Work Package Service

Work Package Service

Description

The work package service allows creating work packages for downloading or uploading dataset files and provides an authorization mechanism for these tasks by issuing access and work order tokens.

API endpoints:

POST /work-packages

Creates a work package.

• auth header: internal access token
• request body:
  • dataset_id: string (the ID of a dataset)
  • type: enum (download/upload)
  • file_ids: array of strings (null = all files of the dataset)
  • user_public_crypt4gh_key: string (the user's public Crypt4GH key)
• response body:
  • id: string (the ID of the created work package)
  • token: string (encrypted work and base64 encoded package access token)

GET /work-packages/{work_package_id}

Gets details on the specified work package.

• auth header: work package access token

POST /work-packages/{work_package_id}/files/{file_id}/work-order-tokens

Creates an encrypted work order token for the specified work package and file.

• auth header: work package access token

GET /users/{user_id}/datasets

Gets a list of all dataset IDs that can be downloaded by the user.

• auth header: internal access token with the user context

Installation

We recommend using the provided Docker container.

A pre-build version is available at docker hub:

docker pull ghga/work-package-service:2.0.6

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

# Execute in the repo's root dir:
docker build -t ghga/work-package-service:2.0.6 .

For production-ready deployment, we recommend using Kubernetes, however, for simple use cases, you could execute the service using docker on a single server:

# The entrypoint is preconfigured:
docker run -p 8080:8080 ghga/work-package-service:2.0.6 --help

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

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

# To run the service:
wps --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", "TRACE"]. Default: "INFO".

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

• service_instance_id (string, required): A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.

  Examples:

  "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:

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

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

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

• datasets_collection (string): The name of the database collection for datasets. Default: "datasets".

• work_packages_collection (string): The name of the database collection for work packages. Default: "workPackages".

• work_package_valid_days (integer): How many days a work package (and its access token) stays valid. Default: 30.

• work_package_signing_key (string, format: password, required): The private key for signing work order tokens.

  Examples:

  "{\"crv\": \"P-256\", \"kty\": \"EC\", \"x\": \"...\", \"y\": \"...\"}"

• db_connection_str (string, format: password, required): MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/.

  Examples:

  "mongodb://localhost:27017"

• db_name (string): Default: "work-packages".

• kafka_servers (array, required): A list of connection strings to connect to Kafka bootstrap servers.

  • Items (string)

  Examples:

  [
      "localhost:9092"
  ]

• kafka_security_protocol (string): Protocol used to communicate with brokers. Valid values are: PLAINTEXT, SSL. Must be one of: ["PLAINTEXT", "SSL"]. Default: "PLAINTEXT".

• kafka_ssl_cafile (string): Certificate Authority file path containing certificates used to sign broker certificates. If a CA is not specified, the default system CA will be used if found by OpenSSL. Default: "".

• kafka_ssl_certfile (string): Optional filename of client certificate, as well as any CA certificates needed to establish the certificate's authenticity. Default: "".

• kafka_ssl_keyfile (string): Optional filename containing the client private key. Default: "".

• kafka_ssl_password (string, format: password): Optional password to be used for the client private key. Default: "".

• 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:

  true

  false

• kafka_max_message_size (integer): The largest message size that can be transmitted, in bytes. Only services that have a need to send/receive larger messages should set this. Exclusive minimum: 0. Default: 1048576.

  Examples:

  1048576

  16777216

• dataset_change_event_topic (string, required): Name of the topic for events that inform about datasets.

  Examples:

  "metadata_datasets"

• dataset_upsertion_event_type (string, required): The type of events that inform about new and changed datasets.

  Examples:

  "dataset_created"

• dataset_deletion_event_type (string, required): The type of events that inform about deleted datasets.

  Examples:

  "dataset_deleted"

• download_access_url (string, required): URL pointing to the internal download access API.

  Examples:

  "http://127.0.0.1/download-access"

• auth_key (string, required): The GHGA internal public key for validating the token signature.

  Examples:

  "{\"crv\": \"P-256\", \"kty\": \"EC\", \"x\": \"...\", \"y\": \"...\"}"

• auth_algs (array): A list of all algorithms used for signing GHGA internal tokens. Default: ["ES256"].

  • Items (string)

• auth_check_claims (object): A dict of all GHGA internal claims that shall be verified. Default: {"id": null, "name": null, "email": null, "iat": null, "exp": null}.

• auth_map_claims (object): A mapping of claims to attributes in the GHGA auth context. Can contain additional properties. Default: {}.

  • 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.

• 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:

  [
      "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:

  [
      "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:

  [
      "*"
  ]

• 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 headers. The Accept, Accept-Language, Content-Language and Content-Type headers are always allowed for CORS requests. Default: null.

  • Any of

    • array

      • Items (string)

    • null

  Examples:

  []

Usage:

A template YAML for configurating the service can be found at ./example-config.yaml. Please adapt it, rename it to .wps.yaml, and place it into one of the following locations:

• in the current working directory were you are execute the service (on unix: ./.wps.yaml)
• in your home directory (on unix: ~/.wps.yaml)

The config yaml 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 could also be set using environment variables or file secrets.

For naming the environment variables, just prefix the parameter name with wps_, e.g. for the host set an environment variable named wps_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 corresponding section of the pydantic documentation.

HTTP API

An OpenAPI specification for this service can be found here.

Architecture and Design:

This is a Python-based service following the Triple Hexagonal Architecture pattern. It uses protocol/provider pairs and dependency injection mechanisms provided by the hexkit library.

Development

For setting up the development environment, we rely on the devcontainer feature 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

Moreover, inside the devcontainer, a convenience commands dev_install is available. It installs the service with all development dependencies, installs pre-commit.

The installation is performed automatically when you build the devcontainer. However, if you update dependencies in the ./pyproject.toml or the ./requirements-dev.txt, please 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.md for details.