metamist 6.10.1

Python API for interacting with the Sample API system

Metamist

Introduction

Metamist is a database designed for storing de-identified -omics metadata.

Purpose

The project provides an interface to interact with the -omics database via the Python client as well as the GraphQL + HTTP APIs.

Features

• Project-Based Resource Organization: Every resource in Metamist is associated with a specific project.
• Access Control: Access to resources is controlled through membership in specific Google Groups:
  • dataset-sample-metadata-main-read: For read-only access.
  • dataset-sample-metadata-main-write: For write access.
• Efficiency Note: Members of Google Groups are cached in a blob to optimize performance, as group-membership identity lookups can be slow.

High-Level Architecture

It comprises three key components:

1. System-Versioned MariaDB Database: A robust database system for managing -omics metadata.

2. Python Web API: This component is responsible for:

   • Managing permissions.
   • Storing frequently used queries.
   • Providing a GraphQL/HTTP API for efficient querying of the database.

3. Installable Python Library: Wraps the Python Web API using the OpenAPI generator, facilitating easier interaction with the system.

Schema

As of Jan 15, 2024 this schema should reflect the data structure on the tables:

You can also find this at DbDiagram.

The codebase contains the following modules worth noting:

• models -> General data models + enums
• db/python/tables -> Interaction with MariaDB / BigQuery
• db/python/layers -> Logic
• api/graphql : GraphQL
• api/routes: HTTP + OpenAPI

And metamist maintains two clients:

• web -> React app that consumes a generated Typescript API + GraphQL
• metamist -> autogenerated Python API

Installation and Running Locally

• Installation and developer setup

License

This project is licensed under the MIT License. You can see it in the LICENSE file in the root directory of this source tree.