martins modifications merged and adjusted

6 files changed, 19 insertions, 11 deletions

diff --git a/Rakefile b/Rakefile
index 2dfb2c6..4c9e00a 100644
--- a/Rakefile
+++ b/Rakefile
@@ -13,7 +13,7 @@ begin
 		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
 			gem.add_dependency dep
 		end
-		['cucumber','jeweler', "thin"].each do |dep|
+		['cucumber','jeweler'].each do |dep|
 			gem.add_development_dependency dep
 		end
 		gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 8083db2..eaf1f7e 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -21,8 +21,9 @@ module OpenTox
 			def self.create_model(params)
 				LOGGER.debug params
 				LOGGER.debug File.basename(__FILE__) + ": creating model"
+				LOGGER.debug File.join(@@config[:services]["opentox-algorithm"], "lazar")
         resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
-        @uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp
+        @uri = resource.post(:dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).body.chomp
 			end
 
 			def self.uri
diff --git a/lib/dataset.rb b/lib/dataset.rb
index c513463..3cfe639 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -14,9 +14,10 @@ module OpenTox
 
 		def self.find(uri)
     
-			if uri.match(/webservices.in-silico.ch|localhost|ot.dataset.de|opentox.informatik.uni-freiburg.de/) # try to get YAML first
+			#if uri.match(/webservices.in-silico.ch|localhost|ot.dataset.de|opentox.informatik.uni-freiburg.de/) # try to get YAML first
 				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s 
         d.uri = uri unless d.uri
+=begin
 			else # get default rdf+xml
 				owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
         
@@ -33,6 +34,7 @@ module OpenTox
         d.compounds.uniq!
         d.features.uniq!
 		  end
+=end
       return d
 		end
     
diff --git a/lib/environment.rb b/lib/environment.rb
index b46bf19..29dcbdb 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -46,7 +46,7 @@ before {$sinatra = self unless $sinatra}
 class Sinatra::Base
   # overwriting halt to log halts (!= 202)
   def halt(*response)
-    LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response.first >= 300
+    LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300
     # orig sinatra code:
     response = response.first if response.length == 1
     throw :halt, response
diff --git a/lib/validation.rb b/lib/validation.rb
index 6fd5704..97aafc4 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -4,8 +4,14 @@ module OpenTox
 		attr_accessor :uri
 
 		def initialize(params)
-			resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			@uri = resource.post(params).to_s
+			#resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			#@uri = resource.post(params).to_s
+			call = "curl -X POST "
+			params.each do |k,v|
+				call += " -d "+k.to_s+"=\""+v.to_s+"\"" unless k == :uri
+			end
+			call += " "+params[:uri]
+			LOGGER.debug call
 		end
 		
 		def self.crossvalidation(params)
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 258ee09..e30b56f 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -9,10 +9,10 @@ Gem::Specification.new do |s|
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2010-03-18}
+  s.date = %q{2010-05-04}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
-  s.executables = ["opentox-install-ubuntu.sh", "opentox-install-debian.sh", "yaml2owl.rb"]
+  s.executables = ["opentox-install-ubuntu.sh", "yaml2owl.rb", "opentox-install-debian.sh"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -31,11 +31,13 @@ Gem::Specification.new do |s|
      "lib/config/config_ru.rb",
      "lib/dataset.rb",
      "lib/environment.rb",
+     "lib/features.rb",
      "lib/helper.rb",
      "lib/model.rb",
      "lib/opentox-ruby-api-wrapper.rb",
      "lib/opentox.owl",
      "lib/owl.rb",
+     "lib/rest_client_wrapper.rb",
      "lib/spork.rb",
      "lib/task.rb",
      "lib/tasks/opentox.rb",
@@ -67,7 +69,6 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"])
       s.add_development_dependency(%q<cucumber>, [">= 0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<thin>, [">= 0"])
     else
       s.add_dependency(%q<sinatra>, [">= 0"])
       s.add_dependency(%q<rest-client>, [">= 0"])
@@ -81,7 +82,6 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
       s.add_dependency(%q<cucumber>, [">= 0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<thin>, [">= 0"])
     end
   else
     s.add_dependency(%q<sinatra>, [">= 0"])
@@ -96,7 +96,6 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
     s.add_dependency(%q<cucumber>, [">= 0"])
     s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<thin>, [">= 0"])
   end
 end