opentox-ruby 0.0.1

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Files changed (21) hide show
  1. data/LICENSE +674 -0
  2. data/README.rdoc +23 -0
  3. data/Rakefile +87 -0
  4. data/VERSION +1 -0
  5. data/bin/opentox-install-debian.sh +105 -0
  6. data/bin/opentox-install-ubuntu.sh +375 -0
  7. data/lib/algorithm.rb +82 -0
  8. data/lib/compound.rb +128 -0
  9. data/lib/config/config_ru.rb +51 -0
  10. data/lib/dataset.rb +226 -0
  11. data/lib/environment.rb +77 -0
  12. data/lib/helper.rb +26 -0
  13. data/lib/model.rb +143 -0
  14. data/lib/opentox.owl +809 -0
  15. data/lib/overwrite.rb +14 -0
  16. data/lib/rest_client_wrapper.rb +168 -0
  17. data/lib/spork.rb +83 -0
  18. data/lib/task.rb +176 -0
  19. data/lib/templates/config.yaml +41 -0
  20. data/lib/validation.rb +20 -0
  21. metadata +437 -0
data/README.rdoc ADDED
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+ = opentox-ruby-api-wrapper
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+
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+ Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
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+
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+ == Installation
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+
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+ Run the following if you haven't already:
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+
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+ gem sources -a http://gems.github.com
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+
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+ Install the gem:
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+
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+ sudo gem install helma-opentox-ruby-api-wrapper
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+
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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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+
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+ == Copyright
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+
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+ Copyright (c) 2009 Christoph Helma. See LICENSE for details.
data/Rakefile ADDED
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+ require 'rubygems'
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+ require 'rake'
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+
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+ begin
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ gem.name = "opentox-ruby-api-wrapper"
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+ gem.summary = %Q{Ruby wrapper for the OpenTox REST API}
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+ gem.description = %Q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
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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, Martin Guetlein"]
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+ # dependencies
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+ [ "sinatra",
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+ "emk-sinatra-url-for",
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+ "sinatra-respond_to",
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+ "sinatra-static-assets",
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+ "rest-client",
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+ "rack",
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+ "rack-contrib",
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+ "rack-flash",
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+ "nokogiri",
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+ "rubyzip",
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+ "builder",
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+ "roo",
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+ "spreadsheet",
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+ "google-spreadsheet-ruby",
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+ "tmail",
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+ "rinruby",
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+ "rjb"
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+ ].each { |dep| gem.add_dependency dep }
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+ [ "dm-core",
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+ 'dm-serializer',
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+ 'dm-timestamps',
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+ 'dm-types',
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+ 'dm-migrations',
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+ "dm-mysql-adapter",
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+ "dm-validations",
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+ ].each {|dep| gem.add_dependency dep, ">= 1" }
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+ gem.add_dependency "haml", ">=3"
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+ ['cucumber','jeweler'].each { |dep| gem.add_development_dependency dep }
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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/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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+ 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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+
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+ require 'rake/testtask'
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+ Rake::TestTask.new(:test) do |test|
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+ test.libs << 'lib' << 'test'
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+ test.pattern = 'test/**/*_test.rb'
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+ test.verbose = true
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+ end
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+
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+ begin
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+ require 'rcov/rcovtask'
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+ Rcov::RcovTask.new do |test|
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+ test.libs << 'test'
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+ test.pattern = 'test/**/*_test.rb'
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+ test.verbose = true
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+ end
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+ rescue LoadError
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+ task :rcov do
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+ abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
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+ end
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+ end
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+
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+ task :test => :check_dependencies
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+
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+ task :default => :test
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+
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+ require 'rake/rdoctask'
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+ Rake::RDocTask.new do |rdoc|
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+ if File.exist?('VERSION')
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+ version = File.read('VERSION')
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+ else
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+ version = ""
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+ end
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "opentox-ruby-api-wrapper #{version}"
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+ rdoc.rdoc_files.include('README*')
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+ rdoc.rdoc_files.include('lib/**/*.rb')
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+ end
data/VERSION ADDED
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+ 1.6.5
data/bin/opentox-install-debian.sh ADDED
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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
data/bin/opentox-install-ubuntu.sh ADDED
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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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+
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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=$1
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+ GEMVERSION="1.3.5"
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+ GITVERSION="1.6.5.2"
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+ RAPTORVERSION="1.4.20"
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+ RASQALVERSION="0.9.16"
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+ RASQALVERSION2="0.9.15"
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+ REDLANDVERSION="1.0.7"
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+ REDBINDVERSION="1.0.7.1"
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+
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+ if [ "$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: $BRANCH"
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+ echo "================================================="
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+ echo "Please enshure that the sudo package is installed"
28
+ echo "on your system. "
29
+ echo "On Ubuntu Linux sudo is installed by default."
30
+ echo "If you are unsure check with it 'sudo ls'"
31
+ echo "and installed it with 'apt-get install sudo'"
32
+ echo "and add your username with visudo."
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+ echo "================================================="
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+ echo "Some programs and the OpenTox webservices will be installed in the current folder."
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+ echo "================================================="
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+ echo -n "To continue installation press y: "
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+ read answer
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+ if [ "$answer" != "y" ]
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+ then
40
+ echo "exiting the script..."
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+ exit 1
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+ fi
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+
44
+ 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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+
49
+ 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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+
52
+ 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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+
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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 ];
58
+ then
59
+ 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`
66
+ if [ "$CHECKGEM" == "$GEMVERSION" ]
67
+ then
68
+ echo "Adding http://gems.github.com to ruby gem sources"
69
+ sudo gem sources -a http://gems.github.com >>$INSTALLLOG 2>>$ERRLOG
70
+
71
+ echo "================================================="
72
+ echo "Rubygems version $GEMVERSION successfully installed."
73
+ echo "================================================="
74
+ else
75
+ echo "Rubygems version $GEMVERSION installation failed."
76
+ FAILED=1
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+ exit $FAILED
78
+ fi
79
+ else
80
+ echo "rubygems-$GEMVERSION folder already exist. "
81
+ fi
82
+
83
+ echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5 libopenssl-ruby libgsl0-dev swig r-base rinruby"
84
+ 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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+
89
+
90
+ #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 sinatra-respond_to | 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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+
106
+ echo "Installing LibRDF-ruby"
107
+ sudo apt-get install librdf0 librdf-ruby | tee -a $INSTALLLOG
108
+
109
+ #GIT
110
+ echo "Installing git from source"
111
+ echo "This could take a while..."
112
+ if [ ! -d $STARTPATH/git-$GITVERSION ];
113
+ then
114
+ wget http://www.kernel.org/pub/software/scm/git/git-$GITVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
115
+ tar xzfv git-$GITVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
116
+ cd git-$GITVERSION
117
+ ./configure >>$INSTALLLOG 2>>$ERRLOG
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+ make >>$INSTALLLOG 2>>$ERRLOG
119
+ sudo make install >>$INSTALLLOG 2>>$ERRLOG
120
+ cd ..
121
+ sudo rm git-$GITVERSION.tar.gz
122
+ CHECKGIT=`git --version`
123
+ if [ "$CHECKGIT" == "git version $GITVERSION" ]
124
+ then
125
+ echo "================================================="
126
+ echo "Git version $GITVERSION successfully installed."
127
+ echo "================================================="
128
+ else
129
+ echo "Git version $GITVERSION installation failed."
130
+ FAILED=1
131
+ exit $FAILED
132
+ fi
133
+ else
134
+ echo "git-$GITVERSION folder exists."
135
+ fi
136
+
137
+ #REDLAND
138
+ if [ ! -d $STARTPATH/redland ];
139
+ then
140
+ echo "Making Redland folder."
141
+ mkdir redland >>$INSTALLLOG 2>>$ERRLOG
142
+ cd redland
143
+ echo "Installing Redland raptor"
144
+ if [ ! -d $STARTPATH/redland/raptor-$RAPTORVERSION ];
145
+ then
146
+ wget wget http://download.librdf.org/source/raptor-$RAPTORVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
147
+ tar xzfv raptor-$RAPTORVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
148
+ cd raptor-$RAPTORVERSION
149
+ ./configure >>$INSTALLLOG 2>>$ERRLOG
150
+ sudo make >>$INSTALLLOG 2>>$ERRLOG
151
+ sudo make install >>$INSTALLLOG 2>>$ERRLOG
152
+ cd ..
153
+ sudo rm raptor-$RAPTORVERSION.tar.gz
154
+ CHECKRAPTOR=`raptor-config --version`
155
+ if [ "$CHECKRAPTOR" == "$RAPTORVERSION" ]
156
+ then
157
+ echo "================================================="
158
+ echo "Raptor version $RAPTORVERSION successfully installed."
159
+ echo "================================================="
160
+ else
161
+ echo "Raptor version $RAPTORVERSION installation failed."
162
+ FAILED=1
163
+ exit $FAILED
164
+ fi
165
+ else
166
+ echo "raptor-$RAPTORVERSION folder exists."
167
+ fi
168
+
169
+ echo "Installing Redland rasqal"
170
+ wget wget http://download.librdf.org/source/rasqal-$RASQALVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
171
+ tar xzfv rasqal-$RASQALVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
172
+ cd rasqal-$RASQALVERSION
173
+ ./configure >>$INSTALLLOG 2>>$ERRLOG
174
+ sudo make >>$INSTALLLOG 2>>$ERRLOG
175
+ sudo make install >>$INSTALLLOG 2>>$ERRLOG
176
+ cd ..
177
+ sudo rm rasqal-$RASQALVERSION.tar.gz
178
+ CHECKRASQAL=`rasqal-config --version`
179
+ if [ "$CHECKRASQAL" == "$RASQALVERSION2" -o "$CHECKRASQAL" == "$RASQALVERSION" ]
180
+ then
181
+ echo "================================================="
182
+ echo "Raptor version $RASQALVERSION2 or higher successfully installed."
183
+ echo "================================================="
184
+ else
185
+ echo "Raptor version $RASQALVERSION2 or higher installation failed."
186
+ FAILED=1
187
+ exit $FAILED
188
+ fi
189
+
190
+ echo "Installing Redland redland"
191
+ wget wget http://download.librdf.org/source/redland-$REDLANDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
192
+ tar xzfv redland-$REDLANDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
193
+ cd redland-$REDLANDVERSION
194
+ ./configure >>$INSTALLLOG 2>>$ERRLOG
195
+ sudo make >>$INSTALLLOG 2>>$ERRLOG
196
+ sudo make install >>$INSTALLLOG 2>>$ERRLOG
197
+ cd ..
198
+ sudo rm redland-$REDLANDVERSION.tar.gz
199
+ CHECKREDLAND=`redland-config --version`
200
+ if [ "$CHECKREDLAND" == "$REDLANDVERSION" ]
201
+ then
202
+ echo "================================================="
203
+ echo "Redland version $REDLANDVERSION successfully installed."
204
+ echo "================================================="
205
+ else
206
+ echo "Redland version $REDLANDVERSION installation failed."
207
+ FAILED=1
208
+ exit $FAILED
209
+ fi
210
+
211
+
212
+ echo "Installing Redland Bindings with ruby"
213
+ wget http://download.librdf.org/source/redland-bindings-$REDBINDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
214
+ tar xzfv redland-bindings-$REDBINDVERSION.tar.gz >>$INSTALLLOG 2>>$ERRLOG
215
+ cd redland-bindings-$REDBINDVERSION
216
+ ./configure --with-ruby >>$INSTALLLOG 2>>$ERRLOG
217
+ sudo make >>$INSTALLLOG 2>>$ERRLOG
218
+ sudo make install >>$INSTALLLOG 2>>$ERRLOG
219
+ cd ..
220
+ sudo rm redland-bindings-$REDBINDVERSION.tar.gz
221
+ cd ..
222
+ #CHECKREDBIND=`??? --version`
223
+ #if [ "$CHECKREDBIND" == "$REDBINDVERSION" ]
224
+ #then
225
+ # echo "================================================="
226
+ # echo "Redland Bindings version $REDBINDVERSION successfully installed."
227
+ # echo "================================================="
228
+ #else
229
+ # echo "Redland Bindings version $REDBINDVERSION installation failed."
230
+ # FAILED=1
231
+ # exit $FAILED
232
+ #fi
233
+ else
234
+ echo "Redland folder exists."
235
+ fi
236
+
237
+ echo "Installing the opentox webservices"
238
+ mkdir webservices
239
+ cd webservices
240
+
241
+ echo "Install the opentox-ruby-api-wrapper"
242
+ echo "This could take a while..."
243
+ git clone git://github.com/helma/opentox-ruby-api-wrapper.git >>$INSTALLLOG 2>>$ERRLOG
244
+ cd opentox-ruby-api-wrapper
245
+ git checkout -b $BRANCH origin/$BRANCH >>$INSTALLLOG 2>>$ERRLOG
246
+ OTAPIVERSION=`cat VERSION`
247
+ sudo rake install | tee -a $INSTALLLOG
248
+ cd ..
249
+ CHECKOTAPI=`gem list | grep "opentox-ruby-api-wrapper" | grep "$OTAPIVERSION"`
250
+ if [ ! "$CHECKOTAPI" = '' ]
251
+ then
252
+ echo "================================================="
253
+ echo "opentox-ruby-api-wrapper ($OTAPIVERSION) successfully installed."
254
+ echo "================================================="
255
+ else
256
+ 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