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other_servers_update_data.sh
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other_servers_update_data.sh
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#!/bin/bash
########################
#
## Servers that do NOT need updating:
# -Gateway HTTPD proxy
# -PC Beacon - hosts Care4Rare exomes, no way to change them?
# -PC Preprod - Old data doesn't matter?
# -PC Dev - Old data doesn't matter
# -PC Playground - Old data doesn't matter
#
########################
########################
#
## Servers that DO need updating:
# - PhenoTips Database: PT Farm, PC Prod2
# - ElasticCompute: Stats
# - Jenkins: CI
# - Nexus: Nexus
#
########################
########################
## Dump PhenoTips Database
#
# Apply to Servers:
# PT Farm
# PC Prod2
#
########################
# Detect where the PhenoTips instance is
if [[ -f /var/lib/tomcat6/webapps/ROOT/WEB-INF/xwiki.properties ]]
then
HIBERNATE_CONFIG="/var/lib/tomcat6/webapps/ROOT/WEB-INF/hibernate.cfg.xml"
elif [[ -f /var/lib/tomcat6/webapps/phenotips/WEB-INF/xwiki.properties ]]
then
HIBERNATE_CONFIG="/var/lib/tomcat6/webapps/phenotips/WEB-INF/hibernate.cfg.xml"
elif [[ -f /var/lib/phenotips/webapp/WEB-INF/xwiki.properties ]]
then
HIBERNATE_CONFIG="/var/lib/phenotips/webapp/WEB-INF/hibernate.cfg.xml"
fi
# Extract the mysql host, DB name, username and password
MHOST=`cat $HIBERNATE_CONFIG | grep 'jdbc:mysql://' | sed -r -e 's/.*\/\/([^\/]+)\/.*/\1/'`
MDB=`cat $HIBERNATE_CONFIG | grep 'jdbc:mysql://' | sed -r -e 's/.*\/\/[^\/]+\/([^?<]+).*/\1/'`
MUSER=`cat $HIBERNATE_CONFIG | grep 'jdbc:mysql://' -A 5 | grep 'connection.username' | sed -r -e 's/.*>([^<]+)<.*/\1/'`
MPASS=`cat $HIBERNATE_CONFIG | grep 'jdbc:mysql://' -A 5 | grep 'connection.password' | sed -r -e 's/.*>([^<]+)<.*/\1/'`
# Compute the backup filename and make sure its parent directory exists
BACKUPDIR=/var/lib/phenotips/backups/mysql
DBFILE=data.sql
# Dump the database
mysqldump --events --single-transaction $MDB -u $MUSER -h $MHOST -p $MPASS > $DBFILE
########################
## Load PhetoTips Database
########################
mysql -u $MUSER -h $MHOST -p $MPASS < $DBFILE
########################
## Upgrade Phenotips Version (Only if out of date)
########################
# Option 1) Install PhenoTips From APT
curl https://phenotips.org/download/PhenoTips/Download/PhenoTips.repo > PhenoTips.repo
sudo chown root:root PhenoTips.repo
sudo mv PhenoTips.repo /etc/yum.repos.d/
sudo yum install -y phenotips
# Option 2) Install PhenoTips From WGET
systemctl stop tomcat || service tomcat stop
mkdir -p /var/lib/phenotips/next
cd /var/lib/phenotips/next
wget https://nexus.phenotips.org/nexus/content/repositories/releases/org/phenotips/phenotips-standalone/1.2.5/phenotips-standalone-1.2.5.zip
unzip phenotips-*.zip && rm phenotips-*.zip
cd phenotips-*
rm -rf ../../solr/ && cp -r data/solr ../../
mkdir /var/lib/phenotips/backup
mv /var/lib/tomcat*/webapps/phenotips /var/lib/phenotips/backup
mv /var/lib/tomcat*/webapps/ROOT /var/lib/phenotips/backup # ? needed
mv webapps/phenotips /var/lib/tomcat*/webapps
rm -rf /var/lib/phenotips/next
chown -R tomcat:tomcat /var/lib/phenotips || chown -R tomcat:tomcat /var/lib/phenotips
# Merge any custom changes done in the following configuration files from the old instance into the new one:
diff xwiki.cfg /var/lib/phenotips/webapp/WEB-INF/xwiki.cfg
diff xwiki.properties /var/lib/phenotips/webapp/WEB-INF/xwiki.properties
diff hibernate.cfg.xml /var/lib/phenotips/webapp/WEB-INF/hibernate.cfg.xml
# Start new version of Phenotips
systemctl start tomcat || service tomcat start
########################
## Elastic Compute
#
# Apply to Server: Stats
#
########################
# Initialize Snapshot Respository
curl -sX PUT http://$ES_HOST:$ES_PORT/_snapshot/$REPOSITORY_NAME -w "\n" -d @- << EOF
{
"type": "fs",
"settings": {
"location": "/root/elastic_backup"
}
}
EOF
# Perform a snapshat
curl -sX PUT -w "\n" http://$ES_HOST:$ES_PORT/_snapshot/$REPOSITORY_NAME/$SNAPNAME?wait_for_completion=true
# Restore from an existing snapshot:
curl -sX POST -w "\n" http://$ES_HOST:$ES_PORT/_snapshot/$REPOSITORY_NAME/$SNAPNAME/_restore
/var/lib
########################
## Nexus
#
# Apply to Server: Nexus
#
########################
cat <<EOF >> /etc/ssh/ssh_config
Host *.local
ProxyCommand ssh -i ~/.ssh/id_rsa.dan -q [email protected] nc %h 22
EOF
rsync -v -e "ssh -i /root/.ssh/id_rsa.dan" nexus.local:/home/nexus /home/nexus
########################
## Jenkins
## https://wiki.jenkins.io/display/JENKINS/Administering+Jenkins
#
# Apply to Server: CI
#
########################
cat <<EOF >> /etc/ssh/ssh_config
Host *.local
ProxyCommand ssh -i ~/.ssh/id_rsa.dan -q [email protected] nc %h 22
EOF
rsync -v -e "ssh -i /root/.ssh/id_rsa.dan" ci.local:/var/lib/jenkins /var/lib/jenkins
```