git commit added to model metadata

5 files changed, 19 insertions, 10 deletions

diff --git a/lib/caret.rb b/lib/caret.rb
index 2c4cd0c..e24c943 100644
--- a/lib/caret.rb
+++ b/lib/caret.rb
@@ -2,10 +2,17 @@ module OpenTox
   module Algorithm
     
     class Caret
-      # TODO classification
       # model list: https://topepo.github.io/caret/modelList.html
 
       def self.create_model_and_predict dependent_variables:, independent_variables:, weights:, method:, query_variables:
+        remove = []
+        # remove independent_variables with single values
+        independent_variables.each_with_index { |values,i| remove << i if values.uniq.size == 1}
+        remove.sort.reverse.each do |i|
+          independent_variables.delete_at i
+          weights.delete_at i
+          query_variables.delete_at i
+        end
         if independent_variables.flatten.uniq == ["NA"] 
           prediction = Algorithm::Regression::weighted_average dependent_variables:dependent_variables, weights:weights
           prediction[:warning] = "No variables for regression model. Using weighted average of similar substances."
diff --git a/lib/compound.rb b/lib/compound.rb
index 6c53cde..e2a55ea 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -76,7 +76,6 @@ module OpenTox
     end
 
     def calculate_properties descriptors=PhysChem::OPENBABEL
-      # TODO: speedup java descriptors
       calculated_ids = properties.keys
       # BSON::ObjectId instances are not allowed as keys in a BSON document.
       new_ids = descriptors.collect{|d| d.id.to_s} - calculated_ids
@@ -95,7 +94,6 @@ module OpenTox
       end
       save
       descriptors.collect{|d| properties[d.id.to_s]}
-      #properties.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
     end
 
     def smarts_match smarts, count=false
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 453fc35..ab55294 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -130,7 +130,6 @@ module OpenTox
     #end
     
     # Create a dataset from CSV file
-    # TODO: document structure
     def self.from_csv_file file, accept_empty_values=false
       source = file
       name = File.basename(file,".*")
diff --git a/lib/model.rb b/lib/model.rb
index d7b072f..7503215 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -23,6 +23,7 @@ module OpenTox
       field :descriptor_means, type: Array, default:[]
       field :descriptor_sds, type: Array, default:[]
       field :scaled_variables, type: Array, default:[]
+      field :version, type: Hash, default:{}
       
       def self.create prediction_feature:nil, training_dataset:nil, algorithms:{}
         bad_request_error "Please provide a prediction_feature and/or a training_dataset." unless prediction_feature or training_dataset
@@ -35,6 +36,16 @@ module OpenTox
         model.prediction_feature_id = prediction_feature.id
         model.training_dataset_id = training_dataset.id
         model.name = "#{prediction_feature.name} (#{training_dataset.name})" 
+        # TODO: check if this works for gem version, add gem versioning?
+        dir = File.dirname(__FILE__)
+        commit = `cd #{dir}; git rev-parse HEAD`.chomp
+        branch = `cd #{dir}; git rev-parse --abbrev-ref HEAD`.chomp
+        url = `cd #{dir}; git config --get remote.origin.url`.chomp
+        if branch
+          model.version = {:url => url, :branch => branch, :commit => commit}
+        else
+          model.version = {:warning => "git is not installed"}
+        end
 
         # set defaults
         substance_classes = training_dataset.substances.collect{|s| s.class.to_s}.uniq
diff --git a/lib/rest-client-wrapper.rb b/lib/rest-client-wrapper.rb
index 9321a75..2073be2 100644
--- a/lib/rest-client-wrapper.rb
+++ b/lib/rest-client-wrapper.rb
@@ -55,14 +55,8 @@ module OpenTox
           if [301, 302, 307].include? response.code and request.method == :get
             response.follow_redirection(request, result)
           elsif response.code >= 400 and !URI.task?(uri)
-            #TODO add parameters to error-report
-            #parameters = request.args
-            #parameters[:headers][:subjectid] = "REMOVED" if parameters[:headers] and parameters[:headers][:subjectid]
-            #parameters[:url] = parameters[:url].gsub(/(http|https|)\:\/\/[a-zA-Z0-9\-]+\:[a-zA-Z0-9]+\@/, "REMOVED@") if parameters[:url]
-            #message += "\nREST parameters:\n#{parameters.inspect}" 
             error = known_errors.collect{|e| e if e[:code] == response.code}.compact.first
             begin # errors are returned as error reports in json, try to parse
-              # TODO: may be the reason for failure of task.rb -n test_11_wait_for_error_task
               content = JSON.parse(response)
               msg = content["message"].to_s
               cause = content["errorCause"].to_s