1 files changed, 75 insertions, 24 deletions
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index 294b9bf..91d402e 100644..100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -1,24 +1,58 @@
 #!/bin/sh
+#
+# Installs Opentox Webservices.
+# Author: Christoph Helma, Andreas Maunz.
+#
 
-echo "Installing OpenTox webservices"
-. ./config
-# Create opentox system user
-id opentox
-if [ $? -ne 0 ] 
-then
-   adduser --system opentox
+. "`pwd`/utils.sh"
+DIR=`pwd`
+
+if [ "$(id -u)" = "0" ]; then
+  echo "This script must be run as non-root." 1>&2
+  exit 1
+fi
+
+# Utils
+WGET="`which wget`"
+if [ ! -e "$WGET" ]; then
+  echo "'wget' missing. Install 'wget' first. Aborting..."
+  exit 1
+fi
+
+RAKE="`which rake`"
+if [ ! -e "$RAKE" ]; then
+  echo "'rake' missing. Install 'rake' first. Aborting..."
+  exit 1
+fi
+
+GIT="`which git`"
+if [ ! -e "$GIT" ]; then
+  echo "'git' missing. Install 'git' first. Aborting..."
+  exit 1
 fi
 
-dir=`pwd`
-mkdir -p /var/www/opentox
-cd /var/www/opentox
-for s in compound dataset algorithm model toxcreate task; do
-    git clone git://github.com/opentox/$s.git $s
-    cd $s
-    git checkout -t origin/$branch
-    mkdir -p public
-    ln -s /var/www/opentox/$s/public /var/www/$s
-    cd -
+LOG="/tmp/`basename $0`-log.txt"
+
+if ! id opentox >>$LOG 2>&1; then
+  cmd="sudo adduser --system opentox" && run_cmd "$cmd" "User 'opentox'"
+fi
+
+echo
+echo "Webservices ('$LOG'):"
+
+mkdir -p "$WWW_DEST/opentox" >>$LOG 2>&1
+cd "$WWW_DEST/opentox" >>$LOG 2>&1
+for s in compound dataset algorithm model toxcreate task validation; do
+    rm -rf "$s" >>$LOG 2>&1
+    $GIT clone "git@github.com:opentox/$s.git" "$s" >>$LOG 2>&1
+    cd "$s" >>$LOG 2>&1
+    $GIT checkout -b $OT_BRANCH origin/$OT_BRANCH >>$LOG 2>&1
+    #rm -rf public >>$LOG 2>&1
+    #mkdir public >>$LOG 2>&1
+    mypath_from="$WWW_DEST/opentox/$s/public"
+    mypath_to="$WWW_DEST/$s"
+    cmd="ln -sf \"$mypath_from\" \"$mypath_to\"" && run_cmd "$cmd" "Linking $s"
+    cd - >>$LOG 2>&1
 done
 
 # validation service
@@ -30,10 +64,27 @@ done
 #ln -s /var/www/opentox/validation/public /var/www/validation
 
 # fminer etc
-cd /var/www/opentox/algorithm
-updatedb
-rake fminer:install
-chown -R opentox /var/www/opentox
-cp -r $HOME/.opentox /home/opentox/
-chown -R opentox /home/opentox/.opentox
-cd $dir
+cmd="test -f $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config present"
+cd "$WWW_DEST/opentox/algorithm" >>$LOG 2>&1
+cmd="$GIT submodule init" && run_cmd "$cmd" "Fminer Init"
+cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update"
+for mylib in bbrc last; do
+  cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ -I$OB_DEST/include/openbabel-2.0,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile; sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ -L$OB_DEST/lib,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)"
+  cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ -I$RUBY_DEST/lib/ruby/1.8/`uname -m`-linux,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)"
+done
+cd "libfminer/libbbrc">>$LOG 2>&1
+$GIT checkout master >>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
+cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
+cd ->>$LOG 2>&1
+cd "libfminer/liblast">>$LOG 2>&1
+$GIT checkout master >>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
+cmd="make ruby" && run_cmd "$cmd" "Make LAST"
+cd ->>$LOG 2>&1
+cd "last-utils">>$LOG 2>&1
+$GIT checkout master >>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
+
+cd "$DIR"
+