From 68ff57c18f9f2f737ecdd8e5c60f42aa2f925416 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Sat, 13 Aug 2011 08:39:22 +0200 Subject: Fixed variance to population --- lib/algorithm.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 3cf4ecf..90049dc 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -923,7 +923,7 @@ module OpenTox # @param [Array] Array to test, must indicate non-occurrence with 0. # @return [Boolean] Whether the feature has variance zero. def self.zero_variance?(array) - return (array.to_scale.variance_sample == 0.0) + return (array.to_scale.variance_population == 0.0) end # Sum of an array for Arrays. -- cgit v1.2.3 From ed3a1a1d85fd6b3d1e00f3193cdbfe9bfbe8866c Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Sat, 13 Aug 2011 08:44:17 +0200 Subject: Checking for metadata nil --- lib/serializer.rb | 42 ++++++++++++++++++++++-------------------- 1 file changed, 22 insertions(+), 20 deletions(-) diff --git a/lib/serializer.rb b/lib/serializer.rb index 03dcf1f..7fe4a3e 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -268,28 +268,30 @@ module OpenTox # @param [Hash] metadata def add_metadata(uri,metadata) id = 0 - metadata.each do |u,v| - #if v.is_a? Array and (u == OT.parameters or u == RDF.type) - if v.is_a? Array and u == OT.parameters#or u == RDF.type) - @object[uri][u] = [] unless @object[uri][u] - v.each do |value| - id+=1 - genid = "_:genid#{id}" - @object[uri][u] << {"type" => "bnode", "value" => genid} - @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] } - value.each do |name,entry| - @object[genid][name] = [{"type" => type(entry), "value" => entry }] - end - end - elsif v.is_a? Array #and u == RDF.type - @object[uri] = {} unless @object[uri] - v.each do |value| + if !metadata.nil? + metadata.each do |u,v| + #if v.is_a? Array and (u == OT.parameters or u == RDF.type) + if v.is_a? Array and u == OT.parameters#or u == RDF.type) @object[uri][u] = [] unless @object[uri][u] - @object[uri][u] << {"type" => type(value), "value" => value } + v.each do |value| + id+=1 + genid = "_:genid#{id}" + @object[uri][u] << {"type" => "bnode", "value" => genid} + @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] } + value.each do |name,entry| + @object[genid][name] = [{"type" => type(entry), "value" => entry }] + end + end + elsif v.is_a? Array #and u == RDF.type + @object[uri] = {} unless @object[uri] + v.each do |value| + @object[uri][u] = [] unless @object[uri][u] + @object[uri][u] << {"type" => type(value), "value" => value } + end + elsif v.is_a? String + @object[uri] = {} unless @object[uri] + @object[uri][u] = [{"type" => type(v), "value" => v }] end - elsif v.is_a? String - @object[uri] = {} unless @object[uri] - @object[uri][u] = [{"type" => type(v), "value" => v }] end end end -- cgit v1.2.3 From ec7faee0180f61e2d1254a67cb9bff7eb95db78d Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Sat, 13 Aug 2011 08:45:46 +0200 Subject: Checking for metadata nil --- lib/opentox.rb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/lib/opentox.rb b/lib/opentox.rb index c76e21a..3ad6f6a 100644 --- a/lib/opentox.rb +++ b/lib/opentox.rb @@ -31,12 +31,14 @@ module OpenTox end def add_metadata(metadata) - metadata.each do |k,v| - if v.is_a? Array - @metadata[k] = [] unless @metadata[k] - @metadata[k] << v - else - @metadata[k] = v + if !metadata.nil? + metadata.each do |k,v| + if v.is_a? Array + @metadata[k] = [] unless @metadata[k] + @metadata[k] << v + else + @metadata[k] = v + end end end end -- cgit v1.2.3 From 5eab9794b1f0df0921b51f1aa4009e24f3db21a4 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 16 Aug 2011 12:12:51 +0000 Subject: old installation scripts removed --- bin/opentox-install-debian.sh | 105 ------------ bin/opentox-install-ubuntu.sh | 375 ------------------------------------------ 2 files changed, 480 deletions(-) delete mode 100644 bin/opentox-install-debian.sh delete mode 100755 bin/opentox-install-ubuntu.sh diff --git a/bin/opentox-install-debian.sh b/bin/opentox-install-debian.sh deleted file mode 100644 index cf173da..0000000 --- a/bin/opentox-install-debian.sh +++ /dev/null @@ -1,105 +0,0 @@ -#!/bin/bash -#Installation is tested on Debian Lenny Ubuntu 9.04 -#Update the system - -ERRLOG='install_err.log' -INSTALLLOG='install_log.log' -DATE=$(date +%Y/%m/%d\ %H:%M:%S) - -echo "=================================================" -echo "Please enshure that the sudo package is installed" -echo "on your system. " -echo "On Ubuntu Linux sudo is installed by default." -echo "If you are unshure check with it 'sudo ls'" -echo "and installed it with 'apt-get install sudo'" -echo "and add your username with visudo." -echo "=================================================" -echo -n "To continue installation press y: " -read answer -if [ "$answer" != "y" ] -then - echo "exiting the script..." - exit 1 -fi - -echo "opentox webservice install log - " $DATE > $INSTALLLOG -echo "Installing: build-essential" -sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG -echo "Installing: ruby 1.8 with its dev files" -sudo apt-get install ruby ruby1.8-dev >> $INSTALLLOG 2>>$ERRLOG -echo "Installing: gems rdoc rubygems and rake" -sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG - -echo "Installing rubygems from source. This may take some time" -wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG -tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG -cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG -sudo ruby setup.rb 2>>$ERRLOG -cd .. - -echo "Adding http://gems.github.com to ruby gem sources" -sudo gem sources -a http://gems.github.com >> $INSTALLLOG 2>>$ERRLOG - -#for debian lenny: -echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5" -sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5 >> $INSTALLLOG 2>>$ERRLOG -echo "Installing git from source" -wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG -tar xzfv git-1.6.5.2.tar.gz 2>>$ERRLOG -cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG -./configure 2>>$ERRLOG -make 2>>$ERRLOG -make install 2>>$ERRLOG - -echo "Installing the opentox webservices" -mkdir webservices >> $INSTALLLOG 2>>$ERRLOG -cd webservices >> $INSTALLLOG 2>>$ERRLOG - -git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG -git clone git://github.com/helma/opentox-feature.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-test.git >> $INSTALLLOG 2>>$ERRLOG - -cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -cd .. >> $INSTALLLOG 2>>$ERRLOG -git clone git://github.com/helma/opentox-ruby-api-wrapper.git >> $INSTALLLOG 2>>$ERRLOG -cd opentox-ruby-api-wrapper >> $INSTALLLOG 2>>$ERRLOG -git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG -rake install >> $INSTALLLOG 2>>$ERRLOG - - -cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG -echo "Installing libopenssl-ruby" -sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG -echo "Installing dtach" -rake dtach:install >> $INSTALLLOG 2>>$ERRLOG -echo "Installing openbabel" -rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG - -#debian lenny missed liblink: -ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG - -rake redis:download >> $INSTALLLOG 2>>$ERRLOG -rake redis:install >> $INSTALLLOG 2>>$ERRLOG -#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices -sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG -sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG -sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG -cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG -echo "Installing fminer" -rake fminer:install >> $INSTALLLOG 2>>$ERRLOG -sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG - - -mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG diff --git a/bin/opentox-install-ubuntu.sh b/bin/opentox-install-ubuntu.sh deleted file mode 100755 index ae4807d..0000000 --- a/bin/opentox-install-ubuntu.sh +++ /dev/null @@ -1,375 +0,0 @@ -#!/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 sinatra-respond_to | 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 -- cgit v1.2.3 From 46d1fa0469d6b6f9c7ec184fcef0c41cbd3b8a9b Mon Sep 17 00:00:00 2001 From: mr Date: Wed, 17 Aug 2011 12:42:51 +0200 Subject: A&A add missing subjectids --- lib/authorization.rb | 2 +- lib/dataset.rb | 4 ++-- lib/helper.rb | 2 +- lib/model.rb | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/lib/authorization.rb b/lib/authorization.rb index 288733a..8023f60 100644 --- a/lib/authorization.rb +++ b/lib/authorization.rb @@ -216,7 +216,7 @@ module OpenTox LOGGER.debug "OpenTox::Authorization.delete_policy policy: #{policy} with token: #{subjectid}" return true if resource.delete(:subjectid => subjectid, :id => policy) rescue - return nil + return false end end diff --git a/lib/dataset.rb b/lib/dataset.rb index 5ebad0f..4102e18 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -84,12 +84,12 @@ module OpenTox copy YAML.load(yaml) end - def load_rdfxml(rdfxml) + def load_rdfxml(rdfxml, subjectid=nil) raise "rdfxml data is empty" if rdfxml.to_s.size==0 file = Tempfile.new("ot-rdfxml") file.puts rdfxml file.close - load_rdfxml_file file + load_rdfxml_file file, subjectid file.delete end diff --git a/lib/helper.rb b/lib/helper.rb index 33774b4..d255b08 100644 --- a/lib/helper.rb +++ b/lib/helper.rb @@ -30,9 +30,9 @@ helpers do def clean_uri(uri) uri = uri.sub(" ", "%20") #dirty hacks => to fix uri = uri[0,uri.index("InChI=")] if uri.index("InChI=") - out = URI.parse(uri) out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/) #cuts after /id/ for a&a + out.path = out.path.split('.').first #cut extension port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}" "#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #" end diff --git a/lib/model.rb b/lib/model.rb index 8a07858..8548e47 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -199,7 +199,7 @@ module OpenTox count += 1 waiting_task.progress( count/d.compounds.size.to_f*100.0 ) if waiting_task rescue => ex - LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message + LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message+" subjectid: #{subjectid}" end end #@prediction_dataset.save(subjectid) @@ -225,7 +225,7 @@ module OpenTox } ) end - if OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type == "regression" + if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "regression" all_activities = [] all_activities = @activities.values.flatten.collect! { |i| i.to_f } @prediction_min_max[0] = (all_activities.to_scale.min/2) -- cgit v1.2.3 From 89b583fbc8e2493bcfd912bed72b8a80d4d2474d Mon Sep 17 00:00:00 2001 From: mguetlein Date: Mon, 22 Aug 2011 11:23:49 +0200 Subject: unify cookies --- lib/environment.rb | 5 +++++ lib/helper.rb | 31 ++++++++++++++++++++++++++++++- lib/to-html.rb | 5 ++--- 3 files changed, 37 insertions(+), 4 deletions(-) diff --git a/lib/environment.rb b/lib/environment.rb index 6d1bb85..ccd5c9e 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -74,6 +74,11 @@ CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorizatio CONFIG[:authorization][:authorize_request] = [""] unless CONFIG[:authorization][:authorize_request] CONFIG[:authorization][:free_request] = [""] unless CONFIG[:authorization][:free_request] +cookie_secret = CONFIG[:authorization] ? CONFIG[:authorization][:cookie_secret] : nil +cookie_secret = cookie_secret ? cookie_secret : "ui6vaiNi-change_me" +use Rack::Session::Cookie, :expire_after => 28800, + :secret => cookie_secret + RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#' DC = OwlNamespace.new 'http://purl.org/dc/elements/1.1/' diff --git a/lib/helper.rb b/lib/helper.rb index 33774b4..da77945 100644 --- a/lib/helper.rb +++ b/lib/helper.rb @@ -1,4 +1,34 @@ helpers do + + def login(username, password) + logout + session[:subjectid] = OpenTox::Authorization.authenticate(username, password) + #LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s + if session[:subjectid] != nil + session[:username] = username + return session[:subjectid] + else + session[:username] = "" + return nil + end + end + + def logout + if session[:subjectid] != nil + session[:subjectid] = nil + session[:username] = "" + return true + end + return false + end + + def logged_in() + return true if !AA_SERVER + if session[:subjectid] != nil + return OpenTox::Authorization.is_token_valid(session[:subjectid]) + end + return false + end # Authentification def protected!(subjectid) @@ -56,7 +86,6 @@ helpers do subjectid = session[:subjectid] if session[:subjectid] subjectid = params[:subjectid] if params[:subjectid] and !subjectid subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !subjectid - subjectid = request.cookies["subjectid"] unless subjectid # see http://rack.rubyforge.org/doc/SPEC.html subjectid = CGI.unescape(subjectid) if subjectid.include?("%23") @subjectid = subjectid diff --git a/lib/to-html.rb b/lib/to-html.rb index 2979062..519688f 100644 --- a/lib/to-html.rb +++ b/lib/to-html.rb @@ -111,7 +111,7 @@ module OpenTox end get '/sign_out/?' do - response.set_cookie("subjectid",{:value=>nil}) + logout content_type "text/html" content = "Sucessfully signed out from "+$url_provider.url_for("",:full) OpenTox.text_to_html(content) @@ -123,9 +123,8 @@ get '/sign_in/?' do end post '/sign_in/?' do - subjectid = OpenTox::Authorization.authenticate(params[:user], params[:password]) + subjectid = login(params[:user], params[:password]) if (subjectid) - response.set_cookie("subjectid",{:value=>subjectid}) content_type "text/html" content = "Sucessfully signed in as '"+params[:user]+"' to "+$url_provider.url_for("",:full) OpenTox.text_to_html(content,subjectid) -- cgit v1.2.3 From 7789591f370c290c265fce0d2103652b6c55687b Mon Sep 17 00:00:00 2001 From: opentox Date: Mon, 22 Aug 2011 09:34:56 +0000 Subject: carcinogen/non-carcinogen added to TRUE|FALSE Regexp --- lib/environment.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/environment.rb b/lib/environment.rb index 6d1bb85..8745c54 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -40,8 +40,8 @@ else end # Regular expressions for parsing classification data -TRUE_REGEXP = /^(true|active|1|1.0|tox|activating)$/i -FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating)$/i +TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen)$/i +FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen)$/i # Task durations DEFAULT_TASK_MAX_DURATION = 36000 -- cgit v1.2.3 From 1e6bf954fb9cbc8a8aad9af3d6f653f79e0f401a Mon Sep 17 00:00:00 2001 From: mguetlein Date: Mon, 22 Aug 2011 12:12:52 +0200 Subject: adjust sign in/out messages --- lib/to-html.rb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/lib/to-html.rb b/lib/to-html.rb index 519688f..678ef29 100644 --- a/lib/to-html.rb +++ b/lib/to-html.rb @@ -33,10 +33,10 @@ module OpenTox user = OpenTox::Authorization.get_user(subjectid) if subjectid html += "
"
       unless user
-        html += "You are currently not signed in to "+$url_provider.url_for("",:full)+
+        html += "You are currently not signed in to "+$url_provider.request.host.to_s+
           ", sign in"
       else
-        html += "You are signed in as '#{user}' to "+$url_provider.url_for("",:full)+
+        html += "You are signed in as '#{user}' to "+$url_provider.request.host.to_s+
           ", sign out"
       end
       html += "
" @@ -61,7 +61,7 @@ module OpenTox html += "
" html += "
"
     html += msg+"\n\n" if msg
-    html += "Please sign in to "+$url_provider.url_for("",:full)+"\n\n"
+    html += "Please sign in to "+$url_provider.request.host.to_s+"\n\n"
     html += ""
     html += ""+
           ""+
@@ -113,7 +113,8 @@ end
 get '/sign_out/?' do
   logout
   content_type "text/html"
-  content = "Sucessfully signed out from "+$url_provider.url_for("",:full)
+  content = "Sucessfully signed out from "+$url_provider.request.host.to_s+" ( Back to "+
+      $url_provider.url_for("",:full)+" )"
   OpenTox.text_to_html(content)
 end
 
@@ -126,7 +127,8 @@ post '/sign_in/?' do
   subjectid = login(params[:user], params[:password])
   if (subjectid)
     content_type "text/html"
-    content = "Sucessfully signed in as '"+params[:user]+"' to "+$url_provider.url_for("",:full)
+    content = "Sucessfully signed in as '"+params[:user]+"' to "+$url_provider.request.host.to_s+" ( Back to "+
+      $url_provider.url_for("",:full)+" )"
     OpenTox.text_to_html(content,subjectid)    
   else
     content_type "text/html"
-- 
cgit v1.2.3


From cb2170529708deb0f711383040aa0ff174d35a36 Mon Sep 17 00:00:00 2001
From: Christoph Helma 
Date: Mon, 22 Aug 2011 16:23:56 +0000
Subject: rdfxml of prediction features fixed

---
 lib/feature.rb    | 11 +++++++++++
 lib/model.rb      |  4 ++--
 lib/opentox.rb    |  1 -
 lib/serializer.rb |  8 +++++++-
 4 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/lib/feature.rb b/lib/feature.rb
index 4ba58ce..0099d41 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -42,4 +42,15 @@ module OpenTox
       end
     end    
   end
+
+  # Get OWL-DL representation in RDF/XML format
+  # @return [application/rdf+xml] RDF/XML representation
+  def to_rdfxml
+    s = Serializer::Owl.new
+    s.add_feature(@uri,@metadata)
+    @metadata.values.grep(/model\/\d+$/).each{ |m| s.add_uri(m,OT.Model)}
+    @metadata.values.grep(/feature/).each{ |f| s.add_uri(f,OT.Feature)}
+    #s.add_parameters(@uri,@parameters) if @parameters
+    s.to_rdfxml
+  end
 end
diff --git a/lib/model.rb b/lib/model.rb
index 8548e47..e9e0b09 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -385,7 +385,7 @@ module OpenTox
         dependent_uri = @metadata[OT.dependentVariables].first
         feature = OpenTox::Feature.new File.join( @uri, "predicted", "value")
         feature.add_metadata( {
-          RDF.type => [OT.ModelPrediction],
+          RDF.type => OT.ModelPrediction,
           OT.hasSource => @uri,
           DC.creator => @uri,
           DC.title => URI.decode(File.basename( dependent_uri )),
@@ -398,7 +398,7 @@ module OpenTox
         dependent_uri = @metadata[OT.dependentVariables].first
         feature = OpenTox::Feature.new File.join( @uri, "predicted", "confidence")
         feature.add_metadata( {
-          RDF.type => [OT.ModelPrediction],
+          RDF.type => OT.ModelPrediction,
           OT.hasSource => @uri,
           DC.creator => @uri,
           DC.title => "#{URI.decode(File.basename( dependent_uri ))} confidence"
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 3ad6f6a..14704ec 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -48,7 +48,6 @@ module OpenTox
   def to_rdfxml
     s = Serializer::Owl.new
     s.add_metadata(@uri,@metadata)
-    #s.add_parameters(@uri,@parameters) if @parameters
     s.to_rdfxml
   end
 
diff --git a/lib/serializer.rb b/lib/serializer.rb
index 9fc034d..87de036 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -21,6 +21,7 @@ module OpenTox
           OT.NominalFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.NumericFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.StringFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
+          OT.ModelPrediction => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.Dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.DataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
           OT.FeatureValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
@@ -69,6 +70,7 @@ module OpenTox
           OT.validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.crossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
           OT.dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
+          OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
 
           DC.title => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           DC.identifier => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
@@ -131,7 +133,7 @@ module OpenTox
           OT.actor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
           OT.errorCode => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
 
-          OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
+          #OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           OT.paramScope => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
           #OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
@@ -216,6 +218,10 @@ module OpenTox
         @@content_id = 1
         add_content uri, content
       end
+
+      def add_uri(uri,type)
+        @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => type }] }
+      end
       
       private
       @@content_id = 1
-- 
cgit v1.2.3


From 067cf2332b85b29ed8054ab249322f8ae2345c2b Mon Sep 17 00:00:00 2001
From: mr 
Date: Tue, 23 Aug 2011 12:46:33 +0200
Subject: optimize helper

---
 lib/helper.rb | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/helper.rb b/lib/helper.rb
index 76226e5..ce13ff1 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -90,10 +90,12 @@ helpers do
       subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
       @subjectid = subjectid
     rescue
-      subjectid = nil
+      @subjectid = nil
     end
   end
   def get_extension
+    @accept = request.env['HTTP_ACCEPT']
+    @accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
     extension = File.extname(request.path_info)
     unless extension.empty?
       case extension.gsub(".","")
@@ -107,6 +109,8 @@ helpers do
         @accept = 'application/rdf+xml'
       when "xls"
         @accept = 'application/ms-excel'
+      when "sdf"
+        @accept = 'chemical/x-mdl-sdfile'
       when "css"
         @accept = 'text/css'
       else
@@ -117,8 +121,8 @@ helpers do
 end
 
 before do 
-  @subjectid = get_subjectid()
-  @accept = get_extension()
+  get_subjectid()
+  get_extension()
   unless !AA_SERVER or login_requests or CONFIG[:authorization][:free_request].include?(env['REQUEST_METHOD'])
     protected!(@subjectid)
   end
-- 
cgit v1.2.3


From 64ab23142ffb068c8b901c73ec227ca484d9efb6 Mon Sep 17 00:00:00 2001
From: mr 
Date: Wed, 24 Aug 2011 11:20:32 +0200
Subject: quickfix to flatten error

---
 lib/feature.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/feature.rb b/lib/feature.rb
index 0099d41..6d14444 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -23,9 +23,9 @@ module OpenTox
     # @return [String] feature type, unknown if OT.isA property is unknown/ not set
     def feature_type
       raise OpenTox::BadRequestError.new("rdf type of feature '"+uri.to_s+"' not set") unless metadata[RDF.type]
-      if metadata[RDF.type].flatten.include?(OT.NominalFeature)
+      if metadata[RDF.type].to_a.flatten.include?(OT.NominalFeature)
         "classification"
-      elsif metadata[RDF.type].flatten.include?(OT.NumericFeature)
+      elsif metadata[RDF.type].to_a.flatten.include?(OT.NumericFeature)
         "regression"
       elsif metadata[OWL.sameAs]
         metadata[OWL.sameAs].each do |f|
-- 
cgit v1.2.3


From 5550566e7c72afd6d70d2d2180b780ffa876a691 Mon Sep 17 00:00:00 2001
From: Christoph Helma 
Date: Wed, 24 Aug 2011 16:07:15 +0000
Subject: datasets stored as json (with Yajl) to improve performance

---
 lib/dataset.rb | 35 +++++++++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 4 deletions(-)

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 4102e18..8061153 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -46,6 +46,12 @@ module OpenTox
       dataset.save(subjectid)
       dataset
     end
+
+    def self.from_json(json, subjectid=nil) 
+      dataset = Dataset.new(nil,subjectid)
+      dataset.copy_hash Yajl::Parser.parse(json)
+      dataset
+    end
     
     # Find a dataset and load all data. This can be time consuming, use Dataset.new together with one of the load_* methods for a fine grained control over data loading.
     # @param [String] uri Dataset URI
@@ -84,6 +90,10 @@ module OpenTox
       copy YAML.load(yaml)
     end
 
+    def load_json(json)
+      copy_hash Yajl::Parser.parse(json)
+    end
+
     def load_rdfxml(rdfxml, subjectid=nil)
       raise "rdfxml data is empty" if rdfxml.to_s.size==0
       file = Tempfile.new("ot-rdfxml")
@@ -146,7 +156,7 @@ module OpenTox
     # Load all data (metadata, data_entries, compounds and features) from URI
     def load_all(subjectid=nil)
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
+        copy_hash Yajl::Parser.parse(RestClientWrapper.get(@uri, {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
         copy parser.load_uri(subjectid)
@@ -170,7 +180,7 @@ module OpenTox
     # @return [Hash]  Features of the dataset
     def load_features(subjectid=nil)
       if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-        @features = YAML.load(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/x-yaml", :subjectid => subjectid}))
+        @features = Yajl::Parser.parse(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
         @features = parser.load_features(subjectid)
@@ -203,6 +213,10 @@ module OpenTox
 =begin
 =end
 
+    def to_json
+      Yajl::Encoder.encode({:uri => @uri, :metadata => @metadata, :data_entries => @data_entries, :compounds => @compounds, :features => @features})
+    end
+
     # Get Spreadsheet representation
     # @return [Spreadsheet::Workbook] Workbook which can be written with the spreadsheet gem (data_entries only, metadata will will be discarded))
     def to_spreadsheet
@@ -359,11 +373,11 @@ module OpenTox
       @compounds.uniq!
       if @uri
         if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
+          #LOGGER.debug self.to_json
+          RestClientWrapper.post(@uri,self.to_json,{:content_type =>  "application/json", :subjectid => subjectid})
         else
           File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
           task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp
-          #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset`
           Task.find(task_uri).wait_for_completion
           self.uri = RestClientWrapper.get(task_uri,{:accept => 'text/uri-list', :subjectid => subjectid})
         end
@@ -379,6 +393,19 @@ module OpenTox
       RestClientWrapper.delete(@uri, :subjectid => subjectid)
     end
 
+    # Copy a hash (eg. from JSON) into a dataset (rewrites URI)
+    def copy_hash(hash)
+      @metadata = hash["metadata"]
+      @data_entries = hash["data_entries"]
+      @compounds = hash["compounds"]
+      @features = hash["features"]
+      if @uri
+        self.uri = @uri 
+      else
+        @uri = hash["metadata"][XSD.anyURI]
+      end
+    end
+
     private
     # Copy a dataset (rewrites URI)
     def copy(dataset)
-- 
cgit v1.2.3


From b4e4ac6a6eee4d05144de7447091e27f624325d4 Mon Sep 17 00:00:00 2001
From: Christoph Helma 
Date: Thu, 25 Aug 2011 10:41:37 +0000
Subject: json store for models

---
 lib/model.rb | 45 +++++++++++++++++++++++++++++++++++++++------
 1 file changed, 39 insertions(+), 6 deletions(-)

diff --git a/lib/model.rb b/lib/model.rb
index e9e0b09..42e5b92 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -11,7 +11,7 @@ module OpenTox
     def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
         if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
-          accept_header = 'application/x-yaml' 
+          accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
         end
@@ -144,7 +144,7 @@ module OpenTox
       # @param [String] uri Model URI
       # @return [OpenTox::Model::Lazar] lazar model
       def self.find(uri, subjectid=nil)
-        YAML.load RestClientWrapper.get(uri,{:accept => 'application/x-yaml', :subjectid => subjectid})
+        OpenTox::Model::Lazar.from_json RestClientWrapper.get(uri,{:accept => 'application/json', :subjectid => subjectid})
       end
 
       # Create a new lazar model
@@ -157,10 +157,42 @@ module OpenTox
         OpenTox::Model::Lazar.find(model_uri, subjectid)      
       end
 
+      def self.from_json(json)
+        hash = Yajl::Parser.parse(json)
+        #LOGGER.debug hash.to_yaml
+        lazar = OpenTox::Model::Lazar.new
+        #hash.each { |k,v| eval("lazar.#{k} = #{v}") }
+        lazar.uri = hash["uri"] if hash["uri"]
+        lazar.metadata = hash["metadata"] if hash["metadata"]
+        lazar.compound = hash["compound"] if hash["compound"]
+        lazar.prediction_dataset = hash["prediction_dataset"] if hash["prediction_dataset"]
+        lazar.features = hash["features"] if hash["features"]
+        lazar.effects = hash["effects"] if hash["effects"]
+        lazar.activities = hash["activities"] if hash["activities"]
+        lazar.p_values = hash["p_values"] if hash["p_values"]
+        lazar.fingerprints = hash["fingerprints"] if hash["fingerprints"]
+        lazar.feature_calculation_algorithm = hash["feature_calculation_algorithm"] if hash["feature_calculation_algorithm"]
+        lazar.similarity_algorithm = hash["similarity_algorithm"] if hash["similarity_algorithm"]
+        lazar.prediction_algorithm = hash["prediction_algorithm"] if hash["prediction_algorithm"]
+        lazar.min_sim = hash["min_sim"] if hash["min_sim"]
+        lazar.subjectid = hash["subjectid"] if hash["subjectid"]
+        lazar.prop_kernel = hash["prop_kernel"] if hash["prop_kernel"]
+        lazar.value_map = hash["value_map"] if hash["value_map"]
+        lazar.nr_hits = hash["nr_hits"] if hash["nr_hits"]
+        lazar.transform = hash["transform"] if hash["transform"]
+        lazar.conf_stdev = hash["conf_stdev"] if hash["conf_stdev"]
+        lazar.prediction_min_max = hash["prediction_min_max"] if hash["prediction_min_max"]
+        lazar
+      end
+
+      def to_json
+        Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :min_sim => @min_sim, :subjectid => @subjectid, :prop_kernel => @prop_kernel, :value_map => @value_map, :nr_hits => @nr_hits, :transform => @transform, :conf_stdev => @conf_stdev, :prediction_min_max => @prediction_min_max})
+      end
+
       def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
         if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
-          accept_header = 'application/x-yaml' 
+          accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
         end
@@ -215,6 +247,7 @@ module OpenTox
         @compound = Compound.new compound_uri
         features = {}
 
+        #LOGGER.debug self.to_yaml
         unless @prediction_dataset
           @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
           @prediction_dataset.add_metadata( {
@@ -255,7 +288,7 @@ module OpenTox
           @prediction_dataset.metadata[OT.predictedVariables] = [value_feature_uri, confidence_feature_uri] unless @prediction_dataset.metadata[OT.predictedVariables] 
 
           if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification"
-            @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction]]
+            @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction].to_s]
           else
             @prediction_dataset.add @compound.uri, value_feature_uri, prediction[:prediction]
           end
@@ -365,7 +398,7 @@ module OpenTox
       def database_activity(subjectid)
         if @activities[@compound.uri]
           if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification"
-            @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act] }
+            @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act.to_s] }
           else
             @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], act }
           end
@@ -408,7 +441,7 @@ module OpenTox
 
       # Save model at model service
       def save(subjectid)
-        self.uri = RestClientWrapper.post(@uri,self.to_yaml,{:content_type =>  "application/x-yaml", :subjectid => subjectid})
+        self.uri = RestClientWrapper.post(@uri,self.to_json,{:content_type =>  "application/json", :subjectid => subjectid})
       end
 
       # Delete model at model service
-- 
cgit v1.2.3


From d408d94cb03f8254ab6cdfb84f3f557d1ca5e536 Mon Sep 17 00:00:00 2001
From: Christoph Helma 
Date: Fri, 26 Aug 2011 13:32:48 +0000
Subject: yaml_hosts changed to json_hosts

---
 lib/dataset.rb | 6 +++---
 lib/feature.rb | 2 +-
 lib/model.rb   | 4 ++--
 lib/task.rb    | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 8061153..0911073 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -155,7 +155,7 @@ module OpenTox
 
     # Load all data (metadata, data_entries, compounds and features) from URI
     def load_all(subjectid=nil)
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
         copy_hash Yajl::Parser.parse(RestClientWrapper.get(@uri, {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
@@ -179,7 +179,7 @@ module OpenTox
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
     def load_features(subjectid=nil)
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
         @features = Yajl::Parser.parse(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/json", :subjectid => subjectid}))
       else
         parser = Parser::Owl::Dataset.new(@uri, subjectid)
@@ -372,7 +372,7 @@ module OpenTox
       # TODO: rewrite feature URI's ??
       @compounds.uniq!
       if @uri
-        if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+        if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
           #LOGGER.debug self.to_json
           RestClientWrapper.post(@uri,self.to_json,{:content_type =>  "application/json", :subjectid => subjectid})
         else
diff --git a/lib/feature.rb b/lib/feature.rb
index 6d14444..55ac678 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -10,7 +10,7 @@ module OpenTox
     def self.find(uri, subjectid=nil)
       return nil unless uri   
       feature = Feature.new uri
-      if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(uri).host))
         feature.add_metadata YAML.load(RestClientWrapper.get(uri,{:accept => "application/x-yaml", :subjectid => subjectid}))
       else
         feature.add_metadata  Parser::Owl::Dataset.new(uri).load_metadata
diff --git a/lib/model.rb b/lib/model.rb
index 42e5b92..0b116c2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -10,7 +10,7 @@ module OpenTox
     # @return [text/uri-list] Task or resource URI
     def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
-        if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
+        if CONFIG[:json_hosts].include?(URI.parse(@uri).host)
           accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
@@ -191,7 +191,7 @@ module OpenTox
 
       def run( params, accept_header=nil, waiting_task=nil )
       unless accept_header
-        if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)
+        if CONFIG[:json_hosts].include?(URI.parse(@uri).host)
           accept_header = 'application/json' 
         else
           accept_header = 'application/rdf+xml'
diff --git a/lib/task.rb b/lib/task.rb
index dbcbe59..e6fa5e1 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -182,7 +182,7 @@ module OpenTox
     end
 
     def load_metadata
-      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+      if (CONFIG[:json_hosts].include?(URI.parse(@uri).host))
         result = RestClientWrapper.get(@uri, {:accept => 'application/x-yaml'}, nil, false)
         @metadata = YAML.load result.to_s
         @http_code = result.code
@@ -209,7 +209,7 @@ module OpenTox
 
     def reload( accept_header=nil )
       unless accept_header 
-        if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host))
+        if (CONFIG[:json_hosts].include?(URI.parse(uri).host))
           accept_header = "application/x-yaml"
         else
           accept_header = 'application/rdf+xml'
-- 
cgit v1.2.3


From 811ced6dfe7178ee985043f8ef9e304140158f96 Mon Sep 17 00:00:00 2001
From: Christoph Helma 
Date: Fri, 26 Aug 2011 15:16:50 +0000
Subject: (non-)mutagenic added to TRUE|FALSE REGEXP

---
 lib/environment.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/environment.rb b/lib/environment.rb
index 35500f7..09830b8 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -40,8 +40,8 @@ else
 end
 
 # Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen)$/i
-FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen)$/i
+TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
 
 # Task durations
 DEFAULT_TASK_MAX_DURATION = 36000
-- 
cgit v1.2.3


From d0ea360e353aacff9eabfe97882726134aec19c1 Mon Sep 17 00:00:00 2001
From: mr 
Date: Wed, 14 Sep 2011 09:37:52 +0200
Subject: register model to ontology service|ECHA Endpoints from ontology
 service

---
 lib/environment.rb |  2 ++
 lib/ontology.rb    | 61 ++++++++++++++++++++++++++++++++++++++++++------------
 2 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/lib/environment.rb b/lib/environment.rb
index 09830b8..3775797 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -74,6 +74,8 @@ CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorizatio
 CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
 CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
 
+ONTOLOGY_SERVER = CONFIG[:services]["opentox-ontology"] ? CONFIG[:services]["opentox-ontology"] : "http://apps.ideaconsult.net:8080/ontology"
+
 cookie_secret =  CONFIG[:authorization] ? CONFIG[:authorization][:cookie_secret] : nil 
 cookie_secret = cookie_secret ? cookie_secret : "ui6vaiNi-change_me"
 use Rack::Session::Cookie, :expire_after => 28800, 
diff --git a/lib/ontology.rb b/lib/ontology.rb
index fa4ea6f..ca957af 100644
--- a/lib/ontology.rb
+++ b/lib/ontology.rb
@@ -1,11 +1,9 @@
 module OpenTox
   module Ontology
     module Echa
-=begin
-      require 'sparql/client'
-      @sparql = SPARQL::Client.new("http://apps.ideaconsult.net:8080/ontology")
-      def self.qs(classname="Endpoints")
-        return "PREFIX ot:
+
+      def self.querystring(classname="Endpoints")
+        return CGI.escape("PREFIX ot:
         PREFIX ota:
         PREFIX owl:
         PREFIX dc:
@@ -17,29 +15,44 @@ module OpenTox
           where {
             ?endpoint  rdfs:subClassOf  otee:#{classname}.
             ?endpoint dc:title ?title.
-          }"
+          }")
       end
       
       def self.make_option_list(endpoint="Endpoints", level=1)
-        out = ""
-        results = @sparql.query(qs(endpoint)) rescue results = []
+      out = ""
+        results = echa_endpoints(endpoint) rescue results = []
         results.each do |result|
-          endpointname = result.Endpoints.to_s.split('#').last
-          title = result.bound?(:title) ? result.title : endpointname     
-          out += "\n"
+          r = result.split(',')
+          endpointname = r.first.split("#").last
+          title = r[1..r.size-1]
+          out += "\n"
           out += make_option_list(endpointname, level + 1)
         end
         return out
       end
     
-      def self.get_endpoint_selectlist(include_blank=true)
+      def self.endpoint_option_list(include_blank=true)
         out = "\n"
         return out
       end
-=end
+
+      # Gets Endpoints of specific level from ontology service
+      # Top level with endpoint="Endpoints"
+      # e.G. Ecotoxic effects endpoints with  endpoint="EcotoxicEffects"
+      # if ontology service is not reachable it returns an empty array
+      # @param [String] endpoint
+      # @return [Array] of endpoints: e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects,Ecotoxic effects"
+      def self.echa_endpoints(endpoint)
+        begin
+          RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{querystring(endpoint)}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.match(/^http/)}.uniq.compact.sort
+        rescue
+          LOGGER.warn "OpenTox::Ontology::Echa.echa_endpoints ontology service is not reachable."
+          []
+        end
+      end
 
       def self.endpoints
         RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/query/ndatasets_endpoint",:accept => "text/csv").collect { |line| line.split(',').first if line.match(/^http/) }.compact
@@ -51,5 +64,27 @@ module OpenTox
 
     end
 
+    # Register an OpenTox resource into ontology service
+    # @param [String] uri, URI of recource to register
+    # @param [String] subjectid
+    def self.register(uri, subjectid=nil)
+      begin
+        RestClientWrapper.post(ONTOLOGY_SERVER, {:uri => uri}, {:subjectid => CGI.escape(subjectid)})
+      rescue
+        false
+      end
+    end
+
+    # Unregister an OpenTox resource into ontology service
+    # @param [String] uri, URI of recource to unregister
+    # @param [String] subjectid
+    def self.unregister(uri, subjectid=nil)
+      begin
+        RestClientWrapper.delete("#{ONTOLOGY_SERVER}?uri=#{CGI.escape(uri)}", {:subjectid => CGI.escape(subjectid)})
+      rescue
+        false
+      end
+    end
+
   end
 end
-- 
cgit v1.2.3


From bd726758d25e44b74b694fb15ac6f348bf350c76 Mon Sep 17 00:00:00 2001
From: mr 
Date: Wed, 14 Sep 2011 15:30:34 +0200
Subject: load json prettifing gem

---
 lib/serializer.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/serializer.rb b/lib/serializer.rb
index 87de036..3a19bf0 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -1,5 +1,6 @@
 require 'spreadsheet'
 require 'yajl'
+require 'yajl/json_gem'
 
 module OpenTox
 
-- 
cgit v1.2.3


From 7727060f8642bd26f837392b2069d89365eadee8 Mon Sep 17 00:00:00 2001
From: mr 
Date: Tue, 20 Sep 2011 13:36:41 +0200
Subject: fix syntax for yard documentation

---
 lib/serializer.rb | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/serializer.rb b/lib/serializer.rb
index 3a19bf0..b62ac45 100644
--- a/lib/serializer.rb
+++ b/lib/serializer.rb
@@ -227,16 +227,16 @@ module OpenTox
       private
       @@content_id = 1
       
-      # Recursiv function to add content
-      # @example
-      # { DC.description => "bla",
-      #   OT.similar_resources => [ "http://uri1", "http://uri2" ],
-      #   OT.matrixCells => 
-      #     [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" },
-      #       { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ],
-      #   OT.info => { RDF.type => OT.ImportantInfo, 
-      #                DC.description => "blub" }
-      # } 
+      #Recursiv function to add content
+      #@example
+      #  { DC.description => "bla",
+      #    OT.similar_resources => [ "http://uri1", "http://uri2" ],
+      #    OT.matrixCells =>
+      #      [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" },
+      #        { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ],
+      #    OT.info => { RDF.type => OT.ImportantInfo,
+      #                 DC.description => "blub" }
+      #  }
       # @param [String] uri
       # @param [Hash] content as hash, uri must already have been added to @object
       def add_content(uri, hash)
-- 
cgit v1.2.3


From 4fc797d5b7869f9d386df2b823168ff76f1359e6 Mon Sep 17 00:00:00 2001
From: mr 
Date: Tue, 20 Sep 2011 13:38:56 +0200
Subject: feature: model registration to ontology service

---
 lib/ontology.rb | 87 ++++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 67 insertions(+), 20 deletions(-)

diff --git a/lib/ontology.rb b/lib/ontology.rb
index ca957af..ad7ba7b 100644
--- a/lib/ontology.rb
+++ b/lib/ontology.rb
@@ -17,7 +17,7 @@ module OpenTox
             ?endpoint dc:title ?title.
           }")
       end
-      
+
       def self.make_option_list(endpoint="Endpoints", level=1)
       out = ""
         results = echa_endpoints(endpoint) rescue results = []
@@ -30,7 +30,7 @@ module OpenTox
         end
         return out
       end
-    
+
       def self.endpoint_option_list(include_blank=true)
         out = "
user:
password: