opentox-ruby 0.0.2 → 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.markdown +41 -0
 - data/Rakefile +4 -0
 - data/VERSION +1 -1
 - data/lib/algorithm.rb +15 -2
 - data/lib/authorization.rb +381 -0
 - data/lib/compound.rb +6 -0
 - data/lib/config/config_ru.rb +1 -0
 - data/lib/dataset.rb +98 -43
 - data/lib/environment.rb +9 -18
 - data/lib/error.rb +99 -0
 - data/lib/feature.rb +30 -2
 - data/lib/helper.rb +90 -17
 - data/lib/model.rb +81 -34
 - data/lib/ontology_service.rb +43 -0
 - data/lib/opentox-ruby.rb +3 -2
 - data/lib/opentox.rb +9 -4
 - data/lib/overwrite.rb +87 -28
 - data/lib/parser.rb +117 -22
 - data/lib/policy.rb +261 -0
 - data/lib/rest_client_wrapper.rb +110 -99
 - data/lib/serializer.rb +130 -1
 - data/lib/task.rb +179 -42
 - data/lib/templates/config.yaml +45 -0
 - data/lib/templates/default_guest_policy.xml +53 -0
 - data/lib/templates/default_policy.xml +53 -0
 - data/lib/to-html.rb +112 -0
 - data/lib/validation.rb +183 -57
 - metadata +31 -94
 - data/README.rdoc +0 -23
 
    
        metadata
    CHANGED
    
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         @@ -1,13 +1,13 @@ 
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            --- !ruby/object:Gem::Specification 
         
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            name: opentox-ruby
         
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            version: !ruby/object:Gem::Version 
         
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            -
              hash:  
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            -
              prerelease:  
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              hash: 23
         
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              prerelease: 
         
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              segments: 
         
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              - 1
         
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              - 0
         
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              - 0
         
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            -
               
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            -
              version: 0.0.2
         
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              version: 1.0.0
         
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            platform: ruby
         
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            authors: 
         
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            - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
         
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         @@ -15,7 +15,7 @@ autorequire: 
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            bindir: bin
         
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            cert_chain: []
         
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            -
            date:  
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            +
            date: 2011-03-09 00:00:00 +01:00
         
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            default_executable: 
         
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            dependencies: 
         
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            - !ruby/object:Gem::Dependency 
         
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         @@ -243,7 +243,7 @@ dependencies: 
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              type: :runtime
         
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              version_requirements: *id016
         
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            - !ruby/object:Gem::Dependency 
         
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            -
              name:  
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              name: ohm
         
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              prerelease: false
         
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              requirement: &id017 !ruby/object:Gem::Requirement 
         
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                none: false
         
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         @@ -257,107 +257,37 @@ dependencies: 
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              type: :runtime
         
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              version_requirements: *id017
         
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            - !ruby/object:Gem::Dependency 
         
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              name:  
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              name: SystemTimer
         
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              prerelease: false
         
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              requirement: &id018 !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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            -
                    hash:  
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                    hash: 3
         
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                    segments: 
         
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            -
                    -  
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                    version: " 
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            +
                    - 0
         
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                    version: "0"
         
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              type: :runtime
         
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              version_requirements: *id018
         
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            - !ruby/object:Gem::Dependency 
         
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              name:  
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              name: rjb
         
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              prerelease: false
         
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              requirement: &id019 !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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            -
                    hash:  
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            +
                    hash: 3
         
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                    segments: 
         
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            -
                    -  
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                    version: " 
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            +
                    - 0
         
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            +
                    version: "0"
         
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              type: :runtime
         
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              version_requirements: *id019
         
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            -
            - !ruby/object:Gem::Dependency 
         
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            -
              name: dm-timestamps
         
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              prerelease: false
         
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            -
              requirement: &id020 !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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            -
                    hash: 1
         
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            -
                    segments: 
         
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                    - 1
         
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            -
                    version: "1"
         
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              type: :runtime
         
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              version_requirements: *id020
         
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            -
            - !ruby/object:Gem::Dependency 
         
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              name: dm-types
         
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              prerelease: false
         
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            -
              requirement: &id021 !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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            -
                    hash: 1
         
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                    segments: 
         
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            -
                    - 1
         
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                    version: "1"
         
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              type: :runtime
         
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              version_requirements: *id021
         
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            -
            - !ruby/object:Gem::Dependency 
         
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              name: dm-migrations
         
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              prerelease: false
         
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              requirement: &id022 !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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            -
                    hash: 1
         
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                    segments: 
         
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                    - 1
         
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                    version: "1"
         
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              type: :runtime
         
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              version_requirements: *id022
         
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            - !ruby/object:Gem::Dependency 
         
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              name: dm-mysql-adapter
         
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              prerelease: false
         
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              requirement: &id023 !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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                    hash: 1
         
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                    segments: 
         
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                    - 1
         
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                    version: "1"
         
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              type: :runtime
         
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              version_requirements: *id023
         
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            - !ruby/object:Gem::Dependency 
         
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              name: dm-validations
         
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              prerelease: false
         
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              requirement: &id024 !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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            -
                    hash: 1
         
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                    segments: 
         
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                    - 1
         
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                    version: "1"
         
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              type: :runtime
         
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            - !ruby/object:Gem::Dependency 
         
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              name: haml
         
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              prerelease: false
         
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              requirement: & 
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              requirement: &id020 !ruby/object:Gem::Requirement 
         
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                none: false
         
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                requirements: 
         
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                - - ">="
         
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                    - 3
         
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                    version: "3"
         
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              type: :runtime
         
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              version_requirements: *id020
         
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            - !ruby/object:Gem::Dependency 
         
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              name: jeweler
         
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              prerelease: false
         
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              requirement: & 
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              requirement: &id021 !ruby/object:Gem::Requirement 
         
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                none: false
         
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                requirements: 
         
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                - - ">="
         
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                    - 0
         
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                    version: "0"
         
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              type: :development
         
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              version_requirements: *id021
         
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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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            - opentox-install-ubuntu.sh
         
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            - opentox-install-debian.sh
         
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            - opentox-install-ubuntu.sh
         
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            extensions: []
         
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            extra_rdoc_files: 
         
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            - LICENSE
         
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            -
            - README. 
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            - README.markdown
         
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            files: 
         
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            - LICENSE
         
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            - README. 
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            - README.markdown
         
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            - Rakefile
         
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            - VERSION
         
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            - bin/opentox-install-debian.sh
         
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            - bin/opentox-install-ubuntu.sh
         
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            - lib/algorithm.rb
         
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            - lib/authorization.rb
         
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            - lib/compound.rb
         
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            - lib/config/config_ru.rb
         
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            - lib/dataset.rb
         
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       406 
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            - lib/environment.rb
         
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            - lib/error.rb
         
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            - lib/feature.rb
         
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            - lib/helper.rb
         
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            - lib/model.rb
         
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            - lib/ontology_service.rb
         
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            - lib/opentox-ruby.rb
         
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            - lib/opentox.owl
         
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            - lib/opentox.rb
         
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            - lib/overwrite.rb
         
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            - lib/parser.rb
         
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            - lib/policy.rb
         
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            - lib/rest_client_wrapper.rb
         
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            - lib/serializer.rb
         
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            - lib/spork.rb
         
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            - lib/task.rb
         
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            - lib/templates/config.yaml
         
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            - lib/templates/default_guest_policy.xml
         
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            +
            - lib/templates/default_policy.xml
         
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            +
            - lib/to-html.rb
         
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       420 
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            - lib/validation.rb
         
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            has_rdoc: true
         
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            homepage: http://github.com/helma/opentox-ruby
         
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            licenses: []
         
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            post_install_message: 
         
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            rdoc_options: 
         
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            -
             
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 363 
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            +
            rdoc_options: []
         
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            +
             
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       428 
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     | 
    
         
             
            require_paths: 
         
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       429 
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            - lib
         
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            required_ruby_version: !ruby/object:Gem::Requirement 
         
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| 
         @@ -448,7 +385,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement 
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       448 
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            requirements: []
         
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            rubyforge_project: 
         
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       451 
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            -
            rubygems_version: 1. 
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| 
      
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            +
            rubygems_version: 1.4.2
         
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            signing_key: 
         
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       453 
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     | 
    
         
             
            specification_version: 3
         
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       454 
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            summary: Ruby wrapper for the OpenTox REST API
         
     | 
    
        data/README.rdoc
    DELETED
    
    | 
         @@ -1,23 +0,0 @@ 
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|
| 
       1 
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            -
            = opentox-ruby
         
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       2 
     | 
    
         
            -
             
     | 
| 
       3 
     | 
    
         
            -
            Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
         
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| 
       4 
     | 
    
         
            -
             
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| 
       5 
     | 
    
         
            -
            == Installation
         
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| 
       6 
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            -
             
     | 
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       7 
     | 
    
         
            -
            Run the following if you haven't already:
         
     | 
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       8 
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            -
             
     | 
| 
       9 
     | 
    
         
            -
            	gem sources -a http://gems.github.com
         
     | 
| 
       10 
     | 
    
         
            -
             
     | 
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       11 
     | 
    
         
            -
            Install the gem:
         
     | 
| 
       12 
     | 
    
         
            -
             
     | 
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       13 
     | 
    
         
            -
            	sudo gem install helma-opentox-ruby 
         
     | 
| 
       14 
     | 
    
         
            -
             
     | 
| 
       15 
     | 
    
         
            -
            == Usage
         
     | 
| 
       16 
     | 
    
         
            -
             
     | 
| 
       17 
     | 
    
         
            -
            - adjust the settings in $HOME/.opentox/config
         
     | 
| 
       18 
     | 
    
         
            -
            - require 'opentox-ruby' in your ruby application
         
     | 
| 
       19 
     | 
    
         
            -
            - consult the rdoc API documentation for details 
         
     | 
| 
       20 
     | 
    
         
            -
             
     | 
| 
       21 
     | 
    
         
            -
            == Copyright
         
     | 
| 
       22 
     | 
    
         
            -
             
     | 
| 
       23 
     | 
    
         
            -
            Copyright (c) 2009-2010 Christoph Helma. See LICENSE for details.
         
     |