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# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
# USE ONLY IF YOUR NGINX PORT IS >1024 (NOT PRIVILEGED)
# Load server config
otconfig() {
source $HOME/.opentox-ui.sh
}
# Update the version
otupdate() {
START_DIR=`pwd`
otconfig
cd $HOME/opentox-ruby/www/opentox
for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ; done
cd $HOME/opentox-ruby/www/opentox/algorithm/libfminer
mv libbbrc/Makefile libbbrc/Makefile~
mv liblast/Makefile liblast/Makefile~
if ! git pull; then
echo "Error! Pull for Fminer failed."
return 1
fi
mv libbbrc/Makefile~ libbbrc/Makefile
mv liblast/Makefile~ liblast/Makefile
make -C libbbrc/ clean
make -C libbbrc/ ruby
make -C liblast/ clean
make -C liblast/ ruby
cd -
cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
if ! git pull; then
echo "Error! Pull for Last-Utils failed."
return 1
fi
cd -
cd opentox-ruby
LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
if [ -h $LINK_DIR ]; then
rm -f $LINK_DIR
fi
rake install
if ! [ -h $LINK_DIR ]; then
echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
rm -rf "$LINK_DIR~"
mv "$LINK_DIR" "$LINK_DIR~"
ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}`
fi
echo "Please execute 'otstart' to restart."
cd "$START_DIR"
}
# Start the server
otstart() {
otconfig
otkill
nice bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
nice bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
sleep 2
if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
}
# Display log
alias otless='less $HOME/.opentox/log/production.log'
# Tail log
alias ottail='tail -f $HOME/.opentox/log/production.log'
# Reload the server
otreload() {
otconfig
bash -c "nginx -s reload"
}
# Kill the server
otkill() {
otconfig
killall nginx >/dev/null 2>&1
bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
}
# Check the server
otcheck() {
check_service=`cat $HOME/.opentox/config/production.yaml | grep opentox-algorithm | sed 's/.*\s//g' | sed 's/"//g'`
if [ -z "`curl -v $check_service 2>&1 | grep '200 OK'`" ]; then
otstart
fi
}
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