Package for biomedical data model and data ingress management
Project description
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
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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:
Project details
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