lazar predictions working in principle

7 files changed, 52 insertions, 112 deletions

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
diff --git a/lib/compound.rb b/lib/compound.rb
index b588c75..6cc4707 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -12,6 +12,10 @@ module OpenTox
       @inchi = inchi
     end
 
+    def  == compound
+      self.inchi == compound.inchi
+    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 bcbacb2..2a777bb 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -4,21 +4,17 @@ module OpenTox
 
   # Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
   class Dataset
-      include Mongoid::Document
+    include Mongoid::Document
 
-    field :feature_ids, type: Array
-    field :inchis, type: Array
-    field :data_entries, type: Array
-    field :warnings, type: Array
+    field :feature_ids, type: Array, default: []
+    field :inchis, type: Array, default: []
+    field :data_entries, type: Array, default: []
+    field :warnings, type: Array, default: []
     field :source, type: String
 
-    def initialize
-      super
-      self.feature_ids = []
-      self.inchis = []
-      self.data_entries = []
-      self.warnings = []
-    end
+    # TODO subclass Datasets
+    field :dependent_variables, type: BSON::ObjectId
+    field :predicted_variables, type: Array
 
     # Readers
 
@@ -53,8 +49,8 @@ module OpenTox
     # @param feature [OpenTox::Feature] OpenTox Feature object
     # @return [Array] Data entry values
     def values(compound, feature)
-      rows = (0 ... inchis.length).select { |r| inchis[r].uri == compound.uri }
-      col = feature_ids.collect{|f| f.uri}.index feature.uri
+      rows = (0 ... inchis.length).select { |r| inchis[r] == compound.inchi }
+      col = feature_ids.index feature.id
       rows.collect{|row| data_entries[row][col]}
     end
 
@@ -63,9 +59,9 @@ module OpenTox
     # Search a dataset for a feature given its URI
     # @param uri [String] Feature URI
     # @return [OpenTox::Feature] Feature object, or nil if not present
-    def find_feature_uri(uri)
-      features.select{|f| f.uri == uri}.first
-    end
+    #def find_feature_uri(uri)
+      #features.select{|f| f.uri == uri}.first
+    #end
 
     # Search a dataset for a compound given its URI
     # @param uri [String] Compound URI
@@ -120,17 +116,18 @@ module OpenTox
     # @param value [Object] (will be converted to String)
     # @return [Array] data_entries
     def add_data_entry compound, feature, value
-      @data["compounds"] << compound unless @data["compounds"].collect{|c| c.uri}.include?(compound.uri)
-      row = @data["compounds"].collect{|c| c.uri}.index(compound.uri)
-      @data["features"] << feature unless @data["features"].collect{|f| f.uri}.include?(feature.uri)
-      col = @data["features"].collect{|f| f.uri}.index(feature.uri)
-      if @data["data_entries"][row] and @data["data_entries"][row][col] # duplicated values
-        @data["compounds"] << compound
-        row = @data["compounds"].collect{|c| c.uri}.rindex(compound.uri)
+      # TODO: optimize
+      add_compound compound unless self.compounds.include?(compound)
+      row = self.compounds.index(compound)
+      add_feature feature unless self.features.include?(feature)
+      col = self.features.index(feature)
+      if self.data_entries[row] and self.data_entries[row][col] # duplicated values
+        add_compound compound
+        row = self.compounds.rindex(compound)
       end
       if value
-        @data["data_entries"][row] ||= []
-        @data["data_entries"][row][col] = value
+        self.data_entries[row] ||= []
+        self.data_entries[row][col] = value
       end
     end
 
diff --git a/lib/feature.rb b/lib/feature.rb
index 43cf7e9..b2ddce4 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -1,10 +1,16 @@
 module OpenTox
 
+  # TODO subclass features
   class Feature
 
     field :string, type: Boolean, default: false
     field :nominal, type: Boolean, default: false
     field :numeric, type: Boolean, default: false
+    field :substructure, type: Boolean, default: false
+    field :prediction, type: Boolean
+    field :smarts, type: String
+    field :pValue, type: Float
+    field :effect, type: String
     field :accept_values, type: Array
     
     # Find out feature type
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index 6358705..40f87cf 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -4,11 +4,11 @@ require "bundler/setup"
 #require 'rdf/raptor'
 #require 'rdf/turtle'
 require "rest-client"
-require 'uri'
+#require 'uri'
 require 'yaml'
 require 'json'
 require 'logger'
-require "securerandom"
+#require "securerandom"
 require 'mongoid'
 
 default_config = File.join(ENV["HOME"],".opentox","config","default.rb")
@@ -50,8 +50,8 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m
   "compound.rb",
   "feature.rb",
   "dataset.rb",
-  "algorithm.rb",
-  "model.rb",
+  #"algorithm.rb",
+  #"model.rb",
   "validation.rb"
 ].each{ |f| require_relative f }
 
@@ -61,7 +61,7 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m
 #end
 
 # defaults to stderr, may be changed to file output (e.g in opentox-service)
-$logger = OTLogger.new(STDERR) 
+$logger = OTLogger.new(STDOUT) # STDERR did not work on my development machine (CH)
 $logger.level = Logger::DEBUG
 #Mongo::Logger.logger = $logger
 Mongo::Logger.level = Logger::WARN 
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 68a841b..554e686 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -15,7 +15,8 @@ module OpenTox
 
       field :title, type: String
       field :description, type: String
-      field :parameters, type: Array
+      field :parameters, type: Array, default: []
+      field :creator, type: String
 
       # TODO check if needed
       def self.subjectid
diff --git a/lib/task.rb b/lib/task.rb
index 55d024d..cd2dd92 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -1,3 +1,5 @@
+# TODO: task seems to run twice, see fminser tests
+# TODO: do we need tasks for internal use
 DEFAULT_TASK_MAX_DURATION = 36000
 module OpenTox
   # TODO: fix error reports
@@ -5,13 +7,16 @@ module OpenTox
 
   # Class for handling asynchronous tasks
   class Task 
+    include Mongoid::Document
+    include Mongoid::Timestamps
 
     field :creator, type: String
     field :percentageCompleted, type: Float
     field :error_code, type: Integer # workaround name, cannot overwrite accessors in current mongoid version
     field :finished, type: Time # workaround name, cannot overwrite accessors in current mongoid version
     # TODO
-    field :result_object, type: String
+    field :result_type, type: String
+    field :result_id, type: BSON::ObjectId
     field :report, type: String
     field :pid, type: Integer
     field :observer_pid, type: Integer
@@ -66,7 +71,7 @@ module OpenTox
     end
 
     def completed(result)
-      update_attributes(:error_code => 200, :finished => Time.now, :percentageCompleted => 100, :result_object => result)
+      update_attributes(:error_code => 200, :finished => Time.now, :percentageCompleted => 100, :result_type => result.type, :result_id => result.id)
     end
 
     # waits for a task, unless time exceeds or state is no longer running
@@ -92,7 +97,11 @@ module OpenTox
   end
 
   def result
-    OpenTox::Task.find(id).result_object
+    c = OpenTox::Task.find(id).result_type.downcase.to_sym
+    rid = OpenTox::Task.find(id).result_id
+    p c, rid
+    p $mongo[collection].all
+    $mongo[collection].find(rid).first
   end
 
   def finished_at