Zotero server setup script

#!/bin/bash

#It is written on the basis of Instructions given here(http://git.27o.de/dataserver/about/) and I have tested it on ubuntu server 16.04.
#Before running this script get full information about inputs required to run this script

#SQL server ROOT password:
#	is password which will be used as root password for MySQL server

#password for Zotero databases:
#	This password will be used for all databases which are required for zotero dataserver

#Web access address:
#	Address where you will access your server if you are installing it on a server you can use servers ip address to access it or a domain name which is pointing to it.

#Port:
#	Port on which you will access your dataserver as it uses https protocol so default port is 443 if you want to access it on an other port which is available enter it.

#salt for user passwords:
#	This salt will be embedded with user passwords before encrypting it to enhance security. You will have to use it during user creation on server.

#API super user name:
#	Super username to access APIs

#API super user password:
#	Superuser password to access APIs

#AWS secret key:
#	This key is used to sync attachments with storage server. Storage server address and key is provided to client by server then client uploads attachment on storage server using this key.

#checking if script is ran as root or not
	if [ "$EUID" -ne 0 ]
	  then echo 'Please run as root!'
	  exit
	fi

# Ask the user for required inputs
	echo 'Note: Do not use "zotero" as credential it cause some unknown problems.'

	read -p 'Enter MySQL server ROOT password: ' sqlRootPassword

	read -p 'Enter password for Zotero databases: ' zoteroDbPassword

	printf 'Enter web/IP address where you will access it.\n'
	printf 'Examples:\n\t127.0.0.1\n\texample.com\n\tsub.example.com\n'
	read -p 'Enter web/IP address: ' webAdress

	printf 'Enter port where you want to access it.\n'
	read -p 'Default HTTPS port is 443 : ' port

	read -p 'Enter salt for user passwords: ' salt

	read -p 'Enter API super user name: ' suName

	read -p 'Enter API super user password: ' suPassword

	read -p 'Enter AWS secret key: ' awsKey

#install packages
	echo 'Installing required packages'
	
	apt-get update
	
	debconf-set-selections <<< "mysql-server mysql-server/root_password password $sqlRootPassword"
	debconf-set-selections <<< "mysql-server mysql-server/root_password_again password $sqlRootPassword"
	apt-get -y install mysql-server

	apt-get install apache2 libapache2-mod-php memcached zend-framework php-cli php-memcached php-mysql php-curl uwsgi uwsgi-plugin-psgi libplack-perl libdigest-hmac-perl libjson-xs-perl libfile-util-perl libapache2-mod-uwsgi git gnutls-bin runit libswitch-perl php-mbstring php-simplexml

#Create DIRECTORIES
	echo 'Creating required directories'

	mkdir -p /srv/zotero/{dataserver,zss,storage}/ /srv/zotero/log/{download,upload,error,api-errors,sync-errors} /etc/sv/zotero-download/log /etc/sv/zotero-upload/log /etc/sv/zotero-error/log

#Download dataserver Source Code
	echo 'Cloning dataserver repository'

	git clone git://git.27o.de/dataserver /srv/zotero/dataserver

#Commenting three lines which doesn't have correct syntax according to php7 and it doesn't have any impact on working
	echo 'Commenting lines with incorect syntax'

	sed -i '508,510 s/^/\/\//' /srv/zotero/dataserver/controllers/ApiController.php

#Prepare directory rights
	echo 'Preparing directory rights'

	chown www-data: /srv/zotero/log/{sync-errors,api-errors}/
	chown www-data:www-data /srv/zotero/dataserver/tmp /srv/zotero/storage

#Zend Linking
	echo 'Linking Zend framework work with zotero dataserver'

	cd /srv/zotero/dataserver/include
	rm -r Zend
	ln -s /usr/share/php/libzend-framework-php/Zend

#Apache2 Configuration
	echo 'Enabling rewrite and ssl mode for apache2'

	a2enmod ssl
	a2enmod rewrite
	
#	SSL Certificate Creation
		echo 'Creating self-signed ssl certificates'

		certtool -p --sec-param high --outfile /etc/apache2/zotero.key
		certtool -s --load-privkey /etc/apache2/zotero.key --outfile /etc/apache2/zotero.cert
	
#	Creating Virtual Host File
		echo 'Creating VirtualHost file for zotero dataserver'

		cat << EOF > /etc/apache2/sites-available/zotero.conf
<VirtualHost *:$port>
  DocumentRoot /srv/zotero/dataserver/htdocs
  SSLEngine on
  SSLCertificateFile /etc/apache2/zotero.cert
  SSLCertificateKeyFile /etc/apache2/zotero.key

  <Location /zotero/>
	SetHandler uwsgi-handler
	uWSGISocket /var/run/uwsgi/app/zss/socket
	uWSGImodifier1 5
  </Location>

  <Directory "/srv/zotero/dataserver/htdocs/">
	Options FollowSymLinks MultiViews
	AllowOverride All
	Require all granted
	Require all granted
  </Directory>

  php_value short_open_tag 1
  ErrorLog /srv/zotero/log/error.log
  CustomLog /srv/zotero/log/access.log common
</VirtualHost>
EOF
	
#	Registering Virtual Host File
	echo 'Loading VirtualHost file of zotero dataserver'

	a2ensite zotero.conf
	
#	Editing .htaccess File
	echo 'Editing /srv/zotero/dataserver/htdocs/.htaccess file'

	sed -i -e 's/RewriteCond %{SCRIPT_FILENAME} !-d/RewriteCond %{SCRIPT_FILENAME} !-d\nRewriteCond %{REQUEST_URI} !^\/zotero/g' /srv/zotero/dataserver/htdocs/.htaccess

#MySQL Configuration
	echo 'Configuring MySQL'

	cat << EOF > /etc/mysql/conf.d/zotero.cnf
[mysqld]
character-set-server = utf8
collation-server = utf8_general_ci
event-scheduler = ON
sql-mode = STRICT_ALL_TABLES
default-time-zone = '+0:00'
EOF

#	Setting up Database
		cd /srv/zotero/dataserver/misc/
#		Script to setup databases
			echo 'Setting up databases'
			
			sed -i -e "s/-pPW/-p$sqlRootPassword/g" /srv/zotero/dataserver/misc/setup_db
			sed -i -e "s/foobar/$zoteroDbPassword/g" /srv/zotero/dataserver/misc/setup_db
			
			./setup_db

#Dataserver Configuration
	echo 'Configuring zotero dataserver settings'

	cat << EOF > /srv/zotero/dataserver/include/config/dbconnect.inc.php
<?
function Zotero_dbConnectAuth(\$db) {
	\$charset = '';

	if (\$db == 'master') {
			\$host = 'localhost';
			\$port = 3306;
			\$db = 'zotero_master';
			\$user = 'zotero';
			\$pass = '$zoteroDbPassword';
	}
	else if (\$db == 'shard') {
			\$host = false;
			\$port = false;
			\$db = false;
			\$user = 'zotero';
			\$pass = '$zoteroDbPassword';
	}
	else if (\$db == 'id1') {
			\$host = 'localhost';
			\$port = 3306;
			\$db = 'zotero_ids';
			\$user = 'zotero';
			\$pass = '$zoteroDbPassword';
	}
	else if (\$db == 'id2') {
			\$host = 'localhost';
			\$port = 3306;
			\$db = 'zotero_ids';
			\$user = 'zotero';
			\$pass = '$zoteroDbPassword';
	}
	else {
			throw new Exception("Invalid db '\$db'");
	}
	return array(
	  'host'=>\$host, 
	  'port'=>\$port, 
	  'db'=>\$db, 
	  'user'=>\$user, 
	  'pass'=>\$pass,
	  'charset'=>\$charset
	);
}
?>
EOF

	cat << EOF > /srv/zotero/dataserver/include/config/config.inc.php
<?
class Z_CONFIG {
	public static \$API_ENABLED = true;
	public static \$SYNC_ENABLED = true;
	public static \$PROCESSORS_ENABLED = true;
	public static \$MAINTENANCE_MESSAGE = 'Server updates in progress. Please try again in a few minutes.';

	public static \$TESTING_SITE = false;
	public static \$DEV_SITE = false;

	public static \$DEBUG_LOG = false;

	public static \$BASE_URI = 'http://zotero.org/';
	public static \$API_BASE_URI = 'https://$webAdress:$port/';//address where you will access it
	public static \$WWW_BASE_URI = '';
	public static \$SYNC_DOMAIN = 'sync';

	public static \$AUTH_SALT = '$salt';//add some salt that will be embeded with password before encrypting it and it will be used during user password setting.
	public static \$API_SUPER_USERNAME = '$suName';
	public static \$API_SUPER_PASSWORD = '$suPassword';

	public static \$AWS_ACCESS_KEY = '';
	public static \$AWS_SECRET_KEY = '$awsKey'; //this key should be similar to key in ZSS.pm file
	public static \$S3_BUCKET = 'zotero';
	public static \$S3_ENDPOINT = '$webAdress:$port';
	public static \$S3_USE_SSL = true;
	public static \$S3_VALIDATE_SSL = false;

	public static \$URI_PREFIX_DOMAIN_MAP = array(
		'/sync/' => 'sync'
	);

	public static \$MEMCACHED_ENABLED = true;
	public static \$MEMCACHED_SERVERS = array(
		'localhost:11211'
	);

	public static \$TRANSLATION_SERVERS = array(
		"translation1.localdomain:1969"
	);

	public static \$CITATION_SERVERS = array(
		"citeserver1.localdomain:8080", "citeserver2.localdomain:8080"
	);

	public static \$ATTACHMENT_SERVER_HOSTS = array("files1.localdomain", "files2.localdomain");
	public static \$ATTACHMENT_SERVER_DYNAMIC_PORT = 80;
	public static \$ATTACHMENT_SERVER_STATIC_PORT = 81;
	public static \$ATTACHMENT_SERVER_URL = "https://files.example.net";
	public static \$ATTACHMENT_SERVER_DOCROOT = "/var/www/attachments/";

	public static \$STATSD_ENABLED = false;
	public static \$STATSD_PREFIX = "";
	public static \$STATSD_HOST = "monitor.localdomain";
	public static \$STATSD_PORT = 8125;

	public static \$LOG_TO_SCRIBE = false;
	public static \$LOG_ADDRESS = '';
	public static \$LOG_PORT = 1463;
	public static \$LOG_TIMEZONE = 'US/Eastern';
	public static \$LOG_TARGET_DEFAULT = 'errors';

	public static \$PROCESSOR_PORT_DOWNLOAD = 3455;
	public static \$PROCESSOR_PORT_UPLOAD = 3456;
	public static \$PROCESSOR_PORT_ERROR = 3457;

	public static \$PROCESSOR_LOG_TARGET_DOWNLOAD = 'sync-processor-download';
	public static \$PROCESSOR_LOG_TARGET_UPLOAD = 'sync-processor-upload';
	public static \$PROCESSOR_LOG_TARGET_ERROR = 'sync-processor-error';

	public static \$SYNC_DOWNLOAD_SMALLEST_FIRST = false;
	public static \$SYNC_UPLOAD_SMALLEST_FIRST = false;

	// Set some things manually for running via command line
	public static \$CLI_PHP_PATH = '/usr/bin/php';
	public static \$CLI_DOCUMENT_ROOT = "/srv/zotero/dataserver/";

	public static \$SYNC_ERROR_PATH = '/srv/zotero/log/sync-errors/';
	public static \$API_ERROR_PATH = '/srv/zotero/log/api-errors/';

	public static \$CACHE_VERSION_ATOM_ENTRY = 1;
	public static \$CACHE_VERSION_BIB = 1;
	public static \$CACHE_VERSION_ITEM_DATA = 1;
}
?>
EOF

#php Configuration
#	Replace "short_open_tag = Off" with "short_open_tag = On"
		echo 'Enabling php short_open_tag for cli use'

		sed -i -e 's/short_open_tag = Off/short_open_tag = On/g' /etc/php/7.0/cli/php.ini

#Creating Processor daemons Using runit
	echo 'Creating Processor daemons Using runit'

	cat << EOF > /etc/sv/zotero-download/run
#!/bin/sh

cd /srv/zotero/dataserver/processor/download
exec 2>&1
exec chpst -u www-data:www-data php daemon.php
EOF

	cat << EOF > /etc/sv/zotero-upload/run
#!/bin/sh

cd /srv/zotero/dataserver/processor/upload
exec 2>&1
exec chpst -u www-data:www-data php daemon.php
EOF

	cat << EOF > /etc/sv/zotero-error/run
#!/bin/sh

cd /srv/zotero/dataserver/processor/error
exec 2>&1
exec chpst -u www-data:www-data php daemon.php
EOF

	cat << EOF > /etc/sv/zotero-download/log/run
#!/bin/sh

exec svlogd /srv/zotero/log/download
EOF

	cat << EOF > /etc/sv/zotero-upload/log/run
#!/bin/sh

exec svlogd /srv/zotero/log/upload
EOF

	cat << EOF > /etc/sv/zotero-error/log/run
#!/bin/sh

exec svlogd /srv/zotero/log/error
EOF

#Fixing file permissions
	echo 'Fixing file permissions'

	chmod 744 /etc/sv/zotero-download/run /etc/sv/zotero-upload/run /etc/sv/zotero-error/run /etc/sv/zotero-download/log/run /etc/sv/zotero-upload/log/run /etc/sv/zotero-error/log/run
	
#Creating File links to run daemons
	echo 'Creating File links to run daemons'

	ln -s /etc/sv/zotero-download /etc/service/
	ln -s /etc/sv/zotero-upload /etc/service/
	ln -s /etc/sv/zotero-error /etc/service/

#Configuring ZSS
	echo 'Cloning zss repository to /srv/zotero/zss'

	git clone git://git.27o.de/zss /srv/zotero/zss
	
	echo 'Configuring ZSS'

	sed -i -e 's/path\/to\/ZSS.pm/srv\/zotero\/zss\//g' /srv/zotero/zss/zss.psgi
	sed -i -e "s/yoursecretkey/$awsKey/g" /srv/zotero/zss/ZSS.pm
	sed -i -e 's/path\/to/srv\/zotero/g' /srv/zotero/zss/ZSS.pm

#Configure uwsgi
	echo 'Configure uwsgi to launch zss'

	cat << EOF > /etc/uwsgi/apps-available/zss.yaml
uwsgi:
  plugin: psgi
  psgi: /srv/zotero/zss/zss.psgi
EOF

	ln -s /etc/uwsgi/apps-available/zss.yaml /etc/uwsgi/apps-enabled/
	
	echo 'Zotero dataserver installation Completed'
	
	read -n1 -t10 -rsp 'System is going to reboot in 10 seconds or press any key to reboot now...';
	printf '\nRebooting...'
	reboot