rbbt-rest 1.7.5 → 1.7.6

data/share/views/compass/old/layout.sass

@@ -0,0 +1,5 @@
+@import "layout/top_menu"
+@import "layout/body"
+@import "layout/reveal"
+@import "layout/result"
+@import "layout/footer"

data/share/views/compass/screen_sizes.sass

@@ -1 +1,16 @@
-@import "base/screen_sizes"
+$very-small-screen: 500px
+$small-screen: 700px
+$medium-screen: 900px
+$large-screen: 1024px 
+$very-large-screen: 1240px 
+
+$not-very-small: "only screen and (min-width: #{$very-small-screen + 1})" 
+$not-small: "only screen and (min-width: #{$small-screen + 1})" 
+$not-large: "only screen and (max-width: #{$large-screen - 1})" 
+$not-very-large: "only screen and (max-width: #{$very-large-screen})" 
+
+$only-very-small: "only screen and (max-width: #{$very-small-screen})" 
+$only-small: "only screen and (max-width: #{$small-screen})" 
+$only-large: "only screen and (min-width: #{$large-screen})" 
+$only-very-large: "only screen and (min-width: #{$very-large-screen})" 
+

data/share/views/compass/tab_menu.sass

@@ -0,0 +1,115 @@
+
+
+@import "compass/css3/animation"
+@import "compass/css3/opacity"
+@import "compass/css3/box-shadow"
+
+$jiffy: 0.28s
+$jiffy: 0.14s
+
++keyframes(scroll-up)
+  100%
+    max-height: 200px
+    margin-top: -400px
+    overflow: hidden
+    z-index: -1
+    +box-shadow(rgba(0,0,0,0))
+  50%
+    max-height: 300px
+    margin-top: -100px
+    overflow: hidden
+    z-index: -1
+    +box-shadow(rgba(0,0,0,0))
+  0%
+    max-height: 500px
+    overflow: hidden
+    z-index: -1
+    +box-shadow(rgba(0,0,0,0))
+
++keyframes(scroll-down)
+  0%
+    max-height: 200px
+    margin-top: -400px
+    overflow: hidden
+    z-index: -1
+    +box-shadow(rgba(0,0,0,0))
+  100%
+    max-height: 500px
+    z-index: -1
+    +box-shadow(rgba(0,0,0,0))
+
++keyframes(grow-down)
+  0%
+    max-height: 0px
+    padding-top: 0px
+    padding-bottom: 0px
+    +opacity(0.2)
+
+  100%
+    max-height: 500px
+
++keyframes(shrink-up)
+  100%
+    border: none
+    max-height: 0px
+    padding-top: 0px
+    padding-bottom: 0px
+    overflow: hidden
+    +opacity(0.1)
+  0%
+    border: none
+    max-height: 500px
+    overflow: hidden
+
+=shifting-up
+  &:not(.show)
+    +animation(scroll-up $jiffy forwards)
+    overflow: hidden
+  &.show
+    +animation(scroll-down $jiffy*2)
+
+=shrinking-up
+  &:not(.show)
+    +animation(shrink-up $jiffy forwards)
+    overflow: hidden
+  &.show
+    +animation(grow-down $jiffy*2)
+    overflow: hidden
+
+dl.rbbt_tabs
+  position: relative
+  overflow: visible
+  margin-top: 14px
+  margin-bottom: 14px
+  font-size: 0
+  &:after
+    content: ""
+    clear: both
+    display: block
+  dt
+    cursor: pointer
+    font-size: 14px
+    padding: 1em
+    display: inline-block
+    min-width: 20%
+    &.active
+      font-weight: bold
+    border: 1px solid #D4D4D5
+    &:hover
+      border: 1px solid darken(#D4D4D5,30)
+  dd
+    font-size: 14px
+    margin: 0px
+    float: left
+    overflow: visible
+    overflow-y: auto
+    min-width: 100%
+    padding: 1em
+
+    &:not(.show)
+      +animation(shrink-up $jiffy forwards)
+
+    &.show
+      +animation(grow-down $jiffy*2)
+      border: 1px solid #D4D4D5
+

data/share/views/entity_partials/entity_list_card.haml

@@ -20,10 +20,10 @@
           %a.list_list.ui.button(href="#{request.path_info + "?_format=list"}") List
 
           - if list.respond_to? :name
-            %a.name_list.ui.button(href="#{request.path_info + "?_format=name"}") Name
+            %a.name_list.ui.button(href="#{request.path_info + "?_format=name"}") As Name
 
           - if list.respond_to? :ensembl
-            %a.ensembl_list.ui.button(href="#{request.path_info + "?_format=ensembl"}") Ensembl
+            %a.ensembl_list.ui.button(href="#{request.path_info + "?_format=ensembl"}") As Ensembl
 
           %a.download_list.ui.button(href="#{request.path_info + "?_format=raw"}") Raw
           %a.edit_list.ui.button(href="#") Edit

data/share/views/entity_partials/entity_map_card.haml

@@ -20,7 +20,7 @@
               %input(name='rename' value=map_id)
               %input(type='submit')
 
-          - if %w(pvalue p.value p-value pvalues p.values p-values).include? map.fields.first.downcase.gsub(/\s/,'')
+          - if %w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values).include? map.fields.first.downcase.gsub(/\s/,'')
             - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
             %a.ui.small.button(href=url) Pvalue score
 

data/share/views/help/UI.haml

@@ -1,4 +1,4 @@
-%dl.tabs.UI.active
+%dl.rbbt_tabs
 
   %dt.next.active.show Report structure
   %dd.show
@@ -29,8 +29,8 @@
       action controller or side-bar
         
     .images
-      %dl.tabs.active.show
-        %dt.next.show Snapshot
+      %dl.rbbt_tabs.active.show
+        %dt.next.active Snapshot
         %dd.show
           %img(src="/img/UI/report.png")
 
@@ -63,8 +63,8 @@
       bookmarking actions latter.
 
     .images
-      %dl.tabs.active.show
-        %dt.next.show Snapshot
+      %dl.rbbt_tabs.active.show
+        %dt.next.active Snapshot
         %dd.show
           %img(src="/img/UI/topbar.png")
 
@@ -98,8 +98,8 @@
       click on the star once the report is shown.
 
     .images
-      %dl.tabs.active.show
-        %dt.next.show Snapshot
+      %dl.rbbt_tabs.active.show
+        %dt.next.active Snapshot
         %dd.show
           %img(src="/img/UI/favourites.png")
 
@@ -151,9 +151,9 @@
       later.
 
     .images
-      %dl.tabs.active.show
+      %dl.rbbt_tabs.active.show
 
-        %dt.next.show.active Action Snapshot
+        %dt.next.active Action Snapshot
         %dd.show
           %img(src="/img/UI/actions.png")
 
@@ -231,7 +231,7 @@
       include a cytoscape plot to the description section of the report.
 
     .images
-      %dl.tabs.active.show
+      %dl.rbbt_tabs.active.show
         %dt.next.show Cytoscape
         %dd.show
           %img(src="/img/UI/cytoscape.png")

data/share/views/layout.haml

@@ -41,4 +41,6 @@
       - record_js file
     =partial_render('layout/coda')
   
+  #extra
+    =partial_render('layout/extra')
 

data/share/views/layout/coda.haml

@@ -39,10 +39,6 @@
     gene.parents("tfacts@genomics").then(draw_entity_list)
   }
 
-  //require_js(["/js-find/rbbt", "/js-find/rbbt.entity", "/js-find/rbbt.entity_list", "/js-find/rbbt.entity_map", "/js-find/rbbt.knowledge_base", "/js-find/rbbt.page", "/js-find/rbbt.aesthetics", "/js-find/rbbt.favourites"], function(){
-  //  //debug("TP53")
-  //})
-
 
 - if @reload_page 
   :javascript

data/share/views/layout/header.haml

@@ -22,7 +22,7 @@
   var main_url = window.location.toString();
   var production = #{production? ? "true" : "false"};
 
-- record_js '/js/defer'
+- record_js '/js/helpers/defer'
 - record_js "/plugins/mithril/js/mithril.js"
 -# record_js "/plugins/requirejs/js/require.js"
 = serve_js
@@ -56,7 +56,7 @@
 
 
 - %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
-  - record_js "/js-find/#{ file }"
+  - record_js "/js-find/helpers/#{ file }"
 
 -# %w(dom_update workflow fragment menu favourites page_type modal reveal actions table list map hide).each do |file|
 - %w(dom_update fragment actions table list map reveal).each do |file|

data/share/views/public/js/app.js

@@ -14,6 +14,7 @@ function update_rbbt(){
  $('.ui.checkbox').checkbox();
 
  $('.rbbt_reveal_trigger').reveal()
+
  //$('table.tablesorter').tablesorter()
  //$('body > #modal').modal()
  //$('#top_menu .favourites').favourites('update_list_selects').favourites('update_map_selects')
@@ -29,10 +30,25 @@ function update_rbbt(){
    rbbt.aesthetics.load()
    rbbt.aesthetics.apply()
  }
+
+
+ rbbt.favourites.update()
 }
 
 $(function(){
 
+ register_dom_update(('.next'), function(elem){
+   elem.click(function(){
+     var trigger = $(this)
+     var next = trigger.next()
+
+     next.siblings().removeClass('show').removeClass('active')
+
+     next.toggleClass('show')
+     trigger.toggleClass('active')
+   })
+ })
+
  register_dom_update('#top_menu > .reload', function(item){
   item.click(function(){
    var url = window.location.toString();