removed obsolete code

3 files changed, 2 insertions, 55 deletions

diff --git a/application.rb b/application.rb
index a702d9a..8a218f4 100644
--- a/application.rb
+++ b/application.rb
@@ -72,24 +72,6 @@ get '/qmrf-report/:id' do
 end
 #=end
 get '/predict/?' do
-  # temporarily outstanding
-  nos = %w(S40.CIT
-    S40.MES
-    S40.MUTA
-    S40.cPEG5K-SH
-    S40.DDT@DOTAP
-    S40.MAA
-    S40.PLL-SH
-    S40.mPEG5K-SH
-    S40.MBA
-    S40.PVA
-    S40.LA
-    S40.AUT
-    S40.HDA
-    S40.SA
-    S40.nPEG5K-SH
-    S40.MHDA
-  )
   @prediction_models = []
   prediction_models = OpenTox::Model::NanoPrediction.all
   prediction_models.each{|m| m.model[:feature_selection_algorithm_parameters]["category"] == "P-CHEM" ? @prediction_models[0] = m : @prediction_models[1] = m}
@@ -97,28 +79,16 @@ get '/predict/?' do
   @prediction_models.each_with_index{|m,idx| idx == 0 ? m[:pc_model] = true : m[:pcp_model] = true}
   # collect nanoparticles by training dataset (Ag + Au)
   dataset = OpenTox::Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
-  # temporarily delete silver 
-  nanoparticles = dataset.nanoparticles#.delete_if{|n| !nos.include?(n.name)}
+  nanoparticles = dataset.nanoparticles
   
-  # select physchem_parameters by relevant_features out of each model; use @@ for global usage (prediction.haml)
+  # select physchem_parameters by relevant_features for of each model
   @pc_relevant_features = @prediction_models[0].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)}
   @pcp_relevant_features = @prediction_models[1].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)}
-  # check for outstanding nanoparticles
   pcp = nanoparticles.sample
-  #while nos.include?(pcp.name)
-  #  pcp = nanoparticles.sample
-  #end
-  # use only relevant features
   pcp.physchem_descriptors.delete_if{|id,v| !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}
   @example_pcp = pcp
   
-  # check for outstanding nanoparticles
   pc = nanoparticles.sample
-  #while nos.include?(pc.name)
-  #  pcp = nanoparticles.sample
-  #end
-  # use only relevant features
-  #pc.physchem_descriptors.delete_if{|id,v| OpenTox::Feature.find(id).category != "P-CHEM"}
   pc.physchem_descriptors.delete_if{|id,v| !@pc_relevant_features.include?(OpenTox::Feature.find(id))}
   @example_pc = pc
 
diff --git a/views/predict.haml b/views/predict.haml
index 0630b2c..5d5d6f0 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -51,7 +51,6 @@
           Neighbor algorithm parameter:
           = "min sim = #{m.model.neighbor_algorithm_parameters["min_sim"]}"
           %p
-          -#- cv = OpenTox::CrossValidation.find(m.repeated_crossvalidation_id)
           %b Independent crossvalidations (log2 transformed):
           - crossvalidations =[]
           - m.repeated_crossvalidation.crossvalidation_ids.each{|cv| c = OpenTox::Validation::CrossValidation.find(cv); crossvalidations << c}
@@ -91,7 +90,6 @@
               %input{:id=>"example_core",:type=>"hidden",:name=>"example_core",:value=>"#{example.core}"}
               %input{:id=>"example_coating",:type=>"hidden",:name=>"example_coating",:value=>"#{example.coating}"}
               %input{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example.physchem_descriptors}"}
-              -#- size = example.physchem_descriptors.size
               - size = relevant_features.size
               %input{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
               %input{:id=>"id",:type=>"hidden",:name=>"example_id",:value=>example.id}
@@ -110,13 +108,8 @@
               // prediction model id 
               %input{:id=>"prediction_model",:type=>"hidden",:name=>"prediction_model",:value=>m.id}
             - relevant_features.sort_by{|d| d.category}.each_with_index do |relf,id|
-              -#- example.physchem_descriptors.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each_with_index do |v,id|
               - feature = relf
-              /%p= feature.id
               - v = example.physchem_descriptors.find{|id,v| id == feature.id.to_s  }
-              /%p= v
-              -#- feature = OpenTox::Feature.find_by(:id => v[0])
-              -#- feature = v
               - name = feature.name
               - if feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?
                 - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
diff --git a/views/prediction.haml b/views/prediction.haml
index e6b4ae4..53a9cfd 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -43,7 +43,6 @@
             Net cell association
             %br
             [mL/ug(Mg)]
-          -#- @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
           - @input.each{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
             - feature = OpenTox::Feature.find_by(:id=>key[0])
             - name = feature.name
@@ -95,16 +94,6 @@
               %h5.th5 Prediction:
               = "not available"
               %br
-            -#- if @prediction[:rmse]
-              %h5.th5
-                %a{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
-              = @prediction[:rmse].round(3)
-              %br
-            -#- if @prediction[:r_squared]
-              %h5.th5
-                %a{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
-              = @prediction[:r_squared].round(3)
-              %br
             - if @prediction[:prediction_interval]
               %h5
                 %a{:href=>"https://en.wikipedia.org/wiki/Prediction_interval", :rel=>"external"} 95% Prediction interval:
@@ -118,7 +107,6 @@
             - if !@prediction[:value] && !@prediction[:measurements]
               %h5.th5 not available
           / physchem
-          -#- @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |v|
           - @input.each do |v|
             %td.physchem
               %div{:style=>"display:inline-block;padding-right:20px;"}
@@ -131,7 +119,6 @@
         - if @prediction[:neighbors]
           - @prediction[:neighbors].each_with_index do |neighbor,idx|
             - nano = OpenTox::Nanoparticle.find(neighbor["_id"])
-            -#- nano.physchem_descriptors.delete_if{|id,v| OpenTox::Feature.find(id).category != "P-CHEM"} if @type == "pc"
             %tr
               / ID
               %td
@@ -152,9 +139,6 @@
                 %h5.th5 Measurement:
                 = neighbor["measurements"][0]
               / Physchem
-              -#- nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| OpenTox::Feature.find(id).category}.each do |k,v|
               - nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| @pc_relevant_features.index OpenTox::Feature.find(id)}.each do |k,v|
                 %td.physchem
-                  -#%div
-                    %div{:style=>"display:inline-block;padding-right:20px;"}
                   = v[0].round(3) unless v.nil?