added Ag

6 files changed, 83 insertions, 53 deletions

diff --git a/Gemfile b/Gemfile
index 3cde411..a33d28e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -2,5 +2,6 @@ source "https://rubygems.org"
 gemspec
 gem "lazar", :path => "../lazar"
 gem "sinatra"
+gem 'sinatra-reloader', '~> 1.0'
 gem "haml"
 gem "rdiscount"
diff --git a/application.rb b/application.rb
index 98e502f..3ffc080 100644
--- a/application.rb
+++ b/application.rb
@@ -18,11 +18,13 @@ get '/predict/?' do
   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}
   @prediction_models.each_with_index{|m,idx| idx == 0 ? m[:pc_model] = true : m[:pcp_model] = true}
-  example = OpenTox::Nanoparticle.all.select{|n| n.core["name"] == "Au"}.sample
-  @example_pcp = example
-  example = OpenTox::Nanoparticle.all.select{|n| n.core["name"] == "Au"}.sample
-  example.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"}
-  @example_pc = example
+  nanoparticles = OpenTox::Nanoparticle.all.select{|n| n.core["name"] == "Au" || n.core["name"] == "Ag"}
+  example = nanoparticles.collect{|n| n if n.physchem_descriptors.size > 16}.compact
+  pcp = example.sample
+  @example_pcp = pcp
+  pc = example.sample
+  pc.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"}
+  @example_pc = pc
 
   haml :predict
 end
@@ -35,32 +37,38 @@ end
 post '/predict/?' do
   prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model])
   size = params[:size].to_i
+  @type = params[:type]
+
+  example_core = eval(params[:example_core])
+  example_coating = eval(params[:example_coating])
   example_pc = eval(params[:example_pc])
-  pc_descriptors = {}
-  (1..size).each{|i| pc_descriptors["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f]}
-  if example_pc == pc_descriptors 
+
+  in_core = eval(params[:in_core])
+  in_core["name"] = params[:input_core]
+  input_core = in_core
+
+  in_coating = eval(params[:in_coating])
+  in_coating[0]["name"] = params[:input_coating]
+  input_coating = in_coating
+
+  input_pc = {}
+  (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f]}
+  if input_pc == example_pc && input_core == example_core && input_coating == example_coating
     # unchanged input = database hit
     nanoparticle = OpenTox::Nanoparticle.find_by(:id => params[:example_id])
-    nanoparticle.physchem_descriptors = pc_descriptors
+    nanoparticle.physchem_descriptors = input_pc
+    @match = true,@nanoparticle = nanoparticle,@name = nanoparticle.name
   else
     # changed input = create nanoparticle to predict
     nanoparticle = OpenTox::Nanoparticle.new
-    nanoparticle.core = eval(params[:core])
-    nanoparticle.coating = eval(params[:coating])
-    nanoparticle.physchem_descriptors = pc_descriptors
+    nanoparticle.core = input_core
+    nanoparticle.coating = input_coating
+    nanoparticle.physchem_descriptors = input_pc
+    @match = false
   end
   # output
-  @input = pc_descriptors
+  @input = input_pc
   @prediction = prediction_model.model.predict_substance nanoparticle
-  @match = true,@nanoparticle = nanoparticle,@name = nanoparticle.name if @prediction[:warning] =~ /identical/
-  #@prediction[:neighbors].each do |n|
-    #puts n
-    #puts nano = OpenTox::Nanoparticle.find(n["_id"])
-    #puts nano.name
-    #puts n["similarity"]
-    #puts n["measurements"]
-    #puts nano.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"}.size
-  #end
 
   haml :prediction
 end
diff --git a/config.ru b/config.ru
index 4f8501e..eec777d 100644
--- a/config.ru
+++ b/config.ru
@@ -3,4 +3,5 @@ SERVICE = "nano-lazar-gui"
 require 'bundler'
 Bundler.require
 require File.expand_path './application.rb'
+require "sinatra/reloader" if development?
 run Sinatra::Application
diff --git a/public/css/style.css b/public/css/style.css
index 93500a6..02b1959 100644
--- a/public/css/style.css
+++ b/public/css/style.css
@@ -11,3 +11,6 @@
 .tablesorter tbody tr.static td {
   background-color: #CCFFCC;
 }
+.th5 {
+  display: inline;
+}
diff --git a/views/predict.haml b/views/predict.haml
index 7c25def..ad263d1 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -11,10 +11,10 @@
       - @prediction_models.each_with_index do |m, idx|
         %li{:class => ("active" if idx == 0)}
           %a{:href => "#model_#{idx}", :id => "linkTab#{idx}", data: {toggle:"tab"}}
-            = "#{idx+1}. #{m.model.feature_selection_algorithm_parameters[:category].nil? ? "P-CHEM & Proteomics" : "P-CHEM" }"
+            = "#{idx+1}. #{m.model.feature_selection_algorithm_parameters[:category].nil? ? "Physchem & Proteomics" : "Physchem" }"
     %div.tab-content
       - @prediction_models.each_with_index do |m, idx|
-        - m[:pc_model] ? example = @example_pc : example = @example_pcp
+        - m[:pc_model] ? (example = @example_pc; type = "pc") : (example = @example_pcp; type = "pcp")
         #model.tab-pane{:id=>"#{idx}", :class => ("active" if idx == 0)}
           %b Model:
           %br
@@ -64,14 +64,33 @@
                 = "R square:\t"
                 = cv.r_squared.round(3) if cv.r_squared
           %br
+          %b QSAR report
+          %br
+          %a{:href=>to('/qsar-report/'+m.id)} download
           %hr
           %form{:id=>idx, :role=>"form", :action=> to("/predict"), :method=>"post"}
             %h3.help-block
               Please characterise a nanoparticle:
             #input
             %div.form-group
+              // type pcp || pc
+              %input{:id=>"type",:type=>"hidden",:name=>"type",:value=>"#{type}"}
+              // example data to compare
+              %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
+              %input{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
+              %input{:id=>"id",:type=>"hidden",:name=>"example_id",:value=>example.id}
+              // input form parameters to transfer
               %h5 Core
-              %input.input-sm.form-control{:id=>"core_name",:type=>"text",:name=>"core_name",:value=>example.core["name"], :disabled=>"true"}
+              %input.input-sm.form-control{:id=>"core",:type=>"text",:name=>"input_core",:value=>example.core["name"]}
+              %input{:id=>"input_core",:type=>"hidden",:name=>"in_core",:value=>"#{example.core}"}
+              %h5 Coating
+              %input.input-sm.form-control{:id=>"coating",:type=>"text",:name=>"input_coating",:value=>example.coating[0]["name"]}
+              %input{:id=>"input_coating",:type=>"hidden",:name=>"in_coating",:value=>example.coating}
+              // prediction model id 
+              %input{:id=>"prediction_model",:type=>"hidden",:name=>"prediction_model",:value=>m.id}
             - example.physchem_descriptors.each_with_index do |v,id|
               - feature = OpenTox::Feature.find_by(:id => v[0])
               - name = feature.name
@@ -82,18 +101,9 @@
               - val = v[1]
               - id = id + 1
               %h5= name
-              %input.form-control{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>v[0]}
+              // input physchem parameters
               %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>val[0]}
-              %input.form-control{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>v[0]}
-              %input.input-sm.form-control{:id=>id,:type=>"hidden",:name=>"input_value_#{id}",:value=>val[0]}
-              %input.form-control{:id=>"example_id",:type=>"hidden",:name=>"example_id",:value=>example.id}
-              %input.form-control{:id=>"core",:type=>"hidden",:name=>"core",:value=>"#{example.core}"}
-              %input.form-control{:id=>"coating",:type=>"hidden",:name=>"coating",:value=>example.coating}
-              %input.form-control{:id=>"prediction_model",:type=>"hidden",:name=>"prediction_model",:value=>m.id}
-              - example_pc = example.physchem_descriptors
-              %input.form-control{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example_pc}"}
-              - size = example.physchem_descriptors.size
-              %input.form-control{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
+              %input{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>v[0]}
             %hr
             #predict
               %button.btn.btn-success{:id=>"submitbutton", :type=>"submit", :onclick=>"showcircle();"} 
diff --git a/views/prediction.haml b/views/prediction.haml
index f8610f5..0438f1f 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -41,7 +41,7 @@
           - @input.each do |key|
             - feature = OpenTox::Feature.find_by(:id=>key[0])
             - name = feature.name
-            - if !feature[:conditions]["MEDIUM"].blank?
+            - if (feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?)
               - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
             - else
               - name = feature.name
@@ -66,34 +66,39 @@
           / composition
           %td
             - if @match
-              %h5 Core
+              %h5.th5 Core:
               = "["+@nanoparticle[:core]["name"]+"]"
-              %h5 Coating
+              %br
+              %h5.th5 Coating:
               = @nanoparticle[:coating][0]["name"]
+              %br
             - else
-              %h5 x
+              %h5.th5 x
           / tox
           %td.tox
             - if @prediction[:value]
-              %h5 Prediction:
+              %h5.th5 Prediction:
               = @prediction[:value].round(3)
+              %br
             - if @prediction[:rmse]
-              %h5 Rmse:
+              %h5.th5 Rmse:
               = @prediction[:rmse].round(3)
+              %br
             - if @prediction[:r_squared]
-              %h5 R_squared:
+              %h5.th5 R_squared:
               = @prediction[:r_squared].round(3)
+              %br
             - if @prediction[:prediction_interval]
               %h5 95% Prediction interval:
               - interval = @prediction[:prediction_interval].nil? ? " - - " : @prediction[:prediction_interval].collect{|i| i.round(2)}
               = "#{interval[0]} - #{interval[1]}"
             - if @prediction[:measurements]
               %hr
-              %h5 Measurement
+              %h5.th5 Measurement:
               - @prediction[:measurements].each do |m|
-                %p= m
+                = m
             - if !@prediction[:value] && !@prediction[:measurements]
-              %h5 not available
+              %h5.th5 not available
           / physchem
           - if @prediction[:match]
             - sorted = {}
@@ -115,7 +120,7 @@
         - if @prediction[:neighbors]
           - @prediction[:neighbors].each_with_index do |neighbor,idx|
             - nano = OpenTox::Nanoparticle.find(neighbor["_id"])
-            - pc_descriptors = nano.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"}
+            - pc_descriptors = nano.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"} if @type == "pc"
             %tr
               / ID
               %td
@@ -126,17 +131,19 @@
                 %h5= neighbor["similarity"].round(3)
               / Composition
               %td
-                %h5 Core
+                %h5.th5 Core:
                 = "["+nano[:core]["name"]+"]"
-                %h5 Coating
+                %br
+                %h5.th5 Coating:
                 = nano[:coating][0]["name"]
               / Tox
               %td.tox
-                %h5 Measurement
-                %p= neighbor["measurements"][0]
+                %h5.th5 Measurement:
+                = neighbor["measurements"][0]
               / Physchem
-              - @input.each do |k,v|
+              -#- @input.each do |k,v|
+              - nano.physchem_descriptors.each do |k,v|
                 %td.physchem
                   %div
                     %div{:style=>"display:inline-block;padding-right:20px;"}
-                      %p= v[0].round(3) unless v.nil?
+                      = v[0].round(3) unless v.nil?