From fc0397cd0d51df4fe7c23f601c2f211c2ebfbf77 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 26 Jul 2012 16:23:44 +0200
Subject: parameter settting for algorithms and models

---
 lib/model.rb          |  5 +++--
 lib/opentox-client.rb | 24 ++++++++++++++----------
 lib/opentox.rb        | 30 +++++++++++++++++++++++++++++-
 3 files changed, 46 insertions(+), 13 deletions(-)

(limited to 'lib')

diff --git a/lib/model.rb b/lib/model.rb
index 95aa9ff..c104e64 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -6,8 +6,9 @@ module OpenTox
     # @param [Hash] params Parameters for OpenTox model
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [text/uri-list] Task or resource URI
-    def run params=nil
-      post params, {:accept => 'text/uri-list'}
+    def run params=nil, wait=true
+      uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
+      wait_for_task uri if wait
     end
 
   end
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index ad7d3cc..276d378 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -24,13 +24,17 @@ RDF_FORMATS = [:rdfxml,:ntriples,:turtle]
 TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
 FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
 
-require File.join(File.dirname(__FILE__),"overwrite.rb")
-require File.join(File.dirname(__FILE__),"error.rb")
-require File.join(File.dirname(__FILE__),"rest-client-wrapper.rb") 
-require File.join(File.dirname(__FILE__),"authorization.rb") 
-require File.join(File.dirname(__FILE__),"policy.rb") 
-require File.join(File.dirname(__FILE__),"otlogger.rb") # avoid require conflicts with logger
-require File.join(File.dirname(__FILE__),"opentox.rb")
-require File.join(File.dirname(__FILE__),"task.rb")
-require File.join(File.dirname(__FILE__),"compound.rb")
-require File.join(File.dirname(__FILE__),"dataset.rb")
+[
+  "overwrite.rb",
+  "error.rb",
+  "rest-client-wrapper.rb", 
+  "authorization.rb", 
+  "policy.rb", 
+  "otlogger.rb", 
+  "opentox.rb",
+  "task.rb",
+  "compound.rb",
+  "dataset.rb",
+  "model.rb",
+].each{ |f| require File.join(File.dirname(__FILE__),f) }
+
diff --git a/lib/opentox.rb b/lib/opentox.rb
index d3b73fb..2c4578f 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -50,6 +50,30 @@ module OpenTox
     append predicate.to_s, values
   end
 
+  def parameters
+    params = {}
+    query = RDF::Query.new({
+      :parameter => {
+        RDF.type  => RDF::OT.Parameter,
+        :property => :value,
+      }
+    })
+    query.execute(@rdf).each do |solution|
+      params[solution.parameter] = {} unless params[solution.parameter] 
+      params[solution.parameter][solution.property.to_s] = solution.value.to_s
+    end
+    params.values
+  end
+
+  def parameters=(parameters)
+    parameters.each do |param|
+      p_node = RDF::Node.new
+      @rdf << [RDF::URI.new(@uri), RDF::OT.parameters, p_node]
+      @rdf << [p_node, RDF.type, RDF::OT.Parameter]
+      param.each{ |p,o| @rdf << [p_node, p, o] }
+    end
+  end
+
   # Append object metadata
   # @param [String] Predicate URI
   # @param [Array, String] Predicate value(s)
@@ -131,7 +155,11 @@ module OpenTox
     end
   end
 
-  {:title => RDF::DC.title, :dexcription => RDF::DC.description}.each do |method,predicate|
+  {
+    :title => RDF::DC.title,
+    :dexcription => RDF::DC.description,
+    :type => RDF.type
+  }.each do |method,predicate|
     send :define_method, method do 
       self.[](predicate) 
     end
-- 
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