Setting up phenotips on Ubuntu Xenial with Tomcat

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

mkdir -p "$directory"/var/lib/phenotips/solr/
if [ ! -e solr-configuration-1.3.7.jar ]; then
	curl https://nexus.phenotips.org/nexus/content/repositories/releases/org/phenotips/solr-configuration/1.3.7/solr-configuration-1.3.7.jar > solr-configuration-1.3.7.jar
fi
echo 0af9a309462f11dd974b6d3a6ab5fa68 solr-configuration-1.3.7.jar | md5sum --check
unzip -d "$directory"/var/lib/phenotips/solr solr-configuration-1.3.7.jar

machinectl shell "$directory" /bin/chown -- -R tomcat8:tomcat8 /var/lib/phenotips
sed -i -r -e 's/^(\s*JAVA_OPTS.*-Xmx)([^" ]+)(.*)/\12g\3/' "$directory/etc/default/tomcat8"

machinectl poweroff "$directory"

wait $pid