From 1985adc474962f590c5e7331e570fde3dfa3dc5b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 13 Aug 2009 11:03:59 +0200 Subject: gemspec and rdoc documentation added --- .gitignore | 1 - LICENSE | 694 +++++++++++++++++++++++- README.rdoc | 29 +- Rakefile | 8 +- lib/opentox-ruby-api-wrapper.rb | 137 +++++ opentox-ruby-api-wrapper.gemspec | 58 ++ rdoc/classes/OpenTox.html | 115 ++++ rdoc/classes/OpenTox/Compound.html | 247 +++++++++ rdoc/classes/OpenTox/Dataset.html | 331 +++++++++++ rdoc/classes/OpenTox/Feature.html | 217 ++++++++ rdoc/classes/OpenTox/Fminer.html | 178 ++++++ rdoc/classes/OpenTox/OpenTox.html | 162 ++++++ rdoc/created.rid | 1 + rdoc/files/README_rdoc.html | 140 +++++ rdoc/files/lib/opentox-ruby-api-wrapper_rb.html | 109 ++++ rdoc/fr_class_index.html | 32 ++ rdoc/fr_file_index.html | 28 + rdoc/fr_method_index.html | 43 ++ rdoc/index.html | 26 + rdoc/rdoc-style.css | 208 +++++++ 20 files changed, 2728 insertions(+), 36 deletions(-) create mode 100644 opentox-ruby-api-wrapper.gemspec create mode 100644 rdoc/classes/OpenTox.html create mode 100644 rdoc/classes/OpenTox/Compound.html create mode 100644 rdoc/classes/OpenTox/Dataset.html create mode 100644 rdoc/classes/OpenTox/Feature.html create mode 100644 rdoc/classes/OpenTox/Fminer.html create mode 100644 rdoc/classes/OpenTox/OpenTox.html create mode 100644 rdoc/created.rid create mode 100644 rdoc/files/README_rdoc.html create mode 100644 rdoc/files/lib/opentox-ruby-api-wrapper_rb.html create mode 100644 rdoc/fr_class_index.html create mode 100644 rdoc/fr_file_index.html create mode 100644 rdoc/fr_method_index.html create mode 100644 rdoc/index.html create mode 100644 rdoc/rdoc-style.css diff --git a/.gitignore b/.gitignore index 00c0b86..00278f4 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ *.sw? .DS_Store coverage -rdoc pkg diff --git a/LICENSE b/LICENSE index b3e4dc8..94a9ed0 100644 --- a/LICENSE +++ b/LICENSE @@ -1,20 +1,674 @@ -Copyright (c) 2009 Christoph Helma - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. 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Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.rdoc b/README.rdoc index 4b593d1..f33ef93 100644 --- a/README.rdoc +++ b/README.rdoc @@ -1,17 +1,22 @@ = opentox-ruby-api-wrapper -Description goes here. - -== Note on Patches/Pull Requests - -* Fork the project. -* Make your feature addition or bug fix. -* Add tests for it. This is important so I don't break it in a - future version unintentionally. -* Commit, do not mess with rakefile, version, or history. - (if you want to have your own version, that is fine but - bump version in a commit by itself I can ignore when I pull) -* Send me a pull request. Bonus points for topic branches. +Ruby wrapper for the OpenTox REST API (http://www.opentox.org) + +== Installation + +Run the following if you haven't already: + + gem sources -a http://gems.github.com + +Install the gem: + + sudo gem install helma-opentox-ruby-api-wrapper + +== Usage + +- set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the OpenTox REST webservices +- require 'opentox-ruby-api-wrapper' in your ruby application +- consult the API documentation for details == Copyright diff --git a/Rakefile b/Rakefile index db42494..a1b950e 100644 --- a/Rakefile +++ b/Rakefile @@ -5,11 +5,13 @@ begin require 'jeweler' Jeweler::Tasks.new do |gem| gem.name = "opentox-ruby-api-wrapper" - gem.summary = %Q{TODO: one-line summary of your gem} - gem.description = %Q{TODO: longer description of your gem} - gem.email = "helma@in-silico.de" + gem.summary = %Q{Ruby wrapper for the OpenTox REST API} + gem.description = %Q{} + gem.email = "helma@in-silico.ch" gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper" gem.authors = ["Christoph Helma"] + gem.add_dependency "rest-client" + gem.add_dependency "crack" gem.add_development_dependency "thoughtbot-shoulda" # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings end diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb index e69de29..647b357 100644 --- a/lib/opentox-ruby-api-wrapper.rb +++ b/lib/opentox-ruby-api-wrapper.rb @@ -0,0 +1,137 @@ +require 'rest_client' +require 'crack/xml' + +module OpenTox + + class OpenTox + attr_reader :uri + + # Escape all nonword characters + def uri_escape(string) + URI.escape(string, /[^\w]/) + end + end + + class Compound < OpenTox + + # Initialize with :uri => uri, :smiles => smiles or :name => name (name can be also an InChI/InChiKey, CAS number, etc) + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + elsif params[:smiles] + @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:smiles => uri_escape(params[:smiles]) + elsif params[:name] + @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:name => uri_escape(params[:name]) + end + end + + # Get the (canonical) smiles + def smiles + RestClient.get @uri + end + + # Matchs a smarts string + def match?(smarts) + if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true' + true + else + false + end + end + + # Match an array of smarts features, returns matching features + def match(smarts_features) + smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact + end + + end + + class Feature < OpenTox + + # Initialize with :uri => uri, or :name => name, :values => hash_of_property_names_and_values + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + else + @uri = ENV['OPENTOX_FEATURES'] + uri_escape(params[:name]) + params[:values].each do |k,v| + @uri += '/' + k.to_s + '/' + v.to_s + end + end + end + + # Get the value of a property + def value(property) + RestClient.get @uri + '/' + property + end + + # Get the name of the feature + def name + RestClient.get @uri + '/name' + end + + end + + class Dataset < OpenTox + + # Initialize with :uri => uri or :name => name (creates a new dataset) + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + elsif params[:name] + @uri = RestClient.post ENV['OPENTOX_DATASETS'], :name => params[:name] + RestClient.delete @uri + '/associations' + end + end + + # Get the dataset name + def name + RestClient.get @uri + '/name' + end + + # Get all compounds from a dataset + def compounds + RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) } + end + + # Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of features as values + def all_compounds_and_features + compounds = {} + Crack::XML.parse(RestClient.get @uri + '/compounds/features')['dataset']['compound'].each do |c| + features = c['feature_uri'].collect{ |f| Feature.new :uri => f } + compounds[c['uri']] = features + end + compounds + end + + # Get all features from a dataset + def all_features + RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)} + end + + # Get all features for a compound + def features(compound) + RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) } + end + + # Add a compound and a feature to a dataset + def add(compound,feature) + RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri + end + + end + + class Fminer < OpenTox + + # Create a new dataset with BBRC features + def initialize(training_dataset) + @dataset_uri = RestClient.post ENV['OPENTOX_FMINER'], :dataset_uri => training_dataset.uri + end + + def dataset + Dataset.new(:uri => @dataset_uri) + end + + end + +end diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec new file mode 100644 index 0000000..cd99a9b --- /dev/null +++ b/opentox-ruby-api-wrapper.gemspec @@ -0,0 +1,58 @@ +# Generated by jeweler +# DO NOT EDIT THIS FILE +# Instead, edit Jeweler::Tasks in Rakefile, and run `rake gemspec` +# -*- encoding: utf-8 -*- + +Gem::Specification.new do |s| + s.name = %q{opentox-ruby-api-wrapper} + s.version = "0.1.0" + + s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= + s.authors = ["Christoph Helma"] + s.date = %q{2009-08-13} + s.description = %q{} + s.email = %q{helma@in-silico.ch} + s.extra_rdoc_files = [ + "LICENSE", + "README.rdoc" + ] + s.files = [ + ".document", + ".gitignore", + "LICENSE", + "README.rdoc", + "Rakefile", + "VERSION", + "lib/opentox-ruby-api-wrapper.rb", + "test/opentox-ruby-api-wrapper_test.rb", + "test/test_helper.rb" + ] + s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper} + s.rdoc_options = ["--charset=UTF-8"] + s.require_paths = ["lib"] + s.rubygems_version = %q{1.3.5} + s.summary = %q{Ruby wrapper for the OpenTox REST API} + s.test_files = [ + "test/test_helper.rb", + "test/opentox-ruby-api-wrapper_test.rb" + ] + + if s.respond_to? :specification_version then + current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION + s.specification_version = 3 + + if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then + s.add_runtime_dependency(%q, [">= 0"]) + s.add_runtime_dependency(%q, [">= 0"]) + s.add_development_dependency(%q, [">= 0"]) + else + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + end + else + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + end +end diff --git a/rdoc/classes/OpenTox.html b/rdoc/classes/OpenTox.html new file mode 100644 index 0000000..21b7032 --- /dev/null +++ b/rdoc/classes/OpenTox.html @@ -0,0 +1,115 @@ + + + + + + Module: OpenTox + + + + + + + + + + +
+ + + + + + + + + + +
ModuleOpenTox
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
+
+ + +
+ + + +
+ + + +
+ + +
+ + + + +
+ +
+

Classes and Modules

+ + Class OpenTox::Compound
+Class OpenTox::Dataset
+Class OpenTox::Feature
+Class OpenTox::Fminer
+Class OpenTox::OpenTox
+ +
+ + + + + + + + + + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/classes/OpenTox/Compound.html b/rdoc/classes/OpenTox/Compound.html new file mode 100644 index 0000000..c892d0e --- /dev/null +++ b/rdoc/classes/OpenTox/Compound.html @@ -0,0 +1,247 @@ + + + + + + Class: OpenTox::Compound + + + + + + + + + + +
+ + + + + + + + + + + + + + +
ClassOpenTox::Compound
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
Parent: + + OpenTox + +
+
+ + +
+ + + +
+ + + +
+ +
+

Methods

+ +
+ match   + match?   + new   + smiles   +
+
+ +
+ + + + +
+ + + + + + + + + +
+

Public Class methods

+ +
+ + +
+ + new(params) + +
+ +
+

+Initialize with :uri => uri, :smiles => smiles or :name => name +(name can be also an InChI/InChiKey, CAS number, etc) +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 18
+                def initialize(params)
+                        if params[:uri]
+                                @uri = params[:uri].to_s
+                        elsif params[:smiles]
+                                @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:smiles => uri_escape(params[:smiles])
+                        elsif params[:name]
+                                @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:name => uri_escape(params[:name])
+                        end
+                end
+
+
+
+
+ +

Public Instance methods

+ +
+ + +
+ + match(smarts_features) + +
+ +
+

+Match an array of smarts features, returns matching features +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 43
+                def match(smarts_features)
+                        smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
+                end
+
+
+
+
+ +
+ + +
+ + match?(smarts) + +
+ +
+

+Matchs a smarts string +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 34
+                def match?(smarts)
+                        if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true'
+                                true
+                        else
+                                false
+                        end
+                end
+
+
+
+
+ +
+ + +
+ + smiles() + +
+ +
+

+Get the (canonical) smiles +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 29
+                def smiles
+                        RestClient.get @uri
+                end
+
+
+
+
+ + +
+ + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/classes/OpenTox/Dataset.html b/rdoc/classes/OpenTox/Dataset.html new file mode 100644 index 0000000..f6966f7 --- /dev/null +++ b/rdoc/classes/OpenTox/Dataset.html @@ -0,0 +1,331 @@ + + + + + + Class: OpenTox::Dataset + + + + + + + + + + +
+ + + + + + + + + + + + + + +
ClassOpenTox::Dataset
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
Parent: + + OpenTox + +
+
+ + +
+ + + +
+ + + +
+ +
+

Methods

+ +
+ add   + all_compounds_and_features   + all_features   + compounds   + features   + name   + new   +
+
+ +
+ + + + +
+ + + + + + + + + +
+

Public Class methods

+ +
+ + +
+ + new(params) + +
+ +
+

+Initialize with :uri => uri or :name => name (creates a new dataset) +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 78
+                def initialize(params)
+                        if params[:uri]
+                                @uri = params[:uri].to_s
+                        elsif params[:name] 
+                                @uri = RestClient.post ENV['OPENTOX_DATASETS'], :name => params[:name]
+                                RestClient.delete @uri + '/associations'
+                        end
+                end
+
+
+
+
+ +

Public Instance methods

+ +
+ + +
+ + add(compound,feature) + +
+ +
+

+Add a compound and a feature to a dataset +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 118
+                def add(compound,feature)
+                        RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
+                end
+
+
+
+
+ +
+ + +
+ + all_compounds_and_features() + +
+ +
+

+Get all compounds and features from a dataset, returns a hash +with compound_uris as keys and arrays of features as values +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 98
+                def all_compounds_and_features
+                        compounds = {}
+                        Crack::XML.parse(RestClient.get @uri + '/compounds/features')['dataset']['compound'].each do |c|
+                                features = c['feature_uri'].collect{ |f| Feature.new :uri => f }
+                                compounds[c['uri']] = features
+                        end
+                        compounds
+                end
+
+
+
+
+ +
+ + +
+ + all_features() + +
+ +
+

+Get all features from a dataset +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 108
+                def all_features
+                        RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)}
+                end
+
+
+
+
+ +
+ + +
+ + compounds() + +
+ +
+

+Get all compounds from a dataset +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 93
+                def compounds
+                        RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) }
+                end
+
+
+
+
+ +
+ + +
+ + features(compound) + +
+ +
+

+Get all features for a compound +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 113
+                def features(compound)
+                        RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) }
+                end
+
+
+
+
+ +
+ + +
+ + name() + +
+ +
+

+Get the dataset name +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 88
+                def name
+                        RestClient.get @uri + '/name'
+                end
+
+
+
+
+ + +
+ + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/classes/OpenTox/Feature.html b/rdoc/classes/OpenTox/Feature.html new file mode 100644 index 0000000..5e53a12 --- /dev/null +++ b/rdoc/classes/OpenTox/Feature.html @@ -0,0 +1,217 @@ + + + + + + Class: OpenTox::Feature + + + + + + + + + + +
+ + + + + + + + + + + + + + +
ClassOpenTox::Feature
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
Parent: + + OpenTox + +
+
+ + +
+ + + +
+ + + +
+ +
+

Methods

+ +
+ name   + new   + value   +
+
+ +
+ + + + +
+ + + + + + + + + +
+

Public Class methods

+ +
+ + +
+ + new(params) + +
+ +
+

+Initialize with :uri => uri, or :name => name, :values => +hash_of_property_names_and_values +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 52
+                def initialize(params)
+                        if params[:uri]
+                                @uri = params[:uri].to_s
+                        else
+                                @uri = ENV['OPENTOX_FEATURES'] + uri_escape(params[:name]) 
+                                params[:values].each do |k,v|
+                                        @uri += '/' + k.to_s + '/' + v.to_s
+                                end
+                        end
+                end
+
+
+
+
+ +

Public Instance methods

+ +
+ + +
+ + name() + +
+ +
+

+Get the name of the feature +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 69
+                def name
+                        RestClient.get @uri + '/name'
+                end
+
+
+
+
+ +
+ + +
+ + value(property) + +
+ +
+

+Get the value of a property +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 64
+                def value(property)
+                        RestClient.get @uri + '/' + property
+                end
+
+
+
+
+ + +
+ + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/classes/OpenTox/Fminer.html b/rdoc/classes/OpenTox/Fminer.html new file mode 100644 index 0000000..6c3b4fe --- /dev/null +++ b/rdoc/classes/OpenTox/Fminer.html @@ -0,0 +1,178 @@ + + + + + + Class: OpenTox::Fminer + + + + + + + + + + +
+ + + + + + + + + + + + + + +
ClassOpenTox::Fminer
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
Parent: + + OpenTox + +
+
+ + +
+ + + +
+ + + +
+ +
+

Methods

+ +
+ dataset   + new   +
+
+ +
+ + + + +
+ + + + + + + + + +
+

Public Class methods

+ +
+ + +
+ + new(training_dataset) + +
+ +
+

+Create a new dataset with BBRC features +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 127
+                def initialize(training_dataset)
+                        @dataset_uri = RestClient.post ENV['OPENTOX_FMINER'], :dataset_uri => training_dataset.uri
+                end
+
+
+
+
+ +

Public Instance methods

+ +
+ + +
+ + dataset() + +
+ +
+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 131
+                def dataset
+                        Dataset.new(:uri => @dataset_uri)
+                end
+
+
+
+
+ + +
+ + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/classes/OpenTox/OpenTox.html b/rdoc/classes/OpenTox/OpenTox.html new file mode 100644 index 0000000..35611f8 --- /dev/null +++ b/rdoc/classes/OpenTox/OpenTox.html @@ -0,0 +1,162 @@ + + + + + + Class: OpenTox::OpenTox + + + + + + + + + + +
+ + + + + + + + + + + + + + +
ClassOpenTox::OpenTox
In: + + lib/opentox-ruby-api-wrapper.rb + +
+
Parent: + Object +
+
+ + +
+ + + +
+ + + +
+ +
+

Methods

+ +
+ uri_escape   +
+
+ +
+ + + + +
+ + + + + +
+

Attributes

+ +
+ + + + + + +
uri [R] 
+
+
+ + + + +
+

Public Instance methods

+ +
+ + +
+ + uri_escape(string) + +
+ +
+

+Escape all nonword characters +

+

[Source]

+
+
+# File lib/opentox-ruby-api-wrapper.rb, line 10
+                def uri_escape(string)
+                        URI.escape(string, /[^\w]/)
+                end
+
+
+
+
+ + +
+ + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/created.rid b/rdoc/created.rid new file mode 100644 index 0000000..8dc2058 --- /dev/null +++ b/rdoc/created.rid @@ -0,0 +1 @@ +Thu, 13 Aug 2009 11:01:58 +0200 diff --git a/rdoc/files/README_rdoc.html b/rdoc/files/README_rdoc.html new file mode 100644 index 0000000..3342971 --- /dev/null +++ b/rdoc/files/README_rdoc.html @@ -0,0 +1,140 @@ + + + + + + File: README.rdoc + + + + + + + + + + +
+

README.rdoc

+ + + + + + + + + +
Path:README.rdoc +
Last Update:Thu Aug 13 11:00:51 +0200 2009
+
+ + +
+ + + +
+ +
+

opentox-ruby-api-wrapper

+

+Ruby wrapper for the OpenTox REST API +(www.opentox.org) +

+

Installation

+

+Run the following if you haven‘t already: +

+
+        gem sources -a http://gems.github.com
+
+

+Install the gem: +

+
+        sudo gem install helma-opentox-ruby-api-wrapper
+
+

Usage

+
    +
  • set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, +OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the OpenTox REST webservices + +
    • +
  • require ‘opentox-ruby-api-wrapper’ in your ruby application + +
    • +
  • consult the API documentation for details + +
    • +
+

Copyright

+

+Copyright (c) 2009 Christoph Helma. See LICENSE for details. +

+ +
+ + +
+ + +
+ + + + +
+ + + + + + + + + + + +
+ + + + + + \ No newline at end of file diff --git a/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html new file mode 100644 index 0000000..be6ca28 --- /dev/null +++ b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html @@ -0,0 +1,109 @@ + + + + + + File: opentox-ruby-api-wrapper.rb + + + + + + + + + + +
+

opentox-ruby-api-wrapper.rb

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Path:lib/opentox-ruby-api-wrapper.rb +
Last Update:Thu Aug 13 10:44:46 +0200 2009
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Required files

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+ rest_client   + crack/xml   +
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+ + + + + + \ No newline at end of file diff --git a/rdoc/fr_class_index.html b/rdoc/fr_class_index.html new file mode 100644 index 0000000..7242f18 --- /dev/null +++ b/rdoc/fr_class_index.html @@ -0,0 +1,32 @@ + + + + + + + + Classes + + + + + + + + \ No newline at end of file diff --git a/rdoc/fr_file_index.html b/rdoc/fr_file_index.html new file mode 100644 index 0000000..eac1d09 --- /dev/null +++ b/rdoc/fr_file_index.html @@ -0,0 +1,28 @@ + + + + + + + + Files + + + + + + + + \ No newline at end of file diff --git a/rdoc/fr_method_index.html b/rdoc/fr_method_index.html new file mode 100644 index 0000000..63abf5e --- /dev/null +++ b/rdoc/fr_method_index.html @@ -0,0 +1,43 @@ + + + + + + + + Methods + + + + + + + + \ No newline at end of file diff --git a/rdoc/index.html b/rdoc/index.html new file mode 100644 index 0000000..bb24624 --- /dev/null +++ b/rdoc/index.html @@ -0,0 +1,26 @@ + + + + + + + opentox-ruby-api-wrapper 0.1.0 + + + + + + + + + + + + \ No newline at end of file diff --git a/rdoc/rdoc-style.css b/rdoc/rdoc-style.css new file mode 100644 index 0000000..44c7b3d --- /dev/null +++ b/rdoc/rdoc-style.css @@ -0,0 +1,208 @@ + +body { + font-family: Verdana,Arial,Helvetica,sans-serif; + font-size: 90%; + margin: 0; + margin-left: 40px; + padding: 0; + background: white; +} + +h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; } +h1 { font-size: 150%; } +h2,h3,h4 { margin-top: 1em; } + +a { background: #eef; color: #039; text-decoration: none; } +a:hover { background: #039; color: #eef; } + +/* Override the base stylesheet's Anchor inside a table cell */ +td > a { + background: transparent; + color: #039; + text-decoration: none; +} + +/* and inside a section title */ +.section-title > a { + background: transparent; + color: #eee; + text-decoration: none; +} + +/* === Structural elements =================================== */ + +div#index { + margin: 0; + margin-left: -40px; + padding: 0; + font-size: 90%; +} + + +div#index a { + margin-left: 0.7em; +} + +div#index .section-bar { + margin-left: 0px; + padding-left: 0.7em; + background: #ccc; + font-size: small; +} + + +div#classHeader, div#fileHeader { + width: auto; + color: white; + padding: 0.5em 1.5em 0.5em 1.5em; + margin: 0; + margin-left: -40px; + border-bottom: 3px solid #006; +} + +div#classHeader a, div#fileHeader a { + background: inherit; + color: white; +} + +div#classHeader td, div#fileHeader td { + background: inherit; + color: white; +} + + +div#fileHeader { + background: #057; +} + +div#classHeader { + background: #048; +} + + +.class-name-in-header { + font-size: 180%; + font-weight: bold; +} + + +div#bodyContent { + padding: 0 1.5em 0 1.5em; +} + +div#description { + padding: 0.5em 1.5em; + background: #efefef; + border: 1px dotted #999; +} + +div#description h1,h2,h3,h4,h5,h6 { + color: #125;; + background: transparent; +} + +div#validator-badges { + text-align: center; +} +div#validator-badges img { border: 0; } + +div#copyright { + color: #333; + background: #efefef; + font: 0.75em sans-serif; + margin-top: 5em; + margin-bottom: 0; + padding: 0.5em 2em; +} + + +/* === Classes =================================== */ + +table.header-table { + color: white; + font-size: small; +} + +.type-note { + font-size: small; + color: #DEDEDE; +} + +.xxsection-bar { + background: #eee; + color: #333; + padding: 3px; +} + +.section-bar { + color: #333; + border-bottom: 1px solid #999; + margin-left: -20px; +} + + +.section-title { + background: #79a; + color: #eee; + padding: 3px; + margin-top: 2em; + margin-left: -30px; + border: 1px solid #999; +} + +.top-aligned-row { vertical-align: top } +.bottom-aligned-row { vertical-align: bottom } + +/* --- Context section classes ----------------------- */ + +.context-row { } +.context-item-name { font-family: monospace; font-weight: bold; color: black; } +.context-item-value { font-size: small; color: #448; } +.context-item-desc { color: #333; padding-left: 2em; } + +/* --- Method classes -------------------------- */ +.method-detail { + background: #efefef; + padding: 0; + margin-top: 0.5em; + margin-bottom: 1em; + border: 1px dotted #ccc; +} +.method-heading { + color: black; + background: #ccc; + border-bottom: 1px solid #666; + padding: 0.2em 0.5em 0 0.5em; +} +.method-signature { color: black; background: inherit; } +.method-name { font-weight: bold; } +.method-args { font-style: italic; } +.method-description { padding: 0 0.5em 0 0.5em; } + +/* --- Source code sections -------------------- */ + +a.source-toggle { font-size: 90%; } +div.method-source-code { + background: #262626; + color: #ffdead; + margin: 1em; + padding: 0.5em; + border: 1px dashed #999; + overflow: hidden; +} + +div.method-source-code pre { color: #ffdead; overflow: hidden; } + +/* --- Ruby keyword styles --------------------- */ + +.standalone-code { background: #221111; color: #ffdead; overflow: hidden; } + +.ruby-constant { color: #7fffd4; background: transparent; } +.ruby-keyword { color: #00ffff; background: transparent; } +.ruby-ivar { color: #eedd82; background: transparent; } +.ruby-operator { color: #00ffee; background: transparent; } +.ruby-identifier { color: #ffdead; background: transparent; } +.ruby-node { color: #ffa07a; background: transparent; } +.ruby-comment { color: #b22222; font-weight: bold; background: transparent; } +.ruby-regexp { color: #ffa07a; background: transparent; } +.ruby-value { color: #7fffd4; background: transparent; } \ No newline at end of file -- cgit v1.2.3