helma-opentox-ruby-api-wrapper 0.1.4 → 0.1.5

data/Rakefile

@@ -11,7 +11,6 @@ begin
     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

data/VERSION

@@ -1 +1 @@
-0.1.4
+0.1.5

data/lib/opentox-ruby-api-wrapper.rb

@@ -1,4 +1,6 @@
-[ 'rest_client', 'crack/xml', 'spork', 'helper' ].each do |lib|
+
+#['rubygems', 'rest_client', 'spork', 'helper' ].each do |lib|
+['rubygems', 'rest_client', 'spork' ].each do |lib|
 	require lib
 end
 
@@ -102,12 +104,7 @@ module OpenTox
 
 		# 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
+			YAML.load(RestClient.get(@uri + '/compounds/features'))
 		end
 
 		# Get all features from a dataset
@@ -143,8 +140,12 @@ module OpenTox
 	class Lazar < OpenTox
 
 		# Create a new prediction model from a dataset
-		def initialize(training_dataset)
-			@uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models/' , :dataset_uri => training_dataset.uri
+		def initialize(params)
+			if params[:uri]
+				@uri = params[:uri]
+			elsif params[:dataset_ur]
+				@uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models/' , :dataset_uri => training_dataset.uri
+			end
 		end
 
 		# Predict a compound

data/opentox-ruby-api-wrapper.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "0.1.4"
+  s.version = "0.1.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
@@ -46,16 +46,13 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<rest-client>, [">= 0"])
-      s.add_runtime_dependency(%q<crack>, [">= 0"])
       s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     else
       s.add_dependency(%q<rest-client>, [">= 0"])
-      s.add_dependency(%q<crack>, [">= 0"])
       s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     end
   else
     s.add_dependency(%q<rest-client>, [">= 0"])
-    s.add_dependency(%q<crack>, [">= 0"])
     s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: helma-opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 0.1.4
+  version: 0.1.5
 platform: ruby
 authors: 
 - Christoph Helma
@@ -22,16 +22,6 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
-- !ruby/object:Gem::Dependency 
-  name: crack
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
-    version: 
 - !ruby/object:Gem::Dependency 
   name: thoughtbot-shoulda
   type: :development