rbbt-rest 1.6.14 → 1.6.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 96f5e042d8f089b55dcbd883dd14ccbad0820d80
-  data.tar.gz: 0ab035fcfdf2838540047d8943c03ad0aa03ea6e
+  metadata.gz: cc4a9b93a28766b814c3dbb6d08f85c021603760
+  data.tar.gz: 975818bfe4d4439652a52744bed51bd171c8bf85
 SHA512:
-  metadata.gz: f7a7be6a47e7b15131ac8abaf3cd303d00f5d77c791321f68ac54d1af6c1299b865793c93964fc0ead18bc9d3021cadcac9572d8d20e436cc6e4c470c6e6dd0c
-  data.tar.gz: ad2e577ef5ecd4e50f08512784311395e62b9767d0c765cb91fc83f59efb4e7cab1de7d3b59e83ee1d1eed06762c59c4ac7a5cdac712b71a0d11332a77ac2844
+  metadata.gz: b4da80d08b5243a647ad31296c4027de08bf63355fb2c2f9d6dd7a51f0b8473b84b61494fa77161f6b519bdad9d5eea0f20d2cd6c5191bc3779cf6bc444b1a8e
+  data.tar.gz: 0a18077ebf5a6a70b6bffe253909c405c585f40ccb4923638736c8df06979b43efdc6cc304e6444a5d6a7f513228d9eac37146edccaaf123a8b795d5eed9209d

data/lib/rbbt/rest/workflow/jobs.rb

@@ -109,7 +109,6 @@ module WorkflowRESTHelpers
     when :entities
       tsv = tsv_process(load_tsv(job.path).first)
       list = tsv.column_values(tsv.fields.first).flatten
-      iif list
       if not AnnotatedArray === list and Annotated === list.first
         list.first.annotate list 
         list.extend AnnotatedArray

data/share/views/compass/app.sass

@@ -323,3 +323,36 @@ label[title]
   &.error
     .header
       color: red
+
+
+
+#footer
+  clear: both
+
+  border: none !important
+  padding: 0px !important
+  margin: 0px !important
+  .card
+    width: 100%
+    height: 100%
+  .contact
+    &:before
+      content: "Contact: "
+      font-weight: bold
+    span.where:before
+      content: " at "
+  .image 
+    font-size: 0px
+    width: 241px 
+  .content
+    width: calc(100% - 241px -8px)
+  .image, .content
+    display: inline-block
+    margin-left: 8px
+
+  .ui.segment:after
+    content: " "
+    display:inline-block
+    float:left
+    clear:both
+

data/share/views/layout/footer.haml

@@ -1,37 +1,3 @@
-:sass
-
-  #footer
-    clear: both
-
-    border: none !important
-    padding: 0px !important
-    margin: 0px !important
-    .card
-      width: 100%
-      height: 100%
-    .contact
-      &:before
-        content: "Contact: "
-        font-weight: bold
-      span.where:before
-        content: " at "
-    .image 
-      font-size: 0px
-      width: 241px 
-    .content
-      width: calc(100% - 241px -8px)
-    .image, .content
-      //float: left
-      display: inline-block
-      margin-left: 8px
-
-    .ui.segment
-      &:after
-        content: " "
-        display:inline-block
-        float:left
-        clear:both
-
 .ui.segment
   .image
     %a(href="http://www.cnio.es/")

data/share/views/layout/top_menu.haml

@@ -1,17 +1,22 @@
 :sass
   #top_menu
+    .favourite
+      width: 100%
     & > .dropdown
       display: inline-block !important
       min-width: 10em
     & > .favourite > .dropdown, & > .favourite > .item.pointer
       display: inline-block !important
-    .favourite
-      width: 100%
+
 #top_menu.ui.fixed.menu
   %a.header.item(href='/')= $title
 
   %span.favourite
 
+  - if settings.respond_to?(:finder) and settings.finder and settings.finder.instances.any?
+    .finder.right.item
+      %form.collapse(action='/find' method="POST")
+        %input(type="search" name="term" placeholder='Search')
 
   - if defined? Sinatra::RbbtRESTWorkflow and Sinatra::RbbtRESTWorkflow::WORKFLOWS
     - expoted_workflows = Sinatra::RbbtRESTWorkflow::WORKFLOWS.collect do |workflow|
@@ -27,10 +32,6 @@
           - expoted_workflows.each do |workflow|
             %a.item(href='#{'/' + workflow.to_s}')= workflow.to_s
 
-  - if settings.respond_to?(:finder) and settings.finder and settings.finder.instances.any?
-    .finder.right.item
-      %form.collapse(action='/find' method="POST")
-        %input(type="search" name="term" placeholder='Search')
 
   %a.item.login.right(href='/login')
     %i.icon.user

data/share/views/public/js/helpers.js

@@ -137,3 +137,30 @@ function unique(arrayName) {
   return newArray;
 }
 
+function forHash(obj, fn, thisObj){
+  var key, i = 0;
+  function exec(fn, obj, key, thisObj){
+    return fn.call(thisObj, key, obj[key], obj);
+  }
+  for (key in obj) {
+    if (exec(fn, obj, key, thisObj) === false) {
+      break;
+    }
+  }
+  return forHash;
+}
+
+function forArray(obj, fn, thisObj){
+  var key, i = 0;
+  function exec(fn, obj, prop, thisObj){
+    return fn.call(thisObj, obj[prop], obj);
+  }
+  for (var prop in obj) {
+    if (obj.hasOwnProperty(prop)) { 
+      if (exec(fn, obj, prop, thisObj) === false) {
+        break;
+      }
+    }
+  }
+  return forArray;
+}

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

@@ -38,19 +38,19 @@ var FavouriteEntities = function(by_type){
  }
 }
 
+
 FavouriteEntities.deserialize = function(data){
   data = JSON.parse(data)
   favourite_entities = {}
-  for (type in data){
-   var type_data = data[type]
-   favourite_entities[type] = {}
-   for (code in type_data){
-    var info = type_data[code]
-    info.code = code
-    info.type = type
-    favourite_entities[type][code] = new Entity(info)
-   }
-  }
+
+  forHash(data, function(type, type_data){
+    favourite_entities[type] = {}
+    forHash(type_data, function(code, info){
+      info.code = code
+      info.type = type
+      favourite_entities[type][code] = new Entity(info)
+    })
+  })
   return favourite_entities
 } 
 

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

@@ -39,16 +39,15 @@ FavouriteLists.get = function(){
 FavouriteLists.deserialize = function(data){
   data = JSON.parse(data)
   favourite_lists = {}
-  for (type in data){
-   var type_data = data[type]
-   favourite_lists[type] = {}
-   for (i in type_data){
-    var info = {}
-    id = type_data[i]
-    info.id = id
-    info.type = type
-    favourite_lists[type][id] = new EntityList(info)
-   }
-  }
+
+  forHash(data, function(type, type_data){
+    favourite_lists[type] = {}
+    forArray(type_data, function(id){
+      var info = {}
+      info.id = id
+      info.type = type
+      favourite_lists[type][id] = new EntityList(info)
+    })
+  })
   return favourite_lists
 } 

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

@@ -9,7 +9,7 @@ var EntityMap = function(data){
  }
 
  this.url = function(){
-  var url = "/entity_map/" + this.full_type() + "/" + this.column + "/" + this.id
+  var url = "/entity_map/" + this.full_type() + "/" + clean_element(this.column) + "/" + clean_element(this.id)
   return url
  }
 
@@ -33,20 +33,20 @@ FavouriteMaps.get = function(){
 FavouriteMaps.deserialize = function(data){
   data = JSON.parse(data)
   favourite_maps = {}
-  for (type in data){
-   var type_data = data[type]
-   favourite_maps[type] = {}
-   for (column in type_data){
-    var column_data = type_data[column]
-    for (i in column_data){
-     var info = {}
-     id = column_data[i]
-     info.id = id
-     info.column = column
-     info.type = type
-     favourite_maps[type][id] = new EntityMap(info)
-    }
-   }
-  }
+
+  forHash(data, function(type, type_data){
+    favourite_maps[type] = {}
+    forHash(type_data, function(column, column_data){
+      forArray(column_data, function(id){
+        var info = {}
+        info.id = id
+        info.column = column
+        info.type = type
+        favourite_maps[type][id] = new EntityMap(info)
+      })
+    })
+  })
   return favourite_maps
 } 
+
+

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

@@ -37,8 +37,6 @@ fav_module.isFavourite_map = function(map){
 
 fav_module.toggleFavourite_entity = function(){
  var entity = rbbt.page.entity();
- console.log(entity)
- console.log(entity.code)
 
  if (fav_module.isFavourite_entity(entity)){
   rbbt.post({url: '/remove_favourite_entity/' + entity.type + '/' + clean_element(entity.code)}).then(fav_module.update)
@@ -68,16 +66,12 @@ fav_module.toggleFavourite_map = function(){
 }
 
 fav_module.toggleFavourite = function(){
- if (! rbbt.page.entity())
-  if (! rbbt.page.list())
-   if (! rbbt.page.map())
-    return
-   else
-    fav_module.toggleFavourite_map()
-  else
-   fav_module.toggleFavourite_list()
- else
-   fav_module.toggleFavourite_entity()
+  if (rbbt.page.entity())
+    return fav_module.toggleFavourite_entity()
+  if (rbbt.page.list())
+    return fav_module.toggleFavourite_list()
+  if (rbbt.page.map())
+    return fav_module.toggleFavourite_map()
 }
 
 //{{{ VIEWS
@@ -280,5 +274,6 @@ fav_module.hooks = function(){
 }
 
 fav_module.update = function(){
+ //fav_module.update_favourites().then(fav_module.view).then(function(){ $('.dropdown:not([tabindex])').dropdown()}).then(fav_module.hooks)
  fav_module.update_favourites().then(fav_module.view).then(function(){ $('.dropdown:not([tabindex])').dropdown()}).then(fav_module.hooks)
 }

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

@@ -28,6 +28,7 @@ rbbt.modal.controller = function(){
     controller._set(content, title)
     $(rbbt.modal.element).addClass('active')
     m.redraw()
+    update_rbbt()
   }
 
   controller.error = function(content, title){
@@ -35,6 +36,7 @@ rbbt.modal.controller = function(){
     $(rbbt.modal.element).addClass('active')
     $(rbbt.modal.element).addClass('error')
     m.redraw()
+    update_rbbt()
   }
 
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.6.14
+  version: 1.6.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-01 00:00:00.000000000 Z
+date: 2015-07-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -1828,7 +1828,6 @@ files:
 - share/views/public/plugins/springy/springyui.js
 - share/views/public/plugins/underscore/js/underscore.js
 - share/views/tasks.haml
-- share/views/tools/cytoscape.haml
 - share/views/wait.haml
 homepage: http://github.com/mikisvaz/rbbt-rest
 licenses:

data/share/views/tools/cytoscape.haml

@@ -1,312 +0,0 @@
-- 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 .window
-    height: 700px
-.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
-  })
-
-