schematicpy 1.0.0

Package for biomedical data model and metadata ingress management

Schematic

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 dataset annotation, metadata validation and submission to an asset store for various data contributors.

Installation Requirements and Pre-requisites

• Python 3.7.1 or higher

Note: 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.

Installing

Create and activate a virtual environment within which you can install the package:

python -m venv .venv
source .venv/bin/activate

Install and update the package using pip:

python -m pip install schematicpy

Command Line Client Usage

Initialization

schematic init --config ~/path/to/config.yml    # initialize mode of authentication

Manifest

schematic manifest --config ~/path/to/config.yml get    # generate manifest based on data type

schematic manifest --config ~/path/to/config.yml validate   # validate manifest

Model

schematic model --config ~/path/to/config.yml submit    # validate and submit manifest

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