Covid-19 Cell Atlas

Covid-19 Cell Atlas Portal is a Flask web application development based on flaskstarter boilerplate. It has all the ready-to-use bare minimum essentials.

Demo

Video: https://d24h-my.sharepoint.com/:v:/g/personal/junyichen_d24h_hk/EZz9CeDLpq1Hl2snWY2f-dsBIP4Fq1Dx9hR4WRAWuzm22A?e=awW1nz

Table of Contents

1. Deployment
2. Getting Started
3. Project Structure
4. Modules
5. Testing
6. Features
7. Need Help?

Deployment

start D24H server at port 5000: execute "source run.sh" Below is run.sh snippet

#!/bin/bash
source venv/bin/activate
export FLASK_ENV=development
export FLASK_APP=manage.py
nohup python3 -m flask run --host='0.0.0.0' > /home/d24h_prog5/flasklog/log.txt 2>&1 &

Getting Started

clone the project

$ git clone https://github.com/ksh7/flask-starter.git
$ cd flask-starter

create virtual environment using python3 and activate it (keep it outside our project directory)

$ python3 -m venv /path/to/your/virtual/environment
$ source <path/to/venv>/bin/activate

For MAC/Linux local development

$ cd ../../
$ virtualenv venv
$ source venv/bin/activate
$ cd covid19_cell_atlas_portal

install dependencies in virtualenv

$ pip install -r requirements.txt

setup flask command for our app

$ export FLASK_APP=manage.py
$ export FLASK_ENV=development

create instance folder in /tmp directory (sqlite database, temp files stay here)

$ mkdir /tmp/flaskstarter-instance

initialize database and get two default users (admin & demo), check manage.py for details

$ flask initdb

start test server at localhost:5000

$ flask run

Project Structure

d24h_prog5@d24hp5ubuntu:~/covid19_cell_atlas_portal$ tree -I "venv|__pycache__"
.
├── flaskstarter
│   ├── app.py
│   ├── config.py
│   ├── covid2k_dense
│   │   ├── __init__.py
│   │   └── models.py
│   ├── covid2k_meta
│   │   ├── __init__.py
│   │   └── models.py
│   ├── decorators.py
│   ├── emails
│   │   └── __init__.py
│   ├── extensions.py
│   ├── frontend
│   │   ├── forms.py
│   │   ├── __init__.py
│   │   ├── models.py
│   │   └── views.py
│   ├── __init__.py
│   ├── model
│   │   ├── meta.py
│   │   └── umap.py
│   ├── naso_tableview
│   │   ├── __init__.py
│   │   └── views.py
│   ├── sample_meta_all
│   │   ├── __init__.py
│   │   └── models.py
│   ├── settings
│   │   ├── forms.py
│   │   ├── __init__.py
│   │   └── views.py
│   ├── static
│   │   ├── bootstrap.bundle.min.js
│   │   ├── bootstrap.min.css
│   │   ├── chevron-down.png
│   │   ├── css
│   │   │   └── template.css
│   │   ├── D24H_Logo.png
│   │   ├── Dataset_Banner.jpeg
│   │   ├── download-file 1.svg
│   │   ├── explore.png
│   │   ├── folder-2.png
│   │   ├── folder.png
│   │   ├── Group 36.png
│   │   ├── Group 37.png
│   │   ├── Group 38.png
│   │   ├── Group.png
│   │   ├── jquery-3.6.0.min.js
│   │   ├── jquery.slim.min.js
│   │   ├── Login_Banner.jpeg
│   │   ├── Mask_Group.png
│   │   ├── microscope.png
│   │   ├── newspaper.png
│   │   └── Pointer.png
│   ├── tasks
│   │   ├── forms.py
│   │   ├── __init__.py
│   │   ├── models.py
│   │   └── views.py
│   ├── templates
│   │   ├── admin
│   │   │   └── index.html
│   │   ├── dashboard
│   │   │   └── dashboard.html
│   │   ├── frontend
│   │   │   ├── change_password.html
│   │   │   ├── contact_us.html
│   │   │   ├── landing.html
│   │   │   ├── login.html
│   │   │   ├── reset_password.html
│   │   │   └── signup.html
│   │   ├── layouts
│   │   │   ├── banner.html
│   │   │   ├── base.html
│   │   │   ├── footer.html
│   │   │   └── header.html
│   │   ├── macros
│   │   │   ├── _confirm_account.html
│   │   │   ├── _flash_msg.html
│   │   │   ├── _form.html
│   │   │   └── _reset_password.html
│   │   ├── settings
│   │   │   ├── password.html
│   │   │   └── profile.html
│   │   └── tasks
│   │       ├── add_task.html
│   │       ├── contribute.html
│   │       ├── edit_task.html
│   │       ├── landing.html
│   │       ├── my_tasks.html
│   │       ├── naso_tableview.html
│   │       ├── show_plot.html
│   │       ├── show_scfeature.html
│   │       ├── table_view.html
│   │       └── view_task.html
│   ├── user
│   │   ├── constants.py
│   │   ├── __init__.py
│   │   └── models.py
│   └── utils.py
├── manage.py
├── README.md
├── requirements.txt
├── run.old.sh
├── run.sh
├── screenshots
│   ├── admin.png
│   ├── dashboard.png
│   ├── homepage.png
│   ├── login.png
│   ├── profile.png
│   ├── signup.png
│   └── tasks.png
└── tests
    ├── __init__.py
    └── test_flaskstarter.py

Modules

This application uses the following modules

• Flask[async]
• Flask-SQLAlchemy
• Flask-WTF
• Flask-Mail
• Flask-Caching
• Flask-Login
• Flask-Admin
• email-validator
• itsdangerous
• WTForms==2.3.3
• pytest
• pandas
• plotly
• numpy
• pymongo
• shortuuid
• seaborn
• dashbio
• gunicorn

Testing

Note: This web application has been tested thoroughly during multiple large projects, however tests for this bare minimum version would be added in tests folder very soon to help you get started.

Features

• Flask 2.0, Python (PEP8)
• Signup, Login with (email, password)
• Forget/reset passwords
• Email verification
• User profile/password updates
• User roles (admin, user, staff)
• User profile status (active, inactive)
• Admin dashboard for management
• Contact us form
• Bootstrap template (minimal)
• Utility scripts (initiate dummy database, run test server)
• Test & Production Configs

Flask 2.0 async or not async

• asynchronous support in Flask 2.0 is an amazing feature
• however, use it only when it has a clear advantage over the equivalent synchronous code
• write asynchronous code, if your application's routes, etc. are making heavy I/O-bound operations, like:
  • sending emails, making API calls to external servers, working with the file system, etc
• otherwise, if your application is doing CPU-bound operations or long-running tasks, like:
  • processing images or large files, creating backups or running AI/ML models, etc
  • it is advised to use tools like "Celery" or "Huey", etc.

async demo in our application

Check emails/__init__.py to see how emails being sent in async mode

Need Help? 🤝

If you need further help, reach out to me via Twitter DM.