Added ot-tools (config/start/kill/less/tail).

1 files changed, 188 insertions, 0 deletions

diff --git a/ot-tools-user.sh b/ot-tools-user.sh
new file mode 100644
index 0000000..846b075
--- /dev/null
+++ b/ot-tools-user.sh
@@ -0,0 +1,188 @@
+# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby')
+
+# Load server config
+otconfig() {
+  source $HOME/.opentox/opentox-ui.sh
+}
+
+# Update the 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 ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; 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 $HOME/opentox-ruby/www/opentox/algorithm/bbrc-sample
+#  if ! git pull; then
+#    echo "Error! Pull for Bbrc-Sample 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}-3}`
+#  fi
+#  echo "Please execute 'otstart' to restart."
+#  cd "$START_DIR"
+#}
+
+# Start the server
+otstart() {
+  if [ $# != 1 ]
+  then
+    echo "One argument required: [service_name] or 'all'"
+    echo "usage: $0 [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
+    return 1
+  fi 
+
+  otconfig
+  otkill $1
+  DIR=`pwd`
+  case "$1" in
+    "algorithm") 
+      cd $HOME/opentox-ruby/$1;
+      nice bash -c "nohup unicorn -p 8081 >/dev/null 2>&1 &"; 
+      ;;
+    "compound") 
+      echo "$1 not available yet."
+      #cd $HOME/opentox-ruby/$1;
+      #nice bash -c "nohup unicorn -p 8082 >/dev/null 2>&1 &"; 
+      ;;
+    "dataset")
+      cd $HOME/opentox-ruby/$1;
+      nice bash -c "nohup unicorn -p 8083 >/dev/null 2>&1 &"; 
+      ;;
+    "feature")
+      cd $HOME/opentox-ruby/$1;
+      nice bash -c "nohup unicorn -p 8084 >/dev/null 2>&1 &"; 
+      ;;
+    "model") 
+      echo "$1 not available yet."
+      #cd $HOME/opentox-ruby/$1;
+      #nice bash -c "nohup unicorn -p 8085 >/dev/null 2>&1 &"; 
+      ;;
+    "task")
+      cd $HOME/opentox-ruby/$1;
+      nice bash -c "nohup unicorn -p 8086 >/dev/null 2>&1 &"; 
+      ;;
+    "validation") 
+      echo "$1 not available yet."
+      #cd $HOME/opentox-ruby/$1;
+      #nice bash -c "nohup unicorn -p 8087 >/dev/null 2>&1 &"; 
+      ;;
+    "4store") 
+      nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-backend opentox >/dev/null 2>&1 &"; 
+      sleep 1; 
+      nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-httpd -D -H localhost -p 8088 opentox >/dev/null 2>&1 &"; 
+      sleep 1; 
+      if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi
+      if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi     
+      ;;
+    "all")
+      otstart 4store;
+      otstart algorithm;
+      otstart dataset;
+      otstart feature;
+      otstart task;
+      ;;
+  esac
+  cd $DIR
+}
+
+# Display log
+alias otless='less $HOME/.opentox/log/development.log'
+
+# Tail log
+alias ottail='tail -f $HOME/.opentox/log/development.log'
+
+# Reload the server
+#otreload() {
+  #otconfig
+  #bash -c "nginx -s reload"
+#}
+
+# Kill the server
+otkill() {
+  if [ $# != 1 ]
+  then
+    echo "One argument required: [service_name] or 'all'"
+    echo "usage: $0 [all|algorithm|compound|dataset|feature|model|task|validation|4store]"
+    return 1
+  fi 
+
+  otconfig
+  case "$1" in
+    "algorithm") 
+      for p in `ps x | grep 'unicorn' | grep 8081 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "compound") 
+      #for p in `ps x | grep 'unicorn' | grep 8082 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "dataset")
+      for p in `ps x | grep 'unicorn' | grep 8083 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "feature")
+      for p in `ps x | grep 'unicorn' | grep 8084 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "model") 
+      #for p in `ps x | grep 'unicorn' | grep 8085 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "task")
+      for p in `ps x | grep 'unicorn' | grep 8086 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "validation") 
+      echo "$1 not available yet."
+      #for p in `ps x | grep 'unicorn' | grep 8087 | grep -v grep | awk '{print $1}'`; do kill -9 $p; done;
+      ;;
+    "4store") 
+      killall 4s-httpd >/dev/null 2>&1;
+      killall 4s-backend >/dev/null 2>&1;
+      ;;
+    "all")
+      otkill algorithm;
+      #otkill compound;
+      otkill dataset;
+      otkill feature;
+      #otkill model;
+      otkill task;
+      #otkill validation;
+      otkill 4store;
+      ;;
+  esac
+}
+
+# Check the server
+#otcheck() {
+#  check_service=`cat $HOME/.opentox/config/production.yaml  | grep opentox-algorithm | sed 's/.*\s//g' | sed 's/"//g'`
+#  if [ -z "`curl -v $check_service 2>&1 | grep '200 OK'`" ]; then
+#    otstart
+#  fi
+#}
+