Merge branch 'development' of github.com:opentox/install into development

2 files changed, 142 insertions, 138 deletions

diff --git a/config.sh b/config.sh
index 9cdbca7..38e7772 100755
--- a/config.sh
+++ b/config.sh
@@ -19,7 +19,7 @@ OB_NUM_VER="2.3.1"
 RAPTOR2_NUM_VER="2.0.8"
 RASQAL_NUM_VER="0.9.29"
 REDIS_NUM_VER="2.4.4"
-RUBY_NUM_VER="1.9.3-p194"
+RUBY_NUM_VER="2.0.0-p0"
 FOUR_STORE_VER="4store-v1.1.5"
 REDIS_URL="http://redis.googlecode.com/files"
 REDLAND_DWL="http://download.librdf.org"
@@ -50,7 +50,7 @@ REDIS_VER="redis-$REDIS_NUM_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
 R_DEST="$OT_PREFIX/r-packages"
-RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
+RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/2.0"
 RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz"
 RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz"
 REDIS_DWL="$REDIS_URL/$REDIS_VER.tar.gz"
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 47f0f66..15b46a7 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -27,8 +27,8 @@ start_unicorn() {
 # @example start_unicorn algorithm 8081
 start_4s() {
   nice bash -c "nohup $OT_PREFIX/4S/bin/4s-backend $1 >/dev/null 2>&1 &";
-  sleep 2;
-  nice bash -c "nohup $OT_PREFIX/4S/bin/4s-httpd -H localhost -p $2 -s -1 $1 >/dev/null 2>&1 &"; #-D for testing        
+  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;
 
 }
@@ -50,9 +50,9 @@ _ottoolcompletion()
     ' "$word")) ;
 }
 complete -o default -F _ottoolcompletion otstart
-complete -o default -F _ottoolcompletion otreload
+#complete -o default -F _ottoolcompletion otreload
 complete -o default -F _ottoolcompletion otkill
-complete -o default -F _ottoolcompletion otcheck
+#complete -o default -F _ottoolcompletion otcheck
 
 # Start the server
 otstart() {
@@ -66,7 +66,11 @@ otstart() {
   otkill $1
   DIR=`pwd`
   case "$1" in
-    "algorithm")  start_unicorn $1 8081;;
+    "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;;
@@ -78,12 +82,12 @@ otstart() {
                   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 algorithm;
                   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]";
@@ -95,62 +99,62 @@ otstart() {
 # 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_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
-}
+#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
@@ -197,85 +201,85 @@ 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
 # @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_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
-}
+#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
+#}