Merge branch 'release/v3.0.1'v3.0.1

15 files changed, 258 insertions, 72 deletions

diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..51762ea
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,6 @@
+v3.0.1 2011-10-19
+    * assign a model to an endpoints on creating a new model,
+      endpoint-list from ontology service,
+      endpoint uri in "Training dataset" 
+    * fix missing "measured activity" predicting a classification model
+
diff --git a/application.rb b/application.rb
index 6d9ea76..6cdfcfb 100644
--- a/application.rb
+++ b/application.rb
@@ -96,8 +96,22 @@ get '/models/?' do
   sort_by = params["sort_by"]
   if sort_by
     case sort_by
-    when "name", "created_at", "type"
-      @models = ToxCreateModel.all.sort_by(sort_by.to_sym, :order => "#{order} ALPHA")
+    when "created_at"
+      @models = ToxCreateModel.all.sort(:order => "#{order}")
+    when "name"
+      @models = ToxCreateModel.all.sort
+      if order == "ASC"
+        @models = @models.sort_by{|x| x.name.downcase}
+      else
+        @models = @models.sort{|x, y| y.name.downcase <=> x.name.downcase}
+      end
+    when "type", "endpoint"
+      @models = ToxCreateModel.all.sort
+      if order == "ASC"
+        @models = @models.sort_by{|x| [x.send(sort_by.to_sym),x.name.downcase]}
+      else
+        @models = @models.sort{|x,y|[y.send(sort_by.to_sym),x.name.downcase] <=> [x.send(sort_by.to_sym), y.name.downcase]}
+      end
     when "id"
       @models = ToxCreateModel.all.sort(:order => "#{order}")
     end
@@ -186,8 +200,9 @@ get '/model/:id/:view/?' do
 end
 
 get '/predict/?' do 
-  @models = ToxCreateModel.all.sort(:order => "DESC")
+  @models = ToxCreateModel.all.sort
   @models = @models.collect{|m| m if m.status == 'Completed'}.compact
+  @models = @models.sort_by{|x| [x.endpoint ? x.endpoint : "",x.name.downcase]}
   haml :predict
 end
 
@@ -232,8 +247,8 @@ end
 
 post '/models' do # create a new model
 
-  unless (params[:dataset] and params[:prediction_feature]) or (params[:file] and params[:file][:tempfile]) #params[:endpoint] and 
-    flash[:notice] = "Please upload a Excel or CSV file or select an AMBIT dataset."
+  unless (params[:dataset] and params[:prediction_feature]) or (params[:endpoint] and params[:file] and params[:file][:tempfile]) #params[:endpoint] and 
+    flash[:notice] = "Please upload a Excel or CSV file and select an endpoint or select an AMBIT dataset."
     redirect url_for('/create')
   end
 
@@ -280,6 +295,8 @@ post '/models' do # create a new model
         else
           raise "#{params[:file][:filename]} has an unsupported file type."
         end
+        @dataset.features[@dataset.features.keys.first][OWL.sameAs] = params[:endpoint].split(',').first if params[:endpoint]
+        @model.update :endpoint_uri => params[:endpoint].split(',').first, :endpoint => params[:endpoint].split(',')[1..99].to_s.gsub(/^"(.*?)"$/,'\1') if params[:endpoint]
         @dataset.save(@subjectid)
       rescue => e
         error "Dataset creation failed '#{e.message}'",e
@@ -289,8 +306,12 @@ post '/models' do # create a new model
       else
         @prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,@subjectid)
       end
+    #else
+      # test when external dataset is enabled: 
+      #if @dataset.features[@dataset.features.keys.first][OWL.sameAs] 
+      #  @model.update :endpoint_uri => @dataset.features[@dataset.features.keys.first][OWL.sameAs], :endpoint => OpenTox::Ontology::Echa.get_endpoint_name(@dataset.features[@dataset.features.keys.first][OWL.sameAs]) 
+      #end
     end
-
     task.progress(10)
     if @dataset.compounds.size < 10
       error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/help"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
diff --git a/helper.rb b/helper.rb
index 9b47142..11f99f7 100644
--- a/helper.rb
+++ b/helper.rb
@@ -96,9 +96,14 @@ helpers do
     haml :models_navigation, :layout => false
   end
 
+  def models_navigation_bottom
+    @page = 0 unless @page
+    haml :models_navigation_bottom, :layout => false
+  end
+
   def endpoint_option_list(max_time=3600)
     out = ""
-    tmpfile = File.join(TMP_DIR, "endpoint_option_list")
+    tmpfile = File.join(TMP_DIR, 'endpoint_option_list')
     if File.exists? tmpfile
       if Time.now-File.mtime(tmpfile) <= max_time
         f = File.open(tmpfile, 'r+')
@@ -108,12 +113,39 @@ helpers do
         File.unlink(tmpfile)
       end
     end
-    result = OpenTox::Ontology::Echa.endpoint_option_list()
+    result = endpoint_selection()
     if result.lines.count > 3
-      f = File.new(tmpfile,"w")
+      f = File.new(tmpfile,'w')
       f.print result
       f.close
     end
-    return result
+    result
+  end
+
+  def endpoint_level(endpoint="Endpoints", level=1)
+    results = OpenTox::Ontology::Echa.echa_endpoints(endpoint) rescue results = []
+    out = ""
+    out += "<ul id='list_#{endpoint}' class='endpoint level_#{level}'>\n" if results.size > 0
+    results.each do |result|
+      r = result.split(',')
+      endpointname = CGI.escape(r.first.split("#").last).gsub(".","")
+      title = r[1..r.size-1].to_s
+      out += "  <li class='level_#{level}'><input type='radio' name='endpoint' value='#{result}' id='#{endpointname}' class='endpoint_list' /><label for='#{endpointname}' id='label_#{endpointname}'>#{title.gsub("\"","")}</label>\n"
+      out += endpoint_level(endpointname, level + 1)
+      out += "</li>\n"
+    end
+    out += "</ul>\n" if results.size > 0
+    return out
   end
-end
+
+  def endpoint_selection()
+    out = "<span id='endpoint_label'></span><input type='button' id='endpoint_list_button' value='Select endpoint' /> \n
+    <div id='div_endpoint'>\n"
+    out += "<b>Please select:</b>\n"
+    out += endpoint_level
+    js = ""
+    out += "</div>\n"
+    return out
+  end
+
+end
\ No newline at end of file
diff --git a/model.rb b/model.rb
index bab5bde..05075f8 100644
--- a/model.rb
+++ b/model.rb
@@ -19,6 +19,8 @@ class ToxCreateModel < Ohm::Model
 
 	attribute :training_dataset
 	attribute :feature_dataset
+	attribute :endpoint_uri
+	attribute :endpoint
 	#attributey :validation_task_uri
 	attribute :validation_uri
 
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index 0e82040..ef2a953 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -25,12 +25,12 @@ $(function() {
     $.each(stati, function(){
       checkProgress(this);
       if(checkStatus(this) > 0) newstati.push(this);
-    });  
+    });
     if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '")',10000);
   };
-  
+
   checkStatus = function(id) {
-    if(id == "") return -1; 
+    if(id == "") return -1;
     var opts = {method: 'get', action: 'model/' + id + '/status', id: id};
     var status_changed = $.ajax({
       type: opts.method,
@@ -43,15 +43,15 @@ $(function() {
       success: function(data) {
         var status_before = "";
         if ($("span#model_" + id + "_status") != null) status_before = $("span#model_" + id + "_status").html().trim();
-        if (status_before == "Deleting") return -1;         
+        if (status_before == "Deleting") return -1;
         var status_after  = data.trim();
         $("span#model_" + id + "_status").animate({"opacity": "0.2"},1000);
         $("span#model_" + id + "_status").animate({"opacity": "1"},1000);
         if( status_before != status_after) {
-          $("span#model_" + id + "_status").html(data);        
+          $("span#model_" + id + "_status").html(data);
           loadModel(id, 'model');
           if (status_after == "Completed" || status_after == "Error") id = -1;
-        }        
+        }
       },
       error: function(data) {
         //alert("status check error");
@@ -60,8 +60,8 @@ $(function() {
     });
     return id;
   };
-  
-  
+
+
   checkProgress = function(id) {
     var task = $("input#model_" + id + "_task").attr('value');
     var opts = {action: task + "/percentageCompleted" , id: id};
@@ -74,9 +74,8 @@ $(function() {
       },
       success: function(data) {
         var progress = data.trim();
-        if (progress == "100") return -1;         
-        
-        $("div#model_" + id + "_progress").progressbar("value", parseInt(progress)); 
+        if (progress == "100") return -1;
+        $("div#model_" + id + "_progress").progressbar("value", parseInt(progress));
         $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%"});
       },
       error: function(data) {
@@ -84,10 +83,10 @@ $(function() {
       }
     });
     return id;
-  };    
+  };
 
   loadModel = function(id, view) {
-    if(id == "") return -1; 
+    if(id == "") return -1;
     var opts = {method: 'get', action: 'model/' + id + '/' + view, view: view };
     var out = id;
     $.ajax({
@@ -118,7 +117,7 @@ jQuery.fn.editModel = function(options) {
     trigger_on: 'click'
   };
   var opts = $.extend(defaults, options);
-  this.bind(opts.trigger_on, function() {  
+  this.bind(opts.trigger_on, function() {
     $.ajax({
          type: opts.method,
          url:  opts.action,
@@ -126,7 +125,7 @@ jQuery.fn.editModel = function(options) {
          data: {
            '_method': 'get'
          },
-         success: function(data) {         
+         success: function(data) {
            $("div#model_" + opts.id + "_name").html(data);
            $("input#model_" + opts.id + "_name").focus();
          },
@@ -145,8 +144,8 @@ jQuery.fn.cancelEdit = function(options) {
     trigger_on: 'click'
   };
   var opts = $.extend(defaults, options);
-  
-  this.bind(opts.trigger_on, function() { 
+
+  this.bind(opts.trigger_on, function() {
     $.ajax({
          type: opts.method,
          url:  opts.action,
@@ -154,7 +153,7 @@ jQuery.fn.cancelEdit = function(options) {
          data: {
            '_method': 'get'
          },
-         success: function(data) {         
+         success: function(data) {
            $("div#model_" + opts.id + "_name").html(data);
          },
          error: function(data) {
@@ -172,9 +171,9 @@ jQuery.fn.saveModel = function(options) {
     trigger_on: 'click'
   };
   var opts = $.extend(defaults, options);
-  
-  this.bind(opts.trigger_on, function() {  
-    var name =  $("input#model_" + opts.id + "_name").val();  
+
+  this.bind(opts.trigger_on, function() {
+    var name =  $("input#model_" + opts.id + "_name").val();
     $.ajax({
          type: opts.method,
          url:  opts.action,
@@ -183,7 +182,7 @@ jQuery.fn.saveModel = function(options) {
            '_method': 'put',
            'name': name
          },
-         success: function(data) {         
+         success: function(data) {
            $("div#model_" + opts.id + "_name").html(data);
          },
          error: function(data) {
@@ -215,7 +214,7 @@ jQuery.fn.deleteModel = function(type, options) {
          data: {
            '_method': 'delete'
          },
-         success: function(data) {         
+         success: function(data) {
            $("div#model_" + opts.id).fadeTo("slow",0).slideUp("slow").remove();
          },
          error: function(data) {
@@ -236,9 +235,6 @@ addExternalLinks = function() {
   $('A[rel="external"]').each(function() {
     $(this).attr('alt', 'Link opens in new window.');
     $(this).attr('title', 'Link opens in new window.');
-  });
-  $('A[rel="external"]').click(function() {
-    window.open($(this).attr('href'));
-    return false;
+    $(this).attr('target', '_blank');
   });
 };
diff --git a/views/create.haml b/views/create.haml
index da85382..9b0ca09 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -1,3 +1,30 @@
+:javascript
+  $(document).ready(function() {
+   $(".endpoint_list").click(function() {
+     elem  = this.id;
+     title = $("label#label_" + elem).html();
+     if($("ul#list_" + elem)) {
+       if ($("ul#list_" + elem).is(":hidden")) {
+         $("ul#list_" + elem).slideDown("slow");
+       } else {
+         $("ul#list_" + elem).slideUp("slow");
+       }
+     }
+     $("span#endpoint_label").html(title);
+   });
+   $("#endpoint_list_button").click(function() {
+     if ($("div#div_endpoint").is(":hidden")) {
+       $("div#div_endpoint").slideDown("slow");
+       $("input#endpoint_list_button").val("Hide");
+       $("input#endpoint_list_button").toggleClass("ok_button", true);
+     } else {
+       $("div#div_endpoint").slideUp("slow");
+       $("input#endpoint_list_button").val("Select endpoint");
+       $("input#endpoint_list_button").toggleClass("ok_button", false);
+     }
+   });
+  });
+
 .input
 
   %p
@@ -25,7 +52,8 @@
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
       %br
-      -# = haml :model_echa, :layout => false
+      = haml :create_echa, :layout => false
+    %br
     %input{ :type => "submit", :value => "Create model"}
     =# link_to "Cancel", '/create'
 
diff --git a/views/create_echa.haml b/views/create_echa.haml
new file mode 100644
index 0000000..4815c35
--- /dev/null
+++ b/views/create_echa.haml
@@ -0,0 +1,2 @@
+For endpoint:
+= endpoint_option_list()
\ No newline at end of file
diff --git a/views/model.haml b/views/model.haml
index 356ec65..fb264ca 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -40,6 +40,9 @@
       - if model.nr_compounds
         %dt Training compounds:
         %dd= model.nr_compounds 
+      - if model.endpoint
+        %dt Endpoint:
+        %dd= model.endpoint
       - if model.error_messages
         %dt Errors:
         %dd= model.error_messages
diff --git a/views/model_echa.haml b/views/model_echa.haml
deleted file mode 100644
index 257a28a..0000000
--- a/views/model_echa.haml
+++ /dev/null
@@ -1,2 +0,0 @@
-Select an endpoint:
-= endpoint_option_list
\ No newline at end of file
diff --git a/views/models.haml b/views/models.haml
index 1419e37..af11a32 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -26,3 +26,4 @@
     = haml :model, :locals=>{:model=>model}, :layout => false
 -if @models.size == 0
   .notice There are currently no models. You have to create a model first.
+= models_navigation_bottom if @models.size > 1
\ No newline at end of file
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
index b491cb5..c5eda97 100644
--- a/views/models_navigation.haml
+++ b/views/models_navigation.haml
@@ -1,12 +1,12 @@
 .models_navigation
-
+  - js = ""
   %form{:name => "nav", :action => url_for('/models'), :method => "get", :id => "nav"}
     %input{:type => :hidden, :name => :sort_by, :id => "sort_by", :value => params[:sort_by]}
     %input{:type => :hidden, :name => :order, :id => "order", :value => params[:order]}
     %input{:type => :hidden, :name => :page, :id => "page", :value => params[:page]}
 
     Sort by:
-    - ["created_at","name","type"].each do |s|
+    - ["created_at","name","type","endpoint"].each do |s|
       - idname = s == "created_at" ? "date" : s
       - if params[:sort_by] == s
         %div{:id => idname, :class => "active"}
@@ -22,32 +22,42 @@
     - if @models.size > 5
       |
       Models:
-      = "#{@models.size}"
-      - unless @page.to_i == 0
-        #prev
-          %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
-      -else
-        %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
-  
       - if @models.size < 5*@page+5
         - last = @models.size
       - else
         - last = 5*@page+5
-  
-      = "(#{5*@page+1}-#{last}/#{@models.size})"
+ 
+      = "#{5*@page+1}-#{last} / #{@models.size}"
+
+      | Page:
+      - unless @page.to_i == 0
+        #prev{:class => "link"}
+          %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
+      -else
+        %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
+
+      - (0..(@models.size/5).to_f.ceil-1).each do |p|
+        -if p != @page.to_f
+          %a{:href => '#', :id => "page_link_#{p}", :class => "page page_link"} #{p+1}
+          - js += "$('#page_link_#{p}').click(function() \{ \n"
+          - js += "  $('#page').val('#{p}');\n"
+          - js += "  $('#nav').submit();\n"
+          - js += "});\n"
+        -else
+          %span{:class => "page page_active"} #{p+1}
+
       - unless 5*@page.to_i+5 >= @models.size
-        #next
+        #next{:class => "link"}
           %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
       -else
         %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
 
-    - js = ""
-    - ["id","created_at","name","type"].each do |s|
+    - ["created_at","name","type","endpoint"].each do |s|
       - idname = s == "created_at" ? "date" : s
-      - js += "$('##{idname}').click(function() \{ \n "
-      - js += "  $('#sort_by').val('#{s}');\n "
-      - js += "  $('#nav').submit();\n "
-      - js += "});\n "
+      - js += "$('##{idname}').click(function() \{ \n"
+      - js += "  $('#sort_by').val('#{s}');\n"
+      - js += "  $('#nav').submit();\n"
+      - js += "});\n"
 
     :javascript
       $("#prev").click(function() {
diff --git a/views/models_navigation_bottom.haml b/views/models_navigation_bottom.haml
new file mode 100644
index 0000000..b2425fa
--- /dev/null
+++ b/views/models_navigation_bottom.haml
@@ -0,0 +1,42 @@
+.models_navigation
+  - js = ""
+  - if @models.size > 5
+    Models:
+    - if @models.size < 5*@page+5
+      - last = @models.size
+    - else
+      - last = 5*@page+5
+    = "#{5*@page+1}-#{last} / #{@models.size}"
+    | Page:
+    - unless @page.to_i == 0
+      #prevbot{:class => "link"}
+        %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
+    -else
+      %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
+
+    - (0..(@models.size/5).to_f.ceil-1).each do |p|
+      -if p != @page.to_f
+        %a{:href => '#', :id => "page_linkbot_#{p}", :class => "page page_link"} #{p+1}
+        - js += "$('#page_linkbot_#{p}').click(function() \{ \n"
+        - js += "  $('#page').val('#{p}');\n"
+        - js += "  $('#nav').submit();\n"
+        - js += "});\n"
+      -else
+        %span{:class => "page page_active"}  #{p+1}
+
+    - unless 5*@page.to_i+5 >= @models.size
+      #nextbot{:class => "link"}
+        %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
+    -else
+      %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
+
+  :javascript
+    $("#prevbot").click(function() {
+      $("#page").val(#{@page-1});
+      $("#nav").submit();
+    });
+    $("#nextbot").click(function() {
+      $("#page").val(#{@page+1});
+      $("#nav").submit();
+    });
+    #{js}
\ No newline at end of file
diff --git a/views/neighbors.haml b/views/neighbors.haml
index e2d65fa..49b72b7 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -14,7 +14,7 @@
   - compound = OpenTox::Compound.new(neighbor[OT.compound])
   %tr
     %td.image= compound_image(compound,@prediction.descriptors(compound),@value_map)
-    %td= activity_markup(neighbor[OT.measuredActivity], @value_map)
+    %td= activity_markup(neighbor[OT.measuredActivity].to_s, @value_map)
     %td= sprintf('%.03g', neighbor[OT.similarity])
     %td
       %ul
diff --git a/views/predict.haml b/views/predict.haml
index 670ca44..c6097ac 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -30,7 +30,12 @@
         %legend
           Choose one or more prediction models
         %br
+        - endpoint = ''
         - @models.each do |model|
+          -if model.endpoint != endpoint
+            -endpoint = model.endpoint
+            %b #{endpoint}:
+            %br
           %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => "model#{model.id}", :disabled => false}
           %label{:for => "model#{model.id}"}
             = model.name
diff --git a/views/style.sass b/views/style.sass
index c2a74cb..230c13c 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -5,6 +5,7 @@ $ot_purple: #5d308a
 $body_color: white
 $text_color: black
 $notice_border: red
+$mouseover: #FFFF69
 
 body
   min-width: 30em
@@ -269,14 +270,7 @@ dl
   float: left
 
 .models_navigation
-  #prev
-    @extend a
-    display: inline
-    cursor: pointer
-  #next
-    @extend a
-    display: inline
-    cursor: pointer
+  margin-top: 4px
   .link
     @extend a
     display: inline
@@ -287,13 +281,59 @@ dl
     font-weight: bold
   .thin
     font-weight: 100
+  .page
+    border: solid 1px #999
+    background-color: #FFF
+    padding: 0px 3px
+    font-size: 94%
+    font-weight: bold
+  .page_link:hover
+    border-color: #000
+    color: #000
+  .page_active
+    background-color: #ccd2dc
+    color: #000
+    font-weight: bold
+    border-right-color: #000
+    border-bottom-color: #000
+
+ul.endpoint
+  list-style-type: none
+  margin-left: 0px
+  padding-left: 0px
+
+ul.level_2
+  display: none
+ul.level_3
+  display: none
+ul.level_4
+  display: none
 
 .level_1
-  padding-left: 10px
+  margin-left: 0px
   font-weight: bold
 .level_2
-  padding-left: 20px
+  margin-left: 20px
+  font-weight: normal
 .level_3
-  padding-left: 30px
+  margin-left: 40px
+  font-weight: normal
 .level_4
-  padding-left: 40px
+  margin-left: 60px
+  font-weight: normal
+
+#endpoint_label
+  font-weight: bold
+  margin: 0 10px
+
+ul.endpoint
+  label:hover, label:active
+    background-color: $mouseover
+    border-bottom: solid #999 1px
+    border-top: solid #999 1px
+
+#div_endpoint
+  display: none
+
+.ok_button
+  background-color: $mouseover