Setting up phenotips on Ubuntu Xenial with Tomcat and MySQL

phenotips_tomcat_mysql.sh

#!/bin/sh

set -exu

directory=ubuntu-xenial-robot

debootstrap --variant=minbase --include=dbus,systemd-sysv xenial "$directory" http://archive.ubuntu.com/ubuntu/

systemd-nspawn --boot --resolv-conf=copy-host --directory="$directory" &
pid=$!

sleep 10 # wait for the system to boot

machinectl shell "$directory" /bin/sh -c "
set -exu

apt update
apt install --yes tomcat8
mkdir /var/lib/phenotips
chown -R tomcat8:tomcat8 /var/lib/phenotips

cat << END > /tmp/preseed
mysql-server mysql-server/root_password password password
mysql-server mysql-server/root_password_again password password
END
debconf-set-selections /tmp/preseed
rm /tmp/preseed
apt install --yes mysql-server

mysql -u root -ppassword -e 'create database phenotips default character set utf8 default collate utf8_bin;'
mysql -u root -ppassword -e 'grant all privileges on phenotips.* to phenotips@localhost identified by \"password\";'
"

mkdir "$directory"/var/lib/tomcat8/webapps/phenotips
if [ ! -e phenotips-war-1.3.7.war ]; then
	curl https://nexus.phenotips.org/nexus/content/repositories/releases/org/phenotips/phenotips-war/1.3.7/phenotips-war-1.3.7.war > phenotips-war-1.3.7.war
fi
echo 0f1b9e1bea6ad479e46a6fbda253ad45  phenotips-war-1.3.7.war | md5sum --check
unzip -d "$directory"/var/lib/tomcat8/webapps/phenotips phenotips-war-1.3.7.war

xmlstarlet edit --inplace --pf \
	--update "//session-factory/property[@name='connection.url']" --expr "string('jdbc:mysql://localhost/phenotips')" \
	--update "//session-factory/property[@name='connection.username']" --expr "string('phenotips')" \
	--update "//session-factory/property[@name='connection.password']" --expr "string('password')" \
	--update "//session-factory/property[@name='connection.driver_class']" --expr "string('com.mysql.jdbc.Driver')" \
	--update "//session-factory/property[@name='dialect']" --expr "string('org.hibernate.dialect.MySQL5InnoDBDialect')" \
	--subnode "//session-factory" -t elem -n myprop -v true \
	--insert "//myprop" -t attr -n "name" -v dbcp.poolPreparedStatements \
	--rename "//myprop" -v "property" \
	--subnode "//session-factory" -t elem -n myprop -v 20 \
	--insert "//myprop" -t attr -n "name" -v dbcp.maxOpenPreparedStatements \
	--rename "//myprop" -v "property" \
	"$directory"/var/lib/tomcat8/webapps/phenotips/WEB-INF/hibernate.cfg.xml
echo xwiki.db=phenotips >> "$directory"/var/lib/tomcat8/webapps/phenotips/WEB-INF/xwiki.cfg

machinectl poweroff "$directory"

wait $pid