tests fixed

7 files changed, 40 insertions, 34 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 9c07626..8b4bb48 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -10,7 +10,6 @@ module OpenTox
     field :inchikey, type: String
     field :names, type: Array
     field :cid, type: String
-    #field :chemblid, type: String
     field :png_id, type: BSON::ObjectId
     field :svg_id, type: BSON::ObjectId
     field :sdf_id, type: BSON::ObjectId
@@ -232,15 +231,6 @@ module OpenTox
       self["cid"]
     end
 
-=begin
-    # Get ChEMBL database compound id, obtained via REST call to ChEMBL
-    # @return [String] 
-    def chemblid
-      update(:chemblid => JSON.parse(RestClientWrapper.get(File.join CHEMBL_URI,URI.escape(smiles)+".json"))["molecule_chembl_id"])
-      self["chemblid"]
-    end
-=end
-
     def db_neighbors min_sim: 0.2, dataset_id:
       #p fingerprints[DEFAULT_FINGERPRINT]
       # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 78f5633..4543e42 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -41,12 +41,14 @@ module OpenTox
     end
 
     # Get all values for a given substance and feature
-    # @param [OpenTox::Substance,BSON::ObjectId] substance or substance id
-    # @param [OpenTox::Feature,BSON::ObjectId] feature or feature id
+    # @param [OpenTox::Substance,BSON::ObjectId,String] substance or substance id
+    # @param [OpenTox::Feature,BSON::ObjectId,String] feature or feature id
     # @return [Array<TrueClass,FalseClass,Float>] values
     def values substance,feature
       substance = substance.id if substance.is_a? Substance
       feature = feature.id if feature.is_a? Feature
+      substance = BSON::ObjectId.from_string(substance) if substance.is_a? String
+      feature = BSON::ObjectId.from_string(feature) if feature.is_a? String
       data_entries.select{|row| row[0] == substance and row[1] == feature}.collect{|row| row[2]}
     end
 
@@ -86,6 +88,8 @@ module OpenTox
       features.select{|f| f._type.match("SubstanceProperty")}
     end
 
+    # Get nominal and numeric prediction features
+    # @return [Array<OpenTox::NominalLazarPrediction,OpenTox::NumericLazarPrediction>]
     def prediction_features
       features.select{|f| f._type.match("Prediction")}
     end
@@ -377,19 +381,6 @@ module OpenTox
 
     # Dataset operations
 
-    # Merge an array of datasets 
-    # @param [Array<OpenTox::Dataset>] datasets to be merged
-    # @return [OpenTox::Dataset] merged dataset
-    def self.merge datasets
-      dataset = self.create(:source => datasets.collect{|d| d.id.to_s}.join(", "), :name => datasets.collect{|d| d.name}.uniq.join(", "))
-      datasets.each do |d|
-        dataset.data_entries += d.data_entries
-        dataset.warnings += d.warnings
-      end
-      dataset.save
-      dataset
-    end
-
     # Copy a dataset
     # @return OpenTox::Dataset dataset copy
     def copy
@@ -434,6 +425,27 @@ module OpenTox
       end
       chunks
     end
+=begin
+    # Merge an array of datasets 
+    # @param [Array<OpenTox::Dataset>] datasets to be merged
+    # @return [OpenTox::Dataset] merged dataset
+    def self.merge datasets: datasets, features: features, value_maps: value_maps, keep_original_features: keep_original_features, remove_duplicates: remove_duplicates
+      dataset = self.create(:source => datasets.collect{|d| d.id.to_s}.join(", "), :name => datasets.collect{|d| d.name}.uniq.join(", ")+" merged")
+      datasets.each_with_index do |d,i|
+        dataset.data_entries += d.data_entries
+        dataset.warnings += d.warnings
+      end
+      feature_classes = features.collect{|f| f.class}.uniq
+      if feature_classes.size == 1
+        if features.first.nominal?
+          merged_feature = MergedNominalBioActivity.find_or_create_by(:name => features.collect{|f| f.name} + " (merged)", :original_feature_id => feature.id, :transformation => map, :accept_values => map.values.sort)
+      compounds.each do |c|
+        values(c,feature).each { |v| dataset.add c, new_feature, map[v] }
+      end
+      dataset.save
+      dataset
+    end
+=end
 
     # Change nominal feature values
     # @param [NominalFeature] Original feature
diff --git a/lib/import.rb b/lib/import.rb~
index 0857717..0857717 100644
--- a/lib/import.rb
+++ b/lib/import.rb~
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 7e813e4..69a6f15 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -97,5 +97,5 @@ CLASSES = ["Feature","Substance","Dataset","CrossValidation","LeaveOneOutValidat
   "train-test-validation.rb",
   "leave-one-out-validation.rb",
   "crossvalidation.rb",
-  "import.rb",
+  #"import.rb",
 ].each{ |f| require_relative f }
diff --git a/lib/model.rb b/lib/model.rb
index 7eaa469..6d5cf7b 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -46,6 +46,7 @@ module OpenTox
         model.prediction_feature_id = prediction_feature.id
         model.training_dataset_id = training_dataset.id
         model.name = "#{prediction_feature.name} (#{training_dataset.name})" 
+        
         # git or gem versioning
         dir = File.dirname(__FILE__)
         path = File.expand_path("../", File.expand_path(dir))
@@ -485,6 +486,8 @@ module OpenTox
         model.is_a? LazarClassification
       end
 
+      # TODO from_pubchem_aid
+
       # Create and validate a lazar model from a csv file with training data and a json file with metadata
       # @param [File] CSV file with two columns. The first line should contain either SMILES or InChI (first column) and the endpoint (second column). The first column should contain either the SMILES or InChI of the training compounds, the second column the training compounds toxic activities (qualitative or quantitative). Use -log10 transformed values for regression datasets. Add metadata to a JSON file with the same basename containing the fields "species", "endpoint", "source" and "unit" (regression only). You can find example training data at https://github.com/opentox/lazar-public-data.
       # @return [OpenTox::Model::Validation] lazar model with three independent 10-fold crossvalidations
@@ -533,6 +536,14 @@ module OpenTox
 
     end
 
+    # TODO
+    def to_json
+      "{\n  metadata:#{super},\n  model:#{model.to_json},  repeated_crossvalidations:#{repeated_crossvalidations.to_json}\n}"
+    end
+
+    def from_json_file
+    end
+
   end
 
 end
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 9cc8260..fb2a579 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -11,13 +11,6 @@ module OpenTox
       include Mongoid::Timestamps
       store_in collection: klass.downcase.pluralize
       field :name,  type: String
-      #field :source,  type: String
-      #field :warnings, type: Array, default: []
-
-#      def warn warning
-        #$logger.warn warning
-#        warnings << warning
-#      end
     end
     OpenTox.const_set klass,c
   end
diff --git a/lib/train-test-validation.rb b/lib/train-test-validation.rb
index 8231728..bffee8c 100644
--- a/lib/train-test-validation.rb
+++ b/lib/train-test-validation.rb
@@ -28,7 +28,7 @@ module OpenTox
         end
         predictions.select!{|cid,p| p[:value] and p[:measurements]}
         # hack to avoid mongos file size limit error on large datasets
-        predictions.each{|cid,p| p[:neighbors] = []} #if model.training_dataset.name.match(/mutagenicity/i)
+        predictions.each{|cid,p| p.delete(:neighbors)} #if model.training_dataset.name.match(/mutagenicity/i)
         validation = self.new(
           :model_id => validation_model.id,
           :test_dataset_id => test_set.id,