From d262dbc79c9f5d8e2d74647df52a9c44e1af511d Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 6 May 2010 17:42:03 +0200
Subject: martins modifications merged and adjusted

---
 lib/algorithm.rb   |  3 ++-
 lib/dataset.rb     |  4 +++-
 lib/environment.rb |  2 +-
 lib/validation.rb  | 10 ++++++++--
 4 files changed, 14 insertions(+), 5 deletions(-)

(limited to 'lib')

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)
-- 
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