V2 (#82)

* remove DI framework (GSI-536) (#78)

- removes the DI framework.
- removes  dependency_injector from dependencies
- example app shown DI without dedicated framework
- added tests for the CLI of the example app

This is a breaking change.

Bumps version to 2.0.0.

* Tools for Structured Logging (GSI 510) (#77)

* Add basic logging tools

* Use configurable class rather than instance

* Add service name and instance id to config

* Explicitly get service/instance from log record

* Use capitalized LogLevel literal for log_level arg

* Add __all__ and rename Adapter to StructuredLogger

* Add RecordCompiler handler

* Add log_format config option

* Bump version from 1.2.0 -> 2.0.0

* Add tests

* remove DI framework (GSI-536) (#78)

- removes the DI framework.
- removes  dependency_injector from dependencies
- example app shown DI without dedicated framework
- added tests for the CLI of the example app

This is a breaking change.

Bumps version to 2.0.0.

* Rename function and remove second config in fixture

* Integrate Kersten's suggestions for simpler config

---------

Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>
Co-authored-by: Kersten Breuer <kersten-breuer@outlook.com>

* Upgrade pytest-asyncio (GSI-534) (#80)

* Remove cap on pytest-asyncio and update lock files

* Use module-scoped kafka fixture in correlation tests

Place the publishing tests at the end of the module, rather than in the middle.

* Specify minimum ver so lower version doesn't get installed

---------

Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>

* Log all config (GSI-546) (#81)

* Log complete config when configuring logging

* Make no-secrets log test more robust

* Add suggested changes

---------

Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>

---------

Co-authored-by: Kersten Breuer <kersten-breuer@outlook.com>
Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>

.pre-commit-config.yaml

@@ -51,7 +51,7 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.1.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

examples/stream_calc/sc_tests/integration/test_cli.py

@@ -0,0 +1,57 @@
+# Copyright 2021 - 2023 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");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+#
+
+"""Test the stream_calc app via the CLI."""
+
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+from func_timeout import func_timeout
+
+from hexkit.providers.akafka.testutils import KafkaFixture, kafka_fixture  # noqa:F401
+from sc_tests.integration.test_event_api import (
+    CASES,
+    check_problem_outcomes,
+    submit_test_problems,
+)
+
+APP_DIR = Path(__file__).parent.parent.parent.absolute()
+
+
+def test_cli(kafka_fixture: KafkaFixture, monkeypatch):  # noqa:F811
+    """Test the stream_calc app via the CLI."""
+    os.chdir(APP_DIR)
+    monkeypatch.setenv(
+        name="STREAM_CALC_KAFKA_SERVERS", value=f'["{kafka_fixture.kafka_servers[0]}"]'
+    )
+    monkeypatch.setenv(
+        name="PYTHONPATH", value=(os.environ.get("PYTHONPATH", "") + f":{APP_DIR}")
+    )
+
+    submit_test_problems(CASES, kafka_server=kafka_fixture.kafka_servers[0])
+
+    with subprocess.Popen(
+        args=["-m", "stream_calc"],
+        executable=sys.executable,
+    ) as process:
+        func_timeout(
+            10,
+            check_problem_outcomes,
+            kwargs={"cases": CASES, "kafka_server": kafka_fixture.kafka_servers[0]},
+        )
+        process.terminate()

examples/stream_calc/sc_tests/integration/test_event_api.py

@@ -22,7 +22,6 @@
 """
 
 import json
-from copy import deepcopy
 from typing import NamedTuple
 
 import pytest
@@ -203,7 +202,7 @@ def check_problem_outcomes(
 
 
 @pytest.mark.asyncio
-async def test_receive_calc_publish(cases: list[Case] = deepcopy(CASES)):
+async def test_receive_calc_publish():
     """
     Test the receipt of new arithmetic problems, the calculation, and the publication of
     the results.
@@ -212,12 +211,12 @@ async def test_receive_calc_publish(cases: list[Case] = deepcopy(CASES)):
     with KafkaContainer(image=KAFKA_IMAGE) as kafka:
         kafka_server = kafka.get_bootstrap_server()
 
-        submit_test_problems(cases, kafka_server=kafka_server)
+        submit_test_problems(CASES, kafka_server=kafka_server)
 
         # run the stream_calc app:
         # (for each problem separately to avoid running forever)
         config = Config(kafka_servers=[kafka_server])
-        for _ in cases:
+        for _ in CASES:
             await main(config=config, run_forever=False)
 
-        check_problem_outcomes(cases, kafka_server=kafka_server)
+        check_problem_outcomes(CASES, kafka_server=kafka_server)

examples/stream_calc/stream_calc/config.py

@@ -18,13 +18,15 @@
 
 from typing import Literal
 
+from hexkit.config import config_from_yaml
 from hexkit.providers.akafka.provider import KafkaConfig
 from stream_calc.translators.eventpub import EventResultEmitterConfig
 from stream_calc.translators.eventsub import EventProblemReceiverConfig
 
 LOGLEVEL = Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
 
+@config_from_yaml(prefix="stream_calc")
 class Config(KafkaConfig, EventProblemReceiverConfig, EventResultEmitterConfig):
     """Config parameters and their defaults."""
 

examples/stream_calc/stream_calc/inject.py

@@ -0,0 +1,58 @@
+# Copyright 2021 - 2023 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");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+
+"""Module hosting the dependency injection container."""
+
+from collections.abc import AsyncGenerator
+from contextlib import asynccontextmanager
+
+from hexkit.providers.akafka import KafkaEventPublisher, KafkaEventSubscriber
+from stream_calc.config import Config
+from stream_calc.core.calc import StreamCalculator
+from stream_calc.ports.problem_receiver import ArithProblemHandlerPort
+from stream_calc.translators.eventpub import EventResultEmitter
+from stream_calc.translators.eventsub import EventProblemReceiver
+
+
+@asynccontextmanager
+async def prepare_core(
+    *,
+    config: Config,
+) -> AsyncGenerator[ArithProblemHandlerPort, None]:
+    """Constructs and initializes all core components and their outbound dependencies."""
+
+    async with KafkaEventPublisher.construct(config=config) as event_pub_provider:
+        result_emitter = EventResultEmitter(
+            config=config, event_publisher=event_pub_provider
+        )
+
+        yield StreamCalculator(result_emitter=result_emitter)
+
+
+@asynccontextmanager
+async def prepare_event_subscriber(
+    *,
+    config: Config,
+) -> AsyncGenerator[KafkaEventSubscriber, None]:
+    """Construct and initialize an event subscriber with all its dependencies."""
+    async with prepare_core(config=config) as stream_calculator:
+        event_problem_receiver = EventProblemReceiver(
+            config=config, problem_handler=stream_calculator
+        )
+
+        async with KafkaEventSubscriber.construct(
+            config=config, translator=event_problem_receiver
+        ) as event_subscriber:
+            yield event_subscriber

examples/stream_calc/stream_calc/main.py

@@ -20,22 +20,7 @@
 import logging
 
 from stream_calc.config import Config
-from stream_calc.container import Container  # type: ignore
-
-
-def get_container(config: Config) -> Container:
-    """
-    Get a pre-configures container for the stream calc app.
-
-    Args:
-        config: App config object.
-    """
-    logging.basicConfig(level=config.log_level)
-
-    container = Container()
-    container.config.load_config(config)
-
-    return container
+from stream_calc.inject import prepare_event_subscriber
 
 
 async def main(
@@ -52,8 +37,9 @@ async def main(
         run_forever:
             If set too `False`, will exit after handling one arithmetic problem.
     """
-    async with get_container(config) as container:
-        event_subscriber = await container.event_subscriber()
+    logging.basicConfig(level=config.log_level)
+
+    async with prepare_event_subscriber(config=config) as event_subscriber:
         await event_subscriber.run(forever=run_forever)
 
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hexkit"
-version = "1.2.0"
+version = "2.0.0"
 description = "A Toolkit for Building Microservices using the Hexagonal Architecture"
 readme = "README.md"
 authors = [
@@ -27,7 +27,6 @@ dependencies = [
     "pydantic >=2, <3",
     "pydantic_settings >=2, <3",
     "PyYAML >=6.0, <7",
-    "dependency-injector >=4.41.0, <5",
 ]
 
 [project.optional-dependencies]

requirements-dev.in

@@ -5,4 +5,5 @@
 
 # additional requirements can be listed her
 cryptography >= 41
-pytest-asyncio < 0.23.0
+func-timeout >= 4.3.5
+pytest-asyncio >= 0.23.0