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-rw-r--r--aa-local.yaml41
-rw-r--r--aa-server.yaml41
-rwxr-xr-x[-rw-r--r--]base-install.sh20
-rwxr-xr-xconfig.sh16
-rwxr-xr-xenvironment_update.sh77
-rwxr-xr-xinstall14
-rw-r--r--jl_keys.yaml38
-rwxr-xr-xkernlab.sh68
-rw-r--r--nginx.conf43
-rwxr-xr-xopenbabel.sh39
-rwxr-xr-xopentox-ruby.sh92
-rw-r--r--ot-tools-root.sh82
-rw-r--r--ot-tools-user.sh83
-rw-r--r--packs.R6
-rw-r--r--production.yaml26
-rwxr-xr-xredis.sh79
-rwxr-xr-xruby.sh83
-rw-r--r--test-ob-rb.rb1
18 files changed, 69 insertions, 780 deletions
diff --git a/aa-local.yaml b/aa-local.yaml
deleted file mode 100644
index 75cccd0..0000000
--- a/aa-local.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-# OpenSSO Authorization
-# set ":server: " to disable A&A
-:authorization:
- :server: AA
- :free_request: #request-method not controlled by A&A
- - "GET"
- - "POST"
- - "HEAD"
- - "DELETE"
- - "PUT"
- :authenticate_request: #only for authenticated user
- - ""
- :authorize_request: #only for authenticated and authorizeduser
- - ""
-# Exceptions:
- :free_uris: #request-method for uri not controlled by A&A
- ? - :GET
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
- - "http://SERVERNAMENGINX_PORT/model"
- - "http://SERVERNAMENGINX_PORT/dataset"
- - "http://SERVERNAMENGINX_PORT/validation"
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
- ? - :GET
- - :POST
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/
- - !ruby/regexp /sign_(in|out)$/
- ? - :PUT
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
- ? - :DELETE
- : - "http://SERVERNAMENGINX_PORT/task/cleanup"
-
- :authorize_exceptions: #request-method for uri only authenticated, no authorization
- ? - :POST
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
- - "http://SERVERNAMENGINX_PORT/dataset"
- - "http://SERVERNAMENGINX_PORT/model"
- - "http://SERVERNAMENGINX_PORT/validation"
- - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
diff --git a/aa-server.yaml b/aa-server.yaml
deleted file mode 100644
index 75cccd0..0000000
--- a/aa-server.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-# OpenSSO Authorization
-# set ":server: " to disable A&A
-:authorization:
- :server: AA
- :free_request: #request-method not controlled by A&A
- - "GET"
- - "POST"
- - "HEAD"
- - "DELETE"
- - "PUT"
- :authenticate_request: #only for authenticated user
- - ""
- :authorize_request: #only for authenticated and authorizeduser
- - ""
-# Exceptions:
- :free_uris: #request-method for uri not controlled by A&A
- ? - :GET
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
- - "http://SERVERNAMENGINX_PORT/model"
- - "http://SERVERNAMENGINX_PORT/dataset"
- - "http://SERVERNAMENGINX_PORT/validation"
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
- ? - :GET
- - :POST
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
- - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/
- - !ruby/regexp /sign_(in|out)$/
- ? - :PUT
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
- ? - :DELETE
- : - "http://SERVERNAMENGINX_PORT/task/cleanup"
-
- :authorize_exceptions: #request-method for uri only authenticated, no authorization
- ? - :POST
- : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
- - "http://SERVERNAMENGINX_PORT/dataset"
- - "http://SERVERNAMENGINX_PORT/model"
- - "http://SERVERNAMENGINX_PORT/validation"
- - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
diff --git a/base-install.sh b/base-install.sh
index 73c9e37..e9e0860 100644..100755
--- a/base-install.sh
+++ b/base-install.sh
@@ -16,6 +16,7 @@ fi
# Utils
APTITUDE="`which aptitude`"
+GIT="`which git`"
APT_CACHE="`which apt-cache`"
DPKG="`which dpkg`"
@@ -24,10 +25,15 @@ if [ ! -e "$APTITUDE" ]; then
exit 1
fi
+if [ ! -e "$GIT" ]; then
+ echo "Git missing. Install git first." 1>&2
+ exit 1
+fi
+
touch $OT_UI_CONF
# Pkgs
-packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 wget xsltproc zlib1g-dev"
+packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev"
echo
echo "Base Packages:"
@@ -65,7 +71,6 @@ if [ -n "$pack_fail" ]; then
sleep 5
fi
-echo sun-java6-jdk shared/accepted-sun-dlj-v1-1 select true | sudo /usr/bin/debconf-set-selections
echo
if [ -n "$pack_arr" ]; then
echo "Installing missing packages:"
@@ -92,5 +97,16 @@ if [ ! -f $JAVA_CONF ]; then
fi
fi
+if [ ! -d ~/.rbenv ]; then
+ cmd="$GIT clone git://github.com/sstephenson/rbenv.git ~/.rbenv" && run_cmd "$cmd" "rbenv"
+else
+ echo "'rbenv' already installed. Leaving untouched."
+fi
+
+if ! grep "rbenv" $OT_UI_CONF >/dev/null 2>&1 ; then
+ echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> $OT_UI_CONF
+ echo 'eval "$(rbenv init -)"' >> $OT_UI_CONF
+fi
+
cd "$DIR"
diff --git a/config.sh b/config.sh
index 8ece62e..bd7f1ab 100755
--- a/config.sh
+++ b/config.sh
@@ -14,37 +14,29 @@ OT_PREFIX="$HOME/opentox-ruby"
OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
# 3) What versions to install.
-RUBY_NUM_VER="1.8.7-2011.03"
-OB_NUM_VER="2.2.3"
-KL_NUM_VER="0.9-11"
-REDIS_NUM_VER="2.4.4"
+RUBY_NUM_VER="1.9.3-p125"
+OB_NUM_VER="2.3.1"
+REDIS_NUM_VER="2.2.2"
# 4) Server settings.
NGINX_SERVERNAME="toxcreate3.in-silico.ch"
WWW_DEST="$OT_PREFIX/www"
-NGINX_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
-OHM_PORT="6379" # set to port (no colon)
+OHM_PORT="6381" # set to port (no colon)
# Done.
### Nothing to gain from changes below this line.
JAVA_CONF="$OT_PREFIX/.sh_java_ot"
-RUBY_CONF="$OT_PREFIX/.sh_ruby_ot"
-REDIS_CONF="$OT_PREFIX/.sh_redis_ot"
-NGINX_CONF="$OT_PREFIX/.sh_nginx_ot"
OB_CONF="$OT_PREFIX/.sh_OB_ot"
R_CONF="$OT_PREFIX/.sh_R_ot"
-RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
OB_VER="openbabel-$OB_NUM_VER"
REDIS_VER="$REDIS_NUM_VER"
-RUBY_DEST="$OT_PREFIX/$RUBY_VER"
OB_DEST="$OT_PREFIX/$OB_VER"
OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
R_DEST="$OT_PREFIX/r-packages"
-NGINX_DEST="$OT_PREFIX/nginx"
REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
REDIS_SERVER_CONF="$REDIS_DEST/redis.conf"
diff --git a/environment_update.sh b/environment_update.sh
deleted file mode 100755
index d0beae4..0000000
--- a/environment_update.sh
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/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/install b/install
index b0422b5..7b8a4a8 100755
--- a/install
+++ b/install
@@ -45,22 +45,10 @@ echo "Cleaning up $HOME/tmp files."
rm -rf $HOME/tmp/openbabel* $HOME/tmp/kernlab* $HOME/tmp/ruby*
. "./base-install.sh"
-. "./ruby.sh"
. "./openbabel.sh"
-. "./kernlab.sh"
-. "./opentox-ruby.sh"
-
-if [ "$install" != "gem" ]
-then
- . "./nginx.sh"
- . "./redis.sh"
- . "./opentox-webservices.sh"
-fi
echo
echo "Installation finished and system configured."
echo "Destination: '$OT_PREFIX'"
-echo "Nginx: '$NGINX_DEST'"
-echo "Redis: '$REDIS_DEST'"
-echo "IMPORTANT: Include the file '$OT_UI_CONF' in your shell or system startup to have the system automatically configured."
+echo "IMPORTANT: Include '$OT_UI_CONF' in your shell or system startup to have the system automatically configured."
echo
diff --git a/jl_keys.yaml b/jl_keys.yaml
new file mode 100644
index 0000000..22f26ae
--- /dev/null
+++ b/jl_keys.yaml
@@ -0,0 +1,38 @@
+[
+ "joelib2.feature.types.FractionRotatableBonds",
+ "joelib2.feature.types.GeometricalDiameter",
+ "joelib2.feature.types.GeometricalRadius",
+ "joelib2.feature.types.GeometricalShapeCoefficient",
+ "joelib2.feature.types.GraphShapeCoefficient",
+ "joelib2.feature.types.KierShape1",
+ "joelib2.feature.types.KierShape2",
+ "joelib2.feature.types.KierShape3",
+ "joelib2.feature.types.LogP",
+ "joelib2.feature.types.MolarRefractivity",
+ "joelib2.feature.types.MolecularWeight",
+ "joelib2.feature.types.PolarSurfaceArea",
+ "joelib2.feature.types.FractionRotatableBonds",
+ "joelib2.feature.types.RotatableBonds",
+ "joelib2.feature.types.TopologicalDiameter",
+ "joelib2.feature.types.TopologicalRadius",
+ "joelib2.feature.types.ZagrebIndex1",
+ "joelib2.feature.types.count.AcidicGroups",
+ "joelib2.feature.types.count.AliphaticOHGroups",
+ "joelib2.feature.types.count.AromaticBonds",
+ "joelib2.feature.types.count.AromaticOHGroups",
+ "joelib2.feature.types.count.BasicGroups",
+ "joelib2.feature.types.count.HBA1",
+ "joelib2.feature.types.count.HBA2",
+ "joelib2.feature.types.count.HBD1",
+ "joelib2.feature.types.count.HBD2",
+ "joelib2.feature.types.count.HeavyBonds",
+ "joelib2.feature.types.count.HeteroCycles",
+ "joelib2.feature.types.count.HydrophobicGroups",
+ "joelib2.feature.types.count.NO2Groups",
+ "joelib2.feature.types.count.NumberOfAtoms",
+ "joelib2.feature.types.count.NumberOfBonds",
+ "joelib2.feature.types.count.NumberOfHal",
+ "joelib2.feature.types.count.OSOGroups",
+ "joelib2.feature.types.count.SO2Groups",
+ "joelib2.feature.types.count.OSOGroups"
+]
diff --git a/kernlab.sh b/kernlab.sh
deleted file mode 100755
index aad125d..0000000
--- a/kernlab.sh
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/bin/sh
-#
-# Installs Kernlab.
-# Author: Christoph Helma, Andreas Maunz.
-#
-
-. "`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 "$WGET" ]; then
- echo "'wget' missing. Install 'wget' first. Aborting..."
- exit 1
-fi
-
-R="`which R`"
-if [ ! -e "$R" ]; then
- echo "'R' missing. Install 'R' first. Aborting..."
- exit 1
-fi
-
-# Pkg
-LOG="$HOME/tmp/`basename $0`-log.txt"
-
-echo
-echo "Kernlab ('$LOG')."
-
-R_DONE=false
-mkdir "$R_DEST" >/dev/null 2>&1
-if [ ! -d "$R_DEST" ]; then
- echo "Install directory '$R_DEST' is not available! Aborting..."
- exit 1
-else
- if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail
- R_DONE=true
- else
- mkdir "$R_DEST" >/dev/null 2>&1
- fi
-fi
-
-
-if ! $R_DONE; then
- export R_LIBS="$R_DEST" # To install non-global
- cmd="$R CMD BATCH packs.R" && run_cmd "$cmd" "R packages"
- eval "$cmd"
-fi
-
-
-if [ ! -f $R_CONF ]; then
-
- echo "if echo \"\$R_LIBS\" | grep -v \"$R_DEST\">/dev/null 2>&1; then export R_LIBS=\"$R_DEST\"; fi" >> "$R_CONF"
- echo "if ! [ -d \"$R_DEST\" ]; then echo \"\$0: '$R_DEST' is not a directory!\"; fi" >> "$R_CONF"
- echo "R package destination has been stored in '$R_CONF'."
-
- if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
- echo ". \"$R_CONF\"" >> $OT_UI_CONF
- fi
-
-fi
-
-cd "$DIR"
-
diff --git a/nginx.conf b/nginx.conf
deleted file mode 100644
index c15dc02..0000000
--- a/nginx.conf
+++ /dev/null
@@ -1,43 +0,0 @@
-worker_processes 10;
-
-events {
- worker_connections 1024;
-}
-
-http {
-
- server_names_hash_bucket_size 256;
-
- passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
- passenger_ruby RUBY_DEST/bin/ruby;
- passenger_default_user USER;
- passenger_log_level 2;
- passenger_spawn_method conservative;
- #passenger_use_global_queue on;
- passenger_max_pool_size 30;
-
- include NGINX_DEST/conf/mime.types;
- default_type application/octet-stream;
-
- sendfile on;
- keepalive_timeout 65;
-
- # webservices
- server {
- listen NGINX_PORT;
- client_max_body_size 5000m;
- server_name SERVERNAME;
- location / {
- root WWW_DEST;
- passenger_enabled on;
- }
- passenger_base_uri /compound;
- passenger_base_uri /dataset;
- passenger_base_uri /algorithm;
- passenger_base_uri /model;
- passenger_base_uri /task;
- passenger_base_uri /validation;
- passenger_base_uri /toxcreate;
- }
-
-}
diff --git a/openbabel.sh b/openbabel.sh
index 3016d95..b51ed17 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -19,6 +19,11 @@ if [ ! -e "$WGET" ]; then
echo "'wget' missing. Install 'wget' first. Aborting..."
exit 1
fi
+CMAKE="`which cmake`"
+if [ ! -e "$CMAKE" ]; then
+ echo "'cmake' missing. Install 'cmake' first. Aborting..."
+ exit 1
+fi
# Pkg
LOG="$HOME/tmp/`basename $0`-log.txt"
@@ -45,9 +50,8 @@ if [ ! $OB_DONE ]; then
cmd="tar zxf $OB_VER.tar.gz?use_mirror=kent $OB_VER" && run_cmd "$cmd" "Unpack"
fi
cd "$HOME/tmp/$OB_VER">>$LOG 2>/dev/null
-
- cmd="./configure --prefix=$OB_DEST" && run_cmd "$cmd" "Configure"
- cmd="make" && run_cmd "$cmd" "Make"
+ cmd="$CMAKE -DCMAKE_INSTALL_PREFIX=$OB_DEST" && run_cmd "$cmd" "Configure"
+ cmd="make -j2" && run_cmd "$cmd" "Make"
cmd="make install" && run_cmd "$cmd" "Install"
fi
@@ -63,9 +67,6 @@ if [ ! -f "$OB_CONF" ]; then
echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF"
echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF"
- echo "if echo \"\$RUBYLIB\" | grep -v \"$OB_DEST_BINDINGS\">/dev/null 2>&1; then export RUBYLIB=\"$OB_DEST_BINDINGS:\$RUBYLIB\"; fi" >> "$RUBY_CONF"
- echo "if ! [ -d \"$OB_DEST_BINDINGS\" ]; then echo \"\$0: '$OB_DEST_BINDINGS' is not a directory!\"; fi" >> "$RUBY_CONF"
-
echo "Openbabel configuration has been stored in '$OB_CONF'."
if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
echo ". \"$OB_CONF\"" >> $OT_UI_CONF
@@ -73,28 +74,4 @@ if [ ! -f "$OB_CONF" ]; then
fi
-echo "Bindings:"
-OB_DONE=false
-. "$OT_UI_CONF"
-mkdir -p "$OB_DEST_BINDINGS">/dev/null 2>&1
-if [ ! -d "$OB_DEST_BINDINGS" ]; then
- echo "Install directory '$OB_DEST_BINDINGS' is not available! Aborting..."
- exit 1
-else
- if [ "`ls $OB_DEST_BINDINGS | wc -l`" -gt 0 ]; then
- OB_DONE=true
- fi
-fi
-
-if ! $OB_DONE ; then
- OB_SRC_DIR="$HOME/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 -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
-
+cd "$DIR"
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
deleted file mode 100755
index 64ac93a..0000000
--- a/opentox-ruby.sh
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/bin/sh
-#
-# Installs Opentox-ruby gem.
-# Author: Christoph Helma, Andreas Maunz.
-#
-
-. "`pwd`/utils.sh"
-DIR="`pwd`"
-
-if [ "$(id -u)" = "0" ]; then
- echo "This script must be run as non-root." 1>&2
- exit 1
-fi
-
-# Utils
-GIT="`which git`"
-if [ ! -e "$GIT" ]; then
- echo "'git' missing. Install 'git' first. Aborting..."
- exit 1
-fi
-
-GEM="`which gem`"
-if [ ! -e "$GEM" ]; then
- echo "'gem' missing. Install 'gem' first. Aborting..."
- exit 1
-fi
-
-RAKE="`which rake`"
-if [ ! -e "$RAKE" ]; then
- echo "'rake' missing. Install 'rake' first. Aborting..."
- exit 1
-fi
-
-
-# Pkg
-LOG="$HOME/tmp/`basename $0`-log.txt"
-
-echo
-echo "Opentox-ruby ('$LOG'):"
-
-for mygem in opentox-ruby builder jeweler; do
- if ! $GEM list | sed 's/\ .*//g' | grep -x "$mygem" >/dev/null 2>&1; then
- cmd="$GEM install $mygem" && run_cmd "$cmd" "$mygem"
- fi
-done
-
-
-servername="`hostname`"
-serverdomain="`dnsdomainname`"
-if [ -n "$serverdomain" ]; then
- servername="$servername"."$serverdomain"
-fi
-escapedserver="`echo $servername | sed 's/\/\\\//'`"
-
-if [ "$OT_BRANCH" = "development" ]; then
- logger=":logger: backtrace"
-else
- logger=""
-fi
-
-if [ "$OT_INSTALL" = "server" ]; then
- aa="https:\/\/opensso.in-silico.ch"
-else
- aa=""
-fi
-
-mkdir -p "$HOME/.opentox/config" >>$LOG 2>&1
-mkdir -p "$HOME/.opentox/log" >>$LOG 2>&1
-mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1
-
-$GIT checkout production.yaml >>$LOG 2>&1
-$GIT checkout aa-$OT_INSTALL.yaml >>$LOG 2>&1
-
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
-cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit"
-
-if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
- mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
- cd $WWW_DEST/opentox >>$LOG 2>&1
- rm -rf opentox-ruby >>$LOG 2>&1
- $GIT clone git://github.com/opentox/opentox-ruby.git >>$LOG 2>&1
- cd opentox-ruby >>$LOG 2>&1
- $GIT checkout -b $OT_BRANCH origin/$OT_BRANCH >>$LOG 2>&1
- cmd="$RAKE install" && run_cmd "$cmd" "Install"
- GEM_LIB=`$GEM which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
- rm -rf "$GEM_LIB~" >>$LOG 2>&1
- mv "$GEM_LIB" "$GEM_LIB~" >>$LOG 2>&1
- cmd="ln -sf $WWW_DEST/opentox/opentox-ruby/lib $GEM_LIB" && run_cmd "$cmd" "Linking back"
-fi
-
-cd "$DIR"
diff --git a/ot-tools-root.sh b/ot-tools-root.sh
deleted file mode 100644
index 064ea29..0000000
--- a/ot-tools-root.sh
+++ /dev/null
@@ -1,82 +0,0 @@
-# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
-# USE ONLY IF YOUR NGINX PORT IS less or equal to 1024 (PRIVILEGED)
-
-# Load server config
-otconfig() {
- source $HOME/.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 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() {
- otconfig
- otkill
- sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
- sudo bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
- sleep 2
- if ! pgrep -u root nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
- if ! pgrep -u root redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
-}
-
-# Display log
-alias otless='less $HOME/.opentox/log/production.log'
-
-# Tail log
-alias ottail='tail -f $HOME/.opentox/log/production.log'
-
-# Reload the server
-otreload() {
- otconfig
- sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
-}
-
-# Kill the server
-otkill() {
- otconfig
- sudo killall -u root nginx >/dev/null 2>&1
- sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
- while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
- while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
- for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done
-}
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
deleted file mode 100644
index 57c6c00..0000000
--- a/ot-tools-user.sh
+++ /dev/null
@@ -1,83 +0,0 @@
-# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
-# USE ONLY IF YOUR NGINX PORT IS >1024 (NOT PRIVILEGED)
-
-# Load server config
-otconfig() {
- source $HOME/.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 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() {
- otconfig
- otkill
- bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
- bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
- sleep 2
- if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
- if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
-}
-
-# Display log
-alias otless='less $HOME/.opentox/log/production.log'
-
-# Tail log
-alias ottail='tail -f $HOME/.opentox/log/production.log'
-
-# Reload the server
-otreload() {
- otconfig
- bash -c "nginx -s reload"
-}
-
-# Kill the server
-otkill() {
- otconfig
- killall nginx >/dev/null 2>&1
- bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
- while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
- while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
- for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
-}
-
diff --git a/packs.R b/packs.R
deleted file mode 100644
index b6b1930..0000000
--- a/packs.R
+++ /dev/null
@@ -1,6 +0,0 @@
-# CRAN package installer for opentox-ruby
-# AM, 2012
-
-# set mirror to avoid questioning the user
-options(repos="http://mirrors.softliste.de/cran")
-install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN"))
diff --git a/production.yaml b/production.yaml
deleted file mode 100644
index e0f39d4..0000000
--- a/production.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-:base_dir: WWW_DEST
-
-:services:
-# make sure to enter a full uri (including training slash)
- opentox-compound: "http://SERVERNAMENGINX_PORT/compound/"
- opentox-dataset: "http://SERVERNAMENGINX_PORT/dataset/"
- opentox-algorithm: "http://SERVERNAMENGINX_PORT/algorithm/"
- opentox-model: "http://SERVERNAMENGINX_PORT/model/"
- opentox-task: "http://SERVERNAMENGINX_PORT/task/"
- opentox-toxcreate: "http://SERVERNAMENGINX_PORT/toxcreate/"
- opentox-validation: "http://SERVERNAMENGINX_PORT/validation/"
- opentox-ontology: "http://apps.ideaconsult.net:8080/ontology"
-
-:json_hosts:
- - "localhost"
- - "SERVERNAME"
- - "webservices.in-silico.ch"
- - "opentox.informatik.uni-freiburg.de"
-
-:ohm_port: OHM_PORT
-
-# Uncomment for verbose logging
-LOGGER
-:logger: debug
-:backtrace: true
-
diff --git a/redis.sh b/redis.sh
deleted file mode 100755
index f07d119..0000000
--- a/redis.sh
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/bin/sh
-#
-# Installs Redis.
-# Author: Christoph Helma, Andreas Maunz.
-#
-
-. "`pwd`/utils.sh"
-DIR=`pwd`
-
-if [ "$(id -u)" = "0" ]; then
- echo "This script must be run as non-root." 1>&2
- exit 1
-fi
-
-# Utils
-WGET="`which wget`"
-if [ ! -e "$WGET" ]; then
- echo "'wget' missing. Install 'wget' first. Aborting..."
- exit 1
-fi
-
-LOG="$HOME/tmp/`basename $0`-log.txt"
-
-echo
-echo "Redis ('$LOG'):"
-
-
-REDIS_DONE=false
-mkdir "$REDIS_DEST" >/dev/null 2>&1
-if [ ! -d "$REDIS_DEST" ]; then
- echo "Install directory '$REDIS_DEST' is not available! Aborting..."
- exit 1
-else
- if ! rmdir "$REDIS_DEST" >/dev/null 2>&1; then # if not empty this will fail
- REDIS_DONE=true
- fi
-fi
-
-if ! $REDIS_DONE; then
- echo "vm.overcommit_memory = 1" | sudo tee -a /etc/sysctl.conf >>$LOG 2>&1
-
- cd $OT_PREFIX
- URI="http://redis.googlecode.com/files/redis-$REDIS_VER.tar.gz"
- if ! [ -d "redis-$REDIS_VER" ]; then
- cmd="$WGET $URI" && run_cmd "$cmd" "Download"
- cmd="tar zxf redis-$REDIS_VER.tar.gz" && run_cmd "$cmd" "Unpack"
- fi
- cd redis-$REDIS_VER >>$LOG 2>&1
- cmd="make" && run_cmd "$cmd" "Make"
-
- if ! grep "daemonize yes" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then
- echo "daemonize yes" > $REDIS_SERVER_CONF 2>$LOG
- fi
-
- if ! grep "dir `pwd`" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then
- echo "dir `pwd`" >> $REDIS_SERVER_CONF 2>$LOG
- fi
-
- if ! grep "save 900 1" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then
- echo "save 900 1" >> $REDIS_SERVER_CONF 2>$LOG
- fi
-
- if ! grep "port $OHM_PORT" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then
- echo "port $OHM_PORT" >> $REDIS_SERVER_CONF 2>$LOG
- fi
-fi
-
-if [ ! -f $REDIS_CONF ]; then
- echo "if ! echo \"\$PATH\" | grep \"$REDIS_DEST\">/dev/null 2>&1; then export PATH=$REDIS_DEST/src:\$PATH; fi" >> "$REDIS_CONF"
- echo "export OHM_PORT=$OHM_PORT" >> "$REDIS_CONF"
- echo "Redis configuration has been stored in '$REDIS_CONF'."
-
- if ! grep ". \"$REDIS_CONF\"" $OT_UI_CONF; then
- echo ". \"$REDIS_CONF\"" >> $OT_UI_CONF
- fi
-
-fi
-
-cd "$DIR"
diff --git a/ruby.sh b/ruby.sh
deleted file mode 100755
index 2e53384..0000000
--- a/ruby.sh
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/bin/sh
-#
-# Installs Ruby enterprise edition and passenger gem.
-# A configuration file is created and included in your '$OT_UI_CONF'.
-# Author: Christoph Helma, Andreas Maunz.
-#
-
-. "`pwd`/utils.sh"
-DIR="`pwd`"
-
-if [ "$(id -u)" = "0" ]; then
- echo "This script must be run as non-root." 1>&2
- exit 1
-fi
-
-# Utils
-WGET="`which wget`"
-if [ ! -e "$WGET" ]; then
- echo "'wget' missing. Install 'wget' first. Aborting..."
- exit 1
-fi
-
-# Pkg
-LOG="$HOME/tmp/`basename $0`-log.txt"
-
-echo
-echo "Ruby Enterprise edition ('$RUBY_DEST', '$LOG')."
-
-
-mkdir "$RUBY_DEST" >/dev/null 2>&1
-if [ ! -d "$RUBY_DEST" ]; then
- echo "Install directory '$RUBY_DEST' is not available! Aborting..."
- exit 1
-else
- if ! rmdir "$RUBY_DEST" >/dev/null 2>&1; then # if not empty this will fail
- RUBY_DONE=true
- fi
-fi
-
-if [ ! $RUBY_DONE ]; then
- cd $HOME/tmp
- URI="http://rubyenterpriseedition.googlecode.com/files/$RUBY_VER.tar.gz"
- if ! [ -d "$HOME/tmp/$RUBY_VER" ]; then
- cmd="$WGET $URI" && run_cmd "$cmd" "Download"
- cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack"
- fi
- cmd="sh $HOME/tmp/$RUBY_VER/installer --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install"
-fi
-
-
-
-if ! [ -f "$RUBY_CONF" ]; then
- echo "if echo \"\$PATH\" | grep -v \"$RUBY_DEST\">/dev/null 2>&1; then export PATH=\"$RUBY_DEST/bin:\$PATH\"; fi" >> "$RUBY_CONF"
-
- echo "Ruby configuration has been stored in '$RUBY_CONF'."
- if ! grep "$RUBY_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
- echo ". \"$RUBY_CONF\"" >> $OT_UI_CONF
- fi
-fi
-. "$RUBY_CONF"
-
-
-GEM="`which gem`"
-if [ ! -e "$GEM" ]; then
- echo "'gem' missing. Install 'gem' first. Aborting..."
- exit 1
-fi
-
-if [ "$PASSENGER_SKIP" != "s" ]; then
- export PATH="$RUBY_DEST/bin:$PATH"
- cmd="$GEM sources -a http://gemcutter.org" && run_cmd "$cmd" "Add Gemcutter"
- cmd="$GEM sources -a http://rubygems.org" && run_cmd "$cmd" "Add Rubygems"
- GEMCONF="gem: --no-ri --no-rdoc"
- if ! grep "$GEMCONF" $HOME/.gemrc >>$LOG 2>&1; then
- echo "$GEMCONF" | tee -a $HOME/.gemrc >>$LOG 2>&1
- fi
- if ! $GEM list | grep passenger >/dev/null 2>&1; then
- cmd="$GEM install passenger" && run_cmd "$cmd" "Install Passenger"
- fi
-
-fi
-
-cd "$DIR"
diff --git a/test-ob-rb.rb b/test-ob-rb.rb
deleted file mode 100644
index 62fda1e..0000000
--- a/test-ob-rb.rb
+++ /dev/null
@@ -1 +0,0 @@
-require 'openbabel'
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-19 14:06:17 +0000