From cd90cdd3fb486b550c2d4de65cbd11682e7aefe9 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 26 Mar 2012 16:04:47 +0200
Subject: Initial version

---
 Gemfile               |   4 ++
 Gemfile.lock          | 103 ++++++++++++++++++++++++++++++++++
 README.md             |   1 +
 application.rb        |  55 +++++++++---------
 bin/algorithm-install | 150 ++++++++++++++++++++++++++++++++------------------
 config.ru             |  10 ++--
 libfminer             |   2 +-
 7 files changed, 234 insertions(+), 91 deletions(-)
 create mode 100644 Gemfile
 create mode 100644 Gemfile.lock

diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..cbb6d62
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source :gemcutter
+
+gem 'opentox-server', :path => "~/opentox-ruby/opentox-server"
+gem "opentox-client", :path => "~/opentox-ruby/opentox-client"
diff --git a/Gemfile.lock b/Gemfile.lock
new file mode 100644
index 0000000..a6d93fe
--- /dev/null
+++ b/Gemfile.lock
@@ -0,0 +1,103 @@
+PATH
+  remote: ~/opentox-ruby/opentox-client
+  specs:
+    opentox-client (0.0.1pre)
+      bundler
+      open4
+      rdf
+      rdf-raptor
+      rest-client
+
+PATH
+  remote: ~/opentox-ruby/opentox-server
+  specs:
+    opentox-server (0.0.1pre)
+      emk-sinatra-url-for
+      opentox-client
+      rack
+      rack-contrib
+      roo
+      sinatra
+      sinatra-contrib
+      unicorn
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    addressable (2.2.7)
+    backports (2.5.0)
+    choice (0.1.5)
+    emk-sinatra-url-for (0.2.1)
+      sinatra (>= 0.9.1.1)
+    eventmachine (0.12.10)
+    faraday (0.7.6)
+      addressable (~> 2.2)
+      multipart-post (~> 1.1)
+      rack (~> 1.1)
+    ffi (1.0.11)
+    google-spreadsheet-ruby (0.1.8)
+      nokogiri (>= 1.4.3.1)
+      oauth (>= 0.3.6)
+      oauth2 (>= 0.5.0)
+    kgio (2.7.4)
+    log4r (1.1.10)
+    mime-types (1.18)
+    multi_json (1.1.0)
+    multipart-post (1.1.5)
+    nokogiri (1.5.2)
+    oauth (0.4.5)
+    oauth2 (0.5.2)
+      faraday (~> 0.7)
+      multi_json (~> 1.0)
+    open4 (1.3.0)
+    rack (1.4.1)
+    rack-contrib (1.1.0)
+      rack (>= 0.9.1)
+    rack-protection (1.2.0)
+      rack
+    rack-test (0.6.1)
+      rack (>= 1.0)
+    raindrops (0.8.0)
+    rdf (0.3.5.1)
+      addressable (>= 2.2.6)
+    rdf-raptor (0.4.1)
+      ffi (>= 1.0)
+      rdf (~> 0.3.0)
+    rest-client (1.6.7)
+      mime-types (>= 1.16)
+    roo (1.10.1)
+      choice (>= 0.1.4)
+      google-spreadsheet-ruby (>= 0.1.5)
+      nokogiri (>= 1.5.0)
+      rubyzip (>= 0.9.4)
+      spreadsheet (> 0.6.4)
+      todonotes (>= 0.1.0)
+    ruby-ole (1.2.11.3)
+    rubyzip (0.9.6.1)
+    sinatra (1.3.2)
+      rack (~> 1.3, >= 1.3.6)
+      rack-protection (~> 1.2)
+      tilt (~> 1.3, >= 1.3.3)
+    sinatra-contrib (1.3.1)
+      backports (>= 2.0)
+      eventmachine
+      rack-protection
+      rack-test
+      sinatra (~> 1.3.0)
+      tilt (~> 1.3)
+    spreadsheet (0.6.8)
+      ruby-ole (>= 1.0)
+    tilt (1.3.3)
+    todonotes (0.1.0)
+      log4r
+    unicorn (4.2.0)
+      kgio (~> 2.6)
+      rack
+      raindrops (~> 0.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  opentox-client!
+  opentox-server!
diff --git a/README.md b/README.md
index 344f747..a7fd0a4 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,7 @@ OpenTox Algorithm
 - Implements the OpenTox algorithm API for
     - fminer
     - lazar
+    - feature selection
 
 REST operations
 ---------------
diff --git a/application.rb b/application.rb
index f5b331f..b93d9fd 100644
--- a/application.rb
+++ b/application.rb
@@ -1,35 +1,32 @@
-require 'rubygems'
-# AM LAST: can include both libs, no problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
-require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb') # AM LAST
-gem "opentox-ruby", "~> 3"
-require 'opentox-ruby'
+require 'opentox-server'
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') # include before openbabel
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last') # 
+require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb')
 
-#require 'smarts.rb'
-#require 'similarity.rb'
-require 'openbabel.rb'
-require 'fminer.rb'
-require 'lazar.rb'
-require 'feature_selection.rb'
+#require 'openbabel.rb'
+#require 'fminer.rb'
+#require 'lazar.rb'
+#require 'feature_selection.rb'
 
-set :lock, true
+module OpenTox
+  class Application < Service
+    helpers do
+      def uri_list 
+        uris = [ url_for('/lazar', :full), url_for('/fminer/bbrc', :full), url_for('/fminer/last', :full), url_for('/feature_selection/rfe', :full) ]
+        uris.compact.sort.join("\n") + "\n"
+      end 
+    end
 
-before do
-	LOGGER.debug "Request: " + request.path
-end
+    get '/?' do
+      case @accept
+      when 'text/uri-list'
+        response['Content-Type'] = 'text/uri-list'
+        uri_list
+      else
+        response['Content-Type'] = 'application/rdf+xml'
+        uri_list
+      end
+    end
 
-# Get a list of available algorithms
-#
-# @return [text/uri-list] algorithm URIs
-get '/?' do
-	list = [ url_for('/lazar', :full), url_for('/fminer/bbrc', :full), url_for('/fminer/last', :full), url_for('/feature_selection/rfe', :full) ].join("\n") + "\n"
-  case request.env['HTTP_ACCEPT']
-  when /text\/html/
-    content_type "text/html"
-    OpenTox.text_to_html list,@subjectid
-  else
-    content_type 'text/uri-list'
-    list
   end
 end
diff --git a/bin/algorithm-install b/bin/algorithm-install
index 20bf847..157eeb6 100755
--- a/bin/algorithm-install
+++ b/bin/algorithm-install
@@ -2,90 +2,130 @@
 #
 # Installs Opentox Webservices.
 # Author: Christoph Helma, Andreas Maunz.
-#
-
 
+SELF=$(basename $0 -install)
 OT_PREFIX="$HOME/opentox-ruby"
+OT_CONFIG="$HOME/.opentox"
 RUBY_VER="1.9.3-p125"
 RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
+RUBY_DIR="$HOME/.rbenv/versions/$RUBY_VER"
 FMINER_BRANCH="development"
 
-if [ "$(id -u)" = "0" ]; then
-  echo "This script must be run as non-root." 1>&2
-  exit 1
-fi
+[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
 
-# Enforce main directory
+# check wd is root of service
 DIR=`pwd`
 if echo $DIR | grep "algorithm/bin" >/dev/null 2>&1 ; then cd ..; fi
 
+# check main directories present
+([ -d $OT_PREFIX ] && [ -d $OT_CONFIG ]) || (echo "Main directories missing." 1>&2 && exit 1)
+[ -d $OT_PREFIX/opentox-server ] || (echo "Warning: opentox-server missing." 1>&2)
 
-# Ruby
-. $HOME/.opentox/opentox-ui.sh 
-utils="git rbenv curl"
+# load main config
+! [ -f $OT_CONFIG/opentox-ui.sh ] && echo "Main config file missing." 1>&2 && exit 1 || . $OT_CONFIG/opentox-ui.sh 
+
+# check utils
+utils="git rbenv curl gem make"
 for u in $utils; do
-  eval `echo $u | tr "[:lower:]" "[:upper:]"`=`which $u` || (echo "'$u' missing. Install '$u' first." && exit 1)
+  eval `echo $u | tr "[:lower:]" "[:upper:]"`=`which $u` || (echo "'$u' missing. Install '$u' first." 1>&2 && exit 1)
 done
 
-
-LOG="$OT_PREFIX/tmp/`basename $0`.log"
-echo
-echo "Installation ('$LOG'):"
-
+# util functions
 run_cmd ()
 {
   local cmd="$1"; local title="$2"
-  printf "%30s" "'$title'"
+  printf "%50s" "'$title'"
   if ! eval $cmd >>$LOG 2>&1 ; then  
-    printf "%50s\n" "FAIL"
+    printf "%30s\n" "FAIL"
     echo "Last 10 lines of log:"
     tail -10 "$LOG"
     exit 1
   fi
-  printf "%50s\n" "DONE"
+  printf "%30s\n" "DONE"
 }
-
 install_ruby() {
+  printf "\n%50s\n" "RUBY"
   local DIR=`pwd`
-  [ -d $DIR/tmp ] || mkdir -p $DIR/tmp && cd $DIR/tmp
-  ([ -d $DIR/tmp/ruby-$RUBY_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_VER.tar.gz 2>/dev/null | tar xz) && cd ruby-$RUBY_VER
-  cmd="./configure --prefix=$HOME/.rbenv/versions/$RUBY_VER" && run_cmd "$cmd" "Configure"
-  cmd="make -j2" && run_cmd "$cmd" "Make"
-  cmd="make install" && run_cmd "$cmd" "Install"
-  $RBENV rehash
+  if ! [ $RBENV versions $RUBY_VER | grep $RUBY_VER>/dev/null ]; then
+    [ -d $DIR/tmp ] || mkdir -p $DIR/tmp && cd $DIR/tmp
+    ([ -d $DIR/tmp/ruby-$RUBY_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_VER.tar.gz 2>/dev/null | tar xz) && cd ruby-$RUBY_VER
+    cmd="./configure --prefix=$RUBY_DIR" && run_cmd "$cmd" "Configure"
+    cmd="make -j2" && run_cmd "$cmd" "Make"
+    [ -d $RUBY_DIR ] && rm -rf $RUBY_DIR
+    cmd="make install" && run_cmd "$cmd" "Install"
+  fi
   cd $DIR
+  cmd="$RBENV rehash" && run_cmd "$cmd" "rbenv rehash"
+  cmd="$RBENV local $RUBY_VER" && run_cmd "$cmd" "rbenv set ruby"
+}
+install_ob_ruby() {
+  printf "\n%50s\n" "OB RUBY BINDINGS"
+  local DIR=`pwd`
+  SRC_DIR=$(dirname $(find $OT_PREFIX -name openbabel-ruby.cpp))
+  [ -d "$SRC_DIR" ] || (echo "Sources not found." 1>&2 && exit 1)
+  cd $SRC_DIR
+  sed -i 's/Init_OpenBabel/Init_openbabel/g' openbabel-ruby.cpp # apply fix
+  RUBY=`which ruby`
+  cmd="$RUBY extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs" && run_cmd "$cmd" "Extconf ruby bindings"
+  cmd="$MAKE" && run_cmd "$cmd" "Make OB ruby bindings"
+  cmd="$MAKE install" && run_cmd "$cmd" "Install OB ruby bindings"
+  cd $DIR
+  cmd="$RBENV rehash" && run_cmd "$cmd" "rbenv rehash"
+}
+install_fminer() {
+  printf "\n%50s\n" "FMINER"
+  local DIR=`pwd`
+  eval RUBY_INC="-I`dirname $RUBY_DIR/include/ruby*/*linux/ruby`\ -I`dirname $RUBY_DIR/include/ruby*/ruby`"
+  eval OPBB_INC="-I`dirname $OT_PREFIX/openbabel*/include/openbabel*/openbabel`"
+  cmd="$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 $FMINER_BRANCH>>$LOG 2>&1
+  $GIT pull >>$LOG 2>&1
+  cd - >>$LOG 2>&1
+  cd "libfminer/liblast">>$LOG 2>&1
+  $GIT checkout $FMINER_BRANCH>>$LOG 2>&1
+  $GIT pull >>$LOG 2>&1
+  cd - >>$LOG 2>&1
+  for mylib in bbrc last; do
+    cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ $OPBB_INC,g' `pwd`/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)"
+    cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ $RUBY_INC,g' `pwd`/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)"
+  done
+  cd "libfminer/libbbrc">>$LOG 2>&1
+  cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
+  cd - >>$LOG 2>&1
+  cd "libfminer/liblast">>$LOG 2>&1
+  cmd="make ruby" && run_cmd "$cmd" "Make LAST"
+  cd - >>$LOG 2>&1
+  cd "last-utils">>$LOG 2>&1
+  $GIT checkout $FMINER_BRANCH>>$LOG 2>&1
+  $GIT pull >>$LOG 2>&1
+  cd $DIR
+}
+install_bundler() {
+  $GEM list | grep bundler >/dev/null 2>&1 || (cmd="$GEM install bundler" && run_cmd "$cmd" "Install bundler")
+  cmd="$RBENV rehash" && run_cmd "$cmd" "rbenv rehash"
+  BUNDLER=`which bundle`
+  cmd="$BUNDLER install" && run_cmd "$cmd" "Bundle install"
 }
 
-[ "`$RBENV local`" = "$RUBY_VER" ] || install_ruby
-$RBENV local $RUBY_VER
 
+# # # Install
 
-# fminer etc
-eval RUBY_INC="-I`dirname $HOME/.rbenv/versions/$RUBY_VER/include/ruby*/*linux/ruby`\ -I`dirname $HOME/.rbenv/versions/$RUBY_VER/include/ruby*/ruby`"
-eval OPBB_INC="-I`dirname $OT_PREFIX/openbabel*/include/openbabel*/openbabel`"
-cmd="$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 $FMINER_BRANCH>>$LOG 2>&1
-$GIT pull >>$LOG 2>&1
-cd - >>$LOG 2>&1
-cd "libfminer/liblast">>$LOG 2>&1
-$GIT checkout $FMINER_BRANCH>>$LOG 2>&1
-$GIT pull >>$LOG 2>&1
-cd - >>$LOG 2>&1
-for mylib in bbrc last; do
-  cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ $OPBB_INC,g' `pwd`/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)"
-  cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ $RUBY_INC,g' `pwd`/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)"
-done
-cd "libfminer/libbbrc">>$LOG 2>&1
-cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd - >>$LOG 2>&1
-cd "libfminer/liblast">>$LOG 2>&1
-cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd - >>$LOG 2>&1
-cd "last-utils">>$LOG 2>&1
-$GIT checkout $FMINER_BRANCH>>$LOG 2>&1
-$GIT pull >>$LOG 2>&1
+LOG="$OT_PREFIX/tmp/`basename $0`.log"
+echo
+echo "Installation ('$LOG'):"
+echo
 
-cd "$DIR"
+[ -d $OT_CONFIG/log ] || cmd="mkdir -p $OT_CONFIG/log" && run_cmd "$cmd" "Main log directory"
+[ -d $OT_CONFIG/config/$SELF ] || cmd="mkdir -p $OT_CONFIG/config/$SELF" && run_cmd "$cmd" "$SELF config directory"
+
+[ "`$RBENV local`" = "$RUBY_VER" ] || install_ruby
+[ -z `find $RUBY_DIR -name openbabel.so 2>/dev/null` ] && install_ob_ruby
+( [ -z `find libfminer/ -name bbrc.so 2>/dev/null` ] || [ -z `find libfminer/ -name last.so 2>/dev/null` ] ) && install_fminer
 
+echo
+install_bundler
+
+# return to wd
+cd "$DIR"
diff --git a/config.ru b/config.ru
index a1aab0d..2e5285d 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,4 @@
-require 'rubygems'
-require 'opentox-ruby'
-require 'config/config_ru'
-run Sinatra::Application
-set :raise_errors, false
-set :show_exceptions, false
\ No newline at end of file
+require 'bundler'
+Bundler.require
+require './application.rb'
+run OpenTox::Application
diff --git a/libfminer b/libfminer
index f9e560d..4577dca 160000
--- a/libfminer
+++ b/libfminer
@@ -1 +1 @@
-Subproject commit f9e560dc0a7a5d5af439814ab5fa9ce027a025b7
+Subproject commit 4577dcacb352af3fdca925714dc570de9e02582c
-- 
cgit v1.2.3