Separated raptor2/rasqal and fixes.

9 files changed, 76 insertions, 67 deletions

diff --git a/config.sh b/config.sh
index edc2fd2..e22c3f2 100755
--- a/config.sh
+++ b/config.sh
@@ -17,6 +17,8 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
 
 OB_NUM_VER="2.3.1"
 RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
+RAPTOR2_DWL="http://download.librdf.org/source/raptor2-2.0.8.tar.gz"
+RASQAL_DWL="http://download.librdf.org/source/rasqal-0.9.29.tar.gz"
 
 # Done.
 
diff --git a/debian.list b/debian.list
index 603458d..862ab51 100644
--- a/debian.list
+++ b/debian.list
@@ -22,7 +22,4 @@ libssl-dev install
 libxml2-dev install
 libssl-dev install
 curl install
-wget install
-tar install
 aptitude install
-find install
diff --git a/install b/install
index 3d1793f..dbd9fbc 100755
--- a/install
+++ b/install
@@ -40,7 +40,8 @@ echo
 [ -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)")
 
 . ./base-install # Debian specific; disable this for others.
-./raptor_rasqal-install # Download, compile and build raptor2 and rasqal. Install to OT_PREFIX.
+./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX.
+./rasqal-install # Download, compile and build rasqal. Install to OT_PREFIX.
 ./4store-install # Download, compile and build 4store. Install to OT_PREFIX.
 
 if [ ! -d ~/.rbenv ]; then
@@ -56,6 +57,4 @@ 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")
 
-. ./services-install
-
 notify
diff --git a/raptor2-install b/raptor2-install
new file mode 100755
index 0000000..d4ad138
--- /dev/null
+++ b/raptor2-install
@@ -0,0 +1,34 @@
+#!/bin/sh
+DIR=`pwd`
+
+# Boot
+. ./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"
+
+# Build
+mkdir -p $PREFIX/tmp
+cd $OT_PREFIX/tmp/
+cmd="$WGET $RAPTOR2_DWL && run_cmd "$cmd" "Download $SELF"
+export RAPTOR2_DIR=$OT_PREFIX/$SELF/
+cmd="$TAR xvzf "$SELF*.tar.gz" && run_cmd "$cmd" "Unpack $SELF" 
+rm "$SELF*.tar.gz"
+cd "$SELF*"
+cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure"
+cmd="$MAKE" && run_cmd "$cmd" "Make"
+cmd="$MAKE install" && run_cmd "$cmd" "Make Install"
+
+# Config
+echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RAPTOR2_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RAPTOR2_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RAPTOR2_CONF"
+echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RAPTOR2_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RAPTOR2_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RAPTOR2_CONF"
+echo "$SELF configuration has been stored in '$RAPTOR2_CONF'."
+if ! grep "$RAPTOR2_CONF" $OT_UI_CONF >/dev/null 2>&1; then
+  echo '. '$RAPTOR2_CONF >> $OT_UI_CONF
+fi
+cd ..
+export LD_LIBRARY_PATH=$RAPTOR2_DIR"/lib:"$LD_LIBRARY_PATH
+export PATH=$RAPTOR2_DIR"/bin:"$PATH
+export PKG_CONFIG_PATH=$RAPTOR2_DIR"/lib/pkgconfig:"$PKG_CONFIG_PATH
+
+cd $DIR
diff --git a/raptor_rasqal-install b/raptor_rasqal-install
deleted file mode 100755
index 24d391b..0000000
--- a/raptor_rasqal-install
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/bin/sh
-DIR=`pwd`
-RAPTOR2=raptor2-2.0.8
-RASQAL=rasqal-0.9.29
-# Boot
-. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1)
-SELF=$(basename $0 -install)
-check_log $SELF
-#[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
-check_utils "wget tar make"
-
-# Build
-mkdir -p $PREFIX/tmp
-cd $OT_PREFIX/tmp/
-cmd="$WGET http://download.librdf.org/source/"$RAPTOR2".tar.gz" && run_cmd "$cmd" "Download $RAPTOR2"
-export RAPTOR2_DIR=$OT_PREFIX/$SELF/$RAPTOR2
-cmd="$TAR xvzf "$RAPTOR2".tar.gz" && run_cmd "$cmd" "Unzip $RAPTOR2" 
-rm $RAPTOR2.tar.gz
-cd $RAPTOR2
-cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure"
-cmd="$MAKE" && run_cmd "$cmd" "Make"
-cmd="$MAKE install" && run_cmd "$cmd" "Make Install"
-# Config
-echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RAPTOR2_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RAPTOR2_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RAPTOR2_CONF"
-echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RAPTOR2_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RAPTOR2_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RAPTOR2_CONF"
-echo "$RAPTOR2 configuration has been stored in '$RAPTOR2_CONF'."
-if ! grep "$RAPTOR2_CONF" $OT_UI_CONF >/dev/null 2>&1; then
-  echo '. '$RAPTOR2_CONF >> $OT_UI_CONF
-fi
-cd ..
-export LD_LIBRARY_PATH=$RAPTOR2_DIR"/lib:"$LD_LIBRARY_PATH
-export PATH=$RAPTOR2_DIR"/bin:"$PATH
-export PKG_CONFIG_PATH=$RAPTOR2_DIR"/lib/pkgconfig:"$PKG_CONFIG_PATH
-
-#Build
-cmd="$WGET http://download.librdf.org/source/"$RASQAL".tar.gz" && run_cmd "$cmd" "Download $RASQAL"
-export RASQAL_DIR=$OT_PREFIX/$SELF/$RASQAL
-cmd="$TAR xvzf "$RASQAL".tar.gz" && run_cmd "$cmd" "Unzip $RASQAL"
-rm $RASQAL.tar.gz
-cd $RASQAL
-cmd="./configure --prefix=$RASQAL_DIR" && run_cmd "$cmd" "Configure"
-cmd="$MAKE" && run_cmd "$cmd" "Make"
-cmd="$MAKE install" && run_cmd "$cmd" "Make Install"
-# Config
-echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RASQAL_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RASQAL_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RASQAL_CONF"
-echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RASQAL_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RASQAL_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RASQAL_CONF"
-echo "$RASQAL configuration has been stored in '$RASQAL_CONF'."
-if ! grep "$RASQAL_CONF" $OT_UI_CONF >/dev/null 2>&1; then
-  echo '. '$RASQAL_CONF >> $OT_UI_CONF
-fi
-cd ..
-
-cd $DIR
diff --git a/rasqal-install b/rasqal-install
new file mode 100755
index 0000000..f73ddc7
--- /dev/null
+++ b/rasqal-install
@@ -0,0 +1,31 @@
+#!/bin/sh
+DIR=`pwd`
+
+# Boot
+. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1)
+SELF=$(basename $0 -install)
+check_log $SELF
+check_utils "wget tar make"
+
+# Build
+mkdir -p $PREFIX/tmp
+cd $OT_PREFIX/tmp/
+cmd="$WGET $RASQAL_DWL" && run_cmd "$cmd" "Download $SELF"
+export RASQAL_DIR=$OT_PREFIX/$SELF
+cmd="$TAR xvzf $SELF*.tar.gz" && run_cmd "$cmd" "Unpack $SELF"
+rm "$SELF*.tar.gz"
+cd "$SELF*"
+cmd="./configure --prefix=$RASQAL_DIR" && run_cmd "$cmd" "Configure"
+cmd="$MAKE" && run_cmd "$cmd" "Make"
+cmd="$MAKE install" && run_cmd "$cmd" "Make Install"
+
+# Config
+echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RASQAL_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RASQAL_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RASQAL_CONF"
+echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RASQAL_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RASQAL_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RASQAL_CONF"
+echo "$SELF configuration has been stored in '$RASQAL_CONF'."
+if ! grep "$RASQAL_CONF" $OT_UI_CONF >/dev/null 2>&1; then
+  echo '. '$RASQAL_CONF >> $OT_UI_CONF
+fi
+cd ..
+
+cd $DIR
diff --git a/services-install b/services-install
index bee1719..d47a62c 100755
--- a/services-install
+++ b/services-install
@@ -39,7 +39,7 @@ echo
 [ "`$RBENV local 2>/dev/null`" = "$RUBY_NUM_VER" ] || install_ruby
 
 
-for SERVICE in opentox-client opentox-server dataset algorithm; do
+for SERVICE in opentox-client opentox-server dataset algorithm task feature opentox-test; do
   install_ot_service
 done
 cd $DIR
diff --git a/ubuntu.list b/ubuntu.list
index 603458d..862ab51 100644
--- a/ubuntu.list
+++ b/ubuntu.list
@@ -22,7 +22,4 @@ libssl-dev install
 libxml2-dev install
 libssl-dev install
 curl install
-wget install
-tar install
 aptitude install
-find install
diff --git a/utils.sh b/utils.sh
index 8ca267e..87013d9 100755
--- a/utils.sh
+++ b/utils.sh
@@ -87,10 +87,10 @@ install_ruby() {
 # install a ruby gem using bundler
 install_with_bundler() {
   printf "\n%50s\n" "INSTALL"
-  check_utils "gem rbenv"
+  check_utils "gem rbenv bundle"
   $GEM list | grep bundler >/dev/null 2>&1 || (cmd="$GEM install bundler" && run_cmd "$cmd" "Install bundler")
   cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv rehash"
-  cmd="bundle install" && run_cmd "$cmd" "Install using bundler"
+  cmd="$BUNDLE install" && run_cmd "$cmd" "Install using bundler"
 }
 
 # download opentox git repo
@@ -104,6 +104,7 @@ ot_git_download(){
 # install opentox service
 install_ot_service(){
   printf "\n%50s\n" "$SERVICE"
+  check_utils "git rbenv"
   local DIR=`pwd`
   cd $OT_PREFIX
   ot_git_download
@@ -111,8 +112,9 @@ install_ot_service(){
   $GIT checkout $OT_BRANCH  >>$LOG 2>&1
   $RBENV local $RUBY_NUM_VER 
   case "$SERVICE" in
-    opentox-server) install_with_bundler;;
-    opentox-client) install_with_bundler;;
+    opentox-*) install_with_bundler;;
+    feature) install_with_bundler;;
+    task) install_with_bundler;;
     *) cd bin; for f in `ls`; do ./$f; done;; 
   esac
   cd $DIR