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
}

# 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

# 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 &"
#  sleep 0.5
#  check_service $1 online
}

# Start 4Store
# @param1 [backend_name]
# @param2 integer Port
# @example start_4s opentox 9088
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;
#  check_service four_store online
}

# 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;;
                  #otcheck 4store;;
    "all")        otstart 4store;
                  otstart dataset;
                  otstart model;
                  otstart task;
                  otstart algorithm; #compound and feature is included
                  otstart validation;;
                  #sleep 1;
                  #otcheck all;;
    *)            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;
  sleep 0.5
  for p in `ps x | grep 'unicorn' | grep $1 | grep -v grep | awk '{print $1}'`; do echo "Process with PID $p is still running and belongs to port $1. Please wait and run otkill again."; 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]
# @param2 (optinal) string ["online"] ; output for running services
# @example check_service algorithm online
check_service() {
  check_utils "curl"
  if [ $# != 1 ] && [ $# != 2 ]; then
    echo "One argument required: [service_name]. Second argument optional."
    echo "usage: check_service [algorithm|compound|dataset|feature|model|task|validation|four_store] [online](optional)"
    return 1
  fi
  get_service_uri $1
  MY_SERVICE="IST service"
  if [[ $1 == "four_store" ]]; then
    SERVICE_URI="$SERVICE_URI""/status/"
    MY_SERVICE="HTTP service"
  fi
  if [ -n "`$CURL -i -k -X HEAD $SERVICE_URI 2>&1 | grep '^HTTP' |grep ' 200'`" ]; then
    if [[ $2 == "online" ]]; then
      echo "$MY_SERVICE $1 is running at $SERVICE_URI."
      return 1
    fi
    return 0
  else
    echo "$MY_SERVICE $1 is NOT available at $SERVICE_URI."
    return 1
  fi
}

#check_all_service_offline() {
#  CHECK_RESULT=`otcheck all`
#  if [ -z "$CHECK_RESULT" ]; then
#    echo "IST service(s) is(are) running."
#    otcheck all
#    return 1
#  else
#    echo "IST services are offline."
#  fi
#}


# Check response of web service
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
}

# pull repository
# @param1  service
# @example pull_repo algorithm
pull_repo() {
  otconfig
  cd $OT_PREFIX/$1
  if OUTPUT=`git pull 2>&1`; then echo "Pulled $1."; else echo -e "Pulling $1 failed.\nMessage: $OUTPUT\n";  fi
}

# pulls recent git repoitory of the service
otupdate_repo() {
  if [ $# != 1 ]; then
    echo "One argument required: [service_name] or 'all'"
    echo "usage: otupdate_repo [all|algorithm|compound|dataset|feature|model|opentox-client|opentox-server|opentox-test|task|validation]"
    return 1
  fi
  DIR=`pwd`
  otconfig
  case "$1" in
    "algorithm")       pull_repo algorithm;;
    "compound")        pull_repo compound;;
    "dataset")         pull_repo dataset;;
    "feature")         pull_repo feature;;
    "model")           pull_repo model;;
    "opentox-client")  pull_repo opentox-client;;
    "opentox-server")  pull_repo opentox-server;;
    "opentox-test")    pull_repo opentox-test;;
    "task")            pull_repo task;;
    "validation")      pull_repo validation;;
    "all")             otupdate_repo algorithm;
                       otupdate_repo compound;
                       otupdate_repo dataset;
                       otupdate_repo feature;
                       otupdate_repo model;
                       otupdate_repo opentox-client;
                       otupdate_repo opentox-server;
                       otupdate_repo opentox-test;
                       otupdate_repo task;
                       otupdate_repo validation;;
    *)                 echo "One argument required: [service_name] or 'all'";
                       echo "usage: otupdate_repo [all|algorithm|compound|dataset|feature|model|opentox-client|opentox-server|opentox-test|task|validation]";
                       return 1;;
  esac
  cd $DIR
}