changed for two model selection

9 files changed, 198 insertions, 98 deletions

diff --git a/Gemfile b/Gemfile
index 9ceb553..3cde411 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,6 @@
 source "https://rubygems.org"
 gemspec
+gem "lazar", :path => "../lazar"
 gem "sinatra"
 gem "haml"
-gem "rserve-client"
 gem "rdiscount"
diff --git a/VERSION b/VERSION
index 4e379d2..bcab45a 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.0.2
+0.0.3
diff --git a/application.rb b/application.rb
index 1f7fa00..98e502f 100644
--- a/application.rb
+++ b/application.rb
@@ -1,23 +1,29 @@
-require 'json'
 require 'rdiscount'
-require_relative './nanoparticles.rb'
-
 $ambit_search = "http://data.enanomapper.net/substance?type=name&search="
 
 configure :development do
   $logger = Logger.new(STDOUT)
 end
 
+before do
+  @version = File.read("VERSION").chomp
+end
+
 get '/?' do
   redirect to('/predict') 
 end
 
 get '/predict/?' do
-  @version = File.read("VERSION").chomp
-  data = JSON.parse(File.read("./data.json"))
-  query_features = JSON.parse(File.read("./query-features.json"))
-  @example = data[data.keys.sample]["physchem"].select{|f,v| query_features.include? f}
-  #@json_example = JSON.pretty_generate(@example)
+  @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}
+  @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
+
   haml :predict
 end
 
@@ -27,10 +33,34 @@ get '/license' do
 end
 
 post '/predict/?' do
+  prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model])
   size = params[:size].to_i
-  @input = []
-  (1..size).each{|i| @input << [params["input_key_#{i}"], params["input_value_#{i}"].to_f]}
-  @params = Hash[*@input.flatten]
-  @prediction = predict @params
+  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 
+    # unchanged input = database hit
+    nanoparticle = OpenTox::Nanoparticle.find_by(:id => params[:example_id])
+    nanoparticle.physchem_descriptors = pc_descriptors
+  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
+  end
+  # output
+  @input = pc_descriptors
+  @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 1e7f981..4f8501e 100644
--- a/config.ru
+++ b/config.ru
@@ -1,3 +1,4 @@
+ENV["LAZAR_ENV"] = "development"
 SERVICE = "nano-lazar-gui"
 require 'bundler'
 Bundler.require
diff --git a/nano-lazar.gemspec b/nano-lazar.gemspec
index c6ae2b1..6e322f3 100644
--- a/nano-lazar.gemspec
+++ b/nano-lazar.gemspec
@@ -15,6 +15,7 @@ Gem::Specification.new do |s|
   s.files       = `git ls-files`.split("\n")
   s.required_ruby_version = '>= 2.0.0'
 
+  s.add_runtime_dependency "lazar"
   s.add_runtime_dependency "sinatra"
   s.add_runtime_dependency "rdiscount"
   s.add_runtime_dependency "haml"
diff --git a/public/images/wait30trans.gif b/public/images/wait30trans.gif
new file mode 100644
index 0000000..183fe6f
--- /dev/null
+++ b/public/images/wait30trans.gif
diff --git a/views/layout.haml b/views/layout.haml
index d924f95..f36bdf7 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -35,7 +35,7 @@
         %div.col-md-2
           %h1.media-heading{:style=>"margin: 0 0 0 1em;"}
             %small
-              %a{:href=>"https://lazar.in-silico.ch/predict"} lazar
+              %a{:href=>"https://lazar.in-silico.ch/predict", :rel=>"external"} lazar
 
     %div.container-fluid
       %topline
diff --git a/views/predict.haml b/views/predict.haml
index 7fa52ed..7c25def 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -1,23 +1,102 @@
+:javascript
+  function showcircle() {
+    $("img.circle").show();
+  };
+
 %div.well
-  %form{:role=>"form", :action=> to("/predict"), :method=>"post"}
-    %h3.help-block
-      Please characterise a nanoparticle
-    %hr
-    #input
-    - size = @example.size
-    %div.form-group
-      %h5 Core
-      %input.input-sm.form-control{:id=>"Au",:type=>"text",:name=>"input_value_Au",:value=>"[Au]", :disabled=>"true"}
-    - @example.each_with_index do |v,id|
-      - id = id + 1
-      - key = v[0]
-      - val = v[1]
-      %h5= key.gsub(/\sMean/, '')
-      %input.form-control{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>key}
-      %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>val}
-    %input.form-control{:id=>"example",:type=>"hidden",:name=>"size",:value=>size}
-    %hr
-    #predict
-      %button.btn.btn-success{:type=>"submit"} 
-        Find similar nano particles
-        %span.glyphicon.glyphicon-chevron-right
+  %h3.help-block
+    Select an endpoint:
+  #tabs
+    %ul.nav.nav-tabs{:id=>"modelTab", :role=>"tablist"}
+      - @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" }"
+    %div.tab-content
+      - @prediction_models.each_with_index do |m, idx|
+        - m[:pc_model] ? example = @example_pc : example = @example_pcp
+        #model.tab-pane{:id=>"#{idx}", :class => ("active" if idx == 0)}
+          %b Model:
+          %br
+          Name:
+          = m.model.name
+          %br
+          Type: regression
+          %br
+          Source:
+          %a{:href=>"#{m.source}", :alt=>"source", :rel=>"external"}
+            = m.source
+          %br
+          Species:
+          = m.species
+          %br
+          Training nanoparticles:
+          = m.model.training_dataset.nanoparticles.size
+          %br
+          Endpoint:
+          = m.endpoint
+          %br
+          Unit:
+          = m.unit
+          %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}
+          %div.row{:id=>"validations#{m.id}", :style=>"background-color:#f5f5f5;"}
+            - crossvalidations.each do |cv|
+              %span.col-xs-4.col-sm-4.col-md-4.col-lg-4
+                = "Num folds:\t"
+                = cv.folds
+                %br
+                = "Num instances:\t"
+                = cv.nr_instances
+                %br
+                = "Num unpredicted"
+                = cv.nr_unpredicted
+                %br
+                = "Root mean squared error:\t"
+                = cv.rmse.round(3) if cv.rmse
+                %br
+                = "Mean absolute error:\t"
+                = cv.mae.round(3) if cv.mae
+                %br 
+                = "R square:\t"
+                = cv.r_squared.round(3) if cv.r_squared
+          %br
+          %hr
+          %form{:id=>idx, :role=>"form", :action=> to("/predict"), :method=>"post"}
+            %h3.help-block
+              Please characterise a nanoparticle:
+            #input
+            %div.form-group
+              %h5 Core
+              %input.input-sm.form-control{:id=>"core_name",:type=>"text",:name=>"core_name",:value=>example.core["name"], :disabled=>"true"}
+            - example.physchem_descriptors.each_with_index do |v,id|
+              - feature = OpenTox::Feature.find_by(:id => v[0])
+              - name = feature.name
+              - if feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?
+                - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
+              - else
+                - name = feature.name
+              - val = v[1]
+              - id = id + 1
+              %h5= name
+              %input.form-control{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>v[0]}
+              %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}
+            %hr
+            #predict
+              %button.btn.btn-success{:id=>"submitbutton", :type=>"submit", :onclick=>"showcircle();"} 
+                Find similar nano particles
+                %span.glyphicon.glyphicon-chevron-right{:id=>"span"}
+              %img{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index d22960b..f8610f5 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -25,7 +25,7 @@
 
 
   #neighbors.table-responsive
-    %table.tablesorter
+    %table.tablesorter{:style => "max-width:100%;white-space:nowrap;"}
       %thead
         %tr
           %th
@@ -39,58 +39,60 @@
             %br 
             Net cell association [mL/ug(Mg)]
           - @input.each do |key|
+            - feature = OpenTox::Feature.find_by(:id=>key[0])
+            - name = feature.name
+            - if !feature[:conditions]["MEDIUM"].blank?
+              - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
+            - else
+              - name = feature.name
             %th.physchem
-              = key[0].gsub(/\sMean/, '')
+              = name
       %tbody
         / query and match combined
         %tr.static
           / id
           %td
-            - if @prediction[:match]
-              %a{:href=> $ambit_search+@prediction[:match].keys[0], :rel=>"external"}
-                %h5= @prediction[:match].keys[0]
+            - if @match
+              %a{:href=> $ambit_search+@name, :rel=>"external"}
+                %h5= @name
             - else
               %h5 Query
           / similarity
           %td
-            - if @prediction[:match]
+            - if @match
               %h5 1
             - else
               %h5 x
           / composition
           %td
-            - if @prediction[:match]
-              - surfaceModifier = {}
-              - surfaceModifier["Surface modifier"] = [@prediction[:match].values[0]["composition"]["Surface modifier1"], @prediction[:match].values[0]["composition"]["Surface modifier2"]] 
-              - @prediction[:match].values[0]["composition"].delete("Surface modifier1")
-              - @prediction[:match].values[0]["composition"].delete("Surface modifier2")
-              - @prediction[:match].values[0]["composition"].merge!(surfaceModifier)
-              - @prediction[:match].values[0]["composition"].each do |k,v|
-                %h5= k
-                - if v.class == Array
-                  - v.compact.each do |value|
-                    %p= value
-                - else
-                  %p= v
+            - if @match
+              %h5 Core
+              = "["+@nanoparticle[:core]["name"]+"]"
+              %h5 Coating
+              = @nanoparticle[:coating][0]["name"]
             - else
               %h5 x
           / tox
           %td.tox
-            - if @prediction[:prediction]
-              - @prediction[:prediction].each do |k,v|
-                %h5 Prediction
-                -#%p= k.split.drop(1).join(" ")[1..-2]
-                - if v == nil
-                  %p not available
-                - else
-                  %h5= v.round(5)
-            - if @prediction[:match]
-              - @prediction[:match].values[0]["tox"].each do |k,v|
-                %hr
-                %h5 Measurement
-                -#%p= k.split.drop(1).join(" ")[1..-2]
-                %p= v.round(3)
-            - if !@prediction[:prediction] && !@prediction[:match]
+            - if @prediction[:value]
+              %h5 Prediction:
+              = @prediction[:value].round(3)
+            - if @prediction[:rmse]
+              %h5 Rmse:
+              = @prediction[:rmse].round(3)
+            - if @prediction[:r_squared]
+              %h5 R_squared:
+              = @prediction[:r_squared].round(3)
+            - 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
+              - @prediction[:measurements].each do |m|
+                %p= m
+            - if !@prediction[:value] && !@prediction[:measurements]
               %h5 not available
           / physchem
           - if @prediction[:match]
@@ -99,55 +101,42 @@
             - sorted.each do |k,v|
               %td.physchem
                 %div{:style=>"display:inline-block;padding-right:20px;"}
-                  /= k.gsub(/\sMean/, '')
-                  %p= v.round(3)
+                  %p= v[0].round(3)
           - else
             - @input.each do |v|
               %td.physchem
                 %div{:style=>"display:inline-block;padding-right:20px;"}
-                  //= v[0].gsub(/\sMean/, '')
                   - if v[1].nil?
                     %p x
                   - else
-                    %p= v[1].round(3)
+                    %p= v[1][0].round(3)
 
         / neighbors
         - 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"}
             %tr
               / ID
               %td
-                %a{:href=> $ambit_search+neighbor["id"], :rel=>"external"}
-                  %h5= neighbor["id"]
+                %a{:href=> $ambit_search+nano.name, :rel=>"external"}
+                  %h5= nano.name
               / Similarity
               %td
                 %h5= neighbor["similarity"].round(3)
               / Composition
               %td
-                - surfaceModifier = {}
-                - surfaceModifier["Surface modifier"] = [neighbor["composition"]["Surface modifier1"], neighbor["composition"]["Surface modifier2"]] 
-                - neighbor["composition"].delete("Surface modifier1")
-                - neighbor["composition"].delete("Surface modifier2")
-                - neighbor["composition"].merge!(surfaceModifier)
-                - neighbor["composition"].each do |k,v|
-                  %h5= k
-                  - if v.class == Array
-                    - v.compact.each do |value|
-                      %p= value
-                  - else
-                    %p= v
+                %h5 Core
+                = "["+nano[:core]["name"]+"]"
+                %h5 Coating
+                = nano[:coating][0]["name"]
               / Tox
               %td.tox
-                - neighbor["tox"].each do |k,v|
-                  %h5 Measurement
-                  -#%p= k.split.drop(1).join(" ")[1..-2]
-                  %p= v.round(3)
+                %h5 Measurement
+                %p= neighbor["measurements"][0]
               / Physchem
-              - sorted = {}
-              - @input.each{|i| sorted[i[0]]=neighbor["physchem"][i[0]]}
-              - sorted.each do |k,v|
+              - @input.each do |k,v|
                 %td.physchem
                   %div
                     %div{:style=>"display:inline-block;padding-right:20px;"}
-                      /= k.gsub(/\sMean/, '')
-                      %p= v.round(3)
+                      %p= v[0].round(3) unless v.nil?