Added 4S backbone for each service.

6 files changed, 39 insertions, 18 deletions

diff --git a/4store-install b/4store-install
index c87c2d9..ee04738 100755
--- a/4store-install
+++ b/4store-install
@@ -25,7 +25,7 @@ cmd="make install" && run_cmd "$cmd" "Make Install"
 
 # Config
 echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$FST/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$FST/lib\"; fi" >> "$FST_CONF"
-if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:8088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi
+if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi
 
 echo "$SELF configuration has been stored in '$FST_CONF'."
 if ! grep "$FST_CONF" $OT_UI_CONF >/dev/null 2>&1; then
diff --git a/base-install b/base-install
index b3a7f6e..593bb0c 100755
--- a/base-install
+++ b/base-install
@@ -38,7 +38,7 @@ case "$DISTRIB_INFO" in
 esac
 
 sudo $DPKG --set-selections < "$PACK_LIST"
-sudo $APT_GET -y -u dselect-upgrade
+sudo $APT_GET -y --force-yes -u dselect-upgrade
 
 if [ ! -f $JAVA_CONF ]; then
 
diff --git a/debian.list b/debian.list
index 6093a9b..041a3b2 100644
--- a/debian.list
+++ b/debian.list
@@ -1,8 +1,11 @@
 aptitude install
 automake install
+avahi-daemon install
 build-essential install
 cmake install
 curl install
+libavahi-glib-dev install
+libavahi-client-dev install
 libglib2.0-dev install
 libgsl0-dev install
 libopenbabel4 install
diff --git a/install b/install
index 5105689..10c02a9 100755
--- a/install
+++ b/install
@@ -59,5 +59,6 @@ fi
 [ -f $HOME/.opentox/config/ambit_descriptors.yaml ] || (cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit keys file")
 [ -f $HOME/.opentox/config/jl_keys.yaml ] || (cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Joelib keys file")
 [ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "Created ot-tools (stored in ~/.opentox)")
+if ! cat "$OT_TOOLS_CONF" | grep "OT_PREFIX=">/dev/null 2>&1; then echo "OT_PREFIX=$OT_PREFIX" >> $OT_DEFAULT_CONF; fi
 
 notify
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 4564181..39f7b52 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -20,6 +20,18 @@ start_unicorn() {
   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 0.5;
+  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 0.5;
+
+}
+
 # Start the server
 otstart() {
   if [ $# != 1 ]
@@ -33,22 +45,26 @@ otstart() {
   otkill $1
   DIR=`pwd`
   case "$1" in
-    "algorithm")  start_unicorn $1 8081;;
-    "compound")   #start_unicorn $1 8082;;
+    "algorithm")  start_4s $1 9081;
+                  start_unicorn $1 8081;;
+    "compound")   #start_4s $1 9082;
+                  #start_unicorn $1 8082;;
                   echo "$1 not available yet.";;
-    "dataset")    start_unicorn $1 8083;;
-    "feature")    start_unicorn $1 8084;;
-    "model")      #start_unicorn $1 8085;;
+    "dataset")    start_4s $1 9083;
+                  start_unicorn $1 8083;;
+    "feature")    start_4s $1 9084;
+                  start_unicorn $1 8084;;
+    "model")      #start_4s $1 9085;
+                  #start_unicorn $1 8085;;
                   echo "$1 not available yet.";;
-    "task")       start_unicorn $1 8086;;
-    "validation") #start_unicorn $1 8087;;
+    "task")       start_4s $1 9086;
+                  start_unicorn $1 8086;;
+    "validation") #start_4s $1 9087;
+                  #start_unicorn $1 8087;;
                   echo "$1 not available yet.";;
-    "4store")     nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-backend opentox >/dev/null 2>&1 &"; 
-                  sleep 1; 
-                  nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-httpd -D -H localhost -p 8088 opentox >/dev/null 2>&1 &"; 
-                  sleep 1; 
-                  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;;
+    "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 algorithm;
                   #otstart compound;
diff --git a/utils.sh b/utils.sh
index 0423786..0837f4c 100755
--- a/utils.sh
+++ b/utils.sh
@@ -127,10 +127,11 @@ notify() {
   echo
   if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then
     echo "IMPORTANT: How to configure your system:"
-    echo "IMPORTANT: a) Include '$OT_UI_CONF' in shell startup (e.g. ~/.bashrc)."
-    echo "IMPORTANT: b) Manually source '$OT_UI_CONF' every time."
-    echo "IMPORTANT: The command in both cases: '. $OT_UI_CONF'"
+    echo "IMPORTANT: a) Include '$OT_TOOLS_CONF' in shell startup (e.g. ~/.bashrc)."
+    echo "IMPORTANT: b) Manually source '$OT_TOOLS_CONF' every time."
+    echo "IMPORTANT: The command in both cases: '. $OT_TOOLS_CONF'"
     echo "IMPORTANT: NOW would be the best time to configure!"
+    echo "Visit 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment/' for further information about the usage of ot-tools."
     echo
     echo "Thank you for your attention."
     echo