rbbt-rest 1.1.5 → 1.2.0

data/share/views/compass/top_menu.sass

@@ -0,0 +1,121 @@
+$padding_top_menu: 5px
+
+#content
+  padding-top:  2 * $vindent + $size_menu_item
+
+#top_menu
+
+  @media print
+    display: none
+
+  @media #{$not-large}
+    position: fixed
+  @media #{$only-large}
+    position: fixed
+  top: 0
+  width: 100%
+  z-index: 30
+  
+  background-color: $color_top_menu
+  color: $color_menu_text
+  padding: $padding_top_menu
+  border-bottom: 1px solid darken($color_menu_bg, 15)
+  box-shadow: 0px 3px -4px 4px rgba(0, 0, 0, 0.1)
+  padding-left: 0px
+  & > ul
+    +grid_row()
+    +clean_list
+    +clearfix
+
+    @media #{$only-large}
+      & > li
+        margin-left: $indent
+
+    & > li.title
+      float: left
+      +rbbt_menu_item($color_top_menu)
+      padding-left: 0
+      padding-right: $indent
+      font-weight: bold
+
+    & > li.reload
+      float: left
+      +rbbt_menu_item($color_top_menu)
+      font-size: 1.2em
+      padding-left: 0
+      padding-right: 0px
+      display: inline-block
+      border: 1px $color_menu_border
+      cursor: pointer
+      width: auto
+
+    & > li.container
+      float: right
+
+    & > li.find
+      float: left
+
+    & > li.favourites, & > li.user
+
+      &.favourites
+        float: left
+      &.user
+        float: right
+      background-color: $color_menu_bg
+      dl.rbbt_menu > dd
+        box-shadow: 1px 3px -4px 4px rgba(0, 0, 0, 0.1)
+
+    dl.rbbt_vertical_menu
+      @media #{$only-large}
+        width: 50em
+
+    dt.star.active > i
+      color: gold !important
+
+    ul.new_list
+      +clean_list
+      padding: $vindent $indent
+      li
+        display: block !important
+
+    a.remove_element
+      margin-right: $indent
+
+  li.user
+    ul.jobs
+      @media #{$only-large}
+        min-width: 400px
+
+
+  @media #{$only-large}
+    li.container
+      display: none
+  @media #{$not-large}
+    li.hide
+      display: none !important
+
+    li.hide.shown
+      display: block !important
+      clear: both
+      width: 100% !important
+      margin-top: 5px
+      dl 
+        width: 100% !important
+        padding-left: 0
+        margin-right: 0
+        margin-bottom: 0
+
+    li.hide.hidden
+      display: none !important
+
+    li.container
+      a.hide_toggle
+        display: inline-block
+        width: auto
+        +_rbbt_menu_item
+        border: 1px solid $color_menu_border
+        padding: 3px
+        margin: 3px
+
+
+

data/share/views/compass/user.sass

@@ -0,0 +1,7 @@
+#top_menu
+  li.user
+    dl.rbbt_menu
+      dd
+        right: 0
+        margin-right: -1px
+        padding: $vindent $indent

data/share/views/compass/variables.sass

@@ -0,0 +1,7 @@
+$z-index_menu_content: 10
+$margin_menu_item: 5px
+$size_menu_item: 25px
+
+$width_finder_button: 50px
+
+$width_user_menu: 200px

data/share/views/compass/workflow.sass

@@ -1,10 +1,9 @@
+ul.tasks > li
+  display: block !important
 
-.workflow_task
-  @include grid-row()
 
+.workflow_task
   .title
-    @include grid-column(12)
-    @extend h4
     span.workflow
       font-weight: 600
 
@@ -15,19 +14,12 @@
       margin-left: 2em
 
   .form
-    @include grid-column(12)
+    @extend .action_parameters
 
 dd.job_control
   ul
-    @include inline-list()
-    @include button-group-container()
+    +rbbt_button_list($color_bg: $base3)
+    width: auto
     li a
-      @include button-base
-      @include button-size
-      @include button-style
-      @include radius
-      @include single-transition
-      margin-bottom: 2px
-      font-size: 0.8em
 
 

data/share/views/entity_partials/action_controller.haml

@@ -1,6 +1,5 @@
 - entity = controller.entity
 - if controller.actions.any?
-
   .action_controller
     %ul.controls
 
@@ -12,11 +11,15 @@
         %a(href="#")
           %i.general.foundicon-settings
 
-    %ul.actions
-      %li.select
+      %li.pin
         %a(href="#")
-          %i.general.foundicon-plus
+          %i.general.foundicon-paper-clip
 
+      %li.url
+        %a(href="#")
+          %i.general.foundicon-flag
+
+    %ul.actions
       - last_resource = nil
       - controller.actions.each do |action, text, resource, params|
         %li(class="#{last_resource and last_resource != resource ? "new_resource" : ""}" attr-resource="#{resource}")

data/share/views/entity_partials/entity_card.haml

@@ -1,6 +1,7 @@
 - entity = card.entity
 - entity_id = "entity__" + entity.id
 .entity_card(id=entity_id)
+  /-- title --
   .title
     .name
       - case card.name
@@ -9,7 +10,7 @@
       - when String
         = card.name
       - when Proc
-        = capture_haml &card.name
+        = fragment :name, &card.name
 
     .long_name
       - case card.long_name
@@ -18,9 +19,11 @@
       - when String
         = card.long_name
       - when Proc
-        = capture_haml &card.long_name
+        = fragment :long_name, &card.long_name
 
   .card
+
+    /-- sidebar --
     .sidebar.offcanvas
       .meta
         .entity_info
@@ -33,11 +36,14 @@
         - when Hash
           = hash2dl(card.meta)
         - when Proc
-          = capture_haml &card.meta 
+          = fragment :meta, &card.meta
         - if card.list_container
           .entity_lists
             = list_container_render(card.list_container)
 
+
+
+    /-- content --
     .content
       .description
         - case card.description
@@ -46,10 +52,9 @@
         - when String
           %p= card.description
         - when Proc
-          = capture_haml &card.description
+          = fragment :description, &card.description
 
       - if card.action_controller
         .actions
           = action_controller_render(card.action_controller)
 
-

data/share/views/entity_partials/entity_list.haml

@@ -1,8 +1,5 @@
 
-- text = :length if not defined? text or text.nil?
-.entity_list_button.button.split.dropdown
-  = list.list_link text, list_id
-  %span
-  %ul.entities(style="max-height: 200px; overflow: auto")
-    - list.each do |elem|
-      %li= elem.link
+%span
+%ul.entities(style="max-height: 200px; overflow: auto")
+  - list.each do |elem|
+    %li= elem.link

data/share/views/entity_partials/entity_list_card.haml

@@ -10,6 +10,7 @@
       = Misc.humanize list_id
 
   .card
+
     .sidebar.offcanvas
       .meta
         .list_management
@@ -18,12 +19,17 @@
 
             %li
               %a.compare_list(href="#" data-reveal-id='modal1') Compare
+            %li
               %a.list_list(href="#{request.path_info + "?_format=list"}") List
-              - if list.respond_to? :name
+            - if list.respond_to? :name
+              %li
                 %a.name_list(href="#{request.path_info + "?_format=name"}") Name
-              - if list.respond_to? :ensembl
+            - if list.respond_to? :ensembl
+              %li
                 %a.ensembl_list(href="#{request.path_info + "?_format=ensembl"}") Ensembl
+            %li
               %a.download_list(href="#{request.path_info + "?_format=raw"}") Raw
+            %li
               %a.edit_list(href="#") Edit
 
         .entity_info
@@ -58,6 +64,8 @@
           .entity_lists
             = list_container_render(card.list_container)
 
+
+
     .content
       .description
         - case card.description
@@ -74,4 +82,3 @@
       - if card.action_controller
         .actions
           = action_controller_render(card.action_controller)
-

data/share/views/entity_partials/entity_map_card.haml

@@ -10,6 +10,7 @@
       = Misc.humanize map_id
 
   .card
+
     .sidebar.offcanvas
       .meta
         .map_management
@@ -47,7 +48,7 @@
               %li
                 - $page_entity_base_type = page_entity_base_type 
                 - $page_entity_map_column = page_entity_map_column 
-                = reveal :rank_products do
+                = reveal :rank_products, :title => "Rank Product" do
                   = action_parameters nil, :class => 'rank_products' do
                     - input :map, :select, "Select map to use", nil, :html_options => {:class => 'favourite_maps', :type =>  $page_entity_base_type, :column => $page_entity_map_column}
 
@@ -60,4 +61,3 @@
       - if card.action_controller
         .actions
           = action_controller_render(card.action_controller)
-

data/share/views/entity_partials/list_container.haml

@@ -1,31 +1,36 @@
-%dl.list_container
+%dl.rbbt_accordion
   - container.lists.each do |id, list, text, options|
-    %section.section.accordion(data-section)
-      - if Proc === list
-        = fragment do
-          - list = list.call
-          - next if list.nil?
-          %dt
-            = list.list_link :length, id
-            %span.title
-              = text || id 
-          %dd.content
-            %p
-              - if (defined? force and force) or list.length < 500
-                = list.link * ", "
-              - else
-                = modal_fragment "Too many entities to list" do
-                  = list.link * ", "
-      - else
-        %dt
+    - if Proc === list
+      = fragment do
+        - list = list.call
+        - next if list.nil?
+        %dt.next
           = list.list_link :length, id
           %span.title
             = text || id 
-        %dd.content
-          %p
-            - if (defined? force and force) or list.length < 500
+        %dd
+          - if (defined? force and force) or list.length < 500
+            = list.link * ", "
+          - else
+            = modal_fragment "Too many entities to list" do
               = list.link * ", "
-            - else
-              = reveal "Too many entities to list" do
-                = fragment do
-                  = list.link * ", "
+    - else
+      - if list.empty?
+        %dt
+          = 0
+          %span.title
+            = text || id 
+      - else
+        %dt.next
+          = list.list_link :length, id
+          %span.title
+            = text || id 
+        %dd
+          - if (defined? force and force) or list.length < 500
+            = list.link * ", "
+          - else
+            = reveal "Too many entities to list" do
+              = fragment do
+                = list.link * ", "
+
+

data/share/views/error.haml

@@ -1,10 +1,8 @@
-.row
-  .column.small-12
-    %h5 Error processing #{File.basename(job.name)}
-    - if job.messages and job.messages.any?
-      %span.error_message
-        %pre= job.messages[-2]
-    - backtrace = job.info[:backtrace]
+%h5 Error processing #{File.basename(job.name)}
+- if job.messages and job.messages.any?
+  %span.error_message
+    %pre= job.messages[-2]
+- backtrace = job.info[:backtrace]
 
 %hr
 

data/share/views/help.haml

@@ -1,34 +1,78 @@
-.row.help
-  .column.small-12
-    :markdown
-
-      Overview
-      ========
-
-      The objective of this page is to offer a collection of functionalities in
-      a uniform interface.  It has two operation modes: Centered on the
-      functionalities or centered on the data. The first operation mode is
-      based on *Workflows*, the second on *Entities*. The Entity subsystem is
-      probably the most interesting one, so let us begin there. 
-      
-      We will devote this document to describe the most general aspects of the
-      application.  The information presented and the analysis available depend
-      on the configuration of the application and will be covered elsewhere.
-
-      
-      #### A word on performance
-
-      This application is intended to allow interactive investigation. But be
-      aware, some analysis are slow and will not feel that much interactive. 
-      Some process may require plenty of infrastructure: downloading of
-      datasets, building databases, computing preliminary results, etc. A lot
-      of this processing is reused system-wide. This means that the application
-      starts slow but get quicker. Unlike other applications with a more limited scope
-      this system cannot foresee what the user will be interested in, so not all
-      this infrastructure can be built before hand and must be built on demand. 
-      We pay a price for flexibility by sacrificing responsiveness. But the system
-      has plenty of tricks to be as efficient as possible and to reuse as much
-      as possible.
+:markdown
 
+  Overview
+  ========
+
+  This application is designed for integration of data and functionalities.
+  It design is based on the idea of the `Entity`: any thing that can be 
+  unambiguously identified and be subject of investigation. Examples of
+  entities are: genes, proteins, SNPs, samples, pathways, etc.
+
+  Each entity has a report, which depends on the type of entity it is. 
+  All reports are computed on the fly and cached. In addition to the main
+  report, entities have `actions`, which are sub-reports that implement
+  particular analysis. For instance, for gene entities, one of the actions
+  is to display a summary of the relevance of that gene across the collection
+  of studies that you have access to.
+ 
+  ## Miscellaneous comments
+ 
+  ### A word on performance
+
+  This application is intended to allow interactive investigation. But be
+  aware, some analysis are slow and will not feel that much interactive.  Some
+  process may require plenty of infrastructure: downloading of datasets,
+  building databases, computing preliminary results, etc. A lot of this
+  processing is reused system-wide. This means that the application starts slow
+  but gets quicker. Unlike other applications with a more limited scope this
+  system cannot foresee what the user will be interested in, so not all this
+  infrastructure can be built before hand and must be built on demand.  We pay
+  a price for flexibility by sacrificing responsiveness. But the system has
+  plenty of tricks to be as efficient as possible and to reuse as much as
+  possible.
+
+  ### Entity annotations
+
+  The `Entity` subsystem annotates identifiers for entities with additional information
+  to help their complete and unambiguous identification.
+
+  #### Organisms and builds
+
+  When you identify a gene with the string `TP53` we might think that the gene
+  is unambiguously identified, however, it is not. First of all, we need to
+  know to which organism this gene belongs to, each TP53 gene from different
+  organisms is a different gene. Not only that, but the TP53 gene changes
+  slightly from build to build, in particular, its chromosomal position may
+  shift. For that reason genes are not only characterized by the organism they
+  belong to but also by the version of the build we are considering.
+
+  We annotate entities with their organism and build using the following
+  convention.  The organism is specified with a three letter code, the first is
+  uppercase and is the first letter of the first term in the organism name ("H"
+  for Homo) and the last two the first two letter of the second term ("sa" for
+  sapiens); this is the convention followed by KeGG, it is succinct and
+  collision free in our experience.  The build is specified afterwards with a
+  date code; "Hsa/may2009" represents the _Homo s._ organism as was known in
+  May 2009 i.e. hg18 build; whereas "Hsa/jan2013" corresponds to a recent
+  version of the hg19 build.
+
+
+  #### Identifier formats
+
+  Genes can be identified through a substantial number of identifier formats:
+  Ensembl Gene ID, Entrez Gene ID, Associated Gene Name (gene symbol). We use
+  the Ensembl BioMart to download an identifier translation resource. The name
+  of the formats corresponds to the names used in the Ensembl BioMart and must
+  be *followed to the letter including case*. The gene `Entity` is prepared to handle all the
+  necessary translations between identifiers across different resources
+  transparently. But the user *must* be aware of this fact or may run into
+  trouble.
+
+
+%h2 Subsystems
+%ul
+  %li 
     %a(href='/help/entity' class="help") Entity subsystem
+
+  %li 
     %a(href='/help/workflow' class="help") Workflow subsystem