opentox-ruby-api-wrapper 1.1.0 → 1.1.1

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Files changed (5) hide show
  1. data/README.rdoc +1 -1
  2. data/Rakefile +7 -1
  3. data/VERSION +1 -1
  4. data/bin/install.sh +105 -0
  5. metadata +117 -6
data/README.rdoc CHANGED
@@ -14,7 +14,7 @@ Install the gem:
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  == Usage
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- - set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the OpenTox REST webservices
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+ - adjust the settings in $HOME/.opentox/config
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  - require 'opentox-ruby-api-wrapper' in your ruby application
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  - consult the rdoc API documentation for details
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data/Rakefile CHANGED
@@ -10,17 +10,23 @@ 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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- gem.add_dependency "technoweenie-rest-client"
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+ gem.add_dependency "rest-client"
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  gem.add_dependency "sinatra"
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  gem.add_dependency "rack"
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  gem.add_dependency "rack-contrib"
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  gem.add_dependency "thin"
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  gem.add_dependency "cucumber"
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  gem.add_dependency "ezmobius-redis-rb"
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+ gem.add_dependency "emk-sinatra-url-for"
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+ gem.add_dependency "cehoffman-sinatra-respond_to"
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+ gem.add_dependency "dm-core"
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+ gem.add_dependency "datamapper"
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+ gem.add_dependency "do_sqlite3"
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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/opentox.rb, lib/tasks/redis.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/feature.rb, lib/model.rb, lib/utils.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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  rescue LoadError
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  puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
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  end
data/VERSION CHANGED
@@ -1 +1 @@
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- 1.1.0
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+ 1.1.1
data/bin/install.sh ADDED
@@ -0,0 +1,105 @@
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+ #!/bin/bash
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+ #Installation is tested on Debian Lenny Ubuntu 9.04
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+ #Update the system
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+
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+ ERRLOG='install_err.log'
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+ INSTALLLOG='install_log.log'
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+ DATE=$(date +%Y/%m/%d\ %H:%M:%S)
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+
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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 unshure 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 -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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+
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+ echo "opentox webservice install log - " $DATE > $INSTALLLOG
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+ echo "Installing: build-essential"
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+ sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG
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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 >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing: gems rdoc rubygems and rake"
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+ sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG
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+
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+ echo "Installing rubygems from source. This may take some time"
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+ wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG
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+ tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG
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+ cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG
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+ sudo ruby setup.rb 2>>$ERRLOG
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+ cd ..
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+
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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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+
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+ #for debian lenny:
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+ echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5"
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+ sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5 >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing git from source"
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+ wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG
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+ tar xzfv git-1.6.5.2.tar.gz 2>>$ERRLOG
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+ cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG
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+ ./configure 2>>$ERRLOG
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+ make 2>>$ERRLOG
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+ make install 2>>$ERRLOG
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+
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+ echo "Installing the opentox webservices"
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+ mkdir webservices >> $INSTALLLOG 2>>$ERRLOG
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+ cd webservices >> $INSTALLLOG 2>>$ERRLOG
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+
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+ git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG
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+ git clone git://github.com/helma/opentox-feature.git >> $INSTALLLOG 2>>$ERRLOG
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+ git clone git://github.com/helma/opentox-dataset.git >> $INSTALLLOG 2>>$ERRLOG
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+ git clone git://github.com/helma/opentox-algorithm.git >> $INSTALLLOG 2>>$ERRLOG
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+ git clone git://github.com/helma/opentox-model.git >> $INSTALLLOG 2>>$ERRLOG
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+ git clone git://github.com/helma/opentox-test.git >> $INSTALLLOG 2>>$ERRLOG
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+
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+ cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ cd .. >> $INSTALLLOG 2>>$ERRLOG
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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 >> $INSTALLLOG 2>>$ERRLOG
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+ git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
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+ rake install >> $INSTALLLOG 2>>$ERRLOG
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+
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+
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+ cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing libopenssl-ruby"
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+ sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing dtach"
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+ rake dtach:install >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing openbabel"
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+ rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG
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+
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+ #debian lenny missed liblink:
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+ ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG
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+
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+ rake redis:download >> $INSTALLLOG 2>>$ERRLOG
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+ rake redis:install >> $INSTALLLOG 2>>$ERRLOG
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+ #edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
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+ sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG
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+ sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG
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+ sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG
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+ cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
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+ echo "Installing fminer"
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+ rake fminer:install >> $INSTALLLOG 2>>$ERRLOG
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+ sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG
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+
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+
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+ mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: opentox-ruby-api-wrapper
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  version: !ruby/object:Gem::Version
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- version: 1.1.0
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+ version: 1.1.1
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  platform: ruby
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  authors:
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  - Christoph Helma
@@ -9,11 +9,121 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-10-06 00:00:00 +02:00
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- default_executable:
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+ date: 2009-11-17 00:00:00 +01:00
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+ default_executable: install.sh
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  dependencies:
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  - !ruby/object:Gem::Dependency
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- name: technoweenie-rest-client
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+ name: rest-client
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: sinatra
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: rack
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: rack-contrib
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: thin
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: cucumber
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: ezmobius-redis-rb
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: emk-sinatra-url-for
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: cehoffman-sinatra-respond_to
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: dm-core
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: datamapper
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+ type: :runtime
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: do_sqlite3
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  type: :runtime
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  version_requirement:
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  version_requirements: !ruby/object:Gem::Requirement
@@ -24,8 +134,8 @@ dependencies:
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  version:
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  description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
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  email: helma@in-silico.ch
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- executables: []
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-
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+ executables:
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+ - install.sh
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  extensions: []
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  extra_rdoc_files:
@@ -36,6 +146,7 @@ files:
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  - README.rdoc
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  - Rakefile
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  - VERSION
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+ - bin/install.sh
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  - lib/algorithm.rb
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  - lib/compound.rb
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  - lib/dataset.rb