(`ms-vscode-remote.remote-containers`) installed.
 Then, you just have to open this repo in vscode and run the command
 `Remote-Containers: Reopen in Container` from the vscode "Command Palette".
 
 This will give you a full-fledged, pre-configured development environment including:
 - infrastructural dependencies of the service (databases, etc.)
 - all relevant vscode extensions pre-installed
-- pre-configured linting and auto-formating
+- pre-configured linting and auto-formatting
 - a pre-configured debugger
 - automatic license-header insertion
 
-Moreover, inside the devcontainer, there is follwing convenience command available
-(please type it in the integrated terminal of vscode):
+Additionally, the following convenience command is available inside the devcontainer
+(type it in the integrated terminal of VS Code):
 - `dev_install` - install the lib with all development dependencies and pre-commit hooks
 (please run that if you are starting the devcontainer for the first time
 or if added any python dependencies to the [`./setup.cfg`](./setup.cfg))
 
-If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
-by running the following commands:
+If you prefer not to use vscode, you could get a similar setup (without the editor
+specific features) by running the following commands:
 ``` bash
 # Execute in the repo's root dir:
 cd ./.devcontainer

{hexkit-4.1.1 → hexkit-4.3.0}/README.md

@@ -4,7 +4,7 @@
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/hexkit/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/hexkit?branch=main)
 
 # hexkit
-A chassis library for building domain-focused, infrastructure-agnostic and event-driven
+A chassis library for building domain-focused, infrastructure-agnostic, and event-driven
 microservices in Python.
 
 ## In a Nutshell
@@ -31,8 +31,8 @@ for an individual service is to implement service-specific translators between t
 service's ports and the general-purpose protocols (in addition to implementing the
 domain functionality of the service, of course).
 
-Hexkit is designed as a general-purpose library. However, currently, it only contains a
-very limited collection of protocol-provider pairs that are of immediate interest to the
+Hexkit is designed as a general-purpose library. However, it currently contains only
+a limited collection of protocol-provider pairs that are of immediate interest to the
 authors. We like to add support for more protocols and technologies over time.
 
 The following protocols and providers are currently available:
@@ -49,9 +49,9 @@ for the rest. For example, you could use hexkit for simplifying the exchange of
 between microservices but use a classical web framework such as FastAPI for designing
 REST API and an ORM like SQLAlchemy for interacting with databases.
 
-Please also feel free to develop hexagonal components yourself (using the base classes of
-hexkit or not). Not every protocol or provider has to be general-purpose,
-however, if they are, please consider contributing them to hexkit.
+Feel free to develop hexagonal components yourself, whether or not you use the base
+classes of hexkit. Not every protocol or provider has to be general-purpose, however,
+if they are, please consider contributing them to hexkit.
 
 ## Getting started
 
@@ -87,25 +87,26 @@ The following extras are available:
 For setting up the development environment, we rely on the
 [devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode.
 
-To use it, you have to have Docker as well as vscode with its "Remote - Containers" extension (`ms-vscode-remote.remote-containers`) extension installed.
+To use it, you need Docker and VS Code with the "Remote - Containers" extension
+(`ms-vscode-remote.remote-containers`) installed.
 Then, you just have to open this repo in vscode and run the command
 `Remote-Containers: Reopen in Container` from the vscode "Command Palette".
 
 This will give you a full-fledged, pre-configured development environment including:
 - infrastructural dependencies of the service (databases, etc.)
 - all relevant vscode extensions pre-installed
-- pre-configured linting and auto-formating
+- pre-configured linting and auto-formatting
 - a pre-configured debugger
 - automatic license-header insertion
 
-Moreover, inside the devcontainer, there is follwing convenience command available
-(please type it in the integrated terminal of vscode):
+Additionally, the following convenience command is available inside the devcontainer
+(type it in the integrated terminal of VS Code):
 - `dev_install` - install the lib with all development dependencies and pre-commit hooks
 (please run that if you are starting the devcontainer for the first time
 or if added any python dependencies to the [`./setup.cfg`](./setup.cfg))
 
-If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
-by running the following commands:
+If you prefer not to use vscode, you could get a similar setup (without the editor
+specific features) by running the following commands:
 ``` bash
 # Execute in the repo's root dir:
 cd ./.devcontainer

{hexkit-4.1.1 → hexkit-4.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 requires = [
-    "setuptools>=69",
+    "setuptools>=78.1",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -17,17 +17,19 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
     "Topic :: Software Development :: Libraries",
     "Intended Audience :: Developers",
 ]
 name = "hexkit"
-version = "4.1.1"
+version = "4.3.0"
 description = "A Toolkit for Building Microservices using the Hexagonal Architecture"
 dependencies = [
-    "pydantic >=2, <3",
-    "pydantic_settings >=2, <3",
+    "opentelemetry-api>=1.31.1, <2",
+    "pydantic >=2.10, <3",
+    "pydantic_settings >=2.8, <3",
     "PyYAML >=6, <7",
 ]
 
@@ -40,23 +42,23 @@ akafka = [
     "jsonschema >=4.23, <5",
 ]
 s3 = [
-    "boto3 >=1.35.80, <2",
-    "botocore >=1.35.80, <2",
+    "boto3 >=1.37, <2",
+    "botocore >=1.37, <2",
 ]
 mongodb = [
-    "motor >=3.5.0, <4",
+    "motor >=3.7, <4",
 ]
 test-akafka = [
     "hexkit[akafka]",
-    "testcontainers[kafka] >=4.9.0, <5",
+    "testcontainers[kafka] >=4.9, <5",
 ]
 test-s3 = [
     "hexkit[s3]",
-    "testcontainers >=4.9.0, <5",
+    "testcontainers >=4.9, <5",
 ]
 test-mongodb = [
     "hexkit[mongodb]",
-    "testcontainers[mongo] >=4.9.0, <5",
+    "testcontainers[mongo] >=4.9, <5",
 ]
 test = [
     "hexkit[test-akafka,test-s3,test-mongodb]",
@@ -175,8 +177,9 @@ check_untyped_defs = true
 no_site_packages = false
 
 [tool.pytest.ini_options]
-minversion = "8.0"
+minversion = "8.3"
 asyncio_mode = "strict"
+asyncio_default_fixture_loop_scope = "function"
 
 [tool.coverage.paths]
 source = [
@@ -188,7 +191,7 @@ source = [
 [tool.tox]
 legacy_tox_ini = """
     [tox]
-    env_list = py3{9,12}
+    env_list = py3{9,12,13}
 
     [gh-actions]
     python =
@@ -196,6 +199,7 @@ legacy_tox_ini = """
         3.10: py310
         3.11: py311
         3.12: py312
+        3.13: py313
 
     [testenv]
     pass_env =

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/__main__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/base.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/config.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/correlation.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/custom_types.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/log.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/dao.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/daopub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/daosub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/eventpub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/eventsub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/protocols/objstorage.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/config.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/provider/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/provider/daosub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/provider/eventpub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/provider/eventsub.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -33,6 +33,9 @@ from datetime import datetime, timezone
 from typing import Any, Callable, Literal, Optional, Protocol, TypeVar, Union, cast
 
 from aiokafka import AIOKafkaConsumer
+from opentelemetry import trace
+from opentelemetry.propagate import extract
+from opentelemetry.propagators import textmap
 from pydantic import ValidationError
 
 from hexkit.base import InboundProviderBase
@@ -50,6 +53,32 @@ from hexkit.providers.akafka.provider.utils import (
 CHANGE_EVENT_TYPE = "upserted"
 DELETE_EVENT_TYPE = "deleted"
 EventOrDaoSubProtocol = Union[DaoSubscriberProtocol, EventSubscriberProtocol]
+TextmapHeaders = list[tuple[str, bytes]]
+
+tracer = trace.get_tracer_provider().get_tracer("hexkit.providers.akafka")
+
+
+class AIOKafkaOtelContextExtractor(textmap.Getter[TextmapHeaders]):
+    """OpenTelemetry context extractor.
+
+    This is slighlty adapted from the aiokafka instrumentation library.
+    """
+
+    def get(self, carrier: TextmapHeaders, key: str) -> Optional[list[str]]:
+        """Extract specific OpenTelemetry header from propagated context"""
+        if carrier is None:
+            return None
+
+        for item_key, value in carrier:
+            if item_key == key and value is not None:
+                return [value.decode()]
+        return None
+
+    def keys(self, carrier: TextmapHeaders) -> list[str]:
+        """Get all headers from propagated context"""
+        if carrier is None:
+            return []
+        return [key for (key, value) in carrier]
 
 
 class ComboTranslator(EventSubscriberProtocol):
@@ -610,39 +639,49 @@ class KafkaEventSubscriber(InboundProviderBase):
 
     async def _consume_event(self, event: ConsumerEvent) -> None:
         """Consume an event by passing it down to the translator via the protocol."""
-        event_id = get_event_id(event, service_name=self._service_name)
-        event_info = self._extract_info(event)
-        try:
-            self._validate_extracted_info(event_info)
-        except RuntimeError as err:
-            logging.info(
-                "Ignored event of type '%s': %s, errors: %s",
-                event_info.type_,
-                event_id,
-                str(err),
-            )
-            # Always acknowledge event receipt for ignored events
-            await self._consumer.commit()
-            return
+        otel_extractor = AIOKafkaOtelContextExtractor()
+        extracted_context = extract(
+            event.headers,
+            getter=otel_extractor,
+        )
+        with tracer.start_as_current_span(
+            name="KafkaEventSubscriber._consume_event", context=extracted_context
+        ):
+            event_id = get_event_id(event, service_name=self._service_name)
+            event_info = self._extract_info(event)
+            try:
+                self._validate_extracted_info(event_info)
+            except RuntimeError as err:
+                logging.info(
+                    "Ignored event of type '%s': %s, errors: %s",
+                    event_info.type_,
+                    event_id,
+                    str(err),
+                )
+                # Always acknowledge event receipt for ignored events
+                await self._consumer.commit()
+                return
 
-        try:
-            logging.info("Consuming event of type '%s': %s", event_info.type_, event_id)
-            correlation_id = event_info.headers[HeaderNames.CORRELATION_ID]
-            async with set_correlation_id(correlation_id):
-                await self._handle_consumption(event=event_info, event_id=event_id)
-        except Exception:
-            # Errors only bubble up here if the DLQ isn't used
-            logging.critical(
-                "An error occurred while processing event of type '%s': %s. It was NOT"
-                " placed in the DLQ topic (%s)",
-                event_info.type_,
-                event_id,
-                self._dlq_topic if self._enable_dlq else "DLQ is disabled",
-            )
-            raise
-        else:
-            # Only save consumed event offsets if it was successful or sent to DLQ
-            await self._consumer.commit()
+            try:
+                logging.info(
+                    "Consuming event of type '%s': %s", event_info.type_, event_id
+                )
+                correlation_id = event_info.headers[HeaderNames.CORRELATION_ID]
+                async with set_correlation_id(correlation_id):
+                    await self._handle_consumption(event=event_info, event_id=event_id)
+            except Exception:
+                # Errors only bubble up here if the DLQ isn't used
+                logging.critical(
+                    "An error occurred while processing event of type '%s': %s. It was NOT"
+                    " placed in the DLQ topic (%s)",
+                    event_info.type_,
+                    event_id,
+                    self._dlq_topic if self._enable_dlq else "DLQ is disabled",
+                )
+                raise
+            else:
+                # Only save consumed event offsets if it was successful or sent to DLQ
+                await self._consumer.commit()
 
     async def run(self, forever: bool = True) -> None:
         """Start consuming events and passing them down to the translator.

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/provider/utils.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/testcontainer.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/akafka/testutils.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -152,7 +152,7 @@ def check_recorded_events(
 
     def get_field_mismatch_error(field, index):
         return get_detailed_error(
-            details=f"the {field} of the recorded event no. {index+1}"
+            details=f"the {field} of the recorded event no. {index + 1}"
             " does not match the expectations"
         )
 

{hexkit-4.1.1 → hexkit-4.3.0}/src/hexkit/providers/mongodb/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

{hexkit-4.1.1/src/hexkit/providers/mongokafka → hexkit-4.3.0/src/hexkit/providers/mongodb/migrations}/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,10 +12,24 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-#
 
-"""An implementation of the DaoPublisherFactoryProtocol based on MongoDB and Apache Kafka."""
+"""Database migration tools for MongoDB"""
 
-from .provider import MongoKafkaConfig, MongoKafkaDaoPublisherFactory
+from ._manager import (
+    MigrationConfig,
+    MigrationManager,
+    MigrationMap,
+    MigrationStepError,
+)
+from ._utils import Document, MigrationDefinition, Reversible, validate_doc
 
-__all__ = ["MongoKafkaConfig", "MongoKafkaDaoPublisherFactory"]
+__all__ = [
+    "Document",
+    "MigrationConfig",
+    "MigrationDefinition",
+    "MigrationManager",
+    "MigrationMap",
+    "MigrationStepError",
+    "Reversible",
+    "validate_doc",
+]