ghga/wkvs

Well Known Value Service

Well-Known-Value-Service - Provides access to common values via API

Description

This service is intended to provide access to configured values via API in order to reduce the required config for other GHGA microservices.

Installation

We recommend using the provided Docker container.

A pre-built version is available on https://hub.docker.com/repository/docker/ghga/well-known-value-service:

bash
docker pull ghga/well-known-value-service:3.0.2

Or you can build the container yourself from the ./Dockerfile:

bash
# Execute in the repo's root dir:
docker build -t ghga/well-known-value-service:3.0.2 .

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 pre-configured:
docker run -p 8080:8080 ghga/well-known-value-service:3.0.2 --help

If you prefer not to use containers, you may install the service from source:

bash
# Execute in the repo's root dir:
pip install .

# To run the service:
wkvs --help

Configuration

Parameters

The service requires the following configuration parameters:

• log_level (string): The minimum log level to capture. Must be one of: "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", or "TRACE". Default: "INFO".

• service_name (string): Default: "wkvs".

• service_instance_id (string, required): A string that uniquely identifies this instance across all instances of this service. This is included in log messages.

  Examples:

  json
  "germany-bw-instance-001"
  

• log_format: If set, will replace JSON formatting with the specified string format. If not set, has no effect. In addition to the standard attributes, the following can also be specified: timestamp, service, instance, level, correlation_id, and details. Default: null.

  • Any of
    • string
    • null

  Examples:

  json
  "%(timestamp)s - %(service)s - %(level)s - %(message)s"
  

  json
  "%(asctime)s - Severity: %(levelno)s - %(msg)s"
  

• log_traceback (boolean): Whether to include exception tracebacks in log messages. Default: true.

• dcs_api_url (string, required): URL to the root of the DRS-compatible DCS API.

• ucs_api_url (string, required): URL to the root of the upload controller API.

• wps_api_url (string, required): URL to the root of the WPS API.

• storage_aliases (object, required): Mapping of storage alias to endpoint URL for all available S3 object storages. Can contain additional properties.

  • Additional properties (string, format: uri): Length must be between 1 and 2083 (inclusive).

• storage_labels (object, required): Mapping of storage alias to its human-readable format. Can contain additional properties.

  • Additional properties (string)

  Examples:

  json
  {
      "HD01": "Heidelberg",
      "TUE01": "T\u00fcbingen"
  }
  

• crypt4gh_public_keys (object, required): Mapping of storage alias to Crypt4GH public key. Can contain additional properties.

  • Additional properties (string)

• host (string): IP of the host. Default: "127.0.0.1".

• port (integer): Port to expose the server on the specified host. Default: 8080.

• auto_reload (boolean): A development feature. Set to True to automatically reload the server upon code changes. Default: false.

• workers (integer): Number of workers processes to run. Default: 1.

• timeout_keep_alive (integer): The time in seconds to keep an idle connection open for subsequent requests before closing it. This value should be higher than the timeout used by any client or reverse proxy to avoid premature connection closures. Default: 90.

  Examples:

  json
  5
  

  json
  90
  

  json
  5400
  

• api_root_path (string): Root path at which the API is reachable. This is relative to the specified host and port. Default: "".

• openapi_url (string): Path to get the openapi specification in JSON format. This is relative to the specified host and port. Default: "/openapi.json".

• docs_url (string): Path to host the swagger documentation. This is relative to the specified host and port. Default: "/docs".

• cors_allowed_origins: A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin. Default: null.

  • Any of
    • array
      • Items (string)
    • null

  Examples:

  json
  [
      "https://example.org",
      "https://www.example.org"
  ]
  

• cors_allow_credentials: Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified. Default: null.

  • Any of
    • boolean
    • null

  Examples:

  json
  [
      "https://example.org",
      "https://www.example.org"
  ]
  

• cors_allowed_methods: A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods. Default: null.

  • Any of
    • array
      • Items (string)
    • null

  Examples:

  json
  [
      "*"
  ]
  

• cors_allowed_headers: A list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all request headers. The Accept, Accept-Language, Content-Language, Content-Type and some are always allowed for CORS requests. Default: null.

  • Any of
    • array
      • Items (string)
    • null

  Examples:

  json
  []
  

• cors_exposed_headers: A list of HTTP response headers that should be exposed for cross-origin responses. Defaults to []. Note that you can NOT use ['*'] to expose all response headers. The Cache-Control, Content-Language, Content-Length, Content-Type, Expires, Last-Modified and Pragma headers are always exposed for CORS responses. Default: null.

  • Any of
    • array
      • Items (string)
    • null

  Examples:

  json
  []
  

• generate_correlation_id (boolean): A flag, which, if False, will result in an error when inbound requests don't possess a correlation ID. If True, requests without a correlation ID will be assigned a newly generated ID in the correlation ID middleware function. Default: true.

  Examples:

  json
  true
  

  json
  false
  

Usage:

A template YAML file for configuring the service can be found at ./example_config.yaml. Please adapt it, rename it to .wkvs.yaml, and place it in one of the following locations:

• in the current working directory where you execute the service (on Linux: ./.wkvs.yaml)
• in your home directory (on Linux: ~/.wkvs.yaml)

The config YAML file will be automatically parsed by the service.

Important: If you are using containers, the locations refer to paths within the container.

All parameters mentioned in the ./example_config.yaml can also be set using environment variables or file secrets.

For naming the environment variables, just prefix the parameter name with wkvs_, e.g. for the host set an environment variable named wkvs_host (you may use both upper or lower cases, however, it is standard to define all env variables in upper cases).

To use file secrets, please refer to the corresponding section of the pydantic documentation.

HTTP API

An OpenAPI specification for this service can be found here.

Architecture and Design:

The Well-Known-Value-Service does not currently utilize the ports or core portions of the triple hexagonal architecture, but it does retain the adapters portion of the design in case the service is extended later.

Development

For setting up the development environment, we rely on the 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 VS Code with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) installed. 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 VS Code extensions pre-installed
• pre-configured linting and auto-formatting
• a pre-configured debugger
• automatic license-header insertion

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 or the lock/requirements-dev.txt, run it again.

License

This repository is free to use and modify according to the Apache 2.0 License.

README Generation

This README file is auto-generated, please see .readme_generation/README.md for details.