opentox-ruby-api-wrapper 1.2.7 → 1.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Rakefile +5 -3
- data/VERSION +1 -1
- data/bin/opentox-install-ubuntu.sh +375 -0
- data/lib/algorithm.rb +51 -36
- data/lib/authorization.rb +24 -0
- data/lib/compound.rb +2 -1
- data/lib/config/config_ru.rb +1 -0
- data/lib/dataset.rb +28 -6
- data/lib/environment.rb +17 -0
- data/lib/model.rb +14 -4
- data/lib/opentox-ruby-api-wrapper.rb +1 -1
- data/lib/owl.rb +0 -1
- data/lib/task.rb +38 -9
- data/lib/templates/users.yaml +5 -0
- data/lib/validation.rb +21 -0
- metadata +12 -18
- data/lib/config/database.rb +0 -21
data/Rakefile
CHANGED
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@@ -10,12 +10,14 @@ begin
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gem.email = "helma@in-silico.ch"
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gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
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gem.authors = ["Christoph Helma"]
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-
["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "
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["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
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gem.add_dependency dep
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end
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-
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['cucumber','jeweler', "thin"].each do |dep|
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gem.add_development_dependency dep
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end
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gem.files = FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
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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/*)
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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/*)
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# gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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end
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Jeweler::GemcutterTasks.new
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
1.
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1
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1.3.0
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@@ -0,0 +1,375 @@
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#!/bin/bash
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#Installation is tested on Debian Ubuntu 9.10
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#Update the system
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FAILED=0
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STARTPATH=$PWD
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ERRLOG=$PWD/'install_err.log'
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INSTALLLOG=$PWD/'install_log.log'
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DATE=$(date +%Y/%m/%d\ %H:%M:%S)
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BRANCH=$1
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GEMVERSION="1.3.5"
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GITVERSION="1.6.5.2"
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RAPTORVERSION="1.4.20"
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RASQALVERSION="0.9.16"
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RASQALVERSION2="0.9.15"
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REDLANDVERSION="1.0.7"
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REDBINDVERSION="1.0.7.1"
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if [ "$BRANCH" = '' ]
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then
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echo "Please enter: sudo ./[filename] [brunchtpy]"
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exit 1
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fi
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echo "================================================="
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echo "Selected branch is: $BRANCH"
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echo "================================================="
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echo "Please enshure that the sudo package is installed"
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echo "on your system. "
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echo "On Ubuntu Linux sudo is installed by default."
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echo "If you are unsure check with it 'sudo ls'"
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echo "and installed it with 'apt-get install sudo'"
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echo "and add your username with visudo."
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echo "================================================="
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echo "Some programs and the OpenTox webservices will be installed in the current folder."
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echo "================================================="
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echo -n "To continue installation press y: "
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read answer
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if [ "$answer" != "y" ]
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then
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echo "exiting the script..."
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exit 1
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fi
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echo "opentox webservice install log - " $DATE > $INSTALLLOG
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echo "opentox webservice install err log - " $DATE > $ERRLOG
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echo "Installing: build-essential"
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sudo apt-get install build-essential | tee -a $INSTALLLOG
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echo "Installing: ruby 1.8 with its dev files"
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sudo apt-get install ruby ruby1.8-dev | tee -a $INSTALLLOG
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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"
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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
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#RUBYGEMS
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echo "Installing rubygems from source. This may take some time"
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if [ ! -d $STARTPATH/rubygems-$GEMVERSION ];
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then
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wget http://rubyforge.org/frs/download.php/60718/rubygems-$GEMVERSION.tgz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv rubygems-$GEMVERSION.tgz >>$INSTALLLOG 2>>$ERRLOG
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cd rubygems-$GEMVERSION
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sudo ruby setup.rb >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm rubygems-$GEMVERSION.tgz
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CHECKGEM=`gem -v`
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if [ "$CHECKGEM" == "$GEMVERSION" ]
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then
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echo "Adding http://gems.github.com to ruby gem sources"
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sudo gem sources -a http://gems.github.com >>$INSTALLLOG 2>>$ERRLOG
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echo "================================================="
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echo "Rubygems version $GEMVERSION successfully installed."
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echo "================================================="
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else
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echo "Rubygems version $GEMVERSION installation failed."
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FAILED=1
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exit $FAILED
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fi
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else
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echo "rubygems-$GEMVERSION folder already exist. "
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fi
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echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5 libopenssl-ruby libgsl0-dev swig r-base rinruby"
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sudo apt-get install zlib1g-dev tcl curl perl libopenssl-ruby libgsl0-dev r-base | tee -a $INSTALLLOG
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sudo apt-get install ssh tcl tk8.5 | tee -a $INSTALLLOG
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sudo apt-get install swig | tee -a $INSTALLLOG
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sudo apt-get install postgresql-server-dev-8.4 | tee -a $INSTALLLOG
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#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"
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sudo gem install jeweler | tee -a $INSTALLLOG
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sudo gem install sinatra | tee -a $INSTALLLOG
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sudo gem install emk-sinatra-url-for -s http://gems.github.com | tee -a $INSTALLLOG
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sudo gem install dm-core | tee -a $INSTALLLOG
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sudo gem install cehoffman-sinatra-respond_to -s http://gems.github.com | tee -a $INSTALLLOG
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sudo gem install rest-client | tee -a $INSTALLLOG
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sudo gem install rack-contrib | tee -a $INSTALLLOG
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sudo gem install thin | tee -a $INSTALLLOG
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sudo gem install cucumber | tee -a $INSTALLLOG
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sudo gem install datamapper | tee -a $INSTALLLOG
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sudo gem install data_objects | tee -a $INSTALLLOG
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sudo gem install do_sqlite3 | tee -a $INSTALLLOG
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sudo gem install rinruby | tee -a $INSTALLLOG
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sudo gem cleanup | tee -a $INSTALLLOG
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echo "Installing LibRDF-ruby"
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sudo apt-get install librdf0 librdf-ruby | tee -a $INSTALLLOG
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#GIT
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echo "Installing git from source"
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echo "This could take a while..."
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if [ ! -d $STARTPATH/git-$GITVERSION ];
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then
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wget http://www.kernel.org/pub/software/scm/git/git-$GITVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv git-$GITVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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cd git-$GITVERSION
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./configure >>$INSTALLLOG 2>>$ERRLOG
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make >>$INSTALLLOG 2>>$ERRLOG
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sudo make install >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm git-$GITVERSION.tar.gz
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CHECKGIT=`git --version`
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if [ "$CHECKGIT" == "git version $GITVERSION" ]
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then
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echo "================================================="
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echo "Git version $GITVERSION successfully installed."
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echo "================================================="
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else
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echo "Git version $GITVERSION installation failed."
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FAILED=1
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exit $FAILED
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fi
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else
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echo "git-$GITVERSION folder exists."
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fi
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#REDLAND
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if [ ! -d $STARTPATH/redland ];
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then
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echo "Making Redland folder."
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mkdir redland >>$INSTALLLOG 2>>$ERRLOG
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cd redland
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echo "Installing Redland raptor"
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if [ ! -d $STARTPATH/redland/raptor-$RAPTORVERSION ];
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then
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wget wget http://download.librdf.org/source/raptor-$RAPTORVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv raptor-$RAPTORVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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cd raptor-$RAPTORVERSION
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./configure >>$INSTALLLOG 2>>$ERRLOG
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sudo make >>$INSTALLLOG 2>>$ERRLOG
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sudo make install >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm raptor-$RAPTORVERSION.tar.gz
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CHECKRAPTOR=`raptor-config --version`
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if [ "$CHECKRAPTOR" == "$RAPTORVERSION" ]
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then
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echo "================================================="
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echo "Raptor version $RAPTORVERSION successfully installed."
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echo "================================================="
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else
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echo "Raptor version $RAPTORVERSION installation failed."
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FAILED=1
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exit $FAILED
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fi
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else
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echo "raptor-$RAPTORVERSION folder exists."
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fi
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echo "Installing Redland rasqal"
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wget wget http://download.librdf.org/source/rasqal-$RASQALVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv rasqal-$RASQALVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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cd rasqal-$RASQALVERSION
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./configure >>$INSTALLLOG 2>>$ERRLOG
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sudo make >>$INSTALLLOG 2>>$ERRLOG
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sudo make install >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm rasqal-$RASQALVERSION.tar.gz
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CHECKRASQAL=`rasqal-config --version`
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if [ "$CHECKRASQAL" == "$RASQALVERSION2" -o "$CHECKRASQAL" == "$RASQALVERSION" ]
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then
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echo "================================================="
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echo "Raptor version $RASQALVERSION2 or higher successfully installed."
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echo "================================================="
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else
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echo "Raptor version $RASQALVERSION2 or higher installation failed."
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FAILED=1
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exit $FAILED
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fi
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echo "Installing Redland redland"
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wget wget http://download.librdf.org/source/redland-$REDLANDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv redland-$REDLANDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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cd redland-$REDLANDVERSION
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./configure >>$INSTALLLOG 2>>$ERRLOG
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sudo make >>$INSTALLLOG 2>>$ERRLOG
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sudo make install >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm redland-$REDLANDVERSION.tar.gz
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CHECKREDLAND=`redland-config --version`
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if [ "$CHECKREDLAND" == "$REDLANDVERSION" ]
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then
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echo "================================================="
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echo "Redland version $REDLANDVERSION successfully installed."
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echo "================================================="
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else
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echo "Redland version $REDLANDVERSION installation failed."
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FAILED=1
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exit $FAILED
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fi
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echo "Installing Redland Bindings with ruby"
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wget http://download.librdf.org/source/redland-bindings-$REDBINDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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tar xzfv redland-bindings-$REDBINDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
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cd redland-bindings-$REDBINDVERSION
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./configure --with-ruby >>$INSTALLLOG 2>>$ERRLOG
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sudo make >>$INSTALLLOG 2>>$ERRLOG
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sudo make install >>$INSTALLLOG 2>>$ERRLOG
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cd ..
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sudo rm redland-bindings-$REDBINDVERSION.tar.gz
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cd ..
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#CHECKREDBIND=`??? --version`
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#if [ "$CHECKREDBIND" == "$REDBINDVERSION" ]
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#then
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# echo "================================================="
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# echo "Redland Bindings version $REDBINDVERSION successfully installed."
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# echo "================================================="
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#else
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# echo "Redland Bindings version $REDBINDVERSION installation failed."
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# FAILED=1
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# exit $FAILED
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#fi
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else
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echo "Redland folder exists."
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fi
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echo "Installing the opentox webservices"
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mkdir webservices
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cd webservices
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echo "Install the opentox-ruby-api-wrapper"
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echo "This could take a while..."
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git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$INSTALLLOG 2>>$ERRLOG
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cd opentox-ruby-api-wrapper
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git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
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OTAPIVERSION=`cat VERSION`
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sudo rake install | tee -a $INSTALLLOG
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cd ..
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CHECKOTAPI=`gem list | grep "opentox-ruby-api-wrapper" | grep "$OTAPIVERSION"`
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if [ ! "$CHECKOTAPI" = '' ]
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then
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echo "================================================="
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echo "opentox-ruby-api-wrapper ($OTAPIVERSION) successfully installed."
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echo "================================================="
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255
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else
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256
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echo "opentox-ruby-api-wrapper ($OTAPIVERSION) installation failed."
|
|
257
|
+
FAILED=1
|
|
258
|
+
exit $FAILED
|
|
259
|
+
fi
|
|
260
|
+
|
|
261
|
+
echo "Installing the webservices: compound, dataset, algorithm, model, task, feature"
|
|
262
|
+
git clone git://github.com/helma/opentox-compound.git >>$INSTALLLOG 2>>$ERRLOG
|
|
263
|
+
git clone git://github.com/helma/opentox-dataset.git >>$INSTALLLOG 2>>$ERRLOG
|
|
264
|
+
git clone git://github.com/helma/opentox-algorithm.git >>$INSTALLLOG 2>>$ERRLOG
|
|
265
|
+
git clone git://github.com/helma/opentox-model.git >>$INSTALLLOG 2>>$ERRLOG
|
|
266
|
+
git clone git://github.com/helma/opentox-task.git >>$INSTALLLOG 2>>$ERRLOG
|
|
267
|
+
git clone git://github.com/helma/opentox-feature.git >>$INSTALLLOG 2>>$ERRLOG
|
|
268
|
+
|
|
269
|
+
cd opentox-compound
|
|
270
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
271
|
+
cd ../opentox-dataset
|
|
272
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
273
|
+
cd ../opentox-algorithm
|
|
274
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
275
|
+
cd ../opentox-model
|
|
276
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
277
|
+
cd ../opentox-task
|
|
278
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
279
|
+
cd ../opentox-task
|
|
280
|
+
git checkout -b development origin/development >>$INSTALLLOG 2>>$ERRLOG
|
|
281
|
+
cd ..
|
|
282
|
+
|
|
283
|
+
#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
|
|
284
|
+
|
|
285
|
+
echo "Installing the tests"
|
|
286
|
+
git clone git://github.com/helma/opentox-test.git >>$INSTALLLOG 2>>$ERRLOG
|
|
287
|
+
cd opentox-test
|
|
288
|
+
git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
|
|
289
|
+
|
|
290
|
+
echo "Installing openbabel"
|
|
291
|
+
cd ../opentox-compound
|
|
292
|
+
sudo rake openbabel:install | tee -a $INSTALLLOG
|
|
293
|
+
sudo ldconfig >>$INSTALLLOG 2>>$ERRLOG
|
|
294
|
+
|
|
295
|
+
ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERR
|
|
296
|
+
#VERSION=` --version`
|
|
297
|
+
#if [ "$VERSION" == "$RAPTORVERSION" ]
|
|
298
|
+
#then
|
|
299
|
+
# echo "================================================="
|
|
300
|
+
# echo "Raptor version $RAPTORVERSION successfully installed."
|
|
301
|
+
# echo "================================================="
|
|
302
|
+
#else
|
|
303
|
+
# echo "Raptor version $RAPTORVERSION installation failed."
|
|
304
|
+
# FAILED=1
|
|
305
|
+
# exit $FAILED
|
|
306
|
+
#fi
|
|
307
|
+
|
|
308
|
+
|
|
309
|
+
#check /webservices/opentox-algorithm/fminer.rb for 1,0/ture,false bug
|
|
310
|
+
BUGCHECK1=`grep "@@fminer.AddActivity(true, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
|
|
311
|
+
BUGCHECK2=`grep "@@fminer.AddActivity(false, id)" $STARTPATH/webservices/opentox-algorithm/fminer.rb`
|
|
312
|
+
if [ -z "$BUGCHECK1$BUGCHECK2" ]
|
|
313
|
+
then
|
|
314
|
+
echo "fminer.rb is correct."
|
|
315
|
+
else
|
|
316
|
+
sed -i 's/@@fminer.AddActivity(true, id)/@@fminer.AddActivity(1, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
|
|
317
|
+
sed -i 's/@@fminer.AddActivity(false, id)/@@fminer.AddActivity(0, id)/g' $STARTPATH/webservices/opentox-algorithm/fminer.rb
|
|
318
|
+
echo "fminer.rb updated."
|
|
319
|
+
fi
|
|
320
|
+
|
|
321
|
+
#todo: configure libfminer Makefile (location of ruby.h)
|
|
322
|
+
#-> fixed by using davor's repository
|
|
323
|
+
|
|
324
|
+
|
|
325
|
+
cd ../opentox-algorithm
|
|
326
|
+
echo "Installing fminer"
|
|
327
|
+
echo "This could take a while..."
|
|
328
|
+
sudo updatedb
|
|
329
|
+
sudo rake fminer:install | tee -a $INSTALLLOG
|
|
330
|
+
cd ..
|
|
331
|
+
FMINERVERSION=`ls $STARTPATH/webservices/opentox-algorithm/libfminer | grep "fminer.so"`
|
|
332
|
+
if [ "$FMINERVERSION" == "fminer.so" ]
|
|
333
|
+
then
|
|
334
|
+
echo "================================================="
|
|
335
|
+
echo "Fminer successfully installed."
|
|
336
|
+
echo "================================================="
|
|
337
|
+
else
|
|
338
|
+
echo "Fminer installation failed."
|
|
339
|
+
FAILED=1
|
|
340
|
+
exit $FAILED
|
|
341
|
+
fi
|
|
342
|
+
|
|
343
|
+
if [ $FAILED == 0 ]
|
|
344
|
+
then
|
|
345
|
+
#get username
|
|
346
|
+
echo "Please enter username:"
|
|
347
|
+
read USERNAME
|
|
348
|
+
|
|
349
|
+
#change rights from root to user
|
|
350
|
+
sudo chown -R $USERNAME: $STARTPATH/webservices/
|
|
351
|
+
sudo chown -R $USERNAME: ~/.opentox/
|
|
352
|
+
fi
|
|
353
|
+
|
|
354
|
+
if [ "$FAILED" == "1" ]
|
|
355
|
+
then
|
|
356
|
+
echo "================================================="
|
|
357
|
+
echo "Installation script failed!"
|
|
358
|
+
echo "================================================="
|
|
359
|
+
exit 1
|
|
360
|
+
else
|
|
361
|
+
echo "================================================="
|
|
362
|
+
echo "opentox-install-script is completed."
|
|
363
|
+
echo "================================================="
|
|
364
|
+
echo "Configuration:"
|
|
365
|
+
echo "Edit the settings in $HOME/.opentox/config/{development|production|test}.yaml for your environment."
|
|
366
|
+
echo "================================================="
|
|
367
|
+
echo "Start the webservices local:"
|
|
368
|
+
echo "cd webservices/opentox-test/"
|
|
369
|
+
echo "rake opentox:services:start"
|
|
370
|
+
echo "================================================="
|
|
371
|
+
echo "Test local webservices:"
|
|
372
|
+
echo "rake features"
|
|
373
|
+
echo "================================================="
|
|
374
|
+
fi
|
|
375
|
+
exit 0
|
data/lib/algorithm.rb
CHANGED
|
@@ -1,27 +1,35 @@
|
|
|
1
|
+
LOGGER.progname = File.expand_path(__FILE__)
|
|
2
|
+
|
|
1
3
|
module OpenTox
|
|
2
|
-
|
|
4
|
+
module Algorithm
|
|
3
5
|
|
|
4
|
-
|
|
5
|
-
|
|
6
|
+
class Fminer
|
|
7
|
+
include Owl
|
|
6
8
|
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
9
|
+
def initialize
|
|
10
|
+
super
|
|
11
|
+
self.uri = File.join(@@config[:services]["opentox-algorithm"],'fminer')
|
|
12
|
+
self.title = "fminer"
|
|
13
|
+
self.source = "http://github.com/amaunz/libfminer"
|
|
14
|
+
self.parameters = {
|
|
15
|
+
"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
|
|
16
|
+
"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
|
|
17
|
+
}
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
def self.create_feature_dataset(params)
|
|
21
|
+
LOGGER.debug File.basename(__FILE__) + ": creating feature dataset"
|
|
22
|
+
resource = RestClient::Resource.new(params[:feature_generation_uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
23
|
+
resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
|
|
24
|
+
end
|
|
17
25
|
|
|
18
|
-
def self.
|
|
19
|
-
|
|
26
|
+
def self.uri
|
|
27
|
+
File.join(@@config[:services]["opentox-algorithm"], "fminer")
|
|
20
28
|
end
|
|
21
|
-
|
|
29
|
+
end
|
|
22
30
|
|
|
23
|
-
|
|
24
|
-
|
|
31
|
+
class Lazar
|
|
32
|
+
include Owl
|
|
25
33
|
|
|
26
34
|
def initialize
|
|
27
35
|
super
|
|
@@ -40,26 +48,33 @@ module OpenTox
|
|
|
40
48
|
|
|
41
49
|
def self.create_model(params)
|
|
42
50
|
LOGGER.debug params
|
|
43
|
-
|
|
51
|
+
LOGGER.debug File.basename(__FILE__) + ": creating model"
|
|
52
|
+
#@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")
|
|
53
|
+
resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
54
|
+
@uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
|
|
44
55
|
end
|
|
45
56
|
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
class Similarity
|
|
49
|
-
def self.weighted_tanimoto(fp_a,fp_b,p)
|
|
50
|
-
common_features = fp_a & fp_b
|
|
51
|
-
all_features = fp_a + fp_b
|
|
52
|
-
common_p_sum = 0.0
|
|
53
|
-
if common_features.size > 0
|
|
54
|
-
common_features.each{|f| common_p_sum += p[f]}
|
|
55
|
-
all_p_sum = 0.0
|
|
56
|
-
all_features.each{|f| all_p_sum += p[f]}
|
|
57
|
-
common_p_sum/all_p_sum
|
|
58
|
-
else
|
|
59
|
-
0.0
|
|
60
|
-
end
|
|
57
|
+
def self.uri
|
|
58
|
+
File.join(@@config[:services]["opentox-algorithm"], "lazar")
|
|
61
59
|
end
|
|
62
|
-
end
|
|
63
60
|
|
|
64
|
-
|
|
61
|
+
end
|
|
62
|
+
|
|
63
|
+
class Similarity
|
|
64
|
+
def self.weighted_tanimoto(fp_a,fp_b,p)
|
|
65
|
+
common_features = fp_a & fp_b
|
|
66
|
+
all_features = fp_a + fp_b
|
|
67
|
+
common_p_sum = 0.0
|
|
68
|
+
if common_features.size > 0
|
|
69
|
+
common_features.each{|f| common_p_sum += p[f]}
|
|
70
|
+
all_p_sum = 0.0
|
|
71
|
+
all_features.each{|f| all_p_sum += p[f]}
|
|
72
|
+
common_p_sum/all_p_sum
|
|
73
|
+
else
|
|
74
|
+
0.0
|
|
75
|
+
end
|
|
76
|
+
end
|
|
77
|
+
end
|
|
78
|
+
|
|
79
|
+
end
|
|
65
80
|
end
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
helpers do
|
|
2
|
+
|
|
3
|
+
def protected!
|
|
4
|
+
response['WWW-Authenticate'] = %(Basic realm="Opentox Webservice Authentication") and \
|
|
5
|
+
throw(:halt, [401, "Not authorized\n"]) and \
|
|
6
|
+
return unless authorized?
|
|
7
|
+
end
|
|
8
|
+
|
|
9
|
+
def authorized?
|
|
10
|
+
@auth ||= Rack::Auth::Basic::Request.new(request.env)
|
|
11
|
+
@auth.provided? && @auth.basic? && @auth.credentials && valid_user?
|
|
12
|
+
end
|
|
13
|
+
|
|
14
|
+
def valid_user?
|
|
15
|
+
users = @@users[:users]
|
|
16
|
+
return @auth.credentials == [@auth.username, users.fetch(@auth.username)] if users.has_key?(@auth.username)
|
|
17
|
+
return false
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
before do
|
|
23
|
+
#protected! unless env['REQUEST_METHOD'] == "GET"
|
|
24
|
+
end
|
data/lib/compound.rb
CHANGED
|
@@ -17,7 +17,8 @@ module OpenTox
|
|
|
17
17
|
@inchi = sdf2inchi(params[:sdf])
|
|
18
18
|
@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
|
|
19
19
|
elsif params[:name]
|
|
20
|
-
|
|
20
|
+
# paranoid URI encoding to keep SMILES charges and brackets
|
|
21
|
+
@inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp
|
|
21
22
|
@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
|
|
22
23
|
elsif params[:uri]
|
|
23
24
|
@uri = params[:uri]
|
data/lib/config/config_ru.rb
CHANGED
data/lib/dataset.rb
CHANGED
|
@@ -1,3 +1,5 @@
|
|
|
1
|
+
LOGGER.progname = File.expand_path(__FILE__)
|
|
2
|
+
|
|
1
3
|
module OpenTox
|
|
2
4
|
|
|
3
5
|
class Dataset
|
|
@@ -14,6 +16,8 @@ module OpenTox
|
|
|
14
16
|
data_entry = @model.subject OT['compound'], compound
|
|
15
17
|
if data_entry.nil?
|
|
16
18
|
data_entry = @model.create_resource
|
|
19
|
+
dataset = @model.subject(RDF['type'],OT[self.owl_class])
|
|
20
|
+
@model.add dataset, OT['dataEntry'], data_entry
|
|
17
21
|
@model.add data_entry, RDF['type'], OT["DataEntry"]
|
|
18
22
|
@model.add data_entry, OT['compound'], compound
|
|
19
23
|
end
|
|
@@ -29,6 +33,8 @@ module OpenTox
|
|
|
29
33
|
data_entry = @model.subject OT['compound'], compound
|
|
30
34
|
if data_entry.nil?
|
|
31
35
|
data_entry = @model.create_resource
|
|
36
|
+
dataset = @model.subject(RDF['type'],OT[self.owl_class])
|
|
37
|
+
@model.add dataset, OT['dataEntry'], data_entry
|
|
32
38
|
@model.add data_entry, RDF['type'], OT["DataEntry"]
|
|
33
39
|
@model.add data_entry, OT['compound'], compound
|
|
34
40
|
end
|
|
@@ -57,7 +63,7 @@ module OpenTox
|
|
|
57
63
|
def find_or_create_compound(uri)
|
|
58
64
|
compound = @model.subject(DC["identifier"], uri)
|
|
59
65
|
if compound.nil?
|
|
60
|
-
compound = @model.create_resource
|
|
66
|
+
compound = @model.create_resource(uri)
|
|
61
67
|
@model.add compound, RDF['type'], OT["Compound"]
|
|
62
68
|
@model.add compound, DC["identifier"], uri
|
|
63
69
|
end
|
|
@@ -68,7 +74,7 @@ module OpenTox
|
|
|
68
74
|
def find_or_create_feature(uri)
|
|
69
75
|
feature = @model.subject(DC["identifier"], uri)
|
|
70
76
|
if feature.nil?
|
|
71
|
-
feature = @model.create_resource
|
|
77
|
+
feature = @model.create_resource(uri)
|
|
72
78
|
@model.add feature, RDF['type'], OT["Feature"]
|
|
73
79
|
@model.add feature, DC["identifier"], uri
|
|
74
80
|
@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
|
|
@@ -78,7 +84,8 @@ module OpenTox
|
|
|
78
84
|
end
|
|
79
85
|
|
|
80
86
|
def self.create(data, content_type = 'application/rdf+xml')
|
|
81
|
-
|
|
87
|
+
resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
88
|
+
uri = resource.post data, :content_type => content_type
|
|
82
89
|
dataset = Dataset.new
|
|
83
90
|
dataset.read uri.to_s
|
|
84
91
|
dataset
|
|
@@ -86,7 +93,9 @@ module OpenTox
|
|
|
86
93
|
|
|
87
94
|
def self.find(uri)
|
|
88
95
|
dataset = Dataset.new
|
|
96
|
+
LOGGER.debug "Getting data from #{uri}"
|
|
89
97
|
data = `curl "#{uri}"`
|
|
98
|
+
#LOGGER.debug data
|
|
90
99
|
#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
|
|
91
100
|
dataset.rdf = data
|
|
92
101
|
dataset
|
|
@@ -152,11 +161,24 @@ module OpenTox
|
|
|
152
161
|
|
|
153
162
|
# Delete a dataset
|
|
154
163
|
def delete
|
|
155
|
-
|
|
156
|
-
|
|
164
|
+
resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
165
|
+
resource.delete
|
|
166
|
+
end
|
|
157
167
|
|
|
158
168
|
def save
|
|
159
|
-
|
|
169
|
+
LOGGER.debug "Saving dataset"
|
|
170
|
+
#task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s
|
|
171
|
+
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
|
|
172
|
+
task = OpenTox::Task.find(task_uri)
|
|
173
|
+
LOGGER.debug "Waiting for task #{task_uri}"
|
|
174
|
+
task.wait_for_completion
|
|
175
|
+
LOGGER.debug "Dataset task #{task_uri} completed"
|
|
176
|
+
if task.failed?
|
|
177
|
+
LOGGER.error "Saving dataset failed"
|
|
178
|
+
task.failed
|
|
179
|
+
exit
|
|
180
|
+
end
|
|
181
|
+
task.resource
|
|
160
182
|
end
|
|
161
183
|
|
|
162
184
|
def to_yaml
|
data/lib/environment.rb
CHANGED
|
@@ -6,6 +6,7 @@ ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
|
|
|
6
6
|
basedir = File.join(ENV['HOME'], ".opentox")
|
|
7
7
|
config_dir = File.join(basedir, "config")
|
|
8
8
|
config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
|
|
9
|
+
user_file = File.join(config_dir, "users.yaml")
|
|
9
10
|
|
|
10
11
|
TMP_DIR = File.join(basedir, "tmp")
|
|
11
12
|
LOG_DIR = File.join(basedir, "log")
|
|
@@ -15,6 +16,7 @@ if File.exist?(config_file)
|
|
|
15
16
|
else
|
|
16
17
|
FileUtils.mkdir_p TMP_DIR
|
|
17
18
|
FileUtils.mkdir_p LOG_DIR
|
|
19
|
+
FileUtils.mkdir_p config_dir
|
|
18
20
|
FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/config.yaml'), config_file)
|
|
19
21
|
puts "Please edit #{config_file} and restart your application."
|
|
20
22
|
exit
|
|
@@ -43,6 +45,21 @@ logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
|
|
|
43
45
|
LOGGER = Logger.new(logfile,'daily') # daily rotation
|
|
44
46
|
LOGGER.level = Logger::DEBUG
|
|
45
47
|
|
|
48
|
+
if File.exist?(user_file)
|
|
49
|
+
@@users = YAML.load_file(user_file)
|
|
50
|
+
else
|
|
51
|
+
FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/users.yaml'), user_file)
|
|
52
|
+
puts "Please edit #{user_file} and restart your application."
|
|
53
|
+
exit
|
|
54
|
+
end
|
|
55
|
+
|
|
56
|
+
begin
|
|
57
|
+
0 < @@users[:users].keys.length
|
|
58
|
+
rescue
|
|
59
|
+
puts "Please edit #{user_file} and restart your application. Create at least one user with password."
|
|
60
|
+
exit
|
|
61
|
+
end
|
|
62
|
+
|
|
46
63
|
# RDF namespaces
|
|
47
64
|
RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
|
|
48
65
|
OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
|
data/lib/model.rb
CHANGED
|
@@ -24,7 +24,7 @@ module OpenTox
|
|
|
24
24
|
lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
|
|
25
25
|
lazar.trainingDataset = yaml[:activity_dataset]
|
|
26
26
|
lazar.dependentVariables = yaml[:endpoint]
|
|
27
|
-
lazar.predictedVariables = yaml[:endpoint]
|
|
27
|
+
lazar.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
|
|
28
28
|
lazar
|
|
29
29
|
end
|
|
30
30
|
|
|
@@ -39,15 +39,25 @@ module OpenTox
|
|
|
39
39
|
|
|
40
40
|
# Predict a compound
|
|
41
41
|
def predict(compound)
|
|
42
|
-
|
|
42
|
+
# nicht absichern??
|
|
43
|
+
resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
44
|
+
resource.post(:compound_uri => compound.uri)
|
|
43
45
|
end
|
|
44
46
|
|
|
45
47
|
def self.base_uri
|
|
46
|
-
@@config[:services]["opentox-model"]
|
|
48
|
+
File.join @@config[:services]["opentox-model"],'lazar'
|
|
47
49
|
end
|
|
48
50
|
|
|
49
51
|
def self.create(data)
|
|
50
|
-
|
|
52
|
+
resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
53
|
+
resource.post(data, :content_type => "application/x-yaml").to_s
|
|
54
|
+
end
|
|
55
|
+
|
|
56
|
+
def delete
|
|
57
|
+
resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
58
|
+
resource.delete
|
|
59
|
+
#RestClient.delete @uri if @uri
|
|
60
|
+
#RestClient.delete model.task_uri if model.task_uri
|
|
51
61
|
end
|
|
52
62
|
|
|
53
63
|
# def self.create(task)
|
|
@@ -8,6 +8,6 @@ rescue LoadError
|
|
|
8
8
|
puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
|
|
9
9
|
end
|
|
10
10
|
|
|
11
|
-
['owl', 'compound','dataset','algorithm','model','task','utils'].each do |lib|
|
|
11
|
+
['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization'].each do |lib|
|
|
12
12
|
require lib
|
|
13
13
|
end
|
data/lib/owl.rb
CHANGED
|
@@ -16,7 +16,6 @@ module OpenTox
|
|
|
16
16
|
# reate an anonymous resource for metadata
|
|
17
17
|
# this has to be rewritten with an URI as soon as the resource has been saved at an definitive location
|
|
18
18
|
tmp = @model.create_resource
|
|
19
|
-
@model.add tmp, RDF['type'], OWL['Ontology']
|
|
20
19
|
@model.add tmp, RDF['type'], OT[self.owl_class]
|
|
21
20
|
end
|
|
22
21
|
|
data/lib/task.rb
CHANGED
|
@@ -1,3 +1,5 @@
|
|
|
1
|
+
LOGGER.progname = File.expand_path(__FILE__)
|
|
2
|
+
|
|
1
3
|
module OpenTox
|
|
2
4
|
|
|
3
5
|
class Task
|
|
@@ -10,7 +12,10 @@ module OpenTox
|
|
|
10
12
|
end
|
|
11
13
|
|
|
12
14
|
def self.create
|
|
13
|
-
uri = RestClient.post @@config[:services]["opentox-task"], {}
|
|
15
|
+
#uri = RestClient.post @@config[:services]["opentox-task"], {}
|
|
16
|
+
resource = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
17
|
+
#uri = resource.post(nil)
|
|
18
|
+
uri = resource.post({})
|
|
14
19
|
Task.new(uri)
|
|
15
20
|
end
|
|
16
21
|
|
|
@@ -26,7 +31,7 @@ module OpenTox
|
|
|
26
31
|
task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
|
|
27
32
|
task_uris.collect{|uri| Task.new(uri)}
|
|
28
33
|
end
|
|
29
|
-
|
|
34
|
+
|
|
30
35
|
def created_at
|
|
31
36
|
RestClient.get File.join(@uri, 'created_at')
|
|
32
37
|
end
|
|
@@ -42,7 +47,24 @@ module OpenTox
|
|
|
42
47
|
def resource
|
|
43
48
|
RestClient.get File.join(@uri, 'resource')
|
|
44
49
|
end
|
|
50
|
+
|
|
51
|
+
def started
|
|
52
|
+
LOGGER.info File.join(@uri,'started')
|
|
53
|
+
resource = RestClient::Resource.new(File.join(@uri,'started'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
54
|
+
resource.put({})
|
|
55
|
+
end
|
|
56
|
+
|
|
57
|
+
def cancel
|
|
58
|
+
resource = RestClient::Resource.new(@File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
59
|
+
resource.put({})
|
|
60
|
+
end
|
|
61
|
+
|
|
62
|
+
def completed(uri)
|
|
63
|
+
resource = RestClient::Resource.new(File.join(@uri,'completed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
64
|
+
resource.put :resource => uri
|
|
65
|
+
end
|
|
45
66
|
|
|
67
|
+
=begin
|
|
46
68
|
def started
|
|
47
69
|
RestClient.put File.join(@uri,'started'), {}
|
|
48
70
|
end
|
|
@@ -51,20 +73,27 @@ module OpenTox
|
|
|
51
73
|
RestClient.put File.join(@uri,'cancelled'), {}
|
|
52
74
|
end
|
|
53
75
|
|
|
54
|
-
def
|
|
55
|
-
RestClient.put File.join(@uri,'
|
|
76
|
+
def completed(uri)
|
|
77
|
+
RestClient.put File.join(@uri,'completed'), :resource => uri
|
|
56
78
|
end
|
|
57
79
|
|
|
58
|
-
|
|
59
|
-
|
|
80
|
+
=end
|
|
81
|
+
def failed
|
|
82
|
+
#RestClient.put File.join(@uri,'failed'), {}
|
|
83
|
+
resource = RestClient::Resource.new(@File.join(@uri,'failed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
84
|
+
resource.put({})
|
|
60
85
|
end
|
|
61
86
|
|
|
62
|
-
def
|
|
63
|
-
RestClient.put File.join(@uri,'
|
|
87
|
+
def parent=(task)
|
|
88
|
+
#RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
|
|
89
|
+
resource = RestClient::Resource.new(File.join(@uri,'parent'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
90
|
+
LOGGER.debug "task.rb: #{resource}"
|
|
91
|
+
resource.put :uri => task.uri
|
|
64
92
|
end
|
|
65
93
|
|
|
66
94
|
def pid=(pid)
|
|
67
|
-
|
|
95
|
+
resource = RestClient::Resource.new(File.join(@uri,'pid'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
96
|
+
resource.put :pid => pid
|
|
68
97
|
end
|
|
69
98
|
|
|
70
99
|
def completed?
|
data/lib/validation.rb
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
module OpenTox
|
|
2
|
+
class Validation
|
|
3
|
+
|
|
4
|
+
attr_accessor :uri
|
|
5
|
+
|
|
6
|
+
def initialize(params)
|
|
7
|
+
resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
|
|
8
|
+
@uri = resource.post(params).to_s
|
|
9
|
+
end
|
|
10
|
+
|
|
11
|
+
def self.crossvalidation(params)
|
|
12
|
+
params[:uri] = File.join(@@config[:services]['opentox-validation'], "crossvalidation")
|
|
13
|
+
params[:num_folds] = 10 unless params[:num_folds]
|
|
14
|
+
params[:random_seed] = 2 unless params[:random_seed]
|
|
15
|
+
params[:stratified] = false unless params[:stratified]
|
|
16
|
+
OpenTox::Validation.new(params)
|
|
17
|
+
end
|
|
18
|
+
|
|
19
|
+
end
|
|
20
|
+
end
|
|
21
|
+
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: opentox-ruby-api-wrapper
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.
|
|
4
|
+
version: 1.3.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Christoph Helma
|
|
@@ -9,7 +9,7 @@ autorequire:
|
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
11
|
|
|
12
|
-
date: 2010-
|
|
12
|
+
date: 2010-03-01 00:00:00 +01:00
|
|
13
13
|
default_executable:
|
|
14
14
|
dependencies:
|
|
15
15
|
- !ruby/object:Gem::Dependency
|
|
@@ -62,16 +62,6 @@ dependencies:
|
|
|
62
62
|
- !ruby/object:Gem::Version
|
|
63
63
|
version: "0"
|
|
64
64
|
version:
|
|
65
|
-
- !ruby/object:Gem::Dependency
|
|
66
|
-
name: thin
|
|
67
|
-
type: :runtime
|
|
68
|
-
version_requirement:
|
|
69
|
-
version_requirements: !ruby/object:Gem::Requirement
|
|
70
|
-
requirements:
|
|
71
|
-
- - ">="
|
|
72
|
-
- !ruby/object:Gem::Version
|
|
73
|
-
version: "0"
|
|
74
|
-
version:
|
|
75
65
|
- !ruby/object:Gem::Dependency
|
|
76
66
|
name: emk-sinatra-url-for
|
|
77
67
|
type: :runtime
|
|
@@ -123,8 +113,8 @@ dependencies:
|
|
|
123
113
|
version: "0"
|
|
124
114
|
version:
|
|
125
115
|
- !ruby/object:Gem::Dependency
|
|
126
|
-
name:
|
|
127
|
-
type: :
|
|
116
|
+
name: cucumber
|
|
117
|
+
type: :development
|
|
128
118
|
version_requirement:
|
|
129
119
|
version_requirements: !ruby/object:Gem::Requirement
|
|
130
120
|
requirements:
|
|
@@ -133,8 +123,8 @@ dependencies:
|
|
|
133
123
|
version: "0"
|
|
134
124
|
version:
|
|
135
125
|
- !ruby/object:Gem::Dependency
|
|
136
|
-
name:
|
|
137
|
-
type: :
|
|
126
|
+
name: jeweler
|
|
127
|
+
type: :development
|
|
138
128
|
version_requirement:
|
|
139
129
|
version_requirements: !ruby/object:Gem::Requirement
|
|
140
130
|
requirements:
|
|
@@ -143,7 +133,7 @@ dependencies:
|
|
|
143
133
|
version: "0"
|
|
144
134
|
version:
|
|
145
135
|
- !ruby/object:Gem::Dependency
|
|
146
|
-
name:
|
|
136
|
+
name: thin
|
|
147
137
|
type: :development
|
|
148
138
|
version_requirement:
|
|
149
139
|
version_requirements: !ruby/object:Gem::Requirement
|
|
@@ -155,6 +145,7 @@ dependencies:
|
|
|
155
145
|
description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
|
|
156
146
|
email: helma@in-silico.ch
|
|
157
147
|
executables:
|
|
148
|
+
- opentox-install-ubuntu.sh
|
|
158
149
|
- opentox-install-debian.sh
|
|
159
150
|
- yaml2owl.rb
|
|
160
151
|
extensions: []
|
|
@@ -168,11 +159,12 @@ files:
|
|
|
168
159
|
- Rakefile
|
|
169
160
|
- VERSION
|
|
170
161
|
- bin/opentox-install-debian.sh
|
|
162
|
+
- bin/opentox-install-ubuntu.sh
|
|
171
163
|
- bin/yaml2owl.rb
|
|
172
164
|
- lib/algorithm.rb
|
|
165
|
+
- lib/authorization.rb
|
|
173
166
|
- lib/compound.rb
|
|
174
167
|
- lib/config/config_ru.rb
|
|
175
|
-
- lib/config/database.rb
|
|
176
168
|
- lib/dataset.rb
|
|
177
169
|
- lib/environment.rb
|
|
178
170
|
- lib/helper.rb
|
|
@@ -184,7 +176,9 @@ files:
|
|
|
184
176
|
- lib/task.rb
|
|
185
177
|
- lib/tasks/opentox.rb
|
|
186
178
|
- lib/templates/config.yaml
|
|
179
|
+
- lib/templates/users.yaml
|
|
187
180
|
- lib/utils.rb
|
|
181
|
+
- lib/validation.rb
|
|
188
182
|
has_rdoc: true
|
|
189
183
|
homepage: http://github.com/helma/opentox-ruby-api-wrapper
|
|
190
184
|
licenses: []
|
data/lib/config/database.rb
DELETED
|
@@ -1,21 +0,0 @@
|
|
|
1
|
-
# database
|
|
2
|
-
if @@config[:database]
|
|
3
|
-
require 'dm-core'
|
|
4
|
-
require 'dm-serializer'
|
|
5
|
-
require 'dm-timestamps'
|
|
6
|
-
require 'dm-types'
|
|
7
|
-
case @@config[:database][:adapter]
|
|
8
|
-
when /sqlite/i
|
|
9
|
-
db_dir = File.join(ENV['HOME'], ".opentox", "db")
|
|
10
|
-
FileUtils.mkdir_p db_dir
|
|
11
|
-
DataMapper::setup(:default, "sqlite3://#{db_dir}/opentox.sqlite3")
|
|
12
|
-
else
|
|
13
|
-
DataMapper.setup(:default, {
|
|
14
|
-
:adapter => @@config[:database][:adapter],
|
|
15
|
-
:database => @@config[:database][:database],
|
|
16
|
-
:username => @@config[:database][:username],
|
|
17
|
-
:password => @@config[:database][:password],
|
|
18
|
-
:host => @@config[:database][:host]})
|
|
19
|
-
end
|
|
20
|
-
end
|
|
21
|
-
|