Update mage to 'trunk'

[wmoore]

Mage is currently OMERO.server-4.2.1-DEV-r8660-trunk-b1302.

Need to upgrade to latest code, including database upgrade: 4.2.x to 4.3

First, check that webemdb works in current code (need to populate DB with scripts etc).

[wmoore]

Made backup of DB on mage:

$ pg_dump -h localhost -U omero -Fc -f before_upgrade_from_4_2_1.db.dump omero

[wmoore]

Current UPGRADE.sh on mage:

#!/bin/bash

# First download or svn up the server you want
# unzip if necessary
#
# After it's done, if needed the Apache config is in:
# ~jboss/httpd.conf

set -e
set -u
set -x

DIR=$1

#OMERO-CURRENT/bin/omero admin status --nodeonly && OMERO-CURRENT/bin/omero admin stop
#sudo /etc/init.d/apache2 stop

OMERO-CURRENT/bin/omero admin stop

#find bin/omero web start process and get pid
pid=$(ps ux | awk "/omero web start/ && !/awk/ {print \$2}")
echo "OMERO.web pid: $pid"

kill `cat OMERO-CURRENT/var/django.pid`
echo "runfcgi killed"
# /usr/bin/python2.6 bin/omero web start
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400

set -e
set -u
set -x

DIR=$1

#OMERO-CURRENT/bin/omero admin status --nodeonly && OMERO-CURRENT/bin/omero admin stop
#sudo /etc/init.d/apache2 stop

OMERO-CURRENT/bin/omero admin stop

#find bin/omero web start process and get pid
pid=$(ps ux | awk "/omero web start/ && !/awk/ {print \$2}")
echo "OMERO.web pid: $pid"

kill `cat OMERO-CURRENT/var/django.pid`
echo "runfcgi killed"
# /usr/bin/python2.6 bin/omero web start
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
# \_ /usr/bin/python2.6 manage.py runfcgi workdir=./ method=prefork host=0.0.0.0 port=8000 pidfile=/home/jboss/OMERO.server-5.0.0-DEV-r8077-trunk936/var/django.pid daemonize=false maxchildren=5 minspare=1 maxspare=5 maxrequests=400
#for child in $(ps -o pid,ppid -ax | awk "{ if ( \$2 == $pid ) { print \$1 }}")
#do
#  echo "Killing child process $child"
#  kill $child
#done


rm -f OMERO-CURRENT
#rm -f /home/jboss/web-log/*.log
ln -s $DIR OMERO-CURRENT
cd OMERO-CURRENT
cp ~/config.xml etc/grid
perl -i -pe 's/Xmx512M/Xmx1024M/' etc/grid/templates.xml
bin/omero admin start

#WEB
chmod 755 var
mkdir var/lib
cp ~/custom_settings.py var/lib/custom_settings.py
cp ~/emdb_settings.py var/lib/emdb_settings.py
python var/lib/custom_settings.py
bin/omero web syncmedia
bin/omero web start &
disown %1

[wmoore]

Manual upgrade of mage:

bin/omero admin stop
bin/omero web stop
cd ../
wget http://hudson.openmicroscopy.org.uk/job/OMERO/lastSuccessfulBuild/artifact/src/target/OMERO.server-4.3.2-8fc94b85-b2882.zip
unzip OMERO.server-4.3.2-8fc94b85-b2882.zip 
rm -f OMERO-CURRENT
ln -s OMERO.server-4.3.2-8fc94b85-b2882 OMERO-CURRENT
cd OMERO-CURRENT/
cp ~/config.xml etc/grid/
perl -i -pe 's/Xmx512M/Xmx2048M<\/option><option>-XX:MaxPermSize=128M/' etc/grid/templates.xml
psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/OMERO4.2__0.sql
psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/OMERO4.2__0.sql
bin/omero admin start
bin/omero config set omero.web.use_eman2 True
bin/omero web syncmedia
bin/omero web start
bin/omero web stop
nano lib/python/omeroweb/settings.py    # turning on webemdb...
nano lib/python/omeroweb/urls.py
bin/omero web start

[wmoore]

The following command can be used to move code from local development onto deployment on mage:

rsync -vaPe ssh ~/Desktop/OMERO/components/tools/OmeroWeb/omeroweb jboss@mage.openmicroscopy.org.uk:~/OMERO-CURRENT/lib/python

# then need to ssh to mage and restart web

[wmoore]

Updated and running OK