Added 4store install

5 files changed, 107 insertions, 33 deletions

diff --git a/4store-install b/4store-install
new file mode 100755
index 0000000..a00a07a
--- /dev/null
+++ b/4store-install
@@ -0,0 +1,43 @@
+#!/bin/sh
+
+# Installs 4store on Debian and compatible systems.
+# Author: Andreas Maunz
+
+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
+[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
+check_utils "git make"
+
+# Build
+cd $OT_PREFIX/tmp/
+([ -d $SELF ] && cd $SELF && cmd="$GIT pull" && run_cmd "$cmd" "Git pull") || (cmd="$GIT clone https://github.com/garlik/$SELF" && run_cmd "$cmd" "Git clone")
+cd $SELF
+cmd="./autogen.sh" && run_cmd "$cmd" "Autogen"
+export FST=$HOME/4S
+cmd="./configure --prefix=$FST --exec-prefix=$FST --with-storage-path=$FST/var/lib --with-config-file=$FST/$SELF.conf -with-http-log=$FST/log" && run_cmd "$cmd" "Configure"
+cmd="make" && run_cmd "$cmd" "Make"
+cmd="make install" && run_cmd "$cmd" "Make Install"
+#cmd="make test" && run_cmd "$cmd" "Make Test"
+
+# Config
+echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$FST/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$FST/lib\"; fi" >> "$FST_CONF"
+echo "$SELF configuration has been stored in '$FST_CONF'."
+if ! grep "$FST_CONF" $OT_UI_CONF >/dev/null 2>&1; then
+  echo '. '$FST_CONF >> $OT_UI_CONF
+fi
+
+# Testing code --- unused
+#export LD_LIBRARY_PATH=$FST/lib
+#cd $FST
+#bin/4s-backend-setup test
+#bin/4s-backend test
+#bin/4s-httpd -D -H localhost -p 8000 test # -D only for testing
+
+notify
+
+# return to wd
+cd $DIR
diff --git a/base-install.sh b/base-install
index c9cebdd..7ce7c70 100755
--- a/base-install.sh
+++ b/base-install
@@ -6,27 +6,21 @@
 # NOTE: Your installed packages are safe and will not be updated.
 # Java configuration is included in '$OT_UI_CONF'.
 
-. ./utils.sh
 DIR=`pwd`
 
-if [ "$(id -u)" = "0" ]; then
-  echo "This script must not be run as root" 1>&2
-  exit 1
-fi
-
-# Utils
+# Boot
+. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh" 1>&2 && exit 1)
+# Not logged
+# Not logged
+[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
 check_utils "aptitude git apt-cache dpkg"
 
-touch $OT_UI_CONF
-
 # Pkgs
-packs="binutils build-essential cmake curl gnuplot hostname libcurl4-openssl-dev libgsl0-dev libopenbabel4 libopenbabel-dev libraptor1-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev"
-
+packs="build-essential cmake libgsl0-dev libopenbabel4 libopenbabel-dev libtool openjdk-6-jdk r-base r-base-dev libpcre3-dev librasqal3-dev libtool libraptor1-dev libglib2.0-dev ncurses-dev libreadline-dev uuid-dev"
 echo
 echo "Base Packages:"
-
 echo
-echo "Updating index"
+echo "Updating index..."
 sudo $APTITUDE update -y >/dev/null 2>&1
 
 pack_arr=$packs
@@ -52,7 +46,9 @@ fi
 
 echo
 if [ -n "$pack_arr" ]; then 
-  cmd="sudo $APTITUDE -y install $pack_arr" && run_cmd "$cmd" "Installing packages"
+  echo
+  echo "Installing packages"
+  sudo $APTITUDE -y install $pack_arr
 fi
 
 
diff --git a/config.sh b/config.sh
index e28d259..eb7a23f 100755
--- a/config.sh
+++ b/config.sh
@@ -23,6 +23,7 @@ RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
 
 ### Nothing to gain from changes below this line.
 JAVA_CONF="$HOME/.opentox/sh_java"
+FST_CONF="$HOME/.opentox/sh_4S"
 OB_CONF="$HOME/.opentox/sh_OB"
 R_CONF="$HOME/.opentox/sh_R"
 OT_UI_CONF="$HOME/.opentox/opentox-ui.sh"
diff --git a/install b/install
index 5d0f9e3..0a3a1e7 100755
--- a/install
+++ b/install
@@ -1,11 +1,9 @@
 #!/bin/sh
+
 # Main Opentox-ruby install script
 # Author: Christoph Helma, Andreas Maunz
 
-if [ "$(id -u)" = "0" ]; then
-  echo "This script must not be run as root" 1>&2
-  exit 1
-fi
+[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
 
 echo
 echo "OpenTox Ruby"
@@ -41,7 +39,8 @@ 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)")
 
-. ./base-install.sh # Debian specific; disable for others.
+. ./base-install # Debian specific; disable this for others.
+./4store-install # Download, compile and build 4store. Install to OT_PREFIX.
 
 if [ ! -d ~/.rbenv ]; then
   cmd="$GIT clone git://github.com/sstephenson/rbenv.git ~/.rbenv" && run_cmd "$cmd" "rbenv"
@@ -56,15 +55,5 @@ 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")
 
-echo
-echo "Installation finished."
-echo "Destination (OT_PREFIX): '$OT_PREFIX'" 
-echo
-echo "IMPORTANT: How to configure your system:"
-echo "IMPORTANT: a) Include '$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: NOW would be the best time to configure!"
-echo
-echo "Thank you for your attention."
-echo
+notify
+
diff --git a/utils.sh b/utils.sh
index 8a41433..d5bbe58 100755
--- a/utils.sh
+++ b/utils.sh
@@ -6,6 +6,7 @@
 # Functions to install ruby and install services with bundler.
 # Ensures presence of ~/.opentox (CONFIG) and OT_PREFIX.
 
+# create a temporary directory in OT_PREFIX and a log directory in .opentox
 check_dest() 
 {
   [ -d "$OT_PREFIX/tmp" ] || mkdir -p "$OT_PREFIX/tmp"
@@ -20,11 +21,30 @@ check_dest()
   fi
 }
 
+# export a LOG file name
+check_log()
+{
+  local name="$1"
+  if [ -z "$LOG" ]; then
+    LOG="$OT_PREFIX/tmp/$name.log"
+    echo
+    printf "\033[1m%s\033[m\n" "$name ('$LOG'):"
+    echo
+  fi
+}
+
+# run a shell command
+# Signal exit status by formatted string
+# @param cmd command to execute 
+# @param title textual description of command
+# @example {
+#   run_cmd "ls" "list dir"
+# }
 run_cmd ()
 {
   local cmd="$1"; local title="$2"
   printf "%50s" "$title"
-  if ! eval $cmd >>$LOG 2>&1 ; then  
+  if ! eval "$cmd" >>$LOG 2>&1 ; then  
     printf "                              [ \033[31m%s\033[m ]\n" "FAIL"
     echo "Last 10 lines of log:"
     tail -10 "$LOG"
@@ -34,6 +54,11 @@ run_cmd ()
 }
 
 
+# stop if required binaries not in path
+# @param list of binaries
+# @example {
+#   check_utils "git curl"
+# }
 check_utils() {
   for u in $1; do
     eval `echo $u | tr "[:lower:]" "[:upper:]" | tr "-" "_"`=`which $u` || (echo "'$u' missing. Install '$u' first." 1>&2 && exit 1)
@@ -41,6 +66,8 @@ check_utils() {
 }
 
 
+# install ruby using rbenv
+# configure the version in config.sh
 install_ruby() {
   printf "\n%50s\n" "RUBY"
   local DIR=`pwd`
@@ -57,7 +84,7 @@ install_ruby() {
   cmd="$RBENV local $RUBY_NUM_VER" && run_cmd "$cmd" "Rbenv set ruby"
 }
 
-
+# install a ruby gem using bundler
 install_with_bundler() {
   printf "\n%50s\n" "INSTALL"
   check_utils "gem rbenv"
@@ -66,7 +93,25 @@ install_with_bundler() {
   cmd="bundle install" && run_cmd "$cmd" "Install using bundler"
 }
 
+# emit notification if caller was the shell (the user), see http://goo.gl/grCOk
+notify() {
+  echo
+  echo "Installation succesful"
+  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: NOW would be the best time to configure!"
+    echo
+    echo "Thank you for your attention."
+    echo
+  fi
+}
+
 
+# Force loading configuration from local, if we are installing for the first time
 if [ -z "$OT_PREFIX" ]; then
   . ./config.sh
 else