Merge branch 'builddep' into development

Conflicts:
	4store-install
	base-install
	config.sh
	utils.sh

10 files changed, 103 insertions, 79 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 c7d717e..6e549d8 100755
--- a/base-install
+++ b/base-install
@@ -13,12 +13,20 @@ DIR=`pwd`
 # Not logged
 # Not logged
 [ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
-check_utils "aptitude apt-get apt-cache dpkg"
+check_utils "aptitude apt-get apt-key apt-cache dpkg tee wget"
 
 echo
 echo "Base Packages:"
 echo
 echo "Updating index..."
+
+cmd="$WGET -O redland_key.asc $REDLAND_APT_KEY  >/dev/null 2>&1" && run_cmd "$cmd" "Download redland apt-key"
+cmd="$APT_KEY add redland_key.asc >/dev/null 2>&1; rm redland_key.asc" && run_cmd "$cmd" "Adding redland apt-key"
+if ! cat "/etc/apt/sources.list" | grep "$REDLAND_DEB">/dev/null 2>&1; then
+  echo "deb $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null 
+  echo "deb-src $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null 
+fi
+
 sudo $APTITUDE update -y >/dev/null 2>&1
 
 DISTRIB_INFO=$(cat /proc/version)
@@ -30,7 +38,7 @@ case "$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/config.sh b/config.sh
index dbc42e6..8ca0d2e 100755
--- a/config.sh
+++ b/config.sh
@@ -5,7 +5,7 @@
 
 
 # 1) Base setup
-OT_DIST="debian"            # Linux distribution    (debian)
+OT_DIST="debian"            # Linux distribution    (debian, ubuntu)
 OT_INSTALL="local"          # Type                  (gem, local, server)
 OT_BRANCH="development"     # Maturity              (development -need SSH key at Github-, master)
 
@@ -19,10 +19,11 @@ OB_NUM_VER="2.3.1"
 RAPTOR2_NUM_VER="2.0.8"
 RASQAL_NUM_VER="0.9.29"
 RUBY_NUM_VER="1.9.3-p194"
+REDLAND_DWL="http://download.librdf.org"
+REDLAND_APT_KEY="http://purl.org/net/dajobe/gnupg.asc"
 
 # Done.
 
-
 ### Nothing to gain from changes below this line.
 JAVA_CONF="$HOME/.opentox/java.sh"
 FST_CONF="$HOME/.opentox/4S.sh"
@@ -39,9 +40,8 @@ RAPTOR2_VER="raptor2-$RAPTOR2_NUM_VER"
 RASQAL_VER="rasqal-$RASQAL_NUM_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-
-RAPTOR2_DWL="http://download.librdf.org/source/$RAPTOR2_VER.tar.gz"
-RASQAL_DWL="http://download.librdf.org/source/$RASQAL_VER.tar.gz"
 RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
 RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
-
+RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz"
+RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz"
+REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable"
diff --git a/debian.list b/debian.list
index d16ee3f..73be6d9 100644
--- a/debian.list
+++ b/debian.list
@@ -1,25 +1,25 @@
+aptitude install
+automake install
+avahi-daemon install
 build-essential install
 cmake install
-libgsl0-dev install
-libtool install
-openjdk-6-jdk install
-r-base install
-r-base-dev install
-libpcre3-dev install
-librasqal3-dev install
-libtool install
+curl install
+libavahi-glib-dev install
+libavahi-client-dev install
 libglib2.0-dev install
-ncurses-dev install
-libreadline-dev install
-uuid-dev install
-libraptor1-dev install
+libgsl0-dev install
 libopenbabel4 install
 libopenbabel-dev install
-automake install
-libyaml-dev install
 libopenssl-ruby install
+libpcre3-dev install
+libraptor1-dev install
+libreadline-dev install
 libssl-dev install
+libtool install
 libxml2-dev install
-libssl-dev install
-curl install
-aptitude install
+libyaml-dev install
+ncurses-dev install
+openjdk-6-jdk install
+r-base-dev install
+r-base install
+uuid-dev install
diff --git a/install b/install
index 9046987..fce99dc 100755
--- a/install
+++ b/install
@@ -37,9 +37,8 @@ sudo echo -n ""
 echo
 
 [ -f $OT_PREFIX/install/utils.sh ] || (cmd="mkdir -p $OT_PREFIX/install && cp utils.sh $OT_PREFIX/install" && run_cmd "$cmd" "Install utils.sh to OT_PREFIX")
-[ -f $HOME/.opentox/config/install/config.sh ] || (cmd="mkdir -p $HOME/.opentox/config/install && cp config.sh $HOME/.opentox/config/install" && run_cmd "$cmd" "Install config.sh to CONFIG (~/.opentox/config)")
-[ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "Install default.rb to CONFIG (~/.opentox/config)")
-
+[ -f $HOME/.opentox/config/install/config.sh ] || (cmd="mkdir -p $HOME/.opentox/config/install && cp config.sh $HOME/.opentox/config/install" && run_cmd "$cmd" "Install config.sh to CONFIG (~/.opentox/config/install)")
+[ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "Created default.rb service settings (stored in ~/.opentox/config)")
 
 . ./base-install # Debian specific; disable this for others.
 ./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX.
@@ -59,7 +58,7 @@ 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" "Install ot-tools.sh to CONFIG (~/.opentox/config)")
+[ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "Created ot-tools (stored in ~/.opentox)")
 
 
 # Install global ruby version
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index ca3bdbd..d60a26e 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -3,6 +3,7 @@
 # Load server config
 otconfig() {
   source $HOME/.opentox/opentox-ui.sh
+  source $HOME/.opentox/config/install/config.sh
 }
 
 # Display log
@@ -20,6 +21,18 @@ 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 ]
@@ -33,25 +46,28 @@ 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;;
+    "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.";;
-    "dataset")    start_unicorn $1 8083;;
-    "feature")    start_unicorn $1 8084;;
-    "model")      #start_unicorn $1 8085;;
+    "task")       start_4s $1 9086;
+                  start_unicorn $1 8086;;
+    "validation") #start_4s $1 9087;
+                  #start_unicorn $1 8087;;
                   echo "$1 not available yet.";;
-    "task")       start_unicorn $1 8086;;
-    "validation") #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;
+                  otstart compound;
                   otstart dataset;
                   otstart feature;
                   #otstart model;
@@ -61,6 +77,7 @@ otstart() {
                   echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                   return 1;;
   esac
+  sleep 1
   cd $DIR
 }
 
@@ -94,8 +111,7 @@ otreload() {
   otconfig
   case "$1" in
     "algorithm")  reload_unicorn 8081;;
-    "compound")   #reload_unicorn 8082;;
-                  echo "$1 not available yet.";;
+    "compound")   reload_unicorn 8082;;
     "dataset")    reload_unicorn 8083;;
     "feature")    reload_unicorn 8084;;
     "model")      #reload_unicorn 8085;;
@@ -107,7 +123,7 @@ otreload() {
                   #killall 4s-backend >/dev/null 2>&1;;
                   echo "$1 reload not available yet.";;
     "all")        otreload algorithm;
-                  #otreload compound;
+                  otreload compound;
                   otreload dataset;
                   otreload feature;
                   #otreload model;
@@ -118,6 +134,7 @@ otreload() {
                   echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                   return 1;;
   esac
+  sleep 1
 }
 
 # kill unicorn
@@ -139,8 +156,7 @@ otkill() {
   otconfig
   case "$1" in
     "algorithm")  kill_unicorn 8081;;
-    "compound")   #kill_unicorn 8082;;
-                  echo "$1 not available yet.";;
+    "compound")   kill_unicorn 8082;;
     "dataset")    kill_unicorn 8083;;
     "feature")    kill_unicorn 8084;;
     "model")      #kill_unicorn 8085;;
@@ -151,7 +167,7 @@ otkill() {
     "4store")     killall 4s-httpd >/dev/null 2>&1;
                   killall 4s-backend >/dev/null 2>&1;;
     "all")        otkill algorithm;
-                  #otkill compound;
+                  otkill compound;
                   otkill dataset;
                   otkill feature;
                   #otkill model;
@@ -162,6 +178,7 @@ otkill() {
                   echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                   return 1;;
   esac
+  sleep 1
 }
 
 # get service uri
@@ -232,8 +249,7 @@ otcheck() {
   otconfig
   case "$1" in
     "algorithm")  check_service "algorithm";;
-    "compound")   #check_service "compound";;
-                  echo "$1 not available yet.";;
+    "compound")   check_service "compound";;
     "dataset")    check_service "dataset";;
     "feature")    check_service "feature";;
     "model")      #check_service "model";;
@@ -242,9 +258,8 @@ otcheck() {
     "validation") #check_service "validation";;
                   echo "$1 not available yet.";;
     "4store")     check_service "four_store";; 
-                  #killall 4s-backend >/dev/null 2>&1;;
     "all")        otcheck "algorithm";
-                  #otcheck "compound";
+                  otcheck "compound";
                   otcheck "dataset";
                   otcheck "feature";
                   #otcheck "model";
diff --git a/raptor2-install b/raptor2-install
index ad44ed4..4d3be2e 100755
--- a/raptor2-install
+++ b/raptor2-install
@@ -5,7 +5,7 @@ DIR=`pwd`
 . ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1)
 SELF=$(basename $0 -install)
 check_log $SELF
-check_utils "wget tar make grep"
+check_utils "apt-get wget tar make grep"
 
 # Build
 mkdir -p $OT_PREFIX/tmp
@@ -15,6 +15,7 @@ export RAPTOR2_DIR=$OT_PREFIX/$SELF
 cmd="$TAR xvzf $RAPTOR2_VER.tar.gz" && run_cmd "$cmd" "Unpack" 
 rm $RAPTOR2_VER.tar.gz
 cd $RAPTOR2_VER
+cmd="sudo $APT_GET -y build-dep $SELF" && run_cmd "$cmd" "Build dependencies"
 cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure"
 cmd="$MAKE" && run_cmd "$cmd" "Make"
 cmd="$MAKE install" && run_cmd "$cmd" "Make Install"
diff --git a/rasqal-install b/rasqal-install
index bc06450..8bd9fbd 100755
--- a/rasqal-install
+++ b/rasqal-install
@@ -5,7 +5,7 @@ DIR=`pwd`
 . ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1)
 SELF=$(basename $0 -install)
 check_log $SELF
-check_utils "wget tar make grep"
+check_utils "apt-get wget tar make grep"
 
 # Build
 mkdir -p $OT_PREFIX/tmp
diff --git a/ubuntu.list b/ubuntu.list
index d16ee3f..73be6d9 100644
--- a/ubuntu.list
+++ b/ubuntu.list
@@ -1,25 +1,25 @@
+aptitude install
+automake install
+avahi-daemon install
 build-essential install
 cmake install
-libgsl0-dev install
-libtool install
-openjdk-6-jdk install
-r-base install
-r-base-dev install
-libpcre3-dev install
-librasqal3-dev install
-libtool install
+curl install
+libavahi-glib-dev install
+libavahi-client-dev install
 libglib2.0-dev install
-ncurses-dev install
-libreadline-dev install
-uuid-dev install
-libraptor1-dev install
+libgsl0-dev install
 libopenbabel4 install
 libopenbabel-dev install
-automake install
-libyaml-dev install
 libopenssl-ruby install
+libpcre3-dev install
+libraptor1-dev install
+libreadline-dev install
 libssl-dev install
+libtool install
 libxml2-dev install
-libssl-dev install
-curl install
-aptitude install
+libyaml-dev install
+ncurses-dev install
+openjdk-6-jdk install
+r-base-dev install
+r-base install
+uuid-dev install
diff --git a/utils.sh b/utils.sh
index e06be5d..3b39b1e 100755
--- a/utils.sh
+++ b/utils.sh
@@ -77,8 +77,8 @@ install_ruby() {
   local DIR=`pwd`
   check_utils "rbenv curl make tar"
   if ! $RBENV versions $RUBY_NUM_VER | grep $RUBY_NUM_VER>/dev/null 2>&1; then
-    [ -d $DIR/tmp ] || mkdir -p $DIR/tmp && cd $DIR/tmp
-    ([ -d $DIR/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER
+    [ -d $OT_PREFIX/tmp ] || mkdir -p $OT_PREFIX/tmp && cd $OT_PREFIX/tmp
+    ([ -d $OT_PREFIX/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER
     cmd="./configure --prefix=$RUBY_DIR" && run_cmd "$cmd" "Configure"
     cmd="$MAKE -j2" && run_cmd "$cmd" "Make"
     cmd="$MAKE install" && run_cmd "$cmd" "Install"
@@ -137,10 +137,11 @@ notify() {
   echo
   if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then
     echo "IMPORTANT: How to configure your system if everything went fine:"
-    echo "IMPORTANT: a) Include '$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