version bump;units;general class update;sort by

8 files changed, 88 insertions, 68 deletions

diff --git a/VERSION b/VERSION
index bcab45a..81340c7 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.0.3
+0.0.4
diff --git a/application.rb b/application.rb
index 8a218f4..baba620 100644
--- a/application.rb
+++ b/application.rb
@@ -1,8 +1,9 @@
 require 'qsar-report'
 require 'rdiscount'
+require File.join './npo.rb'
 $ambit_search = "http://data.enanomapper.net/substance?type=name&search="
-$npo_search = "http://bioportal.bioontology.org/search?q=%s&ontologies=NPO&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories="
 
+include OpenTox
 
 configure :development do
   #$logger = Logger.new(STDOUT)
@@ -17,11 +18,11 @@ get '/?' do
 end
 #=begin
 get '/qmrf-report/:id' do
-  prediction_model = OpenTox::Model::NanoPrediction.find(params[:id])
+  prediction_model = Model::NanoPrediction.find(params[:id])
   if prediction_model
     model = prediction_model.model
 		model_type = "regression"
-    report = OpenTox::QMRFReport.new
+    report = QMRFReport.new
 		if File.directory?("#{File.dirname(__FILE__)}/../../lazar")
     	lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip
     	lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}"
@@ -34,38 +35,38 @@ get '/qmrf-report/:id' do
     report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
     report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
     report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
-    report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
+    report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
     report.ref_catalog :model_authors, :authors_catalog, :modelauthor
     report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}"
-    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Rautenberg, Gebele and Helma (2013), Validation of read across predictions for nanoparticle toxicities ", :url => "in preparation"}
+    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma, Rautenberg and Gebele (2013), Validation of read across predictions for nanoparticle toxicities ", :url => "in preparation"}
     report.ref_catalog :references, :publications_catalog, :publications_catalog_1
     report.value "model_species", prediction_model.species
     report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
     report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
     report.value "endpoint_units", "#{prediction_model.unit}"
-    report.value "algorithm_type", "#{model.class.to_s.gsub('OpenTox::Model::Lazar','')}"
-    #TODO add more
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].to_s : '')}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3
-		if model.prediction_algorithm_parameters
-			pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[:method])
-		end
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.prediction_algorithm.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2
+    report.value "algorithm_type", "#{model.class.to_s.gsub('Model::Lazar','')}"
+    #TODO add updated algorithms
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].to_s : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3
+		#if model.prediction_algorithm_parameters
+		#	pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[:method])
+		#end
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.prediction_algorithm.gsub('Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2
 
 		# Descriptors in the model 4.3
-		if model.neighbor_algorithm_parameters[:type]
-			report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
-			report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
-		end
+		#if model.neighbor_algorithm_parameters[:type]
+		#	report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
+		#	report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
+		#end
 
 		# Descriptor selection 4.4
-		report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm  
-    response['Content-Type'] = "application/xml"
+		#report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm  
     
-		return report.to_xml
+    response['Content-Type'] = "application/xml"
+    return report.to_xml
   else
     bad_request_error "model with id: #{params[:id]} does not exist."
   end
@@ -73,23 +74,23 @@ end
 #=end
 get '/predict/?' do
   @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 = Model::NanoPrediction.all
+  prediction_models.each{|m| m.model[:algorithms]["descriptors"]["categories"] == ["P-CHEM"] ? @prediction_models[0] = m : @prediction_models[1] = m}
   # define type (pc or pcp)
   @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")
+  dataset = Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
   nanoparticles = dataset.nanoparticles
   
-  # 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)}
+  # select physchem_parameters by relevant features for each model
+  @pc_relevant_features = @prediction_models[0].model.descriptor_ids.collect{|id, v| Feature.find(id)}
+  @pcp_relevant_features = @prediction_models[1].model.descriptor_ids.collect{|id, v| Feature.find(id)}
   pcp = nanoparticles.sample
-  pcp.physchem_descriptors.delete_if{|id,v| !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}
+  pcp.properties.delete_if{|id,v| !@pcp_relevant_features.include?(Feature.find(id))}
   @example_pcp = pcp
   
   pc = nanoparticles.sample
-  pc.physchem_descriptors.delete_if{|id,v| !@pc_relevant_features.include?(OpenTox::Feature.find(id))}
+  pc.properties.delete_if{|id,v| !@pc_relevant_features.include?(Feature.find(id))}
   @example_pc = pc
 
   haml :predict
@@ -102,7 +103,7 @@ end
 
 post '/predict/?' do
   # choose the right prediction model
-  prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model])
+  prediction_model = Model::NanoPrediction.find(params[:prediction_model])
   size = params[:size].to_i
   @type = params[:type]
 
@@ -123,28 +124,28 @@ post '/predict/?' do
 
   
   # define relevant_features by input
-  @type = "pc" ? (@pc_relevant_features = input_pc.collect{|id,v| OpenTox::Feature.find(id)}) : (@pc_relevant_features = [])
-  @type = "pcp" ? (@pcp_relevant_features = input_pc.collect{|id,v| OpenTox::Feature.find(id)}) : (@pcp_relevant_features = [])
+  @type = "pc" ? (@pc_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pc_relevant_features = [])
+  @type = "pcp" ? (@pcp_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pcp_relevant_features = [])
 
   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 = input_pc
+    nanoparticle = Nanoparticle.find_by(:id => params[:example_id])
+    nanoparticle.properties = input_pc
     @match = true
     @nanoparticle = nanoparticle
     @name = nanoparticle.name
   else
     # changed input = create nanoparticle to predict
-    nanoparticle = OpenTox::Nanoparticle.new
+    nanoparticle = Nanoparticle.new
     nanoparticle.core = input_core
     nanoparticle.coating = input_coating
-    nanoparticle.physchem_descriptors = input_pc
+    nanoparticle.properties = input_pc
     @match = false
     @nanoparticle = nanoparticle
   end
   # prediction output
   @input = input_pc
-  @prediction = prediction_model.model.predict_substance nanoparticle
+  @prediction = prediction_model.model.predict nanoparticle
   
   haml :prediction
 end
diff --git a/bin/nano-lazar-start b/bin/nano-lazar-start
index 0cbaba5..0cbaba5 100644..100755
--- a/bin/nano-lazar-start
+++ b/bin/nano-lazar-start
diff --git a/bin/nano-lazar-stop b/bin/nano-lazar-stop
index b3ef727..b3ef727 100644..100755
--- a/bin/nano-lazar-stop
+++ b/bin/nano-lazar-stop
diff --git a/config.ru b/config.ru
index 36438a3..0662ccd 100644
--- a/config.ru
+++ b/config.ru
@@ -7,7 +7,7 @@ require "sinatra/reloader" if development?
 
 FileUtils.mkdir_p 'log' unless File.exists?('log')
 log = File.new("log/nano-lazar.log", "a")
-$stdout.reopen(log)
-$stderr.reopen(log)
+#$stdout.reopen(log)
+#$stderr.reopen(log)
 
 run Sinatra::Application
diff --git a/npo.rb b/npo.rb
new file mode 100644
index 0000000..8d7075a
--- /dev/null
+++ b/npo.rb
@@ -0,0 +1,11 @@
+$npo = {
+  "Localized Surface Plasmon Resonance (LSPR) index" => "http://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0001136",
+  "ZETA POTENTIAL" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1302",
+  "Total protein (BCA assay)" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOAE_0001659",
+  "Core size" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.enanomapper.org%2Fonto%2FENM_8000039",
+  "Z-Average Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Volume Mean Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Intensity Mean Hydrodynamic Diameter" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1915",
+  "Autot (ICP-AES)" => "http://bioportal.bioontology.org/ontologies/ERO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FERO_0001675",
+  "Polydispersity index" => "http://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1155"
+}
diff --git a/views/predict.haml b/views/predict.haml
index 5d5d6f0..7819698 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -11,7 +11,7 @@
       - @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? ? "Physchem & Proteomics" : "Physchem" }"
+            = "#{idx+1}. #{m[:pcp_model] ? "Physchem & Proteomics" : "Physchem" }"
     %div.tab-content
       - @prediction_models.each_with_index do |m, idx|
         - m[:pc_model] ? (example = @example_pc; type = "pc"; relevant_features = @pc_relevant_features) : (example = @example_pcp; type = "pcp"; relevant_features = @pcp_relevant_features)
@@ -39,17 +39,23 @@
           Unit:
           = m.unit
           %br
-          Prediction algorithm:
-          = m.model.prediction_algorithm.split(".").last.gsub("_"," ")
+          %b Algorithms:
           %br
-          Prediction algorithm parameter:
-          = "random forest" if m.model.prediction_algorithm_parameters["method"] == "rf"
+          Similarity:
+          %a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{m.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"}
+            = m.model.algorithms["similarity"]["method"]
+          = ", min: #{m.model.algorithms["similarity"]["min"]}"
           %br
-          Neighbor algorithm:
-          = m.model.neighbor_algorithm.gsub("_", " ")
+          Prediction:
+          %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{m.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+            = m.model.algorithms["prediction"]["method"]
           %br
-          Neighbor algorithm parameter:
-          = "min sim = #{m.model.neighbor_algorithm_parameters["min_sim"]}"
+          Feature selection:
+          = m.model.algorithms["feature_selection"]["method"].split(".").last
+          %br
+          Descriptors:
+          = m.model.algorithms["descriptors"]["method"]+","
+          = m.model.algorithms["descriptors"]["categories"]
           %p
           %b Independent crossvalidations (log2 transformed):
           - crossvalidations =[]
@@ -89,7 +95,7 @@
               // 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}"}
+              %input{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example.properties}"}
               - size = relevant_features.size
               %input{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
               %input{:id=>"id",:type=>"hidden",:name=>"example_id",:value=>example.id}
@@ -107,9 +113,13 @@
               %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}
-            - relevant_features.sort_by{|d| d.category}.each_with_index do |relf,id|
+            //sort the relevant features
+            - pc = relevant_features.collect{|f| f if f.category == "P-CHEM"}.compact
+            - pcp = relevant_features.collect{|f| f if f.category == "Proteomics"}.compact
+            - relevant_features = pc.sort_by{|f| f.name} + pcp.sort_by{|f| f.name}
+            - relevant_features.each_with_index do |relf,id|
               - feature = relf
-              - v = example.physchem_descriptors.find{|id,v| id == feature.id.to_s  }
+              - v = example.properties.find{|id,v| id == feature.id.to_s  }
               - name = feature.name
               - if feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?
                 - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
@@ -119,12 +129,10 @@
               - id = id + 1
               - if feature.category == "Proteomics"
                 %h5
-                  %a{:href=>"http://www.uniprot.org/uniprot/#{name}", :rel=>"external"}= name
-              - else
-                / prepare name string for npo_search
-                - string = name.split("/").first.downcase.gsub(/%s/, "%20")
+                  %a{:href=>"http://www.uniprot.org/uniprot/#{name}", :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
+              - if feature.category == "P-CHEM"
                 %h5
-                  %a{:href=>$npo_search % string, :rel=>"external"}= name
+                  %a.descriptor{:href=>$npo[feature.name], :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
               // input physchem parameters
               %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>"#{val[0] if val[0]}", :disabled=>("disabled" if val[0] == "-")}
               - if val[0] == "-"
diff --git a/views/prediction.haml b/views/prediction.haml
index 53a9cfd..e451c5f 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -12,7 +12,7 @@
       $(".tablesorter").tablesorter({
         debug: false,
         theme: "bootstrap",
-        headerTemplate: '{content} {icon}',
+        //headerTemplate: '{content} {icon}',
         widgets: ['uitheme', 'staticRow', 'stickyHeaders'],
         widgetOptions: {
           stickyHeaders_attachTo: 'neighbors',
@@ -43,15 +43,15 @@
             Net cell association
             %br
             [mL/ug(Mg)]
-          - @input.each{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
-            - feature = OpenTox::Feature.find_by(:id=>key[0])
+          - @input.each{|d| Feature.find(d[0]).category}.each do |key|
+            - feature = Feature.find_by(:id=>key[0])
             - name = feature.name
             - if (feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?)
               - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
             - else
               - name = feature.name
-            %th.physchem
-              = name
+            %th.physchem.sorter-false
+              %a.descriptor{:href=>$npo[feature.name], :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
       %tbody
         / query and match combined
         %tr.static
@@ -118,7 +118,7 @@
         / neighbors
         - if @prediction[:neighbors]
           - @prediction[:neighbors].each_with_index do |neighbor,idx|
-            - nano = OpenTox::Nanoparticle.find(neighbor["_id"])
+            - nano = Nanoparticle.find(neighbor[:id])
             %tr
               / ID
               %td
@@ -126,7 +126,7 @@
                   %h5.th5= nano.name
               / Similarity
               %td
-                %h5.th5= neighbor["similarity"].round(3)
+                %h5.th5= neighbor[:similarity].round(3)
               / Composition
               %td
                 %h5.th5 Core:
@@ -137,8 +137,8 @@
               / Tox
               %td.tox
                 %h5.th5 Measurement:
-                = neighbor["measurements"][0]
+                = neighbor[:measurement]
               / 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| @pc_relevant_features.index OpenTox::Feature.find(id)}.each do |k,v|
+              - nano.properties.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(Feature.find(id)) : !@pcp_relevant_features.include?(Feature.find(id))}.sort_by{|id,v| @pc_relevant_features.index Feature.find(id)}.each do |k,v|
                 %td.physchem
                   = v[0].round(3) unless v.nil?