rbbt-rest 1.6.2 → 1.6.3

data/share/views/public/js/rbbt.favourites.js.old

@@ -0,0 +1,195 @@
+
+
+rbbt.favourites = {};
+
+var fav_module = rbbt.favourites;
+
+fav_module.update_favourite_entities = function(){
+ return m.request({method: 'GET', url: '/favourite_entities'}).then(function(data){
+  fav_module.favourite_entities = {}
+  for (type in data){
+   var type_data = data[type]
+   fav_module.favourite_entities[type] = {}
+   for (entity in type_data){
+    var info = type_data[entity]
+    info.id = entity
+    info.type = type
+    fav_module.favourite_entities[type][entity] = new Entity(info)
+   }
+  }
+  return data
+ })
+}
+
+fav_module.update_favourite_lists = function(){
+ return m.request({method: 'GET', url: '/favourite_entity_lists'}).then(function(data){
+  fav_module.favourite_lists = {}
+  for (type in data){
+   var type_data = data[type]
+   fav_module.favourite_lists[type] = {}
+   for (i in type_data){
+    var list = type_data[i]
+    info = {}
+    info.id = list
+    info.type = type
+    fav_module.favourite_lists[type][list] = new EntityList(info)
+   }
+  }
+  return data
+ }) //.then(fav_module.update_list_selects)
+}
+
+fav_module.update_favourites = function(){
+ return fav_module.update_favourite_entities().then(fav_module.update_favourite_lists)
+}
+
+fav_module.isFavourite_entity = function(entity){
+ var favourites = fav_module.favourite_entities
+ return favourites[entity.type] !== undefined && favourites[entity.type][entity.id] !== undefined
+}
+
+fav_module.isFavourite_list = function(list){
+ var favourites = fav_module.favourite_lists
+ return favourites[list.type] !== undefined && favourites[list.type][list.id] !== undefined
+}
+
+fav_module.toggleFavourite_entity = function(){
+ var entity = rbbt.page.entity();
+
+ if (fav_module.isFavourite_entity(entity)){
+  rbbt.post({url: '/remove_favourite_entity/' + entity.type + '/' + entity.id}).then(fav_module.update)
+ }else{
+  rbbt.post({url: '/add_favourite_entity/' + entity.type + '/' + entity.id, data: entity.info}).then(fav_module.update)
+ }
+}
+
+fav_module.toggleFavourite_list = function(){
+ var list = rbbt.page.list();
+
+ if (fav_module.isFavourite_list(list)){
+  rbbt.post({url: '/remove_favourite_entity_list/' + list.type + '/' + list.id}).then(fav_module.update)
+ }else{
+  rbbt.post({url: '/add_favourite_entity_list/' + list.type + '/' + list.id}).then(fav_module.update)
+ }
+}
+
+fav_module.toggleFavourite = function(){
+ if (! rbbt.page.entity())
+  if (! rbbt.page.list())
+   return
+  else
+   fav_module.toggleFavourite_list()
+ else
+   fav_module.toggleFavourite_entity()
+}
+
+//{{{ VIEWS
+
+fav_module.star_view = function(){
+ if (! rbbt.page.entity())
+  if (! rbbt.page.list())
+   return
+  else
+   return m('i.icon.star', {class: (fav_module.isFavourite_list(rbbt.page.list()) ? 'favourite' : 'not_favourite')})
+ else
+  return m('i.icon.star', {class: (fav_module.isFavourite_entity(rbbt.page.entity()) ? 'favourite' : 'not_favourite')})
+}
+
+fav_module.draw_favourite_menu = function(){
+ var favourites = fav_module.favourite_entities
+ var types = Object.keys(favourites)
+
+ return m('.ui.menu',
+          m('.ui.dropdown.item', [
+           m('i.icon.dropdown'), 
+           'Entities',
+           m('.menu', types.map(function(type, index){ 
+            var _type = favourites[type]
+            var entities = Object.keys(_type)
+
+            return m('.ui.dropdown.item', [
+             m('i.icon.dropdown'), 
+             type,
+             m('.menu', entities.map(function(entity, index){ url = _type[entity].url(); return m('a.item', {href: url}, _type[entity].name) }))
+            ]);
+           }))
+          ])
+         )
+}
+
+fav_module.draw_favourite_list_menu = function(){
+ var favourites = fav_module.favourite_lists
+ var types = Object.keys(favourites)
+
+ return m('.ui.menu',
+          m('.ui.dropdown.item', [
+           m('i.icon.dropdown'), 
+           'Lists',
+           m('.menu', types.map(function(type, index){ 
+            var _type = favourites[type]
+            var lists = Object.keys(_type)
+
+            return m('.ui.dropdown.item', [
+             m('i.icon.dropdown'), 
+             type,
+             m('.menu', lists.map(function(lists, index){ url = _type[lists].url(); return m('a.item', {href: url}, _type[lists].name) }))
+            ]);
+           }))
+          ])
+         )
+}
+fav_module.view = function(){
+ m.render($('#top_menu > .favourite')[0], [
+  m('.item.pointer', {onclick: fav_module.toggleFavourite}, fav_module.star_view()), 
+  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_menu()),
+  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_list_menu())
+ ])
+}
+
+fav_module.update = function(){
+ fav_module.update_favourites().then(fav_module.view).then(function(){ $('.dropdown:not([tabindex])').dropdown()})
+}
+
+
+fav_module._update_list_select= function(select, type, lists){
+ if (select.attr('attr-allow-empty') == 'true'){
+  var option = $('<option value="none" class="loaded">none</option>')
+  select.append(option);
+ }
+
+ var selected = null;
+
+ if (select.attr('attr-selected') != undefined ){
+  selected = select.attr('attr-selected');
+ }
+
+ $.each(lists, function(name, elems){
+  var option = null;
+  var name = elems
+  if (selected == null || name != selected){
+   option = $('<option attr-entity_type="' + type + '" class="automatic_load" value="' + name.id + '">' + name.id + '</option>');
+  }else{
+   option = $('<option attr-entity_type="' + type + '" class="automatic_load" selected=selected value="' + name.id + '">' + name.id + '</option>');
+  }
+  select.append(option);
+  return true
+ })
+},
+
+fav_module.update_list_selects= function(){
+ $('select.favourite_lists').find('option.automatic_load').remove()
+
+ $.each(fav_module.favourite_lists, function(type, lists){
+  $('select.favourite_lists[type=' + type + ']').each(function(){
+   var select = $(this);
+   fav_module._update_list_select(select, type, lists);
+  })
+  $('select.favourite_lists[type=All]').each(function(){
+   var select = $(this);
+   select.append($('<option class="automatic_load ui" disabled>'+ type +'</option>'));
+   fav_module._update_list_select(select, type, lists);
+  })
+ });
+}
+
+fav_module.update()

data/share/views/public/js/rbbt.js

@@ -0,0 +1,40 @@
+
+rbbt.post = function(params){
+  var req_params = {config: rbbt.post.asFormUrlEncoded, serialize: rbbt.post.serialize_data, method: 'POST'}
+  for (key in params)
+   req_params[key] = params[key]
+
+  return m.request(req_params)
+}
+
+rbbt.post.serialize_data = function(obj) {
+ var str = [];
+ for(var p in obj)
+  if (obj.hasOwnProperty(p)) {
+   str.push(encodeURIComponent(p) + "=" + encodeURIComponent(obj[p]));
+  }
+   
+ return str.join("&");
+}
+
+rbbt.post.asFormUrlEncoded = function(xhr){
+ xhr.setRequestHeader("Content-type","application/x-www-form-urlencoded");
+}
+
+rbbt.log = function(obj){
+ console.log(obj)
+}
+
+rbbt.LS = {}
+
+rbbt.LS.load = function(key){
+ var content = localStorage[key]
+ if (content === undefined)
+  return undefined
+ else
+  return JSON.parse(content)
+}
+
+rbbt.LS.store = function(key, value){
+ localStorage[key] = JSON.stringify(value)
+}

data/share/views/public/js/rbbt.knowledge_base.js

@@ -0,0 +1,24 @@
+
+var KB = rbbt.knowledge_base = {}
+
+KB.children = function(database, entity){
+ var url = '/kb/user/' + database + '/children/' + entity.id
+ url = add_parameter(url, '_format', 'json')
+ return m.request({url: url, method: "GET", type: Entity})
+}
+
+KB.parents = function(database, entity){
+ var url = '/kb/user/' + database + '/parents/' + entity.id
+ url = add_parameter(url, '_format', 'json')
+ return m.request({url: url, method: "GET", type: Entity})
+}
+
+Entity.prototype.children = function(database){
+ return KB.children(database, this)
+}
+
+Entity.prototype.parents = function(database){
+ return KB.parents(database, this)
+}
+
+

data/share/views/public/js/rbbt.page.js

@@ -0,0 +1,32 @@
+
+rbbt.page = {};
+rbbt.page.entity = function(){
+ var card = $('.entity_card')
+ if (card.length == 0) return false
+ 
+ var entity = card.attr('data-entity')
+ var type = card.attr('data-entity-type')
+ var format = card.attr('data-entity-format')
+ var info = card.attr('data-entity-info')
+ var id = card.attr('data-entity-id')
+ return new Entity({id: id, code: entity, type: type, format: format, info: JSON.parse(info)})
+}
+
+rbbt.page.list = function(){
+ var card = $('.entity_list_card')
+ if (card.length == 0) return false
+ 
+ var list = card.attr('data-list')
+ var type = card.attr('data-list-type')
+ return new EntityList({id: list, type: type})
+}
+
+rbbt.page.map = function(){
+ var card = $('.entity_map_card')
+ if (card.length == 0) return false
+ 
+ var map = card.attr('data-map')
+ var type = card.attr('data-type')
+ var column = card.attr('data-column')
+ return new EntityMap({id: map, type: type, column: column})
+}

data/share/views/public/js/rbbt/actions.js

@@ -71,7 +71,7 @@ $.widget("rbbt.action_controller", {
     var tool = this
     var controller = tool.element;
 
-    controller.on('click', '> .actions  .button', function(e){ tool._activate_action(this); return false});
+    controller.on('click', '> .action_menu  .button', function(e){ tool._activate_action(this); return false});
     controller.on('click', '> .controls > .reload', function(e){ tool._reload_action(this); return false});
     controller.on('click', '> .controls > .parameters', function(e){ tool._display_parameters(this); return false});
     controller.on('click', '> .controls > .description', function(e){ tool._display_description(this); return false});
@@ -84,11 +84,11 @@ $.widget("rbbt.action_controller", {
 
     this.options.controller = controller
     this.options.action_controls = controller.find('> .controls')
-    this.options.action_list = controller.find('> .actions')
+    this.options.action_list = controller.find('> .action_menu')
 
     this.options.complete = function(jqXHR, textStatus){
       var action_controller = tool.options.controller
-      var action_list_item = action_controller.find('.actions > .loading, .actions > .active')
+      var action_list_item = action_controller.find('.action_menu > .loading, .action_menu > .active')
       var action_div = action_controller.next('.action_loader');
 
       if (jqXHR.status == 202){
@@ -98,14 +98,14 @@ $.widget("rbbt.action_controller", {
           var response = $(jqXHR.responseText)
           var stat = response.find('span.status').html()
           var message = response.find('.step_messages li:first').html()
+          var progress = response.find('.step.progress')
 
-          if (undefined === message){
-            action_div.html("<span class='loading ui message'>Loading [" + stat + "] ...</span>");
-          }else{
-            action_div.html("<span class='loading ui message'>Loading [" + stat + ": " + message + "] ...</span>");
-          };
+          text = [$('<div class="header">').html(stat), $('<div class="content">').html(message)]
+          action_controller.find('> .progress').html("").append(text).append(progress);
+          update_rbbt()
         }
       }else{ 
+        action_controller.find('> .progress').html("");
         action_controller.removeClass('loading').removeClass('disabled'); 
         action_list_item.removeClass('loading').removeClass('disabled');
 
@@ -142,7 +142,7 @@ $.widget("rbbt.action_controller", {
 
     _activate_action: function(e){
       var action_list_item = $(e)
-      var action_list = action_list_item.parent('.actions');
+      var action_list = action_list_item.parent('.action_menu');
       var link = action_list_item.find('> a')
       link = action_list_item
 
@@ -165,14 +165,14 @@ $.widget("rbbt.action_controller", {
 
       _unpin_parameters: function(){
         var controller = $(this.element)
-        var action = controller.find('.actions .active a').first().html()
+        var action = controller.find('.action_menu .active a').first().html()
         this.options.saved[action] = undefined
         controller.find('> .controls > .pin').removeClass('saved')
       },
 
       _pin_parameters: function(){
         var controller = $(this.element)
-        var action = $(this.element).find('.actions .active a').first().html()
+        var action = $(this.element).find('.action_menu .active a').first().html()
         var loader = $(this.element).next('.action_loader').first();
         this.options.saved[action] = loader.attr('form-params')
         controller.find('> .controls > .pin').addClass('saved')
@@ -180,7 +180,7 @@ $.widget("rbbt.action_controller", {
       },
 
       _toggle_pin: function(){
-       var action = $(this.element).find('.actions .active a').first().html()
+       var action = $(this.element).find('.action_menu .active a').first().html()
 
        if (this.options.saved[action] != undefined){
          this._unpin_parameters();
@@ -212,7 +212,8 @@ $.widget("rbbt.action_controller", {
 
 
      _reload_action: function(e){
-       if(! $(e).hasClass('active')){ return false}
+       if($(e).hasClass('disabled')){ return false}
+       console.log(1)
        var action_list_item = $(e);
        var action_list = action_list_item.parent('.controls');
        var action_controller = action_list.parent('.action_controller');
@@ -264,7 +265,7 @@ $.widget("rbbt.action_controller", {
      _load_action: function(link){
        var action_list_item = link.parent('.button');
        action_list_item = link
-       var action_list = action_list_item.parent('.menu');
+       var action_list = action_list_item.parent('.action_menu');
        var action_controller = action_list.parents('.action_controller').first();
        var action_div = action_controller.next('.action_loader');
        var href = link.attr('href')

data/share/views/public/js/rbbt/table.js

@@ -59,6 +59,7 @@ $.widget("rbbt.table", {
     $.scrollTo(table.find('tfoot'), {axis : 'y', offset: {top: - window.innerHeight + 100 }});
    }else{ complete() }
    if (tool.options.ellipsis !== undefined && ! $(table).hasClass('no_js')){
+     console.log($(table).hasClass('no_js'))
     tool._fix_long_table_cells(5);
    }
   });
@@ -98,7 +99,7 @@ $.widget("rbbt.table", {
 
   //{{{ Pagination
   //
-  table.on('click', 'tfoot > tr > th > .table_pagination > .num > a:not(.active)', function(link){
+  table.on('click', 'tfoot > tr > th > .table_pagination > .num:not(.active)', function(link){
    var link = $(this)
 
    var stat = tool._status()
@@ -108,7 +109,7 @@ $.widget("rbbt.table", {
    return false
   })
 
-  table.on('click', 'tfoot > tr > th > .table_pagination > .arrow > a.prev', function(link){
+  table.on('click', 'tfoot > tr > th > .table_pagination > .arrow.prev', function(link){
    var stat = tool._status()
 
    if (stat.num > 1){ stat.num = stat.num - 1 }
@@ -118,9 +119,9 @@ $.widget("rbbt.table", {
    return false
   })
 
-  table.on('click', 'tfoot > tr > th > .table_pagination > .arrow > a.next', function(evt){
+  table.on('click', 'tfoot > tr > th > .table_pagination > .arrow.next', function(evt){
    var stat = tool._status();
-   var last = parseInt($(this).parents('.table_pagination').first().find('.num').last().find('a').html())
+   var last = parseInt($(this).parents('.table_pagination').first().find('a.num').last().html())
 
    if (stat.num < last){ stat.num = stat.num + 1 }
 
@@ -275,6 +276,7 @@ $.widget("rbbt.table", {
    url = add_parameter(url, '_format', 'map')
    if (undefined != filter){ url = add_parameter(url, '_filter',  escape(filter)) }
 
+   console.log(url)
    modal.modal('show_url', url)
    return false
   });

data/share/views/tools/cytoscape.haml

@@ -0,0 +1,310 @@
+- id = "rand" << (rand * 1000).to_i.to_s unless defined? id and not (id.nil? or id.empty?)
+- id = Misc.snake_case(id)
+- static = false unless defined? static and not static.nil?
+- knowledge_base = nil unless defined? knowledge_base and not knowledge_base.nil?
+- kb_name = 'user' unless defined? kb_name and not kb_name.nil?
+
+= link_css '/stylesheets/cytoscape'
+
+- syndications = {}
+- databases = []
+- cytoscape.knowledge_base.all_databases.each do |database|
+  - database = database.to_s
+  - name, synd = database.split("@")
+  - if synd
+    - syndications[synd] ||= []
+    - syndications[synd] << database
+  - else
+    - databases << database
+
+:sass
+  .tab.content
+    position: relative
+.cytoscape_tool.fixable.preload(id=id)
+
+  .controls.ui.top.attached.tabular.menu
+    .ui.item(data-tab='Close') 
+      %i.icon.close
+    .ui.item(data-tab='Edges') Edges
+    .ui.item(data-tab='Entities') Entities
+    .ui.item(data-tab='Aesthetics') Aesthetics
+    .ui.item(data-tab='Help') Help
+  .ui.tab.bottom.attached.very.basic.segment.content(data-tab='Close')
+  .ui.tab.bottom.attached.segment.content(data-tab='Edges')
+    .database_edges
+
+      %h5 Add edges between entities
+      .action_parameters
+        %form.action_parameter_form
+          - if databases.any?
+            .input.multiple.database
+              - databases.each do |database|
+                - name, *rest = database.split "@"
+                %span.cchoice
+                  %label(for="database[#{database}]")=name
+                  %input(id="database[#{database}]" type="checkbox" value="true" name="database[#{database}]")
+          - if syndications.any?
+            %dl.rbbt_tabs.subtle(style="margin:1em")
+              - syndications.each do |synd, databases|
+                %dt.next=synd
+                %dd
+                  .input.database.multiple
+                    - databases.each do |database|
+                      - name, *rest = database.split "@"
+                      %span.choice
+                        %label(for="database[#{database}]")=name
+                        %input(id="database[#{database}]" type="checkbox" value="true" name="database[#{database}]")
+
+          .input.submit
+            %input(type="submit")
+
+  .ui.tab.bottom.attached.segment.content(data-tab='Entities')
+    .add_gene_list
+      %h5 Add entities from a list
+      = action_parameters nil, {:klass => ''}, :action => '#' do
+        - input :entities, :select, "Entities to add", nil, :html_options => {:class => 'favourite_lists', :type => 'All'}
+
+    .database_neighbours
+      %h5 Add neighbours of entities
+      .action_parameters.ui.raised.segment
+        %form.ui.form
+          .field.input.select.database
+            %label knowledgebase
+            %select(type="All" name="database")
+              - databases.each do |database|
+                - name, *rest = database.split "@"
+                %option(value=database)=name
+              - syndications.each do |synd, databases|
+                %option(disabled=true)=synd
+                - databases.each do |database|
+                  - name, *rest = database.split "@"
+                  %option(value=database)=name
+          .field.submit
+            %input.ui.submit.button(type="submit")
+
+  .ui.tab.bottom.attached.segment.content(data-tab='Aesthetics')
+    .maps
+      %h5 Map entity aesthetic
+      = action_parameters nil, {:klass => ''}, :action => '#' do
+        - input :elem, :select, "Type of element", :nodes, :select_options => [:nodes, :edges]
+        - input :aesthetic, :select, "Aesthetic to map to", :opacity, :select_options => [:shape, :size, :color, :opacity, :borderWidth]
+        - input :field, :string, "Attribute to map", 'id', :select_options => {:textarea => "Use textarea"}, :html_options => {:class => 'favourite_maps', :type => 'All'}
+        - input :map, :select, "Select map to use", nil, :select_options => {:textarea => "Use textarea"}, :html_options => {:class => 'favourite_maps', :type => 'All'}
+        - input :map_tsv, :text, "Map", nil, :no_file => true
+
+    .select_gene_list
+      %h5 Highlight entities from a list
+      = action_parameters nil, {:klass => ''}, :action => '#' do
+        - input :entities, :select, "Genes to add", nil, :html_options => {:class => 'favourite_lists', :type => 'All'}
+
+  .ui.tab.bottom.attached.segment.content(data-tab='Help')
+
+    :documentation
+
+      ### Edges
+      
+      You can connect your nodes using any of the databases in the `knowledgebase`.
+      This is configured in the `Edges` menu: check the databases you want to use, 
+      if none is selected (by default) all of them are used.
+
+      ### Entities
+
+      The network comes preloaded with a list of entities (nodes), but you
+      can remove them or add new ones. To remove them use the context menu
+      (right-click over cytoscape window); you can remove one node, or the
+      selected list of nodes.
+
+      Adding nodes can be done using the `Entity` menu. You can add entities from
+      your `favourite` lists or add the neighbours of your entities using any of
+      the databases in the `knowledgebase`.
+
+      ### Aesthetics
+
+      Use the `Aesthetics` menu to change how your network looks. This can
+      help represent different sources of information. For now it works only
+      on nodes.  You can change the value of different aesthetics, like
+      color, border width, size, shape, and opacity. You can `map` these
+      aesthetics to favourite `Entity Maps`, or use a custom mapping
+      in-place, as a space-separated TSV file (see example below). The
+      mappings can consider the identity of the node (type `id` in `field`;
+      default) or the type of node (type `entity_type` in `field`). For
+      instance:
+
+          aesthetic: color
+          field: entity_type
+          map: use_textarea
+          map_tsv:
+            GOTerm red
+            KeggPathway blue
+            Gene yellow
+            
+      Another example use is to gather the `mutation/protein size` column on
+      the `COSMIC Overview` analysis bellow, and map it to the `opacity`
+      aesthetic of the genes (using the `id` as `field`).
+
+  .window.fixed_size(id="#{id}_window")
+
+
+  :deferjs
+    var cytoscape_id = '##{id}';
+
+    require_js(['/js/cytoscape/js/src/AC_OETags.js', '/js/cytoscape/js/src/cytoscapeweb.js', '/js/cytoscape'], function(){
+
+      $('.preload').removeClass('preload')
+
+      var tool = $(cytoscape_id).cytoscape_tool({
+        knowledge_base: '#{kb_name}',
+        namespace: '#{cytoscape.namespace}',
+        entities: #{cytoscape.entities.to_json},
+        network: #{cytoscape.network.to_json},
+        aesthetics: #{cytoscape.aesthetics.to_json},
+
+        node_click: function(event){
+          var target = event.target;
+
+          for (var i in target.data){
+            var variable_name = i;
+            var variable_value = target.data[i];
+          }
+
+          for (var i in target.data) {
+            var variable_name = i;
+            var variable_value = target.data[i];
+          }
+
+          var url = target.data.url;
+
+          $('#modal').modal('show_url', url, undefined, function(){
+            $('#modal').find(' > .header > .title').attr('entity', target.data.id).attr('type', target.data.entity_type)
+          })
+          return(false)
+        },
+
+        edge_click: function(event){
+          var target = event.target;
+          for (var i in target.data){
+            var variable_name = i;
+            var variable_value = target.data[i];
+          }
+
+          var pair = [target.data.source, target.data.target].join("~")
+          tool.cytoscape_tool('show_info', "user", target.data.database, pair);
+
+          return(false)
+        }
+
+      });
+
+      require_js('/js/controls/context_menu', function(){
+        cytoscape_context_menu(tool)
+      })
+
+      require_js('/js/controls/placement', function(){
+        cytoscape_placement(tool)
+      })
+
+      require_js('/js/controls/save', function(){
+        cytoscape_save(tool)
+      })
+
+
+      ///////////////////////////////////
+      //{{{ NETWORK INIT
+
+      tool.cytoscape_tool('draw');
+
+      //////////////////////////////////////////////////////////////////
+      //{{{ Controls
+
+      $('.cytoscape_tool .database_edges input[type=submit]').click(function(){
+        var form =$(this).parents('form').first()
+        var inputs = form.find('.input.database.multiple')
+        var databases = $.map(inputs.find('input[type=checkbox]:checked'), function(e){
+          return $(e).attr('name').match(/\[(.*)\]/)[1];
+        })
+
+        tool.cytoscape_tool('set_edges', databases)
+        tool.cytoscape_tool('draw');
+
+        return false;
+      })
+
+      $('.cytoscape_tool .database_neighbours input[type=submit]').click(function(){
+        var databases = $.map($(this).parents('form').first().find('.input.database').find('input[type=checkbox]:checked'), function(e){
+          return $(e).attr('name').match(/\[(.*)\]/)[1];
+        })
+        var option = $(this).closest('form').find('select').find('option:selected');
+        var database = option.attr('value')
+
+        tool.cytoscape_tool('add_neighbours', database)
+        tool.cytoscape_tool('draw');
+
+        return false;
+      })
+
+
+      $('.cytoscape_tool .add_gene_list input[type=submit]').click(function(){
+        var option = $(this).closest('form').find('select.favourite_lists').find('option:selected');
+        var type = option.attr('attr-entity_type')
+        var list_id = $(this).parents('form').first().find('select').val();
+        var list = list_entities(type, list_id);
+        var info = list_info(type, list_id);
+
+        tool.cytoscape_tool('add_entities', type, list)
+        tool.cytoscape_tool('draw');
+
+        return false;
+      })
+
+      $('.cytoscape_tool .select_gene_list input[type=submit]').click(function(){
+        var option = $(this).closest('form').find('select.favourite_lists').find('option:selected');
+        var type = option.attr('attr-entity_type')
+        var list_id = $(this).parents('form').first().find('select').val();
+        var list = list_entities(type, list_id);
+
+        tool.cytoscape_tool('select_entities', list)
+
+        return false;
+      })
+
+      $('.cytoscape_tool .maps input[type=submit]').click(function(){
+        var form = $(this).closest('form')
+
+
+        var elem = form.first().find('div.input.elem select').val();
+        var map_id = form.first().find('div.input.map select').val();
+        var field = form.first().find('div.input.field input').val();
+        var map_content = form.first().find('div.input.map_tsv textarea').val();
+        var option = form.first().find('div.input.map option:selected');
+        var type = option.attr('attr-entity_type')
+        var column = form.first().find('div.input.map select').find('option:selected').attr('attr-column');
+        var aesthetic = form.first().find('div.input.aesthetic select').val();
+
+        var map;
+
+        if (map_id == 'textarea'){
+          map_content = "#: :type=:single#:sep=/\\s/#:identifiers=Hsa/jan2013\n" + map_content
+          rbbt_job('TSVWorkflow', 'to_json', {tsv: map_content}, function(data){
+            var map = JSON.parse(data)
+            tool.cytoscape_tool('aesthetic', elem, aesthetic, map, field)
+            tool.cytoscape_tool('draw')
+          })
+        }else{
+          entity_map(type, column, map_id, function(map){
+            tool.cytoscape_tool('aesthetic', elem, aesthetic, map, field)
+            tool.cytoscape_tool('draw')
+          });
+        }
+
+        return false;
+      })
+    })
+:javascript
+  $('.item[data-tab]').tab()
+  $('.item[data-tab=Close]').click(function(item){
+    var tool = $(this).parents('.cytoscape_tool').first()
+    tool.find('.tab.active, .item.active').removeClass('active')
+    return false
+  })
+
+