bam-upload-parsers

Some parsers for openBIS to be used in the bam-masterdata parser interface

This repository is intended to be used as entry point for the parsers from openbis-upload-helper.

Table of Contents

• bam-upload-parsers
  • Table of Contents
  • About
  • Features
  • Getting Started
    • Prerequisites
    • Installation

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About

This repository restructures parser components originally from bam-upload-helper, aiming to improve modularity and maintainability for integration with the bam-masterdata parser interface.

Features

• parser implementations
• Built for integration with openBIS environments
• Includes automated test suite

Getting Started

Prerequisites

• Tested for Python 3.10+
• pip for dependency installation
• Optional: virtualenv or conda environment for isolation

Installation

1. Clone the repository:

   git clone https://github.com/LucasZimm/bam-upload-parsers.git
   cd bam-upload-parsers

2. Create and activate a virtual environment:

   python -m .venv venv
   source venv/bin/activate  # Windows:    venv\Scripts\activate
   

3. Install dependencies:

   pip install .