Depreciation Note:
Please note, this repo was part of an implementation study and is not longer maintained. Please do not use for production.

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Sandbox-Storage - a DRS-compliant service for delivering files from S3

This service implements the GA4GH DRS, while providing the option to serve files from localstack S3.

Documentation:

An extensive documentation can be found here (coming soon).

Quick Start

Installation

We recommend using the provided Docker container.

A pre-build version is available at docker hub:

# Please adapt the version as required:
docker pull ghga/sandbox-storage:<version>

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

# Execute in the repo's root dir:
# (Please feel free to adapt the name/tag.)
docker build -t ghga/sandbox-storage:<version> .

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/sandbox-storage:<version>

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:
sandbox-storage

Configuration:

The ./example-config.yaml gives an overview of the available configuration options. Please adapt it, rename it to .sandbox-storage.yaml, and place it to one of the following locations:

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

Development

For setting up the development environment, we rely on the devcontainer feature of vscode in combination with Docker Compose.

To use it, you have to have Docker Compose as well as vscode 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".

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
• a pre-configured debugger
• automatic license-header insertion

Moreover, inside the devcontainer, there are two convenience commands available (please type them in the integrated terminal of vscode):

• dev_install - install the service with all development dependencies, installs pre-commit, and applies any migration scripts to the test database (please run that if you are starting the devcontainer for the first time or if you added any python dependencies to the ./setup.cfg)
• dev_launcher - starts the service with the development config yaml (located in the ./.devcontainer/ dir)

If you prefer not to use vscode, you could get a similar setup (without the editor specific features) by running the following commands:

# Execute in the repo's root dir:
cd ./.devcontainer

# build and run the environment with docker-compose
docker-compose up

# attach to the main container:
# (you can open multiple shell sessions like this)
docker exec -it devcontainer_app_1 /bin/bash

License

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