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INSTALL MEANDRE

1. Prepare your server

Connection

Connect to you VM with below command and register with you password

ssh user@IP

Create file for auto login and paste your local ssh id_rsa.pub in that file

nano .ssh/authorized_keys

Update

Change password on new VM

passwd

Update apt

sudo apt update
sudo apt upgrade -y

Resize LVM

To see free space

sudo vgdisplay

To see occupy space by partition

sudo lvdisplay

Add suffisant free space to var partition

sudo lvextend -L +200G /dev/vg1/var
sudo resize2fs /dev/vg1/var

2. Download MEANDRE

Clone MEANDRE git

git clone https://github.com/super-lou/MEANDRE.git

Copy the env file from the default one and secure it

cp MEANDRE/install.env MEANDRE/.env

Edit this env file with your info.\ WARNING : KEEP THE .ENV FILE FOR YOU. DO NOT EXPOSE IT.

Load environment variables and move this dir in the right location

source MEANDRE/.env
sudo mv -rv MEANDRE/ $SERVER_DIR

Secure this dir

sudo chown -R root:root $SERVER_DIR/MEANDRE
sudo chmod -R 755 $SERVER_DIR/MEANDRE

2. Install Apache

sudo apt install apache2 python3-certbot-apache -y
sudo systemctl enable apache2
sudo systemctl start apache2

3. Install postgresql

On local computer

Save the database from MEANDRE local dir and export it to server

source .env
sudo -u postgres pg_dump -U postgres -d $DB_NAME -Fc -b -v -f /home/louis/.postgresql/$DB_NAME.backup
scp $DB_NAME.backup $SERVER_USER@$SERVER_IP:~/

You need to be careful with the privileges for the postgres user.\ With the VPN, the bandwidth is significantly limited, so if necessary, use FileSender and then wget.

On remotes server

Create user and database and update it with the local backup

sudo apt install postgresql postgresql-contrib libpq-dev -y
sudo systemctl enable postgresql
sudo systemctl start postgresql
source .env
sudo -u postgres psql -U postgres -c "CREATE DATABASE \"${DB_NAME}\";"
sudo -u postgres psql -U postgres -c "CREATE USER \"${DB_USER}\" WITH PASSWORD '${DB_PASSWORD}';"
sudo -u postgres psql -U postgres -c "GRANT ALL PRIVILEGES ON DATABASE \"${DB_NAME}\" TO \"${DB_USER}\";"
sudo -u postgres pg_restore -U postgres -d $DB_NAME -v ~/$DB_NAME.backup

4. Install python

sudo apt install python3 python3-pip -y
sudo apt install python3-flask python3-sqlalchemy python3-flask-cors python3-psycopg2 python3-numpy python3-pandas python3-dotenv python3-scipy -y

5. Install R

sudo apt install -y r-base
sudo Rscript -e 'install.packages(c("argparse", "jsonlite", "remotes")); remotes::install_github("super-lou/dataSHEEP")'

6. Configure flask app

Source info and install dependency

sudo apt install libapache2-mod-wsgi-py3

Create the Apache configuration file

source .env
sudo bash -c "cat > /etc/apache2/sites-available/MEANDRE.conf <<EOF
<VirtualHost *:80>
    ServerName $SERVER_NAME
    ServerAdmin $SERVER_EMAIL

    <IfDefine !wsgi_init>
        WSGIDaemonProcess MEANDRE processes=4 threads=5 python-path=/usr/lib/python3/dist-packages
        WSGIProcessGroup MEANDRE
        Define wsgi_init 1
    </IfDefine>

    WSGIScriptAlias / $SERVER_DIR/MEANDRE/app.wsgi

    <Directory $SERVER_DIR/MEANDRE>
        WSGIProcessGroup MEANDRE
        WSGIApplicationGroup %{GLOBAL}
        Require all granted

        #Require valid-user
        #AuthType Basic
        #AuthName "Restricted Area"
        #AuthUserFile /path/to/.htpasswd
    </Directory>

    ErrorLog /var/log/apache2/MEANDRE_error.log
    CustomLog /var/log/apache2/MEANDRE_access.log combined
</VirtualHost>
EOF"

Enable the new site and mod_wsgi module

sudo a2ensite MEANDRE
sudo a2enmod wsgi

Restart Apache and certbot for HTTPS

sudo systemctl restart apache2
sudo certbot --apache