opentox-ruby-api-wrapper 1.1.0 → 1.1.1
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- data/README.rdoc +1 -1
- data/Rakefile +7 -1
- data/VERSION +1 -1
- data/bin/install.sh +105 -0
- metadata +117 -6
data/README.rdoc
CHANGED
@@ -14,7 +14,7 @@ Install the gem:
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== Usage
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-
-
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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 "
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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
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
1.1.
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+
1.1.1
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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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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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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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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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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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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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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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mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG
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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.
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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
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@@ -9,11 +9,121 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2009-
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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:
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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:
|
101
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+
- - ">="
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+
- !ruby/object:Gem::Version
|
103
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+
version: "0"
|
104
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+
version:
|
105
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+
- !ruby/object:Gem::Dependency
|
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+
name: dm-core
|
107
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+
type: :runtime
|
108
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+
version_requirement:
|
109
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+
version_requirements: !ruby/object:Gem::Requirement
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+
requirements:
|
111
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+
- - ">="
|
112
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+
- !ruby/object:Gem::Version
|
113
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version: "0"
|
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+
version:
|
115
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+
- !ruby/object:Gem::Dependency
|
116
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+
name: datamapper
|
117
|
+
type: :runtime
|
118
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+
version_requirement:
|
119
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
requirements:
|
121
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+
- - ">="
|
122
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+
- !ruby/object:Gem::Version
|
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version: "0"
|
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+
version:
|
125
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+
- !ruby/object:Gem::Dependency
|
126
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+
name: do_sqlite3
|
17
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|
type: :runtime
|
18
128
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version_requirement:
|
19
129
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version_requirements: !ruby/object:Gem::Requirement
|
@@ -24,8 +134,8 @@ dependencies:
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24
134
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version:
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25
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description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
|
26
136
|
email: helma@in-silico.ch
|
27
|
-
executables:
|
28
|
-
|
137
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+
executables:
|
138
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+
- install.sh
|
29
139
|
extensions: []
|
30
140
|
|
31
141
|
extra_rdoc_files:
|
@@ -36,6 +146,7 @@ files:
|
|
36
146
|
- README.rdoc
|
37
147
|
- Rakefile
|
38
148
|
- VERSION
|
149
|
+
- bin/install.sh
|
39
150
|
- lib/algorithm.rb
|
40
151
|
- lib/compound.rb
|
41
152
|
- lib/dataset.rb
|