rbbt-rest 1.6.2 → 1.6.3

data/share/views/partials/table.haml

@@ -15,6 +15,7 @@
 
 - footer  = table_options[:footer]   unless defined? footer and footer
 - footer = true if footer.nil?
+- footer = false unless table_url
 
 - page = @page unless defined? page and not page.nil?
 
@@ -61,7 +62,7 @@
             = partial_render('partials/table/page', :page => page, :total_size => total_size) 
 
           - if table_url
-            %ul.table_actions
+            .table_actions.ui.buttons
 
               = partial_render('partials/table/filters', :table_url => table_url, :header => header, :id => "rbbt_reveal_" << Misc.digest(table_url)) 
                 

data/share/views/partials/table/column.haml

@@ -1,10 +1,9 @@
 - table_columns_id = "rbbt_table_columns_" << (rand * 1000).to_i.to_s
-%li.table_column
-  = reveal :column do
-    %ul.table_column_selector.clean_list
-      - header.each do |field|
-        %li
-          %span.field= field
-          %a.save_column_map(href="#") save map
-          - if Entity.formats.include? field and Entity.formats[field].include? Entity::REST 
-            %a.save_column_list(href="#") save list
+= reveal :column, table_columns_id, :class => 'ui compact button table_column' do
+  %ul.table_column_selector.clean_list
+    - header.each do |field|
+      %li.ui.basic.segment
+        %span.field= field
+        %a.save_column_map.ui.compact.button(href="#") save map
+        - if Entity.formats.include? field and Entity.formats[field].include? Entity::REST 
+          %a.save_column_list.ui.compact.button(href="#") save list

data/share/views/partials/table/files.haml

@@ -1,4 +1,4 @@
-%li.tsv
+.tsv.ui.wrap.compact.button
   %a(href="#{add_GET_param(table_url, "_format", "tsv")}") tsv
-%li.excel
+.excel.ui.wrap.compact.button
   %a(href="#{add_GET_param(table_url, "_format", "excel")}") excel

data/share/views/partials/table/filters.haml

@@ -1,20 +1,20 @@
-%li.filter
-  = reveal :filter, id do
-    - if @filter
-      - filter_values = Hash[*@filter.split(";;").collect{|f| f.split("~")}.flatten]
-    - else
-      - filter_values = {}
+-#.filter.ui.wrap.button
+= reveal :filter, id, :class => 'ui compact button filter' do
+  - if @filter
+    - filter_values = Hash[*@filter.split(";;").collect{|f| f.split("~")}.flatten]
+  - else
+    - filter_values = {}
 
-    .filters()
-      = action_parameters nil, :class => 'filter_controls' do
-        - header.each do |field|
-          - input field, :string, "Filter for #{ field }", filter_values[field]
+  .filters()
+    = action_parameters nil, :class => 'filter_controls' do
+      - header.each do |field|
+        - input field, :string, "Filter for #{ field }", filter_values[field]
 
-    :markdown
-      Filters can be specified in several ways:
+  :markdown
+    Filters can be specified in several ways:
 
-        - *String of text*: perfect match (e.g. `Cancer`)
-        - *Regular expression*: flexible match (e.g. `/(bladder|breast)\s+cancer/i`)
-        - *Numeric comparison*: lower of grater than (e.g. `< 0.1` or `>= 2`)
-        - *Names: for entities* with names, such as genes or pathways; regular expression accepted (e.g. `:name:SF3B1` or `:name:/CDK\d/`)
+      - *String of text*: perfect match (e.g. `Cancer`)
+      - *Regular expression*: flexible match (e.g. `/(bladder|breast)\s+cancer/i`)
+      - *Numeric comparison*: lower of grater than (e.g. `< 0.1` or `>= 2`)
+      - *Names: for entities* with names, such as genes or pathways; regular expression accepted (e.g. `:name:SF3B1` or `:name:/CDK\d/`)
 

data/share/views/partials/table/page.haml

@@ -4,35 +4,29 @@
 - total_nums += 1 if total_size.to_i % size.to_i > 0
 - start = [1, num - 2].max
 - eend = [total_nums, num + 2].min
-%ul.table_pagination.pagination
-  %li(class="arrow") 
-    %a.prev(href="#") «
+.table_pagination.pagination.ui.buttons
+  %a.ui.compact.arrow.button.prev(href="#") «
 
-  %li(class="arrow") 
-    %a.next(href="#") »
+  %a.ui.compact.arrow.button.next(href="#") »
 
-  %li(class="all") 
-    %a.all(href="#") all 
+  %a.ui.compact.all.button.all(href="#") all 
 
   - if num - 2 > 1
-    %li(class="num") 
-      %a(href="#") 1
+    %a.ui.compact.num.button(href="#") 1
 
   - if num - 2 > 2
-    %li(class="inactive") 
+    .ui.compact.disabled.button
       \...
 
   - (start..eend).each do |p|
-    %li(class="num#{p.to_s == num.to_s ? " active" : "" }") 
-      %a(href="#")= p
+    %a.ui.compact.num.button(class="#{p.to_s == num.to_s ? "active" : "" }" href="#")= p
 
   - if num + 3 < total_nums
-    %li(class="inactive") 
+    .ui.compact.disabled.button
       \...
 
   - if num + 2 < total_nums
-    %li(class="num") 
-      %a(href="#")= total_nums
+    %a.ui.compact.num.button(href="#")= total_nums
 
 
 

data/share/views/public/js/ng-favourites.js

@@ -0,0 +1,13 @@
+var rbbt_angular = angular.module('rbbt', [])
+
+rbbt_angular.controller('FavourtiesController', ['$scope', function($scope){
+ $scope.favourite = 'not_favourite'; 
+ $scope.toggle = function(){
+  if ($scope.favourite == 'favourite'){
+   $scope.favourite = 'not_favourite'
+  }else{
+   $scope.favourite = 'favourite'
+  }
+ }
+}]);
+

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

@@ -0,0 +1,51 @@
+rbbt.aesthetics = {LS_key: "rbbt.aesthetics"}
+
+var aes_module = rbbt.aesthetics 
+
+aes_module.load = function(){
+ this.aesthetics = rbbt.LS.load(this.LS_key)
+ if (undefined === this.aesthetics)
+  this.aesthetics = []
+}
+
+aes_module.store = function(){
+ rbbt.LS.store(this.LS_key, this.aesthetics)
+}
+
+aes_module.add = function(selector, aes, value){
+ this.aesthetics.push({selector: selector, aes: aes, value: value})
+}
+
+aes_module.clear_aesthetic = function(aes){
+ var data_key = 'data-aes-' + aesthetic.aes
+
+ $('[' + data_key + ']').attr(data_key, 'none')
+}
+
+aes_module.apply_aesthetic = function(aesthetic){
+
+ if (typeof aesthetic.selector == "string"){
+  targets = $(aesthetic.selector)
+ }else{
+  var items = aesthetic.selector
+  targets = $('.entity').filter(function(index){ 
+   var id = $(this).attr('data-entity-id')
+   return items.indexOf(id) >= 0
+  })
+ }
+
+ var data_key = 'data-aes-' + aesthetic.aes
+ targets.attr(data_key, aesthetic.value)
+}
+
+aes_module.apply = function(aesthetic){
+ if (undefined === aesthetic)
+  this.aesthetics.map(aes_module.apply_aesthetic)
+ else
+  aes_module.apply_aesthetic(aesthetic)
+}
+
+aes_module.load()
+//aes_module.add(Object.keys(fav_module.entities.types()["Gene"]), 'color', 'red')
+//aes_module.store()
+//aes_module.apply()

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

@@ -0,0 +1,62 @@
+rbbt.entity = {}
+
+var Entity = function(data){
+ this.id = data.id
+ this.code = data.code
+
+ if (data.name !== undefined)
+  this.name = data.name
+ else
+  this.name = data.code
+
+ this.type = data.type
+ this.format = data.format
+ this.info = data.info
+ if (this.format === undefined && this.info !== undefined) this.format = this.info['format']
+
+ this.full_type = function(){
+  var full_type
+  if (this.format){ full_type = this.type + ":" + this.format }
+  else { full_type = this.type }
+  return full_type
+ }
+
+ this.link_info = function(){
+  var link_info = this.info
+  delete link_info['format']
+  return link_info
+ }
+ 
+ this.url = function(){
+  var url = "/entity/" + this.full_type() + "/" + this.code
+  url = add_parameters(url, this.link_info())
+  return url
+ }
+}
+
+var FavouriteEntities = function(by_type){
+ for (type in by_type){
+  this[type] = by_type[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)
+   }
+  }
+  return favourite_entities
+} 
+
+FavouriteEntities.get = function(){
+  return m.request({method: 'GET', url: '/favourite_entities', type: FavouriteEntities, deserialize: FavouriteEntities.deserialize})
+}
+

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

@@ -0,0 +1,54 @@
+
+var EntityList = function(data){
+ this.id = data.id
+ this.name = data.id
+ this.type = data.type
+
+ this.full_type = function(){
+  return this.type
+ }
+
+ this.url = function(){
+  var url = "/entity_list/" + this.full_type() + "/" + this.id
+  return url
+ }
+
+ this.get = function(){ 
+  var url = this.url()
+  url = add_parameter(url, '_format', 'json')
+  return m.request({url: url, method: 'GET'})
+ }
+
+ this.highlight = function(color){
+  this.get().then(function(list){
+   rbbt.aesthetics.apply_aesthetic({selector: list.entities, aes: 'color', value: color})
+  })
+ }
+}
+
+var FavouriteLists = function(by_type){
+ for (type in by_type){
+  this[type] = by_type[type]
+ }
+}
+
+FavouriteLists.get = function(){
+  return m.request({method: 'GET', url: '/favourite_entity_lists', type: FavouriteLists, deserialize: FavouriteLists.deserialize})
+}
+
+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)
+   }
+  }
+  return favourite_lists
+} 

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

@@ -0,0 +1,52 @@
+var EntityMap = function(data){
+ this.id = data.id
+ this.name = data.id
+ this.type = data.type
+ this.column = data.column
+
+ this.full_type = function(){
+  return this.type
+ }
+
+ this.url = function(){
+  var url = "/entity_map/" + this.full_type() + "/" + this.column + "/" + this.id
+  return url
+ }
+
+ this.get = function(){ 
+  var url = this.url()
+  url = add_parameter(url, '_format', 'json')
+  return m.request({url: url, method: 'GET'})
+ }
+}
+
+var FavouriteMaps = function(by_type){
+ for (type in by_type){
+  this[type] = by_type[type]
+ }
+}
+
+FavouriteMaps.get = function(){
+  return m.request({method: 'GET', url: '/favourite_entity_maps', type: FavouriteMaps, deserialize: FavouriteMaps.deserialize})
+}
+
+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)
+    }
+   }
+  }
+  return favourite_maps
+} 

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

@@ -0,0 +1,286 @@
+
+rbbt.favourites = {};
+var fav_module = rbbt.favourites;
+
+fav_module.entities = {types: m.prop({})}
+fav_module.entities.init = function(){
+  return FavouriteEntities.get().then(fav_module.entities.types)
+}
+
+fav_module.lists = {types: m.prop({})}
+fav_module.lists.init = function(){
+  return FavouriteLists.get().then(fav_module.lists.types)
+}
+
+fav_module.maps = {types: m.prop({})}
+fav_module.maps.init = function(){
+  return FavouriteMaps.get().then(fav_module.maps.types)
+}
+
+fav_module.update_favourites = function(){
+ return m.sync([fav_module.lists.init(), fav_module.entities.init(), fav_module.maps.init()])
+}
+
+fav_module.isFavourite_entity = function(entity){
+ return fav_module.entities.types()[entity.type] !== undefined && fav_module.entities.types()[entity.type][entity.code] !== undefined
+}
+
+fav_module.isFavourite_list = function(list){
+ return fav_module.lists.types()[list.type] !== undefined && fav_module.lists.types()[list.type][list.id] !== undefined
+}
+
+fav_module.isFavourite_map = function(map){
+ return fav_module.maps.types()[map.type] !== undefined && fav_module.maps.types()[map.type][map.id] !== undefined
+}
+
+//{{{ TOGGLE
+
+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.code}).then(fav_module.update)
+ }else{
+  rbbt.post({url: '/add_favourite_entity/' + entity.type + '/' + entity.code, 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_map = function(){
+ var map = rbbt.page.map();
+
+ if (fav_module.isFavourite_map(map)){
+  rbbt.post({url: '/remove_favourite_entity_map/' + map.type + '/' + map.column + '/' + map.id}).then(fav_module.update)
+ }else{
+  rbbt.post({url: '/add_favourite_entity_map/' + map.type + '/' + map.column + '/' + map.id}).then(fav_module.update)
+ }
+}
+
+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()
+}
+
+//{{{ VIEWS
+
+fav_module.star_view = function(){
+ if (! rbbt.page.entity())
+  if (! rbbt.page.list())
+   if (! rbbt.page.map())
+    return
+   else
+    return m('i.icon.star', {class: (fav_module.isFavourite_map(rbbt.page.map()) ? 'favourite' : 'not_favourite')})
+  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.entities.types()
+ var types = Object.keys(favourites)
+
+ return m('.ui.menu',
+          m('.ui.dropdown.item', [
+           m('i.icon.dropdown'), 
+           'Entities',
+           m('.menu', [m('a.item',{onclick: fav_module.highlight}, 'highlight')].concat(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.lists.types()
+ 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(list, index){ 
+              url = _type[list].url()
+              var link = m('a.item', {href: url, style: 'display: inline-block; width: 100%'}, _type[list].name)
+              //return [link, m('span.bullet.green', {onclick: function(){_type[list].highlight('green'); return false}},''),m('br')] 
+              return [link, m('span.bullet.green', {onclick: function(){_type[list].highlight('green'); return false}},''),m('br')] 
+             }))
+            ]);
+           }))
+          ])
+         )
+}
+
+fav_module.draw_favourite_map_menu = function(){
+ var favourites = fav_module.maps.types()
+ var types = Object.keys(favourites)
+
+ return m('.ui.menu',
+          m('.ui.dropdown.item', [
+           m('i.icon.dropdown'), 
+           'Maps',
+           m('.menu', types.map(function(type, index){ 
+            var _type = favourites[type]
+            var maps = Object.keys(_type)
+
+            return m('.ui.dropdown.item', [
+             m('i.icon.dropdown'), 
+             type,
+             m('.menu', maps.map(function(map, index){ 
+              url = _type[map].url()
+              var link = m('a.item', {href: url, _style: 'display: inline-block;width:100%'}, _type[map].name)
+              //return [link, m('span.bullet.green', {onclick: function(){_type[map].highlight('green'); return false}},''),m('br')] 
+              return link
+             }))
+            ]);
+           }))
+          ])
+         )
+}
+
+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()),
+  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_map_menu())
+ ])
+}
+
+//{{{ HOOKS
+
+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.lists.types(), 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_map_select= function(select, type, maps){
+ 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');
+ }
+
+ console.log(maps)
+ $.each(maps, function(name, elems){
+  var option = null;
+  var name = elems
+  if (selected == null || name != selected){
+   option = $('<option attr-column="' + name.column + '" attr-entity_type="' + name.type + '" class="automatic_load" value="' + name.id + '">' + name.id + '</option>');
+  }else{                                
+   option = $('<option attr-column="' + name.column + '" attr-entity_type="' + name.type + '" class="automatic_load" selected=selected value="' + name.id + '">' + name.id + '</option>');
+  }
+  select.append(option);
+  return true
+ })
+},
+
+fav_module.update_map_selects= function(){
+ $('select.favourite_maps').find('option.automatic_load').remove()
+
+ $.each(fav_module.maps.types(), function(type, maps){
+  $('select.favourite_maps[type=' + type + ']').each(function(){
+   var select = $(this);
+   fav_module._update_map_select(select, type, maps);
+  })
+  $('select.favourite_maps[type=All]').each(function(){
+   var select = $(this);
+   select.append($('<option class="automatic_load ui" disabled>'+ type +'</option>'));
+   fav_module._update_map_select(select, type, maps);
+  })
+ });
+}
+
+fav_module.highlight = function(){
+ var targets = []
+ for (type in fav_module.entities.types()){
+  var _type = fav_module.entities.types()[type]
+  var n = Object.keys(_type)
+  var nt = n.map(function(e){ return _type[e].id})
+  targets = targets.concat(nt)
+ }
+ rbbt.aesthetics.apply_aesthetic({selector: targets, aes: 'color', value: 'gold'})
+}
+
+fav_module.hooks = function(){
+ fav_module.update_list_selects()
+ fav_module.update_map_selects()
+}
+
+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()