path: root/ot-tools-user.sh

# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby')

# Load server config
otconfig() {
  . $HOME/.opentox/config/install/config.sh
  . $OT_PREFIX/install/utils.sh
}

# Display log
alias otless='less $HOME/.opentox/log/development.log'

# Tail log
alias ottail='tail -f $HOME/.opentox/log/development.log'

# Start unicorn
# @param1 [service_name] 
# @param2 integer Port
# @example start_unicorn algorithm 8081
start_unicorn() {
  cd $HOME/opentox-ruby/$1
  nice bash -c "nohup unicorn -p $2 >/dev/null 2>&1 &"
}

# Start unicorn
# @param1 [backend_name] 
# @param2 integer Port
# @example start_unicorn algorithm 8081
start_4s() {
  nice bash -c "nohup $OT_PREFIX/4S/bin/4s-backend $1 >/dev/null 2>&1 &";
  sleep 4;
  nice bash -c "nohup $OT_PREFIX/4S/bin/4s-httpd -p $2 -s -1 $1 >/dev/null 2>&1 &"; #-D for testing        
  sleep 1;

}

# configure tab completion for ottools
_ottoolcompletion()
{
  word="${COMP_WORDS[COMP_CWORD]}"
  COMPREPLY=(${COMPREPLY[@]:-} $(compgen -W '
    all
    algorithm
    compound
    dataset
    feature
    model
    task
    validation
    4store
    ' "$word")) ;
}
complete -o default -F _ottoolcompletion otstart
#complete -o default -F _ottoolcompletion otreload
complete -o default -F _ottoolcompletion otkill
#complete -o default -F _ottoolcompletion otcheck

# Start the server
otstart() {
  if [ $# != 1 ]; then
    echo "One argument required: [service_name] or 'all'"
    echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
    return 1
  fi 

  otconfig
  otkill $1
  DIR=`pwd`
  case "$1" in
    "algorithm")  otkill compound;
                  otkill feature;
                  otstart compound;
                  otstart feature;
                  start_unicorn $1 8081;;
    "compound")   start_unicorn $1 8082;;
    "dataset")    start_unicorn $1 8083;;
    "feature")    start_unicorn $1 8084;;
    "model")      start_unicorn $1 8085;;
    "task")       start_unicorn $1 8086;;
    "validation") start_unicorn $1 8087;
                  nice bash -c "nohup redis-server $OT_PREFIX/validation/redis-*/redis.conf >/dev/null 2>&1 &";;
    "4store")     start_4s opentox 9088; 
                  if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi
                  if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;;
    "all")        otstart 4store;
                  otstart compound;
                  otstart dataset;
                  otstart feature;
                  otstart model;
                  otstart task;
                  otstart algorithm;
                  otstart validation;;
    *)            echo "One argument required: [service_name] or 'all'";
                  echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                  return 1;;
  esac
  cd $DIR
}

# reload unicorn
# @param1 integer Port
# @example reload_unicorn 8081
#reload_unicorn() {
#  for p in `ps x | grep 'unicorn master' | grep $1 | grep -v grep | awk '{print $1}'`; do 
#    kill -12 $p 
#  done
#  sleep 0.5
#  for p in `ps x | grep 'unicorn master (old)' | grep $1 | grep -v grep | awk '{print $1}'`; do 
#    kill -28 $p
#  done
#  sleep 0.5
#  # ToDo: Check if new master is working properly.
#  for p in `ps x | grep 'unicorn master (old)' | grep $1 | grep -v grep | awk '{print $1}'`; do
#    kill -3 $p
#  done
#}

# Reload the server
#otreload() {
#  if [ $# != 1 ]; then
#    echo "One argument required: [service_name] or 'all'"
#    echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
#    return 1
#  fi 
#
#  otconfig
#  case "$1" in
#    "algorithm")  reload_unicorn 8081;
#                  check_service "algorithm";;
#    "compound")   reload_unicorn 8082;
#                  check_service "compound";;
#    "dataset")    reload_unicorn 8083;
#                  check_service "dataset";;
#    "feature")    reload_unicorn 8084;
#                  check_service "feature";;
#    "model")      reload_unicorn 8085;
#                  check_service "model";;
#    "task")       reload_unicorn 8086;
#                  check_service "task";;
#    "validation") reload_unicorn 8087;
#                  check_service "validation";;
#    "4store")     #killall 4s-httpd >/dev/null 2>&1;
#                  #killall 4s-backend >/dev/null 2>&1;
#                  #check_service "four_store";;
#                  echo "$1 reload not available yet.";;
#    "all")        otreload algorithm;
#                  otreload compound;
#                  otreload dataset;
#                  otreload feature;
#                  otreload model;
#                  otreload task;
#                  otrelaod validation;;
#                  #otreload 4store;;
#    *)            echo "One argument required: [service_name] or 'all'";
#                  echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
#                  return 1;;
#  esac
#}

# kill unicorn
# @param1 integer Port
# @example kill_unicorn 8081
kill_unicorn() {
  for p in `ps x | grep 'unicorn' | grep $1 | grep -v grep | awk '{print $1}'`; do kill -3 $p; done;  
}

# Kill the server
otkill() {
  if [ $# != 1 ]; then
    echo "One argument required: [service_name] or 'all'"
    echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
    return 1
  fi 

  otconfig
  case "$1" in
    "algorithm")  kill_unicorn 8081;;
    "compound")   kill_unicorn 8082;;
    "dataset")    kill_unicorn 8083;;
    "feature")    kill_unicorn 8084;;
    "model")      kill_unicorn 8085;;
    "task")       kill_unicorn 8086;;
    "validation") kill_unicorn 8087;
                  bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1";;
    "4store")     killall 4s-httpd >/dev/null 2>&1;
                  killall 4s-backend >/dev/null 2>&1;;
    "all")        otkill algorithm;
                  otkill compound;
                  otkill dataset;
                  otkill feature;
                  otkill model;
                  otkill task;
                  otkill validation;
                  otkill 4store;;
    *)            echo "One argument required: [service_name] or 'all'";
                  echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                  return 1;;
  esac
}

# get service uri
# sets $SERVICE_URI if found in config files
# @param1 string [service_name]
# @example get_service_uri algorithm
#get_service_uri() {
#  if [ $# != 1 ]; then
#    echo "One argument required: [service_name]"
#    echo "usage: get_service_uri [algorithm|compound|dataset|feature|model|task|validation|four_store]"
#    return 1
#  fi
#  SERVICE_URI=""
#
#  if [ -f $HOME/.opentox/config/$1.rb ]; then
#    SERVICE_URI=`cat $HOME/.opentox/config/$1.rb | grep $1 | grep "uri" | awk -F":uri => " '{print $2}' | awk -F" " '{print $1}' | awk -F"," '{print $1}' |  sed "s/'//g" | sed 's/"//g'`
#  fi
#
#  if [ -f $HOME/.opentox/config/default.rb ]; then
#    [ -n "$SERVICE_URI" ] || SERVICE_URI=`cat $HOME/.opentox/config/default.rb | grep $1 | grep "uri" | awk -F":uri => " '{print $2}' | awk -F" " '{print $1}' | awk -F"," '{print $1}' |  sed "s/'//g" | sed 's/"//g'`
#  fi
#  
#  if [ -z "$SERVICE_URI" ]; then 
#    echo "Cannot find service uri for $1 in config files."
#    return 1
#  else
#    return 0
#  fi
#}

# check service
# @param1 string [service_name]
# @example check_service algorithm
#check_service() {
#  check_utils "curl"
#  if [ $# != 1 ]; then
#    echo "One argument required: [service_name]"
#    echo "usage: get_service_uri [algorithm|compound|dataset|feature|model|task|validation|four_store]"
#    return 1
#  fi
#  get_service_uri $1
#  HEADER="Accept: */*"
#  if [ $1 == "four_store" ]; then
#    SERVICE_URI="$SERVICE_URI""/status/"
#  fi
#  if [ $1 == "compound" ]; then
#    SERVICE_URI="$SERVICE_URI""/InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1"
#    HEADER="Accept: chemical/x-inchi"
#  fi
#  if [ -n "`$CURL -v -H "$HEADER" $SERVICE_URI 2>&1 | grep '200 OK'`" ]; then
#    return 0 
#  else
#    echo "$1 is not available at $SERVICE_URI."
#    return 1
#  fi
#}

# Check the server
#otcheck() {
#  if [ $# != 1 ]; then
#    echo "One argument required: [service_name] or 'all'"
#    echo "usage: otcheck [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
#    return 1
#  fi
#
#  otconfig
#  case "$1" in
#    "algorithm")  check_service "algorithm";;
#    "compound")   check_service "compound";;
#    "dataset")    check_service "dataset";;
#    "feature")    check_service "feature";;
#    "model")      check_service "model";;
#    "task")       check_service "task";;
#    "validation") check_service "validation";;
#    "4store")     check_service "four_store";; 
#    "all")        otcheck "algorithm";
#                  otcheck "compound";
#                  otcheck "dataset";
#                  otcheck "feature";
#                  otcheck "model";
#                  otcheck "task";
#                  otcheck "validation";
#                  otcheck 4store;;
#    *)            echo "One argument required: [service_name] or 'all'";
#                  echo "usage: otcheck [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
#                  return 1;;
#  esac
#}