ConfigureMysql.script

#!/bin/bash

#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#+
#+     Mumps Bioinformatics Software Library
#+     Copyright (C) 2015 by Kevin C. O'Kane
#+
#+     Kevin C. O'Kane
#+     kc.okane@gmail.com
#+     http://www.cs.uni.edu/~okane
#+     http://threadsafebooks.com/
#+
#+ This program is free software; you can redistribute it and/or modify
#+ it under the terms of the GNU General Public License as published by
#+ the Free Software Foundation; either version 2 of the License, or
#+ (at your option) any later version.
#+
#+ This program is distributed in the hope that it will be useful,
#+ but WITHOUT ANY WARRANTY; without even the implied warranty of
#+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#+ GNU General Public License for more details.
#+
#+ You should have received a copy of the GNU General Public License
#+ along with this program; if not, write to the Free Software
#+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#+
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

# this file MUST be run as root
# this file MUST be run as root
# this file MUST be run as root

if [ "$OSTYPE" == "cygwin" ]; then
	echo "This script is not appropriate for Cygwin"
	exit
	fi

if [ `whoami` != "root" ]; then
	echo
	echo "****************************************"
        echo "**** you must be root to run this script"
	echo "****************************************"
	echo
        exit
        fi

# This file will install (if needed) MySQL and configure
# it and mumps.

# If MySQL installation is done, you will need to provide
# a password for the MySQL root (this is not the system root).

# You will also need to provide a password for the MySQL mumps user.

# This file was developed and tested using Linux Mint 17.2 and should be 
# compatible with related Ubuntu/Debian based systems.

# This code is provided with no warranty as per the GPL license.

# Configure MySQL for Mumps usage

# Required software packages 

#	mysql-client
#	mysql-server
#	mysql-common
#	mysql-utilities
#	mysql-workbench
#	libmysqlclient-dev
#	libmysqld-dev

# Adjust the following appropriately.

SOFTWAREROOT="/usr/lib/mysql"

echo
echo "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv"
echo "Grand general Mumps MySQL instalerizer."
echo "This script will install, as needed, MySQL, g++,"
echo "autoconf, libccre-dev and Mumps."
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo

echo "---------------------------------------------------------------"
echo
echo "If MySQL is already installed, you will need to know the"
echo "password for MySQL root (not the operating system root)."
echo
echo "If MySQL needs to be installed, you will need to set the MySQL root"
echo "password. This is not the operating system root. Dialog boxes will "
echo "pop up during the install and ask for the MySQL root password."
echo
echo "NOTE: EVEN THOUGH THE DIALOG SUGGESTS THAT THE PASSWORD IS OPTIONAL"
echo "      IT IS NOT - REPEAT - NOT. TYPE IN A PASSWORD...."	
echo
echo "You will be prompted again for the MySQL root password. The install code"
echo "assumes you used abc123 but you may enter another value"
echo
echo "You will also be asked to set the password for the MySQL user named mumps."
echo "This may or may not be the same as the MySQL root password (your option)."
echo
echo "You must have an Internet connection to install the software."
echo
echo "You will see many messages. The final message is the one that counts."
echo " if you see: ***Done - it worked! it is likely that everything installed correctly."
echo

while true; do
	read -p "Do you wish to proceed? (y/n) " yn
	case $yn in
	[Yy]* ) break;;
	[Nn]* ) exit;;
	* ) echo "Please answer yes or no.";;
	esac
	done
	echo

	apt-get -q update
	apt-get -q -y astyle
	apt-get -q -y install mysql-client
	apt-get -q -y install mysql-server 
	apt-get -q -y install mysql-common 
	apt-get -q -y install mysql-utilities 
	apt-get -q -y install mysql-workbench 
	apt-get -q -y install libmysqlclient-dev
	apt-get -q -y install libmysqld-dev

	apt-get -q -y install autoconf 

	apt-get -q -y install libreadline-dev

	apt-get -q -y install libpcre3 
	apt-get -q -y install libpcre3-dev 

	apt-get -q -y install g++ 
	apt-get -q -y install gcc-doc 

	apt-get -q -y install libgmp-dev
	apt-get -q -y install libmpfr-dev

# compile and install mumps for mysql.
# edit configurations for mumps as needed in this file especially
# passwords and host ip number. see readme.pdf

MumpsPassword=abc123

echo
read -p "What should the MySQL password for user 'mumps' be? (default: abc123) " pass
if [ -z $pass ]; then
	MumpsPassword=abc123
	fi

echo
echo "The password for user 'mumps' will be $MumpsPassword"

	while true; do
		echo
		read -p "Is $MumpsPassword the correct password for user 'mumps'? (y/n) " yn
		case $yn in
			[Yy]* ) break;;
			[Nn]* ) read -p "Enter the password to be used for user 'mumps' " MumpsPassword ;;
			* ) echo "Please answer yes or no.";;
			esac
		done

echo
echo "We will now run BuildMumpsWithGlobalsInMySQL.script"
read -p "Hit enter to begin Mumps configuration script " x
echo

./BuildMumpsWithGlobalsInMySQL.script $MumpsPassword

echo
read -p "What is the MySQL root password? (abc123) " pass
if [ -z $pass ]; then
	pass=abc123
	fi

echo
echo "MySQL root password is $pass"
echo "User mumps MySQL password will be $MumpsPassword"
echo

echo
echo "The password for MySQL root is $pass"

	while true; do
		echo
		read -p "Is $pass the correct password for MySQL root? (y/n) " yn
		case $yn in
			[Yy]* ) break;;
			[Nn]* ) read -p "Enter the correct MySQL root password " pass ;;
			* ) echo "Please answer yes or no.";;
			esac
		done

echo
echo "Note: if user mumps does not exist, you will see an error message to"
echo "that effect next. You may ignore it."
echo

mysql -u root -p$pass -e "drop user 'mumps';"
mysql -u root -p$pass -e "create user 'mumps' identified by '$MumpsPassword';"
mysql -u root -p$pass -e "drop database if exists mumps;"
mysql -u root -p$pass -e "create database mumps;"
mysql -u root -p$pass -e "GRANT ALL PRIVILEGES ON mumps.* TO 'mumps'@'%' WITH GRANT OPTION;"

# create a small mumps program in file gblinit.mps

echo -e "	w \"init database\",!\n	sql/f test 5\n	set ^test(1)=99\n	w \"if you see 99 it worked: \",^test(1),!" > gblinit.mps

# run the program - it will initialize the mumps database

./mumps gblinit.mps 

# done