solve merge conflicts with release/v2.1.0

11 files changed, 157 insertions, 27 deletions

diff --git a/README b/README
index 6746ce7..83ddf02 100644
--- a/README
+++ b/README
@@ -31,6 +31,49 @@ otconfig() {
   source $HOME/.opentox-ui.sh
 }
 
+# Update the development version
+otupdate() {
+  START_DIR=`pwd`
+  otconfig
+  cd $HOME/opentox-ruby/www/opentox
+  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo $d ; cd $d ; git pull  ; echo ; cd - ;  done
+  cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
+  mv libbbrc/Makefile libbbrc/Makefile~
+  mv liblast/Makefile liblast/Makefile~
+  if ! git pull; then
+    echo "Error! Pull for Fminer failed."
+    return 1
+  fi
+  mv libbbrc/Makefile~ libbbrc/Makefile
+  mv liblast/Makefile~ liblast/Makefile
+  make -C libbbrc/ clean
+  make -C libbbrc/ ruby
+  make -C liblast/ clean
+  make -C liblast/ ruby
+  cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
+  if ! git pull; then
+    echo "Error! Pull for Last-Utils failed."
+    return 1
+  fi
+  cd -
+  cd opentox-ruby
+  LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
+  if [ -h $LINK_DIR ]; then 
+    rm -f $LINK_DIR
+  fi
+  rake install
+  if ! [ -h $LINK_DIR ]; then
+    echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
+    rm -rf "$LINK_DIR~"
+    mv "$LINK_DIR" "$LINK_DIR~"
+    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-4}`
+  fi
+  echo "Please execute 'otstart' to restart."
+  cd "$START_DIR"
+>>>>>>> release/v2.1.0
+}
+
 # Start the server
 otstart() {
   otkill
@@ -56,4 +99,7 @@ otreload() {
 otkill() {
   sudo killall nginx >/dev/null 2>&1
   sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  while ps ax | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps ax | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  for p in `pgrep R 2>/dev/null`; do sudo kill -9 $p; done
 }
diff --git a/aa-local.yaml b/aa-local.yaml
index c01c1ed..7c3bbce 100644
--- a/aa-local.yaml
+++ b/aa-local.yaml
@@ -18,13 +18,14 @@
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
       - "http://SERVERNAME/model"
       - "http://SERVERNAME/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/resources/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/toxcreate/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/compound/
-
+      - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
 
diff --git a/aa-server.yaml b/aa-server.yaml
index c01c1ed..7c3bbce 100644
--- a/aa-server.yaml
+++ b/aa-server.yaml
@@ -18,13 +18,14 @@
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
       - "http://SERVERNAME/model"
       - "http://SERVERNAME/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/resources/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/toxcreate/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
       - !ruby/regexp /http:\/\/ESCAPEDSERVER\/compound/
-
+      - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
     : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
 
diff --git a/base-install.sh b/base-install.sh
index 0a13c68..373df1f 100755..100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -27,7 +27,7 @@ fi
 touch $OT_UI_CONF
 
 # Pkgs
-packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline5-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 sun-java6-jdk wget xsltproc zlib1g-dev"
+packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline5-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 sun-java6-jdk wget xsltproc zlib1g-dev"
 
 echo
 echo "Base Packages:"
diff --git a/config.sh b/config.sh
index 5a13b3a..ae90af3 100755
--- a/config.sh
+++ b/config.sh
@@ -7,7 +7,7 @@
 # 1) Base setup
 OT_DIST="debian"       # Linux distribution    (debian)
 OT_INSTALL="local"     # Type                  (gem, local, server)
-OT_BRANCH="master"     # Maturity              (development, master)
+OT_BRANCH="development"     # Maturity              (development, master)
 
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
diff --git a/environment_update.sh b/environment_update.sh
new file mode 100755
index 0000000..d0beae4
--- /dev/null
+++ b/environment_update.sh
@@ -0,0 +1,77 @@
+#!/bin/sh
+# Update script for OpenTox-ruby and webservices
+# Authors: Andreas Maunz, David Vorgrimmler
+# This script updates a productiv version of IST Opentox Services. All data will be saved and recovered.
+# Make sure your web services are down befor running this script.
+# You may modify some variables e.g. HOME, OTPREFIX, BACKUP_DIR.
+# opentox/install is needed and has to be configured
+
+HOME="/home/opentox"
+. $HOME/.opentox-ui.sh
+
+OTPREFIX="$HOME/opentox"
+BACKUP_DIR="$OTPREFIX/ot-server-backup"
+mkdir $BACKUP_DIR >/dev/null 2>&1
+mkdir -p $BACKUP_DIR/tmp/dataset/public >/dev/null 2>&1
+mkdir -p $BACKUP_DIR/tmp/model/public >/dev/null 2>&1
+mkdir -p $BACKUP_DIR/tmp/validation >/dev/null 2>&1
+#mkdir -p $BACKUP_DIR/tmp/log >/dev/null 2>&1
+
+
+echo "Creating backup of www..."
+TAR_NAME=$BACKUP_DIR/"www_`date +%y%m%d`.tar.gz"
+
+if [ -e $TAR_NAME ] || tar czvf $TAR_NAME "$OTPREFIX/opentox-ruby/www"; then
+  echo
+  echo "Will delete www in 10s! Press Ctrl+C to abort..."
+  sleep 10
+  sudo rm -rf "$OTPREFIX/opentox-ruby/www"
+fi
+
+
+NGINX="`which nginx`"
+RAKE="`which rake`"
+
+if ! [ -e "$RAKE" ]; then
+  echo "Rake not found."
+  exit 1
+fi
+if ! [ -e "$NGINX" ]; then
+  echo "Nginx not found."
+  exit 1
+fi
+if ! cd "$OTPREFIX/install"; then
+  echo "$OTPREFIX/install dir not found"
+fi
+
+
+OTINSTALL="$OTPREFIX/install/opentox-webservices.sh"
+if ! [ -e "$OTINSTALL" ]; then
+  echo "$OTINSTALL not found."
+  exit 1
+fi
+chmod +x $OTINSTALL
+`$OTINSTALL`
+echo "$OTINSTALL script end."
+
+
+OTRUBYINSTALL="$OTPREFIX/install/opentox-ruby.sh"
+if ! [ -e "$OTRUBYINSTALL" ]; then
+  echo "$OTRUBYINSTALL not found."
+  exit 1
+fi
+chmod +x $OTRUBYINSTALL
+`$OTRUBYINSTALL`
+echo "$OTRUBYINSTALL script end."
+
+
+echo "Extracting backup of www..."
+cd /
+DEST_DATASET=`echo "$OTPREFIX/opentox-ruby/www/opentox/dataset/public/*yaml" | sed 's/.\(.*\)/\1/'`
+DEST_MODEL=`echo "$OTPREFIX/opentox-ruby/www/opentox/model/public/*yaml" | sed 's/.\(.*\)/\1/'`
+DEST_REPORTS=`echo "$OTPREFIX/opentox-ruby/www/opentox/validation/reports" | sed 's/.\(.*\)/\1/'`
+tar xzvf $TAR_NAME --wildcards $DEST_DATASET
+tar xzvf $TAR_NAME --wildcards $DEST_MODEL
+tar xzvf $TAR_NAME $DEST_REPORTS
+cd -
+echo "End of script."
diff --git a/nginx.conf b/nginx.conf
index d3a8324..c89efe2 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -10,7 +10,7 @@ http {
 
     passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
     passenger_ruby RUBY_DEST/bin/ruby;
-    passenger_default_user opentox;
+    passenger_default_user USER;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
diff --git a/nginx.sh b/nginx.sh
index 6b10a5c..800165e 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -52,6 +52,7 @@ cd - >>$LOG 2>&1
 servername=`hostname`
 $GIT checkout nginx.conf>>$LOG 2>&1
 cmd="sed -i -e \"s,PASSENGER,$passenger,;s,SERVERNAME,$servername,;s,RUBY_DEST,$RUBY_DEST,;s,NGINX_DEST,$NGINX_DEST,;s,WWW_DEST,$WWW_DEST,\" ./nginx.conf" && run_cmd "$cmd" "Config"
+cmd="sed -i -e \"s,USER,`whoami`,\" ./nginx.conf" && run_cmd "$cmd" "User"
 cmd="cp ./nginx.conf \"$NGINX_DEST/conf\"" && run_cmd "$cmd" "Copy"
 
 if [ ! -f $NGINX_CONF ]; then
diff --git a/openbabel.sh b/openbabel.sh
index 3257146..4e55ff8 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -86,14 +86,15 @@ else
   fi
 fi
 
-if ! $OB_DONE ; then
-  cd "/tmp/$OB_VER/scripts/ruby/"
+#if ! $OB_DONE ; then
+  OB_SRC_DIR="/tmp/$OB_VER/scripts/ruby/"
+  cd "$OB_SRC_DIR"
   cmd="ruby extconf.rb --with-openbabel-include=$OB_DEST/include/openbabel-2.0 --with-openbabel-lib=$OB_DEST/lib" && run_cmd "$cmd" "Code"
   cmd="make" && run_cmd "$cmd" "Make"
   cmd="cp openbabel.so $OB_DEST_BINDINGS" && run_cmd "$cmd" "Install"
-  cmd="ln -s $OB_DEST_BINDINGS/openbabel.so $RUBY_DEST/lib/ruby/site_ruby/1.8/`uname -m`-linux/" && run_cmd "$cmd" "Link"
-fi
-
-cd "$DIR"
-
+  cmd="ln -sf $OB_DEST_BINDINGS/openbabel.so $RUBY_DEST/lib/ruby/site_ruby/1.8/`uname -m`-linux/" && run_cmd "$cmd" "Link"
+  cd "$DIR"
+  . "`pwd`/utils.sh"
+  cmd="ruby test-ob-rb.rb" && run_cmd "$cmd" "Load"
+#fi
 
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index fa589cd..ef98ded 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -31,6 +31,12 @@ if [ ! -e "$GIT" ]; then
   exit 1
 fi
 
+RUBY="`which ruby`"
+if [ ! -e "$RUBY" ]; then
+  echo "'ruby' missing. Install 'ruby' first. Aborting..."
+  exit 1
+fi
+
 LOG="/tmp/`basename $0`-log.txt"
 
 echo
@@ -55,35 +61,31 @@ for s in compound dataset algorithm model toxcreate task validation; do
     cd - >>$LOG 2>&1
 done
 
-# validation service
-#git clone http://github.com/mguetlein/opentox-validation.git validation
-#cd /var/www/opentox/validation
-#git checkout -t origin/test
-#gem install ruby-plot
-#mkdir -p public
-#ln -s /var/www/opentox/validation/public /var/www/validation
-
 # fminer etc
 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"
+cd "libfminer/libbbrc">>$LOG 2>&1
+$GIT checkout $OT_BRANCH>>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
+cd -
+cd "libfminer/liblast">>$LOG 2>&1
+$GIT checkout $OT_BRANCH>>$LOG 2>&1
+$GIT pull >>$LOG 2>&1
+cd -
 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 -
 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 ->>$LOG 2>&1
+cd -
 cd "last-utils">>$LOG 2>&1
-$GIT checkout master >>$LOG 2>&1
+$GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
 
 cd "$DIR"
diff --git a/test-ob-rb.rb b/test-ob-rb.rb
new file mode 100644
index 0000000..62fda1e
--- /dev/null
+++ b/test-ob-rb.rb
@@ -0,0 +1 @@
+require 'openbabel'