schematicpy 0.1.13

Package for biomedical data model and data ingress management

Schematic

• Introduction
• Installation Requirements and Pre-requisites
• Package Setup Instructions
• Command Line Interface
• Contributing
• Contributors

Introduction

SCHEMATIC is an acronym for Schema Engine for Manifest Ingress and Curation. The Python based infrastructure provides a novel schema-based, data ingress ecosystem, that is meant to streamline the process of metadata annotation and validation for various data contributors.

Installation Requirements and Pre-requisites

• Python 3.7.1 or higher
• poetry

Important: You need to be a registered and certified user on synapse.org, and also have the right permissions to download the Google credentials files from Synapse.

Package Setup Instructions

• Clone Project Repository
• Virtual Environment Setup
• Install Dependencies
• Fill in Configuration File(s)
• Obtain Credentials File(s)

Command Line Interface

• Schematic Initialization (initialize mode of authentication)

• Metadata Manifest Validation (validate metadata manifest (.csv) files)

• Metadata Manifest Generation (generate metadata manifest (.csv) files)

• Metadata Manifest Validation and Submission (submission and optional validation of metadata manifest (.csv) files)

Contributing

Interested in contributing? Awesome! We follow the typical GitHub workflow of forking a repo, creating a branch, and opening pull requests. For more information on how you can add or propose a change, visit our contributing guide. To start contributing to the package, you can refer to the Getting Started section in our contributing guide.

Contributors

Active contributors and maintainers:

• Milen Nikolov
• Sujay Patil
• Bruno Grande
• Xengie Doan