SynBioSource

SynBio Source is an open-source platform designed for the Synthetic Biology community, enabling easy sharing and management of datasets. It offers intuitive uploading and searching capabilities, with the goal of fostering a unified metadata standard to enhance accessibility and collaboration within the field.

This README provides a comprehensive guide to setting up and running the application locally or otherwise.

Table of Contents

• Setup
• File Structure
• Environment Variables
• Database Configuration
• AWS S3 Configuration
• Local Storage Configuration

Setup

1. Clone the Repository

   git clone https://github.com/AatishDA1/SynBioSource.git
   cd SynBioSource

2. Create a Virtual Environment and Install Dependencies

   python3 -m venv venv
   source venv/bin/activate  # On Windows use `venv\Scripts\activate`
   pip install -r requirements.txt

3. Apply Migrations

   python manage.py migrate

4. Create a Superuser

   python manage.py createsuperuser

5. Run the Server

   python manage.py runserver

File Structure

• synbiosource/: Main Django application
• dashboard/: Contains views and templates for the user dashboard
• dataset/: Manages data upload and dataset-related functionalities
• api/: Provides REST API endpoints for the application

Environment Variables

Create a .env file in the root directory and include the following variables:

SECRET_KEY='your_secret_key'
USE_S3=True  # Set to False if not using AWS S3
AWS_ACCESS_KEY_ID='your_aws_access_key_id'
AWS_SECRET_ACCESS_KEY='your_aws_secret_access_key'
AWS_STORAGE_BUCKET_NAME='your_s3_bucket_name'
SCREATE='your_secret'
EMAIL_HOST_USER='your_email_host_user'
EMAIL_HOST_PASSWORD='your_email_host_password'

DB_NAME='your_db_name'
DB_USER='your_db_user'
DB_PORT='your_db_port'
DB_PASSWORD='your_db_password'
DB_HOST='your_db_host'

TEST_DATABASE_URL='your_test_database_url'

Database Configuration

SynBioSource uses a PostgreSQL database. Update the .env file with your PostgreSQL credentials:

DB_NAME='your_db_name'
DB_USER='your_db_user'
DB_PORT='your_db_port'
DB_PASSWORD='your_db_password'
DB_HOST='your_db_host'

AWS S3 Configuration

To enable AWS S3 for storage, ensure the following variables are set in your .env file:

USE_S3=True
AWS_ACCESS_KEY_ID='your_aws_access_key_id'
AWS_SECRET_ACCESS_KEY='your_aws_secret_access_key'
AWS_STORAGE_BUCKET_NAME='your_s3_bucket_name'

Local Storage Configuration

If not using AWS S3, set USE_S3=False in your .env file. Datasets will be stored in the local file system.