From 6c35e3f8369ba96cb251eac487424bd949fdcf6c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 2 Jul 2013 19:23:01 +0200
Subject: Algorithms and Models are modules instead of classes.

---
 lib/algorithm.rb | 57 +++++++++++++++++++++++++++++++++++++-------------------
 1 file changed, 38 insertions(+), 19 deletions(-)

(limited to 'lib/algorithm.rb')

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 1ffc883..7d9a5a2 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,7 +1,8 @@
 module OpenTox
 
   # Wrapper for OpenTox Algorithms
-  class Algorithm
+  module Algorithm
+    include OpenTox
 
     # Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters
     # @param [optional,Hash] params Algorithm parameters
@@ -11,32 +12,50 @@ module OpenTox
       uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
       wait_for_task uri if wait
     end
-  end
 
-  module Descriptor
+    class Generic
+      include OpenTox
+      include Algorithm
+    end
 
-    class Smarts
+    class Descriptor 
+      include OpenTox
+      include Algorithm
+
+      [:smarts_match,:smarts_count,:openbabel,:cdk,:joelib,:physchem,:lookup].each do |descriptor|
+        Descriptor.define_singleton_method(descriptor) do |compounds,descriptors|
+          descriptors = [descriptors] unless descriptors.is_a? Array
+          case compounds.class.to_s
+          when "Array"
+            klasses = compounds.collect{|c| c.class}.uniq
+            bad_request_error "First argument contains objects with a different class than OpenTox::Compound or OpenTox::Dataset #{klasses.inspect}" unless klasses.size == 1 and klasses.first == Compound
+            JSON.parse(Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s), SUBJECTID).run(:compound_uri => compounds.collect{|c| c.uri}, :descriptors => descriptors))
+          when "OpenTox::Compound"
+            JSON.parse(Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s), SUBJECTID).run(:compound_uri => compounds.uri, :descriptors => descriptors))
+          when "OpenTox::Dataset"
+            task_uri = Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s), SUBJECTID).run(:dataset_uri => compounds.uri, :descriptors => descriptors)
+            puts task_uri
+            #task_uri
+            Dataset.new(Task.new(task_uri).wait_for_task)
+          else
+            bad_request_error "First argument contains objects with a different class than OpenTox::Compound or OpenTox::Dataset" 
+          end
 
-      def self.fingerprint compounds, smarts, count=false
-        matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts","fingerprint")
-        smarts = [smarts] unless smarts.is_a? Array
-        if compounds.is_a? OpenTox::Compound
-          json = matcher.run :compound_uri => compounds.uri, :smarts => smarts, :count => count
-        elsif compounds.is_a? OpenTox::Dataset
-          # TODO: add task and return dataset instead of result
-          json = matcher.run :dataset_uri => compounds.uri, :smarts => smarts, :count => count
-        else
-          bad_request_error "Cannot match smarts on #{compounds.class} objects."
         end
-        
-        JSON.parse json
       end
 
-      def self.count compounds, smarts
-        fingerprint compounds,smarts,true
-      end
     end
 
+    class Fminer 
+      include OpenTox
+      include Algorithm
+      def self.bbrc params
+        Fminer.new(File.join(service_uri, "fminer", "bbrc")).run params
+      end
+      def self.last params
+        Fminer.new(File.join(service_uri, "fminer", "last")).run params
+      end
+    end
 
   end
 end
-- 
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