Opentelemetry instrumentation (#105)

Author: mephenor

.devcontainer/Dockerfile

@@ -8,7 +8,7 @@ ARG USER_GID=$USER_UID
 RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
 
 # [Option] Install Node.js
-ARG INSTALL_NODE="true"
+ARG INSTALL_NODE="false"
 ARG NODE_VERSION="lts/*"
 RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
 

.github/workflows/ci_workflow_dispatch.yaml

@@ -47,9 +47,9 @@ jobs:
         with:
           python-version: 3.12
 
-      - name: Install stringcase and typer
-        id: setup-stringcase
-        run: pip install stringcase typer
+      - name: Install casefy and typer
+        id: setup-casefy
+        run: pip install casefy typer
 
       - name: Extract service name for ${{ matrix.service }}
         id: extract-service-name

.github/workflows/docker_on_release.yaml

@@ -137,9 +137,9 @@ jobs:
         with:
           python-version: 3.12
 
-      - name: Install stringcase and typer
-        id: setup-stringcase
-        run: pip install stringcase typer
+      - name: Install casefy and typer
+        id: setup-casefy
+        run: pip install casefy typer
 
       - name: Extract service name for ${{ matrix.service }}
         id: extract-service-name

.github/workflows/push_to_docker/action.yaml

@@ -54,7 +54,7 @@ runs:
     - name: Prepare Dockerfile
       id: prepare-dockerfile
       shell: bash
-      run: cp Dockerfile services/${{ inputs.service }}/ && sed -i "s/\(ENTRYPOINT \)\[\]/\1[\"${{ inputs.service }}\"]/" services/${{ inputs.service }}/Dockerfile
+      run: cp Dockerfile services/${{ inputs.service }}/ && sed -i "s/\(ENTRYPOINT \)\[\]/\1[\"opentelemetry-instrument\", \"${{ inputs.service }}\"]/" services/${{ inputs.service }}/Dockerfile
 
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v3

.pyproject_generation/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 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");

.pyproject_generation/pyproject_custom.toml

@@ -3,13 +3,23 @@ name = "fsb"
 version = "1.0.0"
 description = "File Services Backend - monorepo housing file services"
 dependencies = [
-    "typer >= 0.12",
-    "ghga-service-commons[api, auth, crypt] >= 3.4",
+    "typer >= 0.15",
+    "ghga-service-commons[api, auth, crypt] >= 4.0",
     "ghga-event-schemas >= 5.0",
-    "hexkit[akafka, s3, mongodb] >= 4.2.0",
-    "crypt4gh>=1.6",
-    "hvac>=2",
-    "httpx>=0.27",
+    "hexkit[akafka, s3, mongodb] >= 4.3.0",
+    "crypt4gh >= 1.7",
+    "hvac >= 2",
+    "httpx >= 0.28",
+    "opentelemetry-api >= 1.31.1",
+    "opentelemetry-sdk >= 1.31.1",
+    "opentelemetry-exporter-otlp-proto-http >= 1.31.1",
+    "opentelemetry-distro >= 0.52b1",
+    "opentelemetry-instrumentation >= 0.52b1",
+    "opentelemetry-instrumentation-aiokafka >= 0.52b1",
+    "opentelemetry-instrumentation-botocore >= 0.52b1",
+    "opentelemetry-instrumentation-fastapi >= 0.52b1",
+    "opentelemetry-instrumentation-httpx >= 0.52b1",
+    "opentelemetry-instrumentation-pymongo >= 0.52b1",
 ]
 
 [project.urls]

.pyproject_generation/pyproject_template.toml

@@ -26,7 +26,8 @@ exclude = [
 ]
 line-length = 88
 src = [
-    "services",
+    "services/**/src",
+    "services/**/tests_*",
     "examples",
     "scripts",
 ]
@@ -40,8 +41,9 @@ fixable = [
     "RUF022", # sort items in __all__
 ]
 ignore = [
-    "E",
-    "W",
+    "E111", # indentation with invalid multiple (for formatter)
+    "E114", # indentation with invalid multiple comment (for formatter)
+    "E116", # over indentation (for formatter)
     "PLW", # pylint warnings
     "RUF001", # ambiguous unicode character strings
     "RUF010", # explicit conversion to string or repr: !s or !r
@@ -76,30 +78,11 @@ select = [
 max-complexity = 10
 
 [tool.ruff.lint.per-file-ignores]
-"scripts/*" = [
-    "PL",
-    "S",
-    "SIM",
-    "D",
-]
-"services/*/tests_*" = [
-    "S",
-    "SIM",
-    "PLR",
-    "B011",
-]
-".devcontainer/*" = [
-    "S",
-    "SIM",
-    "D",
-]
-"examples/*" = [
-    "S",
-    "D",
-]
-"__init__.py" = [
-    "D",
-]
+"scripts/*" = ["PL", "S", "SIM", "D"]
+"services/**/tests_*" = ["S", "SIM", "PLR", "B011"]
+".devcontainer/*" = ["S", "SIM", "D"]
+"examples/*" = ["S","D"]
+"__init__.py" = ["D"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "pep257"
@@ -117,8 +100,9 @@ no_site_packages = false
 explicit_package_bases = true
 
 [tool.pytest.ini_options]
-minversion = "8.0"
+minversion = "8.3"
 asyncio_mode = "strict"
+asyncio_default_fixture_loop_scope = "function"
 
 [tool.coverage.paths]
 source = [

.readme_generation/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 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");

.readme_generation/readme_template_service.md

@@ -10,7 +10,7 @@ $description
 
 We recommend using the provided Docker container.
 
-A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
+A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
 ```bash
 docker pull ghga/$name:$version
 ```
@@ -49,9 +49,9 @@ $config_description
 
 A template YAML for configuring the service can be found at
 [`./example-config.yaml`](./example-config.yaml).
-Please adapt it, rename it to `.$shortname.yaml`, and place it into one of the following locations:
-- in the current working directory were you are execute the service (on unix: `./.$shortname.yaml`)
-- in your home directory (on unix: `~/.$shortname.yaml`)
+Please adapt it, rename it to `.$shortname.yaml`, and place it in one of the following locations:
+- in the current working directory where you execute the service (on Linux: `./.$shortname.yaml`)
+- in your home directory (on Linux: `~/.$shortname.yaml`)
 
 The config yaml will be automatically parsed by the service.
 
@@ -65,7 +65,7 @@ e.g. for the `host` set an environment variable named `${shortname}_host`
 (you may use both upper or lower cases, however, it is standard to define all env
 variables in upper cases).
 
-To using file secrets please refer to the
+To use file secrets, please refer to the
 [corresponding section](https://pydantic-docs.helpmanual.io/usage/settings/#secret-support)
 of the pydantic documentation.
 
@@ -92,8 +92,8 @@ This will give you a full-fledged, pre-configured development environment includ
 - a pre-configured debugger
 - automatic license-header insertion
 
-Moreover, inside the devcontainer, a convenience commands `dev_install` is available.
-It installs the service with all development dependencies, installs pre-commit.
+Moreover, inside the devcontainer, a command `dev_install` is available for convenience.
+It installs the service with all development dependencies, and it installs pre-commit.
 
 The installation is performed automatically when you build the devcontainer. However,
 if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the

.template/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 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");