From 51e7a29c8aac568ff8ef04de5b15d2f6db8f66da Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sun, 19 Jul 2015 21:26:03 +0200
Subject: lazar predictions working in principle

---
 lib/algorithm.rb | 77 --------------------------------------------------------
 1 file changed, 77 deletions(-)
 delete mode 100644 lib/algorithm.rb

(limited to 'lib/algorithm.rb')

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
deleted file mode 100644
index 8f05d6a..0000000
--- a/lib/algorithm.rb
+++ /dev/null
@@ -1,77 +0,0 @@
-module OpenTox
-
-  # Wrapper for OpenTox Algorithms
-  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
-    # @param [optional,Boolean] wait  set to false if method should return a task uri instead of the algorithm result
-    # @return [String] URI of new resource (dataset, model, ...)
-    def run params=nil, wait=true
-      uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list"}
-      wait_for_task uri if wait
-    end
-
-    class Generic
-      include OpenTox
-      include Algorithm
-      include Mongoid::Document
-      include Mongoid::Timestamps
-      field :parameters, type: Array
-    end
-
-    class Descriptor 
-      include OpenTox
-      include Algorithm
-      include Mongoid::Document
-      include Mongoid::Timestamps
-      field :parameters, type: Array
-
-      [:smarts_match,:smarts_count,:physchem,:lookup].each do |descriptor|
-        Descriptor.define_singleton_method(descriptor) do |compounds,descriptors=nil|
-          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)).run(:compound_uri => compounds.collect{|c| c.uri}, :descriptors => descriptors))
-          when "OpenTox::Compound"
-            p descriptor.to_s
-            send descriptor.to_sym, compounds
-            #JSON.parse(Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s)).run(:compound_uri => compounds.uri, :descriptors => descriptors))
-          when "OpenTox::Dataset"
-            task_uri = Descriptor.new(File.join(self.service_uri, "descriptor", descriptor.to_s)).run(:dataset_uri => compounds.uri, :descriptors => descriptors)
-            Dataset.new(wait_for_task task_uri)
-          else
-            bad_request_error "First argument contains objects with a different class than OpenTox::Compound or OpenTox::Dataset" 
-          end
-
-        end
-      end
-
-      # returns a hash, keys: physchem descriptors, values: their description
-      def self.physchem_descriptors
-        Hash[ RestClientWrapper.get(File.join(service_uri, "descriptor", "physchem", "list")).to_s.split("\n").collect{|l| l.split("\t")} ]
-      end
-
-      # returns array of "descriptor-values", as CDK descriptors calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
-      def self.physchem_descriptor_values
-        RestClientWrapper.get(File.join(service_uri, "descriptor", "physchem", "list_values")).to_s.split("\n")
-      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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