clean out; better response codes; prepare for batch

1 files changed, 128 insertions, 1 deletions

diff --git a/helper.rb b/helper.rb
index 54dbd5e..1c1db5f 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,3 +1,130 @@
 helpers do
-  
+
+  def embedded_svg image, options={}
+    doc = Nokogiri::HTML::DocumentFragment.parse image
+    svg = doc.at_css 'svg'
+    title = doc.at_css 'title'
+    if options[:class].present?
+      svg['class'] = options[:class]
+    end
+    if options[:title].present?
+      title.children.remove
+      text_node = Nokogiri::XML::Text.new(options[:title], doc)
+      title.add_child(text_node)
+    end
+    doc.to_html.html_safe
+  end
+
+  def prediction_to_csv(m,c,p)
+    model = m
+    model_name = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
+    model_unit = model.regression? ? "(#{model.unit})" : ""
+    converted_model_unit = model.regression? ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
+
+    csv = ""
+    compound = c
+    prediction = p
+    output = {}
+    line = ""
+    output["model_name"] = model_name
+    output["model_unit"] = model_unit
+    output["converted_model_unit"] = converted_model_unit
+
+    if prediction[:value]
+      inApp = (prediction[:warnings].join(" ") =~ /Cannot/ ? "no" : (prediction[:warnings].join(" ") =~ /may|Insufficient|Weighted/ ? "maybe" : "yes"))
+      if prediction[:info] =~ /\b(identical)\b/i
+        prediction[:info] = "This compound was part of the training dataset. All information "\
+          "from this compound was removed from the training data before the "\
+          "prediction to obtain unbiased results."
+      end
+      note = "\"#{prediction[:warnings].uniq.join(" ")}\""
+
+      output["prediction_value"] = model.regression? ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}"
+      output["converted_value"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" : nil
+
+      if prediction[:measurements].is_a?(Array)
+        output["measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)}"} : prediction[:measurements].collect{|value| "#{value}"}
+        output["converted_measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)}"} : false
+      else
+        output["measurements"] = model.regression? ? "#{prediction[:measurements].delog10.signif(3)}" : "#{prediction[:measurements]}"
+        output["converted_measurements"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)}" : false
+
+      end #db_hit
+
+      if model.regression?
+
+        if !prediction[:prediction_interval].blank?
+          interval = prediction[:prediction_interval]
+          output['interval'] = []
+          output['converted_interval'] = []
+          output['interval'] << interval[1].delog10.signif(3)
+          output['interval'] << interval[0].delog10.signif(3)
+          output['converted_interval'] << compound.mmol_to_mg(interval[1].delog10).signif(3)
+          output['converted_interval'] << compound.mmol_to_mg(interval[0].delog10).signif(3)
+        end #prediction interval
+
+        line += "#{output['model_name']},#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{!output['prediction_value'].blank? ? output['prediction_value'] : ""},"\
+          "#{!output['converted_value'].blank? ? output['converted_value'] : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['interval'].first : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['interval'].last : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].first : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note.chomp}\n"
+      else # Classification
+
+        if !prediction[:probabilities].blank?
+          output['probabilities'] = []
+          prediction[:probabilities].each{|k,v| output['probabilities'] << v.signif(3)}
+        end
+
+        line += "#{output['model_name']},#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{output['prediction_value']},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note}\n"
+
+      end
+      
+      output['warnings'] = prediction[:warnings] if prediction[:warnings]
+
+    else #no prediction value
+      inApp = "no"
+      if prediction[:info] =~ /\b(identical)\b/i
+        prediction[:info] = "This compound was part of the training dataset. All information "\
+          "from this compound was removed from the training data before the "\
+          "prediction to obtain unbiased results."
+      end
+      note = "\"#{prediction[:warnings].join(" ")}\""
+
+      output['warnings'] = prediction[:warnings]
+      output['info'] = prediction[:info] if prediction[:info]
+
+      if model.regression?
+        line += "#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
+          "#{prediction[:measurements].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+      else
+        line += "#{output['model_name']},#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info] && !output['measurements'].blank?}\","\
+          "#{output['prediction_value']},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note}\n"
+      end
+
+    end
+    csv += line
+    # output
+    csv
+  end
+
+  def dataset_storage
+    all = Batch.where(:source => /^tmp/)
+    out = Hash.new
+    all.reverse.each{|d| out[d.id] = [d.name, d.created_at]}
+    out
+  end  
+
 end