TissueHub: Tissue Sample Directory

A Flask-based web application for managing collections of tissue samples and their associated metadata.

Features

1. Display Collections (Home Page)

• Route: /
• Fetches all collections stored in the database.
• Displays a list of collections with their respective titles and associated disease terms.

2. View Collection Details

• Route: /collection/<id>
• Displays detailed information about a specific collection, including its samples (donor count, material type, last updated).

3. Add a Sample to a Collection

• Route: /collection/<id>/add-sample
• Provides a form to input sample details including:
  • Donor count
  • Material type
  • Last updated date (defaults to the current date)
• Saves the new sample to the database.

4. Create a New Collection

• Route: /collection/add
• Allows users to create a new collection by providing the following details:
  • Title
  • Disease term
• Saves the new collection to the database.

Getting Started

Prerequisites

• Python 3.10+
• Poetry (used for managing dependencies)

Installation

1. Clone this repository

git clone https://github.com/bp1183/TissueHub.git
cd TissueHub

2. Install Poetry

If you don't have poetry installed, you can install it by following the official installation guide.

3. Install dependencies using Poetry

poetry install

This will install all required dependencies as specified in the pyproject.toml.

4. Set up the database

First, initialize the Flask-Migrate migration environment:

poetry run flask db init

Next, generate the migration script for creating the initial database tables:

poetry run flask db migrate -m "Initial migration"

Apply the migration to create the tables in the database:

poetry run flask db upgrade

Finally, populate the database with the seed data

poetry run flask init-db

5. Run the application

poetry run start

6. Access the app

Open your browser and navigate to http://127.0.0.1:5000

Tests

Test can be run using pytest:

poetry run pytest