opentox-dataset 5.0.0pre1

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Files changed (13) hide show
  1. data/.gitignore +4 -0
  2. data/.yardopts +1 -0
  3. data/ChangeLog +5 -0
  4. data/Gemfile +4 -0
  5. data/LICENSE +674 -0
  6. data/README.md +47 -0
  7. data/Rakefile +1 -0
  8. data/VERSION +1 -0
  9. data/application.rb +452 -0
  10. data/bin/dataset-install +61 -0
  11. data/config.ru +5 -0
  12. data/dataset.gemspec +25 -0
  13. metadata +90 -0
data/bin/dataset-install ADDED
@@ -0,0 +1,61 @@
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+ #!/bin/sh
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+
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+ # Installs Opentox Webservice.
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+ # Author: Christoph Helma, Andreas Maunz.
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+
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+ SELF=$(basename $0 -install)
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+ [ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
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+
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+ # Adjust ruby version here!
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+ RUBY_NUM_VER="1.9.3-p194"
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+
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+ echo
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+ echo "Welcome to service installation (<Return> to continue)."
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+ read delete_me
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+
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+
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+ # check wd is root of service
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+ DIR=`pwd`
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+ if echo $DIR | grep "$SELF/bin" >/dev/null 2>&1 ; then cd ..; fi
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+
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+ # # # Boot the script
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+
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+ # load base config, helper funs, environment
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+ OT_CONFIG_DIR="$HOME/.opentox"
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+ ! [ -f "$OT_CONFIG_DIR/config/install/config.sh" ] && echo "config.sh not found." 1>&2 && exit 1 || . $OT_CONFIG_DIR/config/install/config.sh
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+ ! [ -f "$OT_PREFIX/install/utils.sh" ] && echo "utils.sh not found." 1>&2 && exit 1 || . $OT_PREFIX/install/utils.sh
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+ [ -f $OT_CONFIG_DIR/opentox-ui.sh ] && . $OT_CONFIG_DIR/opentox-ui.sh # should have been done by user already
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+ RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
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+
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+
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+ # # # Install
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+
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+ check_utils "rbenv find"
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+ check_log $SELF
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+
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+ if [ "$OT_BRANCH" = "development" ]; then
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+ cmd="test -d $OT_PREFIX/opentox-server" && run_cmd "$cmd" "Opentox-server"
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+ cmd="test -d $OT_PREFIX/opentox-client" && run_cmd "$cmd" "Opentox-client"
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+ fi
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+
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+
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+ # log directory for this service
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+ [ -d $OT_CONFIG_DIR/config/$SELF ] || cmd="mkdir -p $OT_CONFIG_DIR/config/$SELF" && run_cmd "$cmd" "Config directory"
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+
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+ # ruby
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+ install_ruby
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+
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+ # self
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+ echo
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+ install_with_bundler
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+
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+ # config
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+ [ -f $OT_CONFIG_DIR/config/$SELF.rb ] || touch $OT_CONFIG_DIR/config/$SELF.rb
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+ if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi
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+ if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "aa">/dev/null 2>&1; then echo '$aa = { :uri => nil }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi
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+ if ! cat "$OT_DEFAULT_CONF" | grep "$SELF">/dev/null 2>&1; then echo '$dataset = { :uri => "http://localhost:8083/dataset" }' >> $OT_DEFAULT_CONF; fi
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+
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+ notify
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+
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+ # return to wd
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+ cd "$DIR"
data/config.ru ADDED
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+ SERVICE = "dataset"
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+ require 'bundler'
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+ Bundler.require
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+ require './application.rb'
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+ run OpenTox::Application
data/dataset.gemspec ADDED
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+ # -*- encoding: utf-8 -*-
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+ $:.push File.expand_path("../lib", __FILE__)
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+
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+ Gem::Specification.new do |s|
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+ s.name = "opentox-dataset"
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+ s.version = File.read("./VERSION")
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+ s.authors = ["Christoph Helma"]
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+ s.email = ["helma@in-silico.ch"]
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+ s.homepage = "http://github.com/opentox/dataset"
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+ s.summary = %q{OpenTox Dataset Service}
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+ s.description = %q{OpenTox Dataset Service}
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+ s.license = 'GPL-3'
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+
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+ s.rubyforge_project = "dataset"
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+
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+ s.files = `git ls-files`.split("\n")
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+ s.required_ruby_version = '>= 1.9.2'
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+
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+ # specify any dependencies here; for example:
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+ s.add_runtime_dependency "opentox-server"
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+ s.add_runtime_dependency 'roo'
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+ #s.add_runtime_dependency 'axlsx'
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+ #s.add_runtime_dependency 'simple_xlsx_writer'
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+ s.post_install_message = "Please configure your service in ~/.opentox/config/dataset.rb"
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: opentox-dataset
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+ version: !ruby/object:Gem::Version
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+ version: 5.0.0pre1
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+ prerelease: 5
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+ platform: ruby
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+ authors:
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+ - Christoph Helma
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2012-08-23 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: opentox-server
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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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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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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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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+ - !ruby/object:Gem::Dependency
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+ name: roo
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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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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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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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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+ description: OpenTox Dataset Service
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+ email:
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+ - helma@in-silico.ch
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - .gitignore
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+ - .yardopts
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+ - ChangeLog
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+ - Gemfile
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+ - LICENSE
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+ - README.md
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+ - Rakefile
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+ - VERSION
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+ - application.rb
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+ - bin/dataset-install
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+ - config.ru
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+ - dataset.gemspec
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+ homepage: http://github.com/opentox/dataset
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+ licenses:
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+ - GPL-3
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+ post_install_message: Please configure your service in ~/.opentox/config/dataset.rb
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 1.9.2
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>'
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+ - !ruby/object:Gem::Version
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+ version: 1.3.1
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+ requirements: []
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+ rubyforge_project: dataset
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+ rubygems_version: 1.8.18
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+ signing_key:
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+ specification_version: 3
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+ summary: OpenTox Dataset Service
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+ test_files: []