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.

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

Setup

Clone the Repository

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

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

Apply Migrations
```
python manage.py migrate
```
Create a Superuser
```
python manage.py createsuperuser
```
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.

AatishDA1/SynBioSource