From b99ee338f6831281de15ffb3ddd14e879e0c1af5 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 7 Jul 2011 16:25:11 +0200
Subject: Added fminer Unit-Tests

---
 opentox-webservices.sh | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index 811d4bc..26835e4 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
@@ -74,10 +80,14 @@ for mylib in bbrc last; do
 done
 cd "libfminer/libbbrc">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd ->>$LOG 2>&1
+cd "test">>$LOG 2>&1
+cmd="$RUBY tc_fminer_ruby.rb" && run_cmd "$cmd" "BBRC Unit Tests"
+cd ../../../ >>$LOG 2>&1
 cd "libfminer/liblast">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd ->>$LOG 2>&1
+cd "test">>$LOG 2>&1
+cmd="$RUBY tc_fminer_ruby.rb" && run_cmd "$cmd" "LAST Unit Tests"
+cd ../../../ >>$LOG 2>&1
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-- 
cgit v1.2.3


From fe1bd0e5c927e55a9ba2a71eec4bba8d1e9c5aa2 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 12 Jul 2011 07:37:33 +0200
Subject: Fixed update of GEM (https://github.com/opentox/install/issues/15)

---
 README | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/README b/README
index 781a37c..697ecdb 100644
--- a/README
+++ b/README
@@ -57,8 +57,11 @@ otupdate() {
   fi
   cd -
   cd opentox-ruby
-  rake install
   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~"
-- 
cgit v1.2.3


From 98fdf4740451067911ed1b8103fec5cc16755f94 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 12 Jul 2011 07:47:19 +0200
Subject: Minor Fixes

---
 README | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README b/README
index 697ecdb..6dd6880 100644
--- a/README
+++ b/README
@@ -33,6 +33,7 @@ otconfig() {
 
 # 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
@@ -41,7 +42,7 @@ otupdate() {
   mv liblast/Makefile liblast/Makefile~
   if ! git pull; then
     echo "Error! Pull for Fminer failed."
-    exit 1
+    return 1
   fi
   mv libbbrc/Makefile~ libbbrc/Makefile
   mv liblast/Makefile~ liblast/Makefile
@@ -53,7 +54,7 @@ otupdate() {
   cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
   if ! git pull; then
     echo "Error! Pull for Last-Utils failed."
-    exit 1
+    return 1
   fi
   cd -
   cd opentox-ruby
@@ -69,6 +70,7 @@ otupdate() {
     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"
 }
 
 
-- 
cgit v1.2.3


From 3a58a09c23087428a4be5488aba5cf13cfbf1a9d Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 12 Jul 2011 07:53:24 +0200
Subject: Removed tests

---
 opentox-webservices.sh | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index 26835e4..ef98ded 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -80,14 +80,10 @@ for mylib in bbrc last; do
 done
 cd "libfminer/libbbrc">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd "test">>$LOG 2>&1
-cmd="$RUBY tc_fminer_ruby.rb" && run_cmd "$cmd" "BBRC Unit Tests"
-cd ../../../ >>$LOG 2>&1
+cd -
 cd "libfminer/liblast">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd "test">>$LOG 2>&1
-cmd="$RUBY tc_fminer_ruby.rb" && run_cmd "$cmd" "LAST Unit Tests"
-cd ../../../ >>$LOG 2>&1
+cd -
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-- 
cgit v1.2.3


From 60b2cbaca5adef4d5806eac782a4c1af19896603 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 12 Jul 2011 10:58:11 +0200
Subject: Kill finished with Watchdog

---
 README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README b/README
index 6dd6880..8d86513 100644
--- a/README
+++ b/README
@@ -99,6 +99,6 @@ 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 PassengerHelperAgent | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps ax | grep PassengerWatchdog | 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
 }
-- 
cgit v1.2.3