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HuBMAP Member Registration and Profile Portal

This repo contains code that handles the HuBMAP member registration and profile management. It's built on top of Python Flask micro-framework and has a tight-coupling with Wordpress and the Connections plugin.

Install dependencies

Create a new Python 3.x virtual environment:

python3 -m venv venv-member-ui
source venv-member-ui/bin/activate

Upgrade pip:

python3 -m pip install --upgrade pip

Then install the dependencies:

pip install -r requirements.txt

Configuration

The confiuration file app.cfg is located under instance folder. You can read more about Flask Instance Folders.

There's an example configuration file instance/app.cfg.example for your quick start.

Start the server

Either methods below will run the search-api web service at http://localhost:5005. Choose one:

Directly via Python

python3 app.py

With the Flask Development Server

cd src
export FLASK_APP=app.py
export FLASK_ENV=development
python3 -m flask run -p 5005

Deployment

For deployment on remote VM, we'll use Nignx as a reverse proxy to forward the requests to uWSGI server.

First copy the nginx/conf.d/member-ui.conf to /etc/nginx/conf.d and edit the configurations with domain and SSL certificate based on the deployment. For example:

server {
    listen 80;
    server_name profile.dev.hubmapconsortium.org;
    
    location / {
        return 301 https://$host$request_uri;
    }
}

server {
    listen 443 ssl;
    server_name profile.dev.hubmapconsortium.org;   
    root /usr/share/nginx/html;

    access_log /var/log/nginx/nginx_access_member-ui.log;
    error_log /var/log/nginx/nginx_error_member-ui.log warn;

    ssl_certificate /etc/letsencrypt/live/profile.dev.hubmapconsortium.org/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/profile.dev.hubmapconsortium.org/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot

    # HTTP requests get passed to the uwsgi server using the "uwsgi" protocol on port 5000
    location / { 
        include uwsgi_params;
        uwsgi_pass uwsgi://127.0.0.1:5000;
    }
    
}

For quick testing:

uwsgi --ini /opt/hubmap/member-ui/uwsgi.ini -H /opt/hubmap/member-ui/venv-member-ui/

Once everything in place, we can copy the hubmap-member-ui.uwsgi.service file to /etc/systemd/system and create a service.

To enable the service with system reboot:

systemctl enable hubmap-member-ui.uwsgi.service

Start and Stop service

systemctl start hubmap-member-ui.uwsgi.service

systemctl stop hubmap-member-ui.uwsgi.service

We can also restart the running service to reflect Python code changes:

systemctl restart hubmap-member-ui.uwsgi.service