Installation
=========================

DRDB system from PNB, McMaster University

This is an open source system to manage participant database, study,
study schedules, and research personnels.

How to deploy the system on a Linux (Ubuntu) sever
-----------------------------------------------------

Prerequisites
~~~~~~~~~~~~~~~~

-  Node.js & npm

.. code-block:: shell

    sudo apt update
    sudo apt install nodejs
    sudo apt install npm

-  MySQL 8 Server
    -  Instructions: https://phoenixnap.com/kb/how-to-install-mysql-on-ubuntu-18-04

-  git

.. code-block:: shell

    sudo apt install git

-  nginx

.. code-block:: shell

    sudo apt install nginx

Download the latest version of the system
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: shell

    cd ~
    git clone https://github.com/naiqixiao/DRDB

All frontend and backend codes should be downloaded to "~/DRDB" folder.

MySQL database setup
~~~~~~~~~~~~~~~~~~~~

-  Create a *user* and *password*

.. code-block:: shell

    # in Terminal, enter mysql shell with root
    # if you haven't set password for root, press 'Enter' key when the password prompt shows up.

    mysql -u root -p

.. code-block:: mysql

    # choose your own username and password to replace the following newuser and password respectively.

    CREATE USER 'newuser'@'localhost' IDENTIFIED BY 'password';

    # provide the user with access to the information they will need.
    # replacing the following newuser with the username that you just created.

    GRANT ALL PRIVILEGES ON * . * TO 'newuser'@'localhost';

    # reload all the privileges

    FLUSH PRIVILEGES;

-  Create a database under the user that you just created.

.. code-block:: shell

    # in Terminal, log in to the MySQL Server using the user just created.

    mysql -u newuser -p

.. code-block:: mysql

    # in MySQL shell, enter the following script to create a database named DRDB.

    CREATE DATABASE IF NOT EXISTS DRDB;

    # quit MySQL shell.

    EXIT

-  Import template database

.. code-block:: shell

    # in Terminal, import the template database with the user just created.
    # the template sql database is in /DRDB/MySQL/Template.sql
    # the following codes assume you import the template database under the user named username. Replacing the following newuser with the username that you just created.

    cd ~/DRDB
    mysql -u newuser -p DRDB < MySQL/Template.sql

    # in Terminal, log in MySQL with the username
    mysql -u newuser -p

.. code-block:: mysql

    # in MySQL, enter the following command to setup automatic Age caculation.

    USE DRDB

    CREATE EVENT
    IF NOT EXISTS age_update
    ON SCHEDULE EVERY 1 Day
    STARTS CURRENT_TIMESTAMP
    DO
    UPDATE DRDB.Child 
        set Age = DATEDIFF(CURDATE(), DoB);

Backend setup and configuration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  Install all required modules

.. code-block:: shell

    cd ~/DRDB/server
    sudo npm install

-  Set up MySQL database connection
-  open '~/DRDB/server/config/general.js'
-  update *Line 5 with the MySQL username and password* that you created
   in the previous step.
-  for example, the following line indicates username of 'admin' and
   password of 'password'

.. code-block:: javascript

    exports.sequelize = new Sequelize("DRDB", "admin", "password", {
    host: "localhost",
    dialect: "mysql",
    logging: false,
    define: {
        // timestamps: false,
        freezeTableName: true,
    },
    timeZone: "America/Toronto",
    pool: {
        max: 10,
        min: 0,
        acquire: 30000,
        idle: 10000,
    },
    });

-  Set up the URL of the system
-  open '~/DRDB/server/config/general.js'
-  update *Line 1* with the URL of the system


- Run backend server with pm2

.. code-block:: shell

    cd ~/DRDB/server

    sudo npm install --save pm2 -g

    pm2 start server.js

- Set up credentials to use Google APIs
Please see this instruction for specific steps: https://mcmasteru365-my.sharepoint.com/:w:/g/personal/xiaon8_mcmaster_ca/EdIxUUOHUeNIgN3pAprvVMoBJZHOp-2dErCY81bENFri-g?e=zKFOIh

Frontend setup
~~~~~~~~~~~~~~

install all required modules

.. code-block:: shell

    cd ~/DRDB/client
    sudo npm install

deploy frontend server

.. code-block:: shell

    cd ~/DRDB/client
    npm run build

Configure nginx

Instructions:
https://www.digitalocean.com/community/tutorials/how-to-install-nginx-on-ubuntu-18-04

You might need to run the following script to enable firewall

.. code-block:: shell

    sudo ufw enable

Run frontend server with nginx

-  Copy the ready-to-be-deployed frontend codes to ngnix folder

.. code-block:: shell

    cd ~/DRDB/client
    sudo cp -r -T dist /var/www/html/DRDB

-  Configure ngnix

.. code-block:: shell

    # Use the following script to configure ngnix services

    sudo nano /etc/nginx/sites-available/default

    # Change 'root /var/www/html;' to 'root /var/www/html/DRDB;'

    # Change ' location / {} ' to 

    location /api/ {
        proxy_pass http://localhost:3000;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection 'upgrade';
        proxy_set_header Host $host;
        proxy_cache_bypass $http_upgrade;
    }

-  Restart ngnix service

.. code-block:: shell

    sudo systemctl restart nginx

You should be able to access the system with the ip address of your
server by now.

Inital setup the system
-------------------------

You should be able to log on to the system with the default admin account:

-  Email: admin@drdb.com
-  Password: password

After logging in to the system, you can start setting up lab information (in Settings page) and personnels (in Personnel management page).

To setup Google account, please see this instruction for details: https://mcmasteru365-my.sharepoint.com/:p:/g/personal/xiaon8_mcmaster_ca/ERk1uev-LENDrca6aWXwSqYBAn1J1OEsJ3tNjPkbpvcwtA?e=xeMbpV

How to upgrade the system
-------------------------

.. code-block:: shell

    cd ~/DRDB
    git pull

    # update npm packages for client folders (i.e., frontend)
    cd ~/DRDB/client
    npm install

    # rebuild the system (frontend)
    npm run build
    #assuming your system is stored at /var/www/html/DRDB
    sudo cp -r -T dist /var/www/html/DRDB  

    # update npm packages for server folders (i.e., backend)
    cd ~/DRDB/server
    npm install

    pm2 restart server.js