migrate DI solution (GSI-440)

Switched to DI based on basic Python constructs like context managers. Upgrades to pydantic v2. Switches to docker-outside-of-docker for the devcontainer environment. Bumps version to 1.0.0. The tests do not use the standard JointFixture setup, however, to keep the PR small, this is not changed. May be reconsidered in a separate PR.
ghga-de · Nov 3, 2023 · d4b048d · d4b048d
1 parent 546cf3c
commit d4b048d
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Showing 35 changed files with 1,989 additions and 1,687 deletions.
diff --git a/.deprecated_files b/.deprecated_files
@@ -21,3 +21,4 @@ setup.cfg
 
 .pylintrc
 .flake8
+.editorconfig
diff --git a/.devcontainer/.dev_config.yaml b/.devcontainer/.dev_config.yaml
@@ -11,7 +11,7 @@ cors_allowed_headers: []
 db_connection_str: "mongodb://mongodb:27017"
 db_name: "dev-db"
 
-service_instance_id: 001
+service_instance_id: "001"
 kafka_servers: ["kafka:9092"]
 
 download_access_url: "http://127.0.0.1:8080/download-access"

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,45 +2,23 @@
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres
 // Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.8, 3.7, 3.6
 {
-	"name": "access-request-service",
+	"name": "${localWorkspaceFolderBasename}",
 	"dockerComposeFile": "docker-compose.yml",
 	"service": "app",
 	"workspaceFolder": "/workspace",
 	"customizations": {
 		"vscode": {
 			// Set *default* container specific settings.json values on container create.
 			"settings": {
+				"files.eol": "\n",
 				"terminal.integrated.profiles.linux": {
 					"bash": {
 						"path": "/bin/bash"
 					}
 				},
-				"sqltools.connections": [
-					{
-						"name": "Container database",
-						"driver": "PostgreSQL",
-						"previewLimit": 50,
-						"server": "localhost",
-						"port": 5432,
-						"database": "postgres",
-						"username": "postgres",
-						"password": "postgres"
-					}
-				],
 				"python.pythonPath": "/usr/local/bin/python",
 				"python.languageServer": "Pylance",
-				"python.linting.enabled": true,
-				"python.linting.pylintEnabled": true,
-				"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
-				"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
-				"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
-				"python.formatting.provider": "black",
 				"python.analysis.typeCheckingMode": "basic",
-				"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
-				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
-				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
-				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
-				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint",
 				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
 				"python.testing.pytestArgs": [
 					"--profile"
@@ -52,6 +30,7 @@
 				"editor.rulers": [
 					88
 				],
+				"editor.defaultFormatter": "ms-python.black-formatter",
 				"licenser.license": "Custom",
 				"licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt"
 			},
@@ -60,7 +39,6 @@
 				"mikestead.dotenv",
 				"ms-azuretools.vscode-docker",
 				"ms-python.python",
-				"ms-python.isort",
 				"ms-python.vscode-pylance",
 				"ms-toolsai.jupyter",
 				"njpwerner.autodocstring",
@@ -73,7 +51,9 @@
 				"yzhang.markdown-all-in-one",
 				"visualstudioexptteam.vscodeintellicode",
 				"ymotongpoo.licenser",
-				"editorconfig.editorconfig"
+				"charliermarsh.ruff",
+				"ms-python.black-formatter",
+				"ms-python.mypy-type-checker"
 			]
 		}
 	},
@@ -83,12 +63,13 @@
 	"postCreateCommand": "dev_install",
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",
+	"containerEnv": {
+		// for testcontainers to connect to the docker host:
+		"TC_HOST": "host.docker.internal",
+		"DOCKER_HOST": "unix:///var/run/docker.sock"
+	},
 	"features": {
-		"ghcr.io/devcontainers/features/docker-in-docker:2": {
-			"version": "latest",
-			"enableNonRootDocker": "true",
-			"moby": true,
-			"azureDnsAutoDetection": false
-		}
+		// details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker
+		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
 	}
 }
diff --git a/.editorconfig b/.editorconfig
diff --git a/.mandatory_files b/.mandatory_files
@@ -6,9 +6,7 @@
 # may differ from that of the template repository.
 
 .devcontainer/dev_launcher
-.devcontainer/devcontainer.json
 .devcontainer/docker-compose.yml
-.devcontainer/Dockerfile
 
 tests/__init__.py
 tests/fixtures/__init__.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -51,16 +51,16 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.1.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.1
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.1
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
diff --git a/.readme_template.md b/.readme_template.md
@@ -1,5 +1,5 @@
 
-[![tests](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml)
+[![tests](https://github.com/ghga-de/$name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml)
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/$name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$name?branch=main)
 
 # $title
@@ -11,6 +11,7 @@ $summary
 $description
 
 ## Installation
+
 We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
@@ -42,6 +43,7 @@ $shortname --help
 ```
 
 ## Configuration
+
 ### Parameters
 
 The service requires the following configuration parameters:
@@ -77,19 +79,20 @@ $openapi_doc
 $design_description
 
 ## Development
+
 For setting up the development environment, we rely on the
-[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode
+[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of VS Code
 in combination with Docker Compose.
 
-To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers"
+To use it, you have to have Docker Compose as well as VS Code with its "Remote - Containers"
 extension (`ms-vscode-remote.remote-containers`) installed.
-Then open this repository in vscode and run the command
-`Remote-Containers: Reopen in Container` from the vscode "Command Palette".
+Then open this repository in VS Code and run the command
+`Remote-Containers: Reopen in Container` from the VS Code "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
+- all relevant VS Code extensions pre-installed
+- pre-configured linting and auto-formatting
 - a pre-configured debugger
 - automatic license-header insertion
 
@@ -101,9 +104,11 @@ if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
 [`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
 
 ## License
+
 This repository is free to use and modify according to the
 [Apache 2.0 License](./LICENSE).
 
-## Readme Generation
-This readme is autogenerate, please see [`readme_generation.md`](./readme_generation.md)
+## README Generation
+
+This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md)
 for details.
diff --git a/.static_files b/.static_files
@@ -11,6 +11,7 @@
 .devcontainer/dev_install
 .devcontainer/license_header.txt
 .devcontainer/Dockerfile
+.devcontainer/devcontainer.json
 
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
@@ -39,7 +40,6 @@ scripts/README.md
 example_data/README.md
 
 .coveragerc
-.editorconfig
 .gitattributes
 .gitignore
 .mypy.ini

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 
-[![tests](https://github.com/ghga-de/access-request-service/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/access-request-service/actions/workflows/unit_and_int_tests.yaml)
+[![tests](https://github.com/ghga-de/access-request-service/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/access-request-service/actions/workflows/unit_and_int_tests.yaml)
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/access-request-service/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/access-request-service?branch=main)
 
 # Access Request Service
@@ -13,25 +13,26 @@ for the GHGA Data Portal.
 
 
 ## Installation
+
 We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/access-request-service):
 ```bash
-docker pull ghga/access-request-service:0.1.2
+docker pull ghga/access-request-service:1.0.0
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/access-request-service:0.1.2 .
+docker build -t ghga/access-request-service:1.0.0 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/access-request-service:0.1.2 --help
+docker run -p 8080:8080 ghga/access-request-service:1.0.0 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
@@ -44,6 +45,7 @@ ars --help
 ```
 
 ## Configuration
+
 ### Parameters
 
 The service requires the following configuration parameters:
@@ -151,19 +153,20 @@ It uses protocol/provider pairs and dependency injection mechanisms provided by
 
 
 ## Development
+
 For setting up the development environment, we rely on the
-[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode
+[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of VS Code
 in combination with Docker Compose.
 
-To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers"
+To use it, you have to have Docker Compose as well as VS Code with its "Remote - Containers"
 extension (`ms-vscode-remote.remote-containers`) installed.
-Then open this repository in vscode and run the command
-`Remote-Containers: Reopen in Container` from the vscode "Command Palette".
+Then open this repository in VS Code and run the command
+`Remote-Containers: Reopen in Container` from the VS Code "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
+- all relevant VS Code extensions pre-installed
+- pre-configured linting and auto-formatting
 - a pre-configured debugger
 - automatic license-header insertion
 
@@ -175,9 +178,11 @@ if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
 [`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
 
 ## License
+
 This repository is free to use and modify according to the
 [Apache 2.0 License](./LICENSE).
 
-## Readme Generation
-This readme is autogenerate, please see [`readme_generation.md`](./readme_generation.md)
+## README Generation
+
+This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md)
 for details.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -21,3 +21,4 @@ setup.cfg

		.pylintrc
		.flake8
		.editorconfig