Test opentelemetry instrumentation

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.1
+    rev: v0.9.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/pyproject_custom.toml

@@ -10,6 +10,19 @@ dependencies = [
     "crypt4gh>=1.6",
     "hvac>=2",
     "httpx>=0.27",
+    "opentelemetry-api==1.29.0",
+    "opentelemetry-sdk==1.29.0",
+    "opentelemetry-distro==0.50b0",
+    "opentelemetry-instrumentation==0.50b0",
+    "opentelemetry-instrumentation-aiokafka==0.50b0",
+    "opentelemetry-instrumentation-asyncio==0.50b0",
+    "opentelemetry-instrumentation-botocore==0.50b0",
+    "opentelemetry-instrumentation-click==0.50b0",
+    "opentelemetry-instrumentation-fastapi==0.50b0",
+    "opentelemetry-instrumentation-httpx==0.50b0",
+    "opentelemetry-instrumentation-logging==0.50b0",
+    "opentelemetry-instrumentation-pymongo==0.50b0",
+    "opentelemetry-instrumentation-urllib3==0.50b0",
 ]
 
 [project.urls]

pyproject.toml

@@ -10,6 +10,19 @@ dependencies = [
     "crypt4gh>=1.6",
     "hvac>=2",
     "httpx>=0.27",
+    "opentelemetry-api==1.29.0",
+    "opentelemetry-sdk==1.29.0",
+    "opentelemetry-distro==0.50b0",
+    "opentelemetry-instrumentation==0.50b0",
+    "opentelemetry-instrumentation-aiokafka==0.50b0",
+    "opentelemetry-instrumentation-asyncio==0.50b0",
+    "opentelemetry-instrumentation-botocore==0.50b0",
+    "opentelemetry-instrumentation-click==0.50b0",
+    "opentelemetry-instrumentation-fastapi==0.50b0",
+    "opentelemetry-instrumentation-httpx==0.50b0",
+    "opentelemetry-instrumentation-logging==0.50b0",
+    "opentelemetry-instrumentation-pymongo==0.50b0",
+    "opentelemetry-instrumentation-urllib3==0.50b0",
 ]
 readme = "README.md"
 authors = [

services/dcs/Dockerfile

@@ -0,0 +1,51 @@
+# Copyright 2021 - 2024 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.
+
+# BASE: a base image with updated packages
+FROM python:3.12-alpine AS base
+RUN apk upgrade --no-cache --available
+
+# BUILDER: a container to build the service wheel
+FROM base AS builder
+RUN pip install build
+COPY . /service
+WORKDIR /service
+RUN python -m build
+
+# DEP-BUILDER: a container to (build and) install dependencies
+FROM base AS dep-builder
+RUN apk update
+RUN apk add build-base gcc g++ libffi-dev zlib-dev
+RUN apk upgrade --available
+WORKDIR /service
+COPY --from=builder /service/lock/requirements.txt /service
+RUN pip install --no-deps -r requirements.txt
+RUN echo $(find / -name opentelemetry-instrument)
+
+# RUNNER: a container to run the service
+FROM base AS runner
+WORKDIR /service
+RUN rm -rf /usr/local/lib/python3.12
+COPY --from=dep-builder /usr/local/lib/python3.12 /usr/local/lib/python3.12
+COPY --from=builder /service/dist/ /service
+COPY --from=dep-builder /usr/local/bin/opentelemetry-instrument /usr/local/bin
+RUN pip install --no-deps *.whl
+RUN rm *.whl
+RUN adduser -D appuser
+WORKDIR /home/appuser
+USER appuser
+ENV PYTHONUNBUFFERED=1
+
+ENTRYPOINT ["opentelemetry-instrument", "--traces_export", "console", "--metrics_exporter", "console", "--logs_export", "console", "dcs"]

services/dcs/lock/README.md

@@ -0,0 +1,56 @@
+<!--
+ 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.
+
+-->
+
+# Lock Files
+
+This directory contains two lock files locking the dependencies of this microservice:
+
+The [`./requirements.txt`](./requirements.txt) contains production dependencies.
+
+The [`./requirements-dev.txt`](./requirements-dev.txt) additionally contains development
+dependencies.
+
+## Sources
+
+For generating the production lock file, only the dependencies specified in the
+[`../pyproject.toml`](../pyproject.toml) are considered as input.
+
+For generating the development lock file, additionally, the
+[`./requirements-dev-template.in`](./requirements-dev-template.in) as well as
+the [`./requirements-dev.in`](./requirements-dev.in) are considered.
+
+The `./requirements-dev-template.in` is automatically updated from the template
+repository and should not be manually modified.
+
+If you require additional dev dependencies not part of the
+`./requirements-dev-template.in`, you can add them to the
+`./requirements-dev.in`.
+
+## Update and Upgrade
+
+The lock files can be updated running the
+[`../scripts/update_lock.py`](../scripts/update_lock.py) script. This will keep the
+dependency versions in the lockfile unchanged unless they are in conflict with the
+the input sources. In that case, the affected dependencies are updated to the latest
+versions compatible with the input.
+
+If you would like to upgrade all dependencies in the lock file to the latest versions
+compatible with the input, you can run `../scripts/update_lock.py --upgrade`.
+
+If you just want to check if the script would do update, you can run
+`../scripts/update_lock.py --check`.

services/dcs/lock/requirements-dev-template.in

@@ -0,0 +1,32 @@
+# common requirements for development and testing of services
+
+pytest>=8.2
+pytest-asyncio>=0.23.7
+pytest-cov>=5
+snakeviz>=2.2
+logot>=1.3
+
+pre-commit>=3.7
+
+mypy>=1.10
+mypy-extensions>=1.0
+
+ruff>=0.4
+
+click>=8.1
+typer>=0.12
+
+httpx>=0.27
+pytest-httpx>=0.30
+
+urllib3>=1.26.18
+requests>=2.31
+
+stringcase>=1.2
+jsonschema2md>=1.1
+setuptools>=69.5
+
+# required since switch to pyproject.toml and pip-tools
+tomli_w>=1.0
+
+uv>=0.2.13

services/dcs/lock/requirements-dev.in

@@ -0,0 +1,7 @@
+# requirements for development and testing this service
+
+# template requirements for development and testing
+-r requirements-dev-template.in
+
+# additional requirements can be listed here
+testcontainers[kafka,mongo]>=4.6.0