File Ingest Service

File Ingest Service - A lightweight service to propagate file upload metadata to the GHGA file backend services

Description

The File Ingest Service provides an endpoint to populate the Encryption Key Store, Internal File Registry and Download Controller with output metadata from the S3 upload script at https://github.com/ghga-de/data-steward-scripts/blob/main/src/s3_upload.py.

Installation

We recommend using the provided Docker container.

A pre-build version is available at docker hub:

docker pull ghga/file-ingest-service:1.4.0

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

# Execute in the repo's root dir:
docker build -t ghga/file-ingest-service:1.4.0 .

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

# The entrypoint is preconfigured:
docker run -p 8080:8080 ghga/file-ingest-service:1.4.0 --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:
fis --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: "fis".

• service_instance_id (string): 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"

• vault_url (string): URL of the vault instance to connect to.

  Examples:

  "http://127.0.0.1.8200"

• vault_role_id: Vault role ID to access a specific prefix. Default: null.

  • Any of

    • string, format: password

    • null

  Examples:

  "example_role"

• vault_secret_id: Vault secret ID to access a specific prefix. Default: null.

  • Any of

    • string, format: password

    • null

  Examples:

  "example_secret"

• vault_verify: SSL certificates (CA bundle) used to verify the identity of the vault, or True to use the default CAs, or False for no verification. Default: true.

  • Any of

    • boolean

    • string

  Examples:

  "/etc/ssl/certs/my_bundle.pem"

• vault_path (string): Path without leading or trailing slashes where secrets should be stored in the vault.

• vault_secrets_mount_point (string): Name used to address the secret engine under a custom mount path. Default: "secret".

  Examples:

  "secret"

• vault_kube_role: Vault role name used for Kubernetes authentication. Default: null.

  • Any of

    • string

    • null

  Examples:

  "file-ingest-role"

• service_account_token_path (string, format: path): Path to service account token used by kube auth adapter. Default: "/var/run/secrets/kubernetes.io/serviceaccount/token".

• private_key (string): Base64 encoded private key of the keypair whose public key is used to encrypt the payload.

• source_bucket_id (string): ID of the bucket the object(s) corresponding to the upload metadata have been uploaded to. This should currently point to the staging bucket.

• token_hashes (array): List of token hashes corresponding to the tokens that can be used to authenticate calls to this service.

  • Items (string)

• selected_storage_alias (string): S3 endpoint alias of the object storage node the bucket and object(s) corresponding to the upload metadata have been uploaded to. This should point to a node containing a staging bucket.

• kafka_servers (array): 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

• publisher_topic (string): Topic name expected by downstream services. Use the topic name from the interrogation room service.

  Examples:

  "file_interrogation"

• publisher_type (string): Type expected by downstream services. Use the type from the interrogation room service.

  Examples:

  "file_validation_success"

• 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 .fis.yaml, and place it into one of the following locations:

• in the current working directory were you are execute the service (on unix: ./.fis.yaml)
• in your home directory (on unix: ~/.fis.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 fis_, e.g. for the host set an environment variable named fis_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.