Algorithms and Models are modules instead of classes.

7 files changed, 98 insertions, 33 deletions

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
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 7f0e840..4b63cef 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -1,6 +1,12 @@
 module OpenTox
-  AA = $aa[:uri] if defined? $aa
-  AA ||= "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb
+  if defined?($aa) and $aa[:uri] 
+    AA = $aa[:uri] 
+    SUBJECTID = OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
+    unauthorized_error "Failed to authenticate user \"#{$aa[:user]}\"." unless OpenTox::Authorization.is_token_valid(SUBJECTID)
+  else
+    AA = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb
+    SUBJECTID = nil
+  end
   #Module for Authorization and Authentication
   #@example Authentication
   #  require "opentox-client"
diff --git a/lib/compound.rb b/lib/compound.rb
index daeabb9..9bd2066 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -6,6 +6,10 @@ module OpenTox
   # Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
   class Compound
 
+    def ==(c)
+      @uri == c.uri
+    end
+
     # Create a compound from smiles string
     # @example
     #   compound = OpenTox::Compound.from_smiles("c1ccccc1")
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 5df20b4..354b443 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -64,6 +64,8 @@ module OpenTox
           RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").each do |row|
             r,c,v = row.split("\t")
             @data_entries[r.to_i] ||= []
+            #v = v.to_f if v.numeric?
+            #v = nil if v.is_a? String and v.empty?
             @data_entries[r.to_i][c.to_i] = v
           end
         # TODO: fallbacks for external and unordered datasets
@@ -169,6 +171,7 @@ module OpenTox
 
     # TODO: remove? might be dangerous if feature ordering is incorrect
     # MG: I would not remove this because add_data_entry is very slow (4 times searching in arrays)
+    # CH: do you have measurements? compound and feature arrays are not that big, I suspect that feature search/creation is the time critical step 
     # @param row [Array] 
     # @example
     #   d = Dataset.new
diff --git a/lib/model.rb b/lib/model.rb
index e49eff3..1dbac6d 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,7 +1,7 @@
 module OpenTox
 
-  class Model
-
+  module Model
+=begin
     # Run a model with parameters
     # @param params [Hash] Parameters for OpenTox model
     # @param wait [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
@@ -10,6 +10,7 @@ module OpenTox
       uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
       wait_for_task uri if wait
     end
+=end
 
     def feature_type # CH: subjectid is a object variable, no need to pass it as a parameter
       unless @feature_type
@@ -41,5 +42,23 @@ module OpenTox
       end
     end
 
+    class Generic
+      include OpenTox
+      include OpenTox::Algorithm
+    end
+
+    class Lazar
+      include OpenTox
+      include OpenTox::Algorithm
+      def self.create params
+        Lazar.new(File.join($algorithm[:uri], "lazar")).run params
+      end
+
+      def predict params
+        run params
+      end
+
+    end
+
   end
 end
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index 02724c2..f25f05a 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -10,6 +10,13 @@ require 'json'
 require 'logger'
 require "securerandom"
 
+default_config = File.join(ENV["HOME"],".opentox","config","default.rb")
+client_config = File.join(ENV["HOME"],".opentox","config","opentox-client.rb")
+
+puts "Could not find configuration files #{default_config} or #{client_config}" unless File.exist? default_config or File.exist? client_config
+require default_config if File.exist? default_config
+require client_config if File.exist? client_config
+
 # define constants and global variables
 RDF::OT =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
 RDF::OT1 =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
@@ -19,7 +26,8 @@ RDF::TB  = RDF::Vocabulary.new "http://onto.toxbank.net/api/"
 RDF::ISA = RDF::Vocabulary.new "http://onto.toxbank.net/isa/"
 RDF::OWL = RDF::Vocabulary.new "http://www.w3.org/2002/07/owl#"
 
-CLASSES = ["Generic", "Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "Investigation"]
+#CLASSES = ["Generic", "Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "Investigation"]
+CLASSES = ["Compound", "Feature", "Dataset", "Validation", "Task", "Investigation"]
 RDF_FORMATS = [:rdfxml,:ntriples,:turtle]
 
 # Regular expressions for parsing classification data
@@ -38,8 +46,8 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m
   "compound.rb",
   "feature.rb",
   "dataset.rb",
-  "model.rb",
   "algorithm.rb",
+  "model.rb",
   "validation.rb"
 ].each{ |f| require_relative f }
 
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 52f705c..044da4b 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -190,6 +190,20 @@ module OpenTox
     end
   end
 
+  # define class methods within module
+  def self.included(base)
+    base.extend(ClassMethods)
+  end
+
+  module ClassMethods
+    def service_uri
+      service = self.to_s.split('::')[1].downcase
+      eval("$#{service}[:uri]")
+    rescue
+      bad_request_error "$#{service}[:uri] variable not set. Please set $#{service}[:uri] or use an explicit uri as first constructor argument "
+    end
+  end
+
   # create default OpenTox classes with class methods
   # (defined in opentox-client.rb)
   CLASSES.each do |klass|
@@ -237,14 +251,6 @@ module OpenTox
           self.new uris.first, subjectid
         end
       end
-
-      def self.service_uri
-        service = self.to_s.split('::').last.downcase
-        eval("$#{service}[:uri]")
-      rescue
-        bad_request_error "$#{service}[:uri] variable not set. Please set $#{service}[:uri] or use an explicit uri as first constructor argument "
-      end
-
     end
     OpenTox.const_set klass,c
   end