MRIdb installation script for EL6

install-mridb.sh

#!/bin/sh

set -exo pipefail

curl -L https://imperialcollegelondon.box.com/shared/static/wm84f86ikub5mceibprp61cd7jxwanzp.gz | tar xz -C /opt
if [ -f /opt/mridb/conf/application-site.conf ]; then
	echo "Updated MRIdb: $(cat /opt/mridb/VERSION)"
	exit
fi

DEPS=/tmp/mridb-deps
if [ ! -d "$DEPS" ]; then
	curl -L https://imperialcollegelondon.box.com/shared/static/gjuidrfqu3n7vvsltdp948ykbqcynwux.tar | tar x -C /tmp
fi

yum upgrade -y
yum install -y unzip patch postgresql-server policycoreutils-python gcc java-1.7.0-openjdk
yum install -y epel-release
yum install -y p7zip
yum install -y centos-release-scl
yum install -y python27-python-devel python27-numpy

RULENUM=$(iptables -L INPUT --line-numbers | grep 'REJECT' | awk '{print $1}')
iptables -I INPUT $RULENUM -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT
iptables -I INPUT $RULENUM -m state --state NEW -m tcp -p tcp --dport 8080 -j ACCEPT
iptables -I INPUT $RULENUM -m state --state NEW -m tcp -p tcp --dport 11112 -j ACCEPT
service iptables save

unzip -d /opt $DEPS/dcm4che-2.0.28-bin.zip
unzip -d /opt $DEPS/dcm4chee-2.17.3-psql.zip
unzip -d /opt $DEPS/lx64.zip
unzip -d /opt $DEPS/play-1.2.x.zip
unzip -d /opt $DEPS/ISD_dicom_tool.zip
tar xf $DEPS/xmedcon-0.13.0.tar.gz -C /opt
tar xf $DEPS/dcmtk-3.6.0-linux-i686-static.tar.bz2 -C /opt

unzip -d /tmp $DEPS/jboss-4.2.3.GA-jdk6.zip
ln -s /opt/dcm4chee-2.17.3-psql /opt/dcm4chee
tar xf $DEPS/jai_imageio-1_1-lib-linux-amd64.tar.gz --strip-components=2 -C /opt/dcm4chee/bin/native jai_imageio-1_1/lib/libclib_jiio.so
/opt/dcm4chee/bin/install_jboss.sh /tmp/jboss-4.2.3.GA
cp $DEPS/weasis.war /opt/dcm4chee/server/default/deploy
cp $DEPS/weasis-pacs-connector.war /opt/dcm4chee/server/default/deploy
patch /opt/dcm4chee/server/default/conf/dcm4chee-attribute-filter.xml <$DEPS/dcm4chee-attribute-filter.patch
patch /opt/dcm4chee/bin/dcm4chee_init_redhat.sh <$DEPS/dcm4chee_init_redhat.patch

mkdir -p /mnt/dcm4chee/archive
ln -s /mnt/dcm4chee/archive /opt/dcm4chee/server/default/archive
echo JBOSS_USER=RUNASIS >/etc/sysconfig/dcm4chee
echo JBOSS_HOME=$(readlink -f /opt/dcm4chee) >>/etc/sysconfig/dcm4chee
ln -s /opt/dcm4chee/bin/dcm4chee_init_redhat.sh /etc/init.d/dcm4chee
chkconfig --add dcm4chee
chkconfig dcm4chee on

chkconfig postgresql on
mkdir -p /mnt/pgsql/data
chown postgres.postgres /mnt/pgsql/data
echo PGDATA=/mnt/pgsql/data >/etc/sysconfig/pgsql/postgresql
semanage fcontext -a -t postgresql_db_t "/mnt/pgsql/data(/.*)?"
restorecon -R /mnt/pgsql/data
service postgresql initdb
sed -i 's/ident$/trust/' /mnt/pgsql/data/pg_hba.conf
service postgresql start
sleep 1
export PGUSER=postgres
createdb pacsdb
psql pacsdb -f /opt/dcm4chee/sql/create.psql
touch /usr/share/pgsql/tsearch_data/empty.stop
psql pacsdb <<EOF
CREATE TEXT SEARCH CONFIGURATION english_nostop (COPY = english);
CREATE TEXT SEARCH DICTIONARY english_nostop (TEMPLATE = simple, STOPWORDS = empty);
ALTER TEXT SEARCH CONFIGURATION english_nostop ALTER MAPPING FOR asciihword, asciiword, hword, hword_asciipart, hword_part, word WITH english_nostop;
EOF

. /opt/rh/python27/enable
(cd $DEPS/pydicom-0.9.7 && python setup.py install)
easy_install -i https://pypi.python.org/simple/ nibabel

/opt/mricron/dcm2nii
sed -i 's/MinReorientMatrix=200/MinReorientMatrix=2000/' ~/.dcm2nii/dcm2nii.ini

touch /opt/mridb/conf/application-site.conf
/opt/play-1.2.x/play secret /opt/mridb
grep -F application.secret /opt/mridb/conf/application.conf >/opt/mridb/conf/application-site.conf
ln -s /opt/mridb/bin/mridb /etc/init.d/mridb
chkconfig --add mridb
chkconfig mridb on

echo "Installed MRIdb: $(cat /opt/mridb/VERSION)"