new gemspec generated

17 files changed, 598 insertions, 76 deletions

diff --git a/.gitignore b/.gitignore
index 00c0b86..fedf1b5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
 coverage
 rdoc
 pkg
+*~
diff --git a/Rakefile b/Rakefile
index e585ca6..d2eaf64 100644
--- a/Rakefile
+++ b/Rakefile
@@ -10,12 +10,14 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets", "do_sqlite3", "do_postgres"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
 			gem.add_dependency dep
 		end
-		gem.add_development_dependency "cucumber"
+		['cucmber','jeweler'].each do |dep|
+			gem.add_development_dependency dep
+		end
 		gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
-		gem.files.include %w(lib/tasks/owl.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/utils.rb, lib/templates/*)
+		gem.files.include %w(lib/tasks/owl.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/utils.rb, lib/validation.rb, lib/templates/*)
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
 	Jeweler::GemcutterTasks.new
diff --git a/VERSION b/VERSION
index c04c650..f0bb29e 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.2.7
+1.3.0
diff --git a/bin/opentox-install-ubuntu.sh b/bin/opentox-install-ubuntu.sh
new file mode 100755
index 0000000..75faff7
--- /dev/null
+++ b/bin/opentox-install-ubuntu.sh
@@ -0,0 +1,375 @@
+#!/bin/bash
+#Installation is tested on Debian Ubuntu 9.10
+#Update the system
+
+FAILED=0
+STARTPATH=$PWD
+ERRLOG=$PWD/'install_err.log'
+INSTALLLOG=$PWD/'install_log.log'
+DATE=$(date +%Y/%m/%d\ %H:%M:%S)
+BRANCH=$1
+GEMVERSION="1.3.5"
+GITVERSION="1.6.5.2"
+RAPTORVERSION="1.4.20"
+RASQALVERSION="0.9.16"
+RASQALVERSION2="0.9.15"
+REDLANDVERSION="1.0.7"
+REDBINDVERSION="1.0.7.1"
+
+if [ "$BRANCH" = '' ]
+then
+  echo "Please enter: sudo ./[filename] [brunchtpy]"
+  exit 1
+fi
+echo "================================================="
+echo "Selected branch is: $BRANCH"
+echo "================================================="
+echo "Please enshure that the sudo package is installed"
+echo "on your system. "
+echo "On Ubuntu Linux sudo is installed by default."
+echo "If you are unsure check with it 'sudo ls'"
+echo "and installed it with 'apt-get install sudo'"
+echo "and add your username with visudo."
+echo "================================================="
+echo "Some programs and the OpenTox webservices will be installed in the current folder."
+echo "================================================="
+echo -n "To continue installation press y: "
+read answer
+if [ "$answer" != "y" ]
+then
+  echo "exiting the script..."
+  exit 1
+fi
+
+echo "opentox webservice install log - " $DATE > $INSTALLLOG
+echo "opentox webservice install err log - " $DATE > $ERRLOG
+echo "Installing: build-essential"
+sudo apt-get install build-essential  | tee -a $INSTALLLOG
+
+echo "Installing: ruby 1.8 with its dev files"
+sudo apt-get install ruby ruby1.8-dev  | tee -a $INSTALLLOG
+
+echo "Installing: gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby sqlite3 libsqlite3-dev libsqlite3-ruby1.8 and rake"
+sudo apt-get install gems rdoc rubygems libxml-parser-ruby1.8 libxml++2.6-dev libyaml-ruby libzlib-ruby rake sqlite3 libsqlite3-dev libsqlite3-ruby1.8 | tee -a $INSTALLLOG  
+
+#RUBYGEMS
+echo "Installing rubygems from source. This may take some time"
+if [ ! -d $STARTPATH/rubygems-$GEMVERSION ]; 
+then
+	wget http://rubyforge.org/frs/download.php/60718/rubygems-$GEMVERSION.tgz >>$INSTALLLOG 2>>$ERRLOG 
+	tar xzfv rubygems-$GEMVERSION.tgz  >>$INSTALLLOG 2>>$ERRLOG
+	cd rubygems-$GEMVERSION  
+	sudo ruby setup.rb  >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm rubygems-$GEMVERSION.tgz  
+	CHECKGEM=`gem -v` 
+	if [ "$CHECKGEM"  == "$GEMVERSION" ]
+	then
+		echo "Adding http://gems.github.com to ruby gem sources"
+		sudo gem sources -a http://gems.github.com  >>$INSTALLLOG 2>>$ERRLOG
+
+		echo "================================================="
+		echo "Rubygems version $GEMVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Rubygems version $GEMVERSION installation failed."
+	    FAILED=1
+        exit $FAILED
+	fi
+else
+	echo "rubygems-$GEMVERSION folder already exist. "
+fi
+
+echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5 libopenssl-ruby libgsl0-dev swig r-base rinruby"
+sudo apt-get install zlib1g-dev tcl curl perl libopenssl-ruby libgsl0-dev r-base | tee -a $INSTALLLOG
+sudo apt-get install ssh tcl tk8.5 | tee -a $INSTALLLOG
+sudo apt-get install swig | tee -a $INSTALLLOG
+sudo apt-get install postgresql-server-dev-8.4 | tee -a $INSTALLLOG
+
+
+#echo "Installing gems jeweler sinatra emk-sinatra-url-for dm-core cehoffman-sinatra-respond_to rest-client rack-contrib thin cucumber datamapper data_objects do_sqlite3 rinruby"
+sudo gem install jeweler  | tee -a $INSTALLLOG
+sudo gem install sinatra | tee -a $INSTALLLOG
+sudo gem install emk-sinatra-url-for -s http://gems.github.com  | tee -a $INSTALLLOG
+sudo gem install dm-core  | tee -a $INSTALLLOG
+sudo gem install cehoffman-sinatra-respond_to -s http://gems.github.com  | tee -a $INSTALLLOG
+sudo gem install rest-client | tee -a $INSTALLLOG
+sudo gem install rack-contrib | tee -a $INSTALLLOG
+sudo gem install thin | tee -a $INSTALLLOG
+sudo gem install cucumber | tee -a $INSTALLLOG
+sudo gem install datamapper | tee -a $INSTALLLOG
+sudo gem install data_objects | tee -a $INSTALLLOG
+sudo gem install do_sqlite3 | tee -a $INSTALLLOG
+sudo gem install rinruby | tee -a $INSTALLLOG
+sudo gem cleanup | tee -a $INSTALLLOG
+
+echo "Installing LibRDF-ruby"
+sudo apt-get install librdf0 librdf-ruby | tee -a $INSTALLLOG
+
+#GIT
+echo "Installing git from source"
+echo "This could take a while..."
+if [ ! -d $STARTPATH/git-$GITVERSION ];  
+then
+	wget http://www.kernel.org/pub/software/scm/git/git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv git-$GITVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd git-$GITVERSION
+	./configure   >>$INSTALLLOG 2>>$ERRLOG
+	make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm git-$GITVERSION.tar.gz
+	CHECKGIT=`git --version`
+	if [ "$CHECKGIT"  == "git version $GITVERSION" ]
+	then
+		echo "================================================="
+    		echo "Git version $GITVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Git version $GITVERSION installation failed."
+	    FAILED=1
+        exit $FAILED
+	fi
+else
+	echo "git-$GITVERSION folder exists."
+fi
+
+#REDLAND
+if [ ! -d $STARTPATH/redland ];
+then
+	echo "Making Redland folder."
+	mkdir redland >>$INSTALLLOG 2>>$ERRLOG
+	cd redland
+	echo "Installing Redland raptor"
+	if [ ! -d $STARTPATH/redland/raptor-$RAPTORVERSION ];
+	then
+		wget wget http://download.librdf.org/source/raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+		tar xzfv raptor-$RAPTORVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+		cd raptor-$RAPTORVERSION
+		./configure  >>$INSTALLLOG 2>>$ERRLOG
+		sudo make   >>$INSTALLLOG 2>>$ERRLOG
+		sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+		cd ..
+		sudo rm raptor-$RAPTORVERSION.tar.gz
+		CHECKRAPTOR=`raptor-config --version`
+		if [ "$CHECKRAPTOR"  == "$RAPTORVERSION" ]
+		then
+			echo "================================================="
+			echo "Raptor version $RAPTORVERSION successfully installed."
+			echo "================================================="
+		else
+		    echo "Raptor version $RAPTORVERSION installation failed."
+		    FAILED=1
+            exit $FAILED
+		fi
+	else
+		echo "raptor-$RAPTORVERSION folder exists."
+	fi
+
+	echo "Installing Redland rasqal"
+	wget wget http://download.librdf.org/source/rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv rasqal-$RASQALVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd rasqal-$RASQALVERSION
+	./configure  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm rasqal-$RASQALVERSION.tar.gz
+	CHECKRASQAL=`rasqal-config --version`
+	if [ "$CHECKRASQAL"  == "$RASQALVERSION2" -o  "$CHECKRASQAL"  == "$RASQALVERSION" ]
+	then
+		echo "================================================="
+		echo "Raptor version $RASQALVERSION2 or higher successfully installed."
+		echo "================================================="
+	else
+	    echo "Raptor version $RASQALVERSION2 or higher installation failed."
+	    FAILED=1
+        exit $FAILED
+	fi
+
+	echo "Installing Redland redland"
+	wget wget http://download.librdf.org/source/redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv redland-$REDLANDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd redland-$REDLANDVERSION
+	./configure  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm redland-$REDLANDVERSION.tar.gz
+	CHECKREDLAND=`redland-config --version`
+	if [ "$CHECKREDLAND"  == "$REDLANDVERSION" ]
+	then
+		echo "================================================="
+		echo "Redland version $REDLANDVERSION successfully installed."
+		echo "================================================="
+	else
+	    echo "Redland version $REDLANDVERSION installation failed."
+	    FAILED=1
+        exit $FAILED
+	fi
+
+
+	echo "Installing Redland Bindings with ruby"
+	wget http://download.librdf.org/source/redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	tar xzfv redland-bindings-$REDBINDVERSION.tar.gz  >>$INSTALLLOG 2>>$ERRLOG
+	cd redland-bindings-$REDBINDVERSION
+	./configure --with-ruby  >>$INSTALLLOG 2>>$ERRLOG
+	sudo make   >>$INSTALLLOG 2>>$ERRLOG
+	sudo make install   >>$INSTALLLOG 2>>$ERRLOG
+	cd ..
+	sudo rm redland-bindings-$REDBINDVERSION.tar.gz
+	cd ..
+	#CHECKREDBIND=`??? --version`
+	#if [ "$CHECKREDBIND"  == "$REDBINDVERSION" ]
+	#then
+	#	echo "================================================="
+	#	echo "Redland Bindings version $REDBINDVERSION successfully installed."
+	#	echo "================================================="
+	#else
+	#    echo "Redland Bindings version $REDBINDVERSION installation failed."
+	#    FAILED=1
+    #    exit $FAILED
+	#fi
+else
+	echo "Redland folder exists."
+fi
+
+echo "Installing the opentox webservices"
+mkdir webservices  
+cd webservices  
+
+echo "Install the opentox-ruby-api-wrapper"
+echo "This could take a while..."
+git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$INSTALLLOG 2>>$ERRLOG
+cd opentox-ruby-api-wrapper
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+OTAPIVERSION=`cat VERSION`
+sudo rake install  | tee -a $INSTALLLOG
+cd ..
+CHECKOTAPI=`gem list | grep "opentox-ruby-api-wrapper" | grep "$OTAPIVERSION"`
+if [ ! "$CHECKOTAPI" = '' ]
+then
+	echo "================================================="
+    	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) successfully installed."
+	echo "================================================="
+else
+	echo "opentox-ruby-api-wrapper ($OTAPIVERSION) installation failed."
+	FAILED=1
+    exit $FAILED
+fi
+
+echo "Installing the webservices: compound, dataset, algorithm, model, task, feature"
+git clone git://github.com/helma/opentox-compound.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-dataset.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-algorithm.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-model.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-task.git >>$INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-feature.git >>$INSTALLLOG 2>>$ERRLOG
+
+cd opentox-compound  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG 
+cd ../opentox-dataset  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-model  
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-task
+git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
+cd ../opentox-task
+git checkout -b development origin/development >>$INSTALLLOG 2>>$ERRLOG
+cd ..  
+
+#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
+
+echo "Installing the tests"                                                   
+git clone git://github.com/helma/opentox-test.git  >>$INSTALLLOG 2>>$ERRLOG   
+cd opentox-test                                                               
+git checkout -b $BRANCH origin/$BRANCH  >>$INSTALLLOG 2>>$ERRLOG       
+
+echo "Installing openbabel"
+cd ../opentox-compound
+sudo rake openbabel:install | tee -a $INSTALLLOG
+sudo ldconfig >>$INSTALLLOG 2>>$ERRLOG
+
+ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERR
+#VERSION=` --version`
+#if [ "$VERSION"  == "$RAPTORVERSION" ]
+#then
+#	echo "================================================="
+#    	echo "Raptor version $RAPTORVERSION successfully installed."
+#	echo "================================================="
+#else
+#    echo "Raptor version $RAPTORVERSION installation failed."
+#    FAILED=1
+#    exit $FAILED
+#fi
+
+
+#check /webservices/opentox-algorithm/fminer.rb for 1,0/ture,false bug
+BUGCHECK1=`grep "@@fminer.AddActivity(true, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
+BUGCHECK2=`grep "@@fminer.AddActivity(false, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
+if [ -z "$BUGCHECK1$BUGCHECK2" ]
+then
+        echo "fminer.rb is correct."
+else
+        sed -i 's/@@fminer.AddActivity(true, id)/@@fminer.AddActivity(1, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
+        sed -i 's/@@fminer.AddActivity(false, id)/@@fminer.AddActivity(0, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
+        echo "fminer.rb updated."
+fi
+
+#todo: configure libfminer Makefile (location of ruby.h)
+#-> fixed by using davor's repository
+
+
+cd ../opentox-algorithm
+echo "Installing fminer"
+echo "This could take a while..."
+sudo updatedb
+sudo rake fminer:install | tee -a $INSTALLLOG
+cd ..
+FMINERVERSION=`ls $STARTPATH/webservices/opentox-algorithm/libfminer | grep "fminer.so"`
+if [ "$FMINERVERSION"  == "fminer.so" ]
+then
+	echo "================================================="
+    	echo "Fminer successfully installed."
+	echo "================================================="
+else
+    echo "Fminer installation failed."
+    FAILED=1
+    exit $FAILED
+fi
+
+if [ $FAILED == 0 ]
+then
+	#get username
+	echo "Please enter username:"
+	read USERNAME
+
+	#change rights from root to user
+	sudo chown -R $USERNAME: $STARTPATH/webservices/
+	sudo chown -R $USERNAME: ~/.opentox/
+fi
+
+if [ "$FAILED" == "1" ]
+then
+	echo "================================================="
+    	echo "Installation script failed!"
+	echo "================================================="
+    	exit 1
+else
+echo "================================================="
+echo "opentox-install-script is completed."
+echo "================================================="
+echo "Configuration:"
+echo "Edit the settings in $HOME/.opentox/config/{development|production|test}.yaml for your environment."
+echo "================================================="
+echo "Start the webservices local:"
+echo "cd webservices/opentox-test/"
+echo "rake opentox:services:start"
+echo "================================================="
+echo "Test local webservices:"
+echo "rake features"
+echo "================================================="
+fi
+exit 0
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 25ae4cb..817340f 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,27 +1,35 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 module OpenTox
-	module Algorithm 
+  module Algorithm 
 
-		class Fminer 
-			include Owl
+    class Fminer 
+      include Owl
 
-			def initialize
-				super
-				self.uri = File.join(@@config[:services]["opentox-algorithm"],'fminer')
-				self.title = "fminer"
-				self.source = "http://github.com/amaunz/libfminer"
-				self.parameters = {
-					"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
-					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
-				}
-			end
+      def initialize
+        super
+        self.uri = File.join(@@config[:services]["opentox-algorithm"],'fminer')
+        self.title = "fminer"
+        self.source = "http://github.com/amaunz/libfminer"
+        self.parameters = {
+          "Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
+          "Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
+        }
+      end
+
+      def self.create_feature_dataset(params)
+				LOGGER.debug File.basename(__FILE__) + ": creating feature dataset"
+        resource = RestClient::Resource.new(params[:feature_generation_uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+        resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
+      end
 
-			def self.create_feature_dataset(params)
-				RestClient.post params[:feature_generation_uri], :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri] 
+			def self.uri
+				File.join(@@config[:services]["opentox-algorithm"], "fminer")
 			end
-		end
+    end
 
-		class Lazar 
-			include Owl
+    class Lazar 
+      include Owl
 
 			def initialize
 				super
@@ -40,26 +48,33 @@ module OpenTox
 			
 			def self.create_model(params)
 				LOGGER.debug params
-				@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
+				LOGGER.debug File.basename(__FILE__) + ": creating model"
+				#@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
+        resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+        @uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
 			end
 
-		end
-
-		class Similarity
-			def self.weighted_tanimoto(fp_a,fp_b,p)
-				common_features = fp_a & fp_b
-				all_features = fp_a + fp_b
-				common_p_sum = 0.0
-				if common_features.size > 0
-					common_features.each{|f| common_p_sum += p[f]}
-					all_p_sum = 0.0
-					all_features.each{|f| all_p_sum += p[f]}
-					common_p_sum/all_p_sum
-				else
-					0.0
-				end
+			def self.uri
+				File.join(@@config[:services]["opentox-algorithm"], "lazar")
 			end
-		end
 
-	end
+    end
+
+    class Similarity
+      def self.weighted_tanimoto(fp_a,fp_b,p)
+        common_features = fp_a & fp_b
+        all_features = fp_a + fp_b
+        common_p_sum = 0.0
+        if common_features.size > 0
+          common_features.each{|f| common_p_sum += p[f]}
+          all_p_sum = 0.0
+          all_features.each{|f| all_p_sum += p[f]}
+          common_p_sum/all_p_sum
+        else
+          0.0
+        end
+      end
+    end
+
+  end
 end
diff --git a/lib/authorization.rb b/lib/authorization.rb
new file mode 100644
index 0000000..9a1760a
--- /dev/null
+++ b/lib/authorization.rb
@@ -0,0 +1,24 @@
+helpers do
+ 
+  def protected!
+    response['WWW-Authenticate'] = %(Basic realm="Opentox Webservice Authentication") and \
+    throw(:halt, [401, "Not authorized\n"]) and \
+    return unless authorized?
+  end
+ 
+  def authorized?
+    @auth ||= Rack::Auth::Basic::Request.new(request.env)
+    @auth.provided? && @auth.basic? && @auth.credentials && valid_user?
+  end
+  
+  def valid_user?
+    users = @@users[:users]
+    return @auth.credentials == [@auth.username, users.fetch(@auth.username)] if users.has_key?(@auth.username)
+    return false
+  end
+ 
+end
+ 
+before do
+  #protected! unless env['REQUEST_METHOD'] == "GET"
+end
diff --git a/lib/compound.rb b/lib/compound.rb
index 56646c0..0ee853d 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -17,7 +17,8 @@ module OpenTox
 				@inchi = sdf2inchi(params[:sdf])
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:name]
-				@inchi = RestClient.get("#{@@cactus_uri}#{params[:name]}/stdinchi").chomp
+				# paranoid URI encoding to keep SMILES charges and brackets
+				@inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@uri = params[:uri]
diff --git a/lib/config/config_ru.rb b/lib/config/config_ru.rb
index 3720ef3..1d32c7e 100644
--- a/lib/config/config_ru.rb
+++ b/lib/config/config_ru.rb
@@ -10,6 +10,7 @@ $stdout.reopen(log)
 $stderr.reopen(log)
 $stdout.sync = true
 $stderr.sync = true
+set :logging, false
 set :raise_errors, true 
 
 ['public','tmp'].each do |dir|
diff --git a/lib/dataset.rb b/lib/dataset.rb
index bd523a3..b5b2e06 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -1,3 +1,5 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 module OpenTox
 
 	class Dataset 
@@ -14,6 +16,8 @@ module OpenTox
 			data_entry = @model.subject OT['compound'], compound
 			if data_entry.nil?
 				data_entry = @model.create_resource
+				dataset = @model.subject(RDF['type'],OT[self.owl_class])
+				@model.add dataset, OT['dataEntry'], data_entry
 				@model.add data_entry, RDF['type'], OT["DataEntry"]
 				@model.add data_entry, OT['compound'], compound
 			end
@@ -29,6 +33,8 @@ module OpenTox
 			data_entry = @model.subject OT['compound'], compound
 			if data_entry.nil?
 				data_entry = @model.create_resource
+				dataset = @model.subject(RDF['type'],OT[self.owl_class])
+				@model.add dataset, OT['dataEntry'], data_entry
 				@model.add data_entry, RDF['type'], OT["DataEntry"]
 				@model.add data_entry, OT['compound'], compound
 			end
@@ -57,7 +63,7 @@ module OpenTox
 		def find_or_create_compound(uri)
 			compound = @model.subject(DC["identifier"], uri)
 			if compound.nil?
-				compound = @model.create_resource
+				compound = @model.create_resource(uri)
 				@model.add compound, RDF['type'], OT["Compound"]
 				@model.add compound, DC["identifier"], uri
 			end
@@ -68,7 +74,7 @@ module OpenTox
 		def find_or_create_feature(uri)
 			feature = @model.subject(DC["identifier"], uri)
 			if feature.nil?
-				feature = @model.create_resource
+				feature = @model.create_resource(uri)
 				@model.add feature, RDF['type'], OT["Feature"]
 				@model.add feature, DC["identifier"], uri
 				@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
@@ -78,7 +84,8 @@ module OpenTox
 		end
 
 		def self.create(data, content_type = 'application/rdf+xml')
-      uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
+      resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])		  
+		  uri = resource.post data, :content_type => content_type
 			dataset = Dataset.new
 			dataset.read uri.to_s
 			dataset
@@ -86,7 +93,9 @@ module OpenTox
 
 		def self.find(uri)
 			dataset = Dataset.new
+			LOGGER.debug "Getting data from #{uri}"
 			data = `curl "#{uri}"`
+			#LOGGER.debug data
 			#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
 			dataset.rdf = data
 			dataset
@@ -152,11 +161,24 @@ module OpenTox
 
 		# Delete a dataset
 		def delete
-			RestClient.delete @uri
-		end
+  		resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+      resource.delete
+    end
 
 		def save
-			RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
+			LOGGER.debug "Saving dataset"
+			#task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
+      task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.rdf, :content_type =>  "application/rdf+xml").to_s		
+			task = OpenTox::Task.find(task_uri)
+			LOGGER.debug "Waiting for task #{task_uri}"
+			task.wait_for_completion
+			LOGGER.debug "Dataset task #{task_uri} completed"
+			if task.failed?
+				LOGGER.error "Saving dataset failed"
+				task.failed
+				exit
+			end
+			task.resource
 		end
 
 		def to_yaml
diff --git a/lib/environment.rb b/lib/environment.rb
index fedc3cf..9338ca5 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -6,6 +6,7 @@ ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
 basedir = File.join(ENV['HOME'], ".opentox")
 config_dir = File.join(basedir, "config")
 config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
+user_file = File.join(config_dir, "users.yaml")
 
 TMP_DIR = File.join(basedir, "tmp")
 LOG_DIR = File.join(basedir, "log")
@@ -15,6 +16,7 @@ if File.exist?(config_file)
 else
 	FileUtils.mkdir_p TMP_DIR
 	FileUtils.mkdir_p LOG_DIR
+	FileUtils.mkdir_p config_dir
 	FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/config.yaml'), config_file)
 	puts "Please edit #{config_file} and restart your application."
 	exit
@@ -43,6 +45,21 @@ logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
 LOGGER = Logger.new(logfile,'daily') # daily rotation
 LOGGER.level = Logger::DEBUG
 
+if File.exist?(user_file)
+  @@users = YAML.load_file(user_file)
+else
+  FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/users.yaml'), user_file)
+  puts "Please edit #{user_file} and restart your application."
+  exit
+end
+
+begin
+  0 < @@users[:users].keys.length
+rescue
+  puts "Please edit #{user_file} and restart your application. Create at least one user with password."
+  exit
+end
+
 # RDF namespaces
 RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
 OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
diff --git a/lib/model.rb b/lib/model.rb
index a585b59..b5129d7 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -24,7 +24,7 @@ module OpenTox
 				lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
 				lazar.trainingDataset = yaml[:activity_dataset]
 				lazar.dependentVariables = yaml[:endpoint]
-				lazar.predictedVariables = yaml[:endpoint] #+ " lazar prediction"
+				lazar.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
 				lazar
 			end
 
@@ -39,15 +39,25 @@ module OpenTox
 			
 			# Predict a compound
 			def predict(compound)
-				RestClient.post(@uri, :compound_uri => compound.uri)
+				# nicht absichern??
+				resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+				resource.post(:compound_uri => compound.uri)
 			end
 
 			def self.base_uri
-				@@config[:services]["opentox-model"]
+				File.join @@config[:services]["opentox-model"],'lazar'
 			end
 
 			def self.create(data)
-				RestClient.post(@@config[:services]["opentox-model"], data, :content_type => "application/x-yaml").to_s
+			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			  resource.post(data, :content_type => "application/x-yaml").to_s
+			end
+
+			def delete
+			  resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+				resource.delete
+				#RestClient.delete @uri if @uri
+				#RestClient.delete model.task_uri if model.task_uri
 			end
 
 #			def self.create(task)
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index ca57fc9..849043c 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -8,6 +8,6 @@ rescue LoadError
 	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
 end
 
-['owl', 'compound','dataset','algorithm','model','task','utils'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization'].each do |lib|
 	require lib
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index a843e59..82d6e0e 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -16,7 +16,6 @@ module OpenTox
 			# reate an anonymous resource for metadata
 			# this has to be rewritten with an URI as soon as the resource has been saved at an definitive location
 			tmp = @model.create_resource
-			@model.add tmp, RDF['type'], OWL['Ontology']
 			@model.add tmp, RDF['type'], OT[self.owl_class]
 		end
 
diff --git a/lib/task.rb b/lib/task.rb
index 70d22bf..f507a22 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -1,3 +1,5 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 module OpenTox
 
 	class Task
@@ -10,7 +12,10 @@ module OpenTox
 		end
 
 		def self.create
-			uri = RestClient.post @@config[:services]["opentox-task"], {}
+			#uri = RestClient.post @@config[:services]["opentox-task"], {}
+      resource = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			#uri = resource.post(nil)
+			uri = resource.post({})
 			Task.new(uri)
 		end
 
@@ -26,7 +31,7 @@ module OpenTox
 			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
 			task_uris.collect{|uri| Task.new(uri)}
 		end
-		 
+
 		def created_at
 			RestClient.get File.join(@uri, 'created_at')
 		end
@@ -42,7 +47,24 @@ module OpenTox
 		def resource
 			RestClient.get File.join(@uri, 'resource')
 		end
+		 
+		def started
+      LOGGER.info File.join(@uri,'started')
+      resource = RestClient::Resource.new(File.join(@uri,'started'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+      resource.put({}) 
+		end
+
+		def cancel
+			resource = RestClient::Resource.new(@File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put({})
+		end
+
+		def completed(uri)
+			resource = RestClient::Resource.new(File.join(@uri,'completed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put :resource => uri
+		end
 
+=begin
 		def started
 			RestClient.put File.join(@uri,'started'), {}
 		end
@@ -51,20 +73,27 @@ module OpenTox
 			RestClient.put File.join(@uri,'cancelled'), {}
 		end
 
-		def failed
-			RestClient.put File.join(@uri,'failed'), {}
+		def completed(uri)
+			RestClient.put File.join(@uri,'completed'), :resource => uri
 		end
 
-		def parent=(task)
-			RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
+=end
+		def failed
+			#RestClient.put File.join(@uri,'failed'), {}
+			resource = RestClient::Resource.new(@File.join(@uri,'failed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put({})
 		end
 
-		def completed(uri)
-			RestClient.put File.join(@uri,'completed'), :resource => uri
+		def parent=(task)
+			#RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
+			resource = RestClient::Resource.new(File.join(@uri,'parent'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			LOGGER.debug "task.rb: #{resource}"
+			resource.put :uri => task.uri
 		end
 		 
 		def pid=(pid)
-			RestClient.put File.join(@uri, 'pid'), :pid => pid
+		  resource = RestClient::Resource.new(File.join(@uri,'pid'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put :pid => pid
 		end
 
 		def completed?
diff --git a/lib/templates/users.yaml b/lib/templates/users.yaml
new file mode 100644
index 0000000..483fd7b
--- /dev/null
+++ b/lib/templates/users.yaml
@@ -0,0 +1,5 @@
+# please insert users and passwords here.
+# one user and password each line. uncomment the line.
+:users:
+# username: "secretpassword"
+# exampleuser: "ih9aiTog"
\ No newline at end of file
diff --git a/lib/validation.rb b/lib/validation.rb
new file mode 100644
index 0000000..6fd5704
--- /dev/null
+++ b/lib/validation.rb
@@ -0,0 +1,21 @@
+module OpenTox
+	class Validation
+
+		attr_accessor :uri
+
+		def initialize(params)
+			resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			@uri = resource.post(params).to_s
+		end
+		
+		def self.crossvalidation(params)
+			params[:uri] = File.join(@@config[:services]['opentox-validation'], "crossvalidation")
+      params[:num_folds] = 10 unless params[:num_folds]
+		 	params[:random_seed] = 2 unless params[:random_seed]
+		 	params[:stratified] = false unless params[:stratified]
+			OpenTox::Validation.new(params)
+		end
+
+	end
+end
+
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 75f5d6b..9500df4 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.2.7"
+  s.version = "1.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2010-02-08}
+  s.date = %q{2010-03-01}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
-  s.executables = ["opentox-install-debian.sh", "yaml2owl.rb"]
+  s.executables = ["opentox-install-ubuntu.sh", "opentox-install-debian.sh", "yaml2owl.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -23,11 +23,12 @@ Gem::Specification.new do |s|
      "Rakefile",
      "VERSION",
      "bin/opentox-install-debian.sh",
+     "bin/opentox-install-ubuntu.sh",
      "bin/yaml2owl.rb",
      "lib/algorithm.rb",
+     "lib/authorization.rb",
      "lib/compound.rb",
      "lib/config/config_ru.rb",
-     "lib/config/database.rb",
      "lib/dataset.rb",
      "lib/environment.rb",
      "lib/helper.rb",
@@ -39,7 +40,9 @@ Gem::Specification.new do |s|
      "lib/task.rb",
      "lib/tasks/opentox.rb",
      "lib/templates/config.yaml",
-     "lib/utils.rb"
+     "lib/templates/users.yaml",
+     "lib/utils.rb",
+     "lib/validation.rb"
   ]
   s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper}
   s.rdoc_options = ["--charset=UTF-8"]
@@ -63,9 +66,8 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<dm-more>, [">= 0"])
       s.add_runtime_dependency(%q<dm-core>, [">= 0"])
       s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"])
-      s.add_runtime_dependency(%q<do_sqlite3>, [">= 0"])
-      s.add_runtime_dependency(%q<do_postgres>, [">= 0"])
-      s.add_development_dependency(%q<cucumber>, [">= 0"])
+      s.add_development_dependency(%q<cucmber>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
     else
       s.add_dependency(%q<sinatra>, [">= 0"])
       s.add_dependency(%q<rest-client>, [">= 0"])
@@ -78,9 +80,8 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<dm-more>, [">= 0"])
       s.add_dependency(%q<dm-core>, [">= 0"])
       s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
-      s.add_dependency(%q<do_sqlite3>, [">= 0"])
-      s.add_dependency(%q<do_postgres>, [">= 0"])
-      s.add_dependency(%q<cucumber>, [">= 0"])
+      s.add_dependency(%q<cucmber>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
     end
   else
     s.add_dependency(%q<sinatra>, [">= 0"])
@@ -94,9 +95,8 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<dm-more>, [">= 0"])
     s.add_dependency(%q<dm-core>, [">= 0"])
     s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
-    s.add_dependency(%q<do_sqlite3>, [">= 0"])
-    s.add_dependency(%q<do_postgres>, [">= 0"])
-    s.add_dependency(%q<cucumber>, [">= 0"])
+    s.add_dependency(%q<cucmber>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
   end
 end