Added otcheck and minor fixes.

1 files changed, 123 insertions, 104 deletions

diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 6680389..f5e6366 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -6,6 +6,27 @@ otconfig() {
   . $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'
 
@@ -19,40 +40,21 @@ alias ottail='tail -f $HOME/.opentox/log/development.log'
 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 unicorn
+# Start 4Store
 # @param1 [backend_name]
 # @param2 integer Port
-# @example start_unicorn algorithm 8081
+# @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 $1 >/dev/null 2>&1 &"; #-D for testing
   sleep 1;
-
-}
-
-# configure tab completion for ottools
-_ottoolcompletion()
-{
-  word="${COMP_WORDS[COMP_CWORD]}"
-  COMPREPLY=(${COMPREPLY[@]:-} $(compgen -W '
-    all
-    algorithm
-    compound
-    dataset
-    feature
-    model
-    task
-    validation
-    4store
-    ' "$word")) ;
+  check_service four_store online
 }
-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() {
@@ -80,15 +82,16 @@ otstart() {
                   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;;
+                  if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;
+                  otcheck 4store;;
     "all")        otstart 4store;
-                  otstart compound;
                   otstart dataset;
-                  otstart feature;
                   otstart model;
                   otstart task;
-                  otstart algorithm;
-                  otstart validation;;
+                  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;;
@@ -161,6 +164,8 @@ otstart() {
 # @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
@@ -201,88 +206,102 @@ otkill() {
 # 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
-#}
+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
+# 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]"
+# @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
-#  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
+#    echo "IST services are offline."
 #  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
-#}
+
+# 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