install.sh

#!/bin/bash

#=============================================================
# HEADER
#=============================================================

#INSTITUTION:ISCIII
#CENTRE:BU-ISCIII
#AUTHOR: Luis Chapado
#CREATED: 02 August 2022
#
#
#DESCRIPTION: This script install on your local server the latest stable
#   version of relecov-platform application
#
#
#================================================================
# END_OF_HEADER
#================================================================

RELECOVPLATFORM_VERSION="0.2.0"
. ./install_settings.txt

db_check(){
    mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist >/tmp/null ###user should have mysql permission on remote server.

    if ! [ $? -eq 0 ]; then
        echo -e "${RED}ERROR : Unable to connect to database. Check if your database is running and accessible${NC}"
        exit 1
    fi
    RESULT=`mysqlshow --user=$DB_USER --password=$DB_PASS --host=$DB_SERVER_IP --port=$DB_PORT | grep -o relecov`

    if  ! [ "$RESULT" == "relecov" ] ; then
        echo -e "${RED}ERROR : Relecov database is not defined yet ${NC}"
        echo -e "${RED}ERROR : Create Relecov database on your mysql server and run again the installation script ${NC}"
        exit 1
    fi
}

apache_check(){
    if [[ $linux_distribution == "Ubuntu" ]]; then
        if ! pidof apache2 > /dev/null ; then
            # web server down, restart the server
            echo "Apache Server is down... Trying to restart Apache"
            systemctl restart apache2.service
            sleep 10
            if pidof apache2 > /dev/null ; then
                echo "Apache Server is up"
            else
                echo -e "${RED}ERROR : Unable to start Apache ${NC}"
                echo -e "${RED}ERROR : Solve the issue with Apache server and run again the installation script ${NC}"
                exit 1
            fi
        fi
    elif [[ $linux_distribution == "CentOs" ]]; then
        if ! pidof httpd > /dev/null ; then
            # web server down, restart the server
            echo "Apache Server is down... Trying to restart Apache"
            systemctl restart httpd
            sleep 10
            if pidof httpd > /dev/null ; then
                echo "Apache Server is up"
            else
                echo -e "${RED}ERROR : Unable to start Apache ${NC}"
                echo -e "${RED}ERROR : Solve the issue with Apache server and run again the installation script ${NC}"
                exit 1
            fi
        fi
    fi
}

python_check(){

    python_version=$(su -c python3 --version $user)
    if [[ $python_version == "" ]]; then
        echo -e "${RED}ERROR : Python3 is not found in your system ${NC}"
        echo -e "${RED}ERROR : Solve the issue with Python and run again the installation script ${NC}"
        exit 1
    fi
    p_version=$(echo $python_version | cut -d"." -f2)
    if (( $p_version < 7 )); then
        echo -e "${RED}ERROR : Application requieres at least the version 3.7.x of Python3  ${NC}"
        echo -e "${RED}ERROR : Solve the issue with Python and run again the installation script ${NC}"
        exit 1
    fi
}
#================================================================
#SET TEMINAL COLORS
#================================================================
YELLOW='\033[0;33m'
WHITE='\033[0;37m'
CYAN='\033[0;36m'
BLUE='\033[0;34m'
RED='\033[0;31m'
GREEN='\033[0;32m'
NC='\033[0m'

#================================================================
# MAIN_BODY
#================================================================

printf "\n\n%s"
printf "${YELLOW}------------------${NC}\n"
printf "%s"
printf "${YELLOW}Starting Relecov Installation version: ${RELECOVPLATFORM_VERSION}${NC}\n"
printf "%s"
printf "${YELLOW}------------------${NC}\n\n"

#================================================================
#CHECK REQUIREMENTS BEFORE STARTING INSTALLATION
#================================================================
# Check that script is run as root
if [[ $EUID -ne 0 ]]; then
    printf "\n\n%s"
    printf "${RED}------------------${NC}\n"
    printf "%s"
    printf "${RED}Exiting installation. This script must be run as root ${NC}\n"
    printf "\n\n%s"
    printf "${RED}------------------${NC}\n"
    printf "%s"
    exit 1
fi

user=$SUDO_USER
group=groups | cut -d" " -f1

#Linux distribution
linux_distribution=$(lsb_release -i | cut -f 2-)

echo "Checking main requirements"
python_check
echo "Valid version of Python"
db_check
echo "Successful check for database"
apache_check
echo "Successful check for apache"

#================================================================

read -p "Are you sure you want to install Relecov-platform in this server? " -n 1 -r
echo    # (optional) move to a new line
if [[ ! $REPLY =~ ^[Yy]$ ]] ; then
    echo "Exiting without running relecov_platform installation"
    exit 1
fi

#================================================================
if [[ $linux_distribution == "Ubuntu" ]]; then
    echo "Software installation for Ubuntu"
    apt-get update && apt-get upgrade -y
    apt-get install -y \
        lightdm git apt-utils libcairo2 libcairo2-dev  wget gnuplot python3-pip \
        libmysqlclient-dev apache2-dev vim libapache2-mod-wsgi-py3
fi

if [[ $linux_distribution == "CentOS" ]]; then
    echo "Software installation for Centos"
    yum groupinstall “Development tools”
    yum install zlib-devel bzip2-devel sqlite sqlite-devel openssl-devel
    yum install git libcairo2 libcairo2-dev libpango1.0 libpango1.0-dev wget gnuplot
fi

echo "Starting relecov-platform installation"
cd /opt/relecov-platform
# git checkout main

mkdir -p /opt/relecov-platform/logs
chown $user:apache /opt/relecov-platform/logs
mkdir -p /opt/relecov-platform/documents
chown $user:apache /opt/relecov-platform/documents
echo "Created folders for logs and documents "

# install virtual environment
if [[ $linux_distribution == "Ubuntu" ]]; then
    echo "Creating virtual environment"
    pip3 install virtualenv
    virtualenv --python=/usr/bin/python3 virtualenv

fi

if [[ $linux_distribution == "CentOS" ]]; then
    echo "Checking virtual environment"
    p_exec=$(which python3)
    p_exec=$(readlink -f $p_exec)
    p_path=$(dirname $p_exec)
    if [ -f $p_path/virtualenv ]; then
        echo "virtualenv alredy defined. Skyping"
    else
        echo "Creating virtual environment"
        $p_path/pip3 install virtualenv
    fi
    su $user bash -c "$p_path/virtualenv --python=$p_exec virtualenv"
fi
echo ""
echo "activate the virtualenv"

source virtualenv/bin/activate

# Starting Relecov Platform
echo "Loading python necessary packages"
su $user bash -c "python3 -m pip install -r conf/requirements.txt"
echo ""
echo "Creating relecov_platform project"
django-admin startproject relecov_platform .
grep ^SECRET relecov_platform/settings.py > ~/.secret


# Copying config files and script
cp conf/template_settings.py /opt/relecov-platform/relecov_platform/settings.py
cp conf/urls.py /opt/relecov-platform/relecov_platform/

sed -i "/^SECRET/c\\$(cat ~/.secret)" relecov_platform/settings.py
sed -i "s/djangouser/${DB_USER}/g" relecov_platform/settings.py
sed -i "s/djangopass/${DB_PASS}/g" relecov_platform/settings.py
sed -i "s/djangohost/${DB_SERVER_IP}/g" relecov_platform/settings.py
sed -i "s/djangoport/${DB_PORT}/g" relecov_platform/settings.py

sed -i "s/localserverip/${LOCAL_SERVER_IP}/g" relecov_platform/settings.py


echo "Creating the database structure for relecov-platform"
python3 manage.py migrate
su $user bash -c "python3 manage.py makemigrations relecov_core"
python3 manage.py migrate

#echo "Change owner of files to Apache user"
#chown -R www-data:www-data /opt/relecov-platform

echo "Loading in database initial data"
python3 manage.py loaddata conf/upload_tables.json


echo "Updating Apache configuration"
if [[ $linux_distribution == "Ubuntu" ]]; then
    cp conf/apache2.conf /etc/apache2/sites-available/000-default.conf
    echo  'LoadModule wsgi_module "/opt/relecov-platform/virtualenv/lib/python3.8/site-packages/mod_wsgi/server/mod_wsgi-py38.cpython-38-x86_64-linux-gnu.so"' >/etc/apache2/mods-available/iskylims.load
    cp conf/relecov_platform.conf /etc/apache2/mods-available/relecov_platform.conf

    # Create needed symbolic links to enable the configurations:

    ln -s /etc/apache2/mods-available/iskylims.load /etc/apache2/mods-enabled/
    ln -s /etc/apache2/mods-available/iskylims.conf /etc/apache2/mods-enabled/
fi

if [[ $linux_distribution == "CentOs" ]]; then
    # cp conf/httpd.conf /etc/httpd/conf.d/relecov_platform.conf
echo "Creating super user "
python3 manage.py createsuperuser

printf "\n\n%s"
printf "${BLUE}------------------${NC}\n"
printf "%s"
printf "${BLUE}Successfuly iSkyLIMS Installation version: ${RELECOVPLATFORM_VERSION}${NC}\n"
printf "%s"
printf "${BLUE}------------------${NC}\n\n"

echo "Installation completed"