rbbt-rest 1.1.4 → 1.1.5

data/share/views/compass/style.sass

@@ -3,7 +3,6 @@
 @import url(http://fonts.googleapis.com/css?family=Open+Sans)
 
 body, p, h1, h2, h3, h4, h5, h6
-  //font-family: Arial, Liberation Sans,DejaVu Sans,sans-serif
   font-family: "Open Sans", "Trebuchet MS", "Noticia Text", Verdana, Arial, "Helvetica Neue", Helvetica, sans-serif
   line-height: 1.4em
 
@@ -86,3 +85,32 @@ footer
 
 ul.clean_list
   list-style: none
+
+span.error_message
+  font-size: 1.2em
+  display: block
+  margin: 1em 0px
+
+ul.error_backtrace, ul.step_messages
+  color: gray
+  
+select.favourite_entities
+  option:disabled
+    font-weight: bold
+
+a.entity.highlighted
+  font-weight: bold
+  
+.help
+  margin: auto
+  ul
+    margin-left: 2em
+    
+  p 
+    max-width: 60em
+
+ 
+a.help
+  display: block
+  font-size: 2em
+  line-height: 2em

data/share/views/compass/style_mixins.sass

@@ -10,7 +10,14 @@
   //border: solid 1px darken($white, 10%)
   @extend .panel
 
-.button-group-list
+=normal_button()
+  @include button-base
+  @include button-size
+  @include button-style
+  @include radius
+  @include single-transition
+
+=button-group-list()
   @include inline-list()
   @include button-group-container()
   margin: 0
@@ -20,11 +27,16 @@
     margin: 0 2px 0 0
       
     a
-      @include button-base
-      @include button-size
-      @include button-style
-      @include radius
-      @include single-transition
+      +normal_button()
       margin-bottom: 2px
       font-size: 0.8em
 
+.button-group-list
+  +button-group-list()
+
+=ellipsis_text()
+  width: 100%
+  overflow: hidden
+  white-space: nowrap
+  text-overflow: ellipsis
+

data/share/views/compass/table.sass

@@ -1,5 +1,8 @@
 $triglecolor: rgba(0,0,0,0.15)
 table
+  //caption
+    width: 100%
+
   &.wide
     td
       max-width: 200px
@@ -18,12 +21,13 @@ table
       @include inline-list()
       @include button-group-container()
       margin-bottom: 0
-      float: right
+      float: left
       li.filter
-        .filter_controls
+      @media print
+        &
           display: none
 
-
+    
   &.sorted
     thead
       tr
@@ -45,3 +49,15 @@ table
           &.headerSortUp:after
             margin-bottom: 5px
             @include css-triangle(5px, $triglecolor, bottom)
+
+.table_column_selector
+  li
+    @include grid-row()
+
+    span
+      @include ellipsis_text()
+      @include grid-column(8)
+    a
+      @include grid-column(2, $last-column:false)
+
+

data/share/views/compass/topbar.sass

@@ -1,11 +1,17 @@
 #header
+  margin-bottom: 1em
   nav.top-bar
     margin-bottom: 0 !important
 
+    section.top-bar-section
+      ul
+        a#reload_page, a#toggle_favourite
+          line-height: 43px
+
     li#top-add-favourite
       cursor: pointer
     li.search
-      width: auto
+      width: 300px
       //@include grid-row(nest-collapse)
       input, button
         display: inline-block
@@ -16,4 +22,4 @@
         left: -5px
         @media #{$not_small}
           top: 9
-      
+           

data/share/views/entity_map/Default.haml

@@ -0,0 +1,5 @@
+- entity_map_card = EntityMapCard.new map, map_id
+
+- entity_map_card.action_controller = default_action_controller map, map_id
+
+= entity_map_card_render entity_map_card

data/share/views/entity_partials/action_card.haml

@@ -6,6 +6,8 @@
         = @entity.respond_to?(:name) ? @entity.name || @entity : @entity
       - when 'entity_list_action'
         = Misc.humanize page_entity_list
+      - when 'entity_map_action'
+        = Misc.humanize page_entity_map
     .long_name
       = Misc.humanize page_action if page_action
 

data/share/views/entity_partials/action_controller.haml

@@ -20,10 +20,17 @@
       - last_resource = nil
       - controller.actions.each do |action, text, resource, params|
         %li(class="#{last_resource and last_resource != resource ? "new_resource" : ""}" attr-resource="#{resource}")
-          - if AnnotatedArray === entity
+          - case
+          - when AnnotatedArray === entity
             - id = params.delete :id if Hash === params
             - id = controller.id if id.nil?
             = entity.list_action_link action, text, id, params.merge(:reuse => true)
+          - when TSV === entity
+            - id = params.delete :id if Hash === params
+            - id = controller.id if id.nil?
+            - type = page_entity_type
+            - column = page_entity_map_column
+            %a.entity_map_action(href="#{Entity::REST.entity_map_action_url id, type, column, action}")= text 
           - else
             = entity.action_link action, text, params
         - last_resource = resource

data/share/views/entity_partials/entity_list_card.haml

@@ -24,7 +24,7 @@
               - if list.respond_to? :ensembl
                 %a.ensembl_list(href="#{request.path_info + "?_format=ensembl"}") Ensembl
               %a.download_list(href="#{request.path_info + "?_format=raw"}") Raw
-              %a.edit_list(href="#" data-reveal-id='modal1') Edit
+              %a.edit_list(href="#") Edit
 
         .entity_info
           - info = list.info.dup
@@ -39,6 +39,7 @@
           = capture_haml &card.meta 
 
         .entities
+          %p #{list.length} entities
           - if (defined? force and force) or list.length < 500
             %ul.entity_list
               - list = list.sort_by{|g| g.name || "Z" << g} if list.respond_to? :name
@@ -46,11 +47,12 @@
                 %li= link
           - else
             %p
-              = modal_fragment "Too many entities to list" do
-                - list = list.sort_by{|g| g.name || "Z" << g} if list.respond_to? :name
-                %ul.entity_list
-                  - list.link.each do |link|
-                    %li= link
+              = reveal "Too many entities to list (#{list.length})" do
+                = fragment do
+                  - list = list.sort_by{|g| g.name || "Z" << g} if list.respond_to? :name
+                  %ul.entity_list
+                    - list.link.each do |link|
+                      %li= link
  
         - if card.list_container
           .entity_lists

data/share/views/entity_partials/entity_map_card.haml

@@ -0,0 +1,63 @@
+- map = card.map
+- map_id = card.map_id
+.entity_map_card(id="#{ map_id.gsub(/\s/,'_') }_card")
+
+  .title
+    .name
+      = map.key_field
+      Map
+    .long_name
+      = Misc.humanize map_id
+
+  .card
+    .sidebar.offcanvas
+      .meta
+        .map_management
+          %ul
+            %li
+              = reveal "Rename" do
+                %form.rename
+                  %label New name
+                  %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/,'')
+              %li
+                - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
+                %a.ensembl(href=url) Pvalue score
+
+            - if Gene == Entity.formats[map.key_field]
+              - if map.key_field != "Ensembl Gene ID"
+                %li
+                  - url = add_GET_param(@fullpath, '_format', 'ensembl')
+                  %a.ensembl(href=url) Ensembl
+              - if map.key_field != "Associated Gene Name"
+                %li
+                  - url = add_GET_param(@fullpath, '_format', 'name')
+                  %a.name(href=url) Name
+            - if "Rank" == map.fields.first
+              %li
+                - url = add_GET_param(@fullpath, '_format', 'invert_ranks')
+                %a.invert_ranks(href=url) Invert ranks
+            - else
+              %li
+                - url = add_GET_param(@fullpath, '_format', 'ranks')
+                %a.ranks(href=url) Ranks
+            - if NumericValue == Entity.formats[map.fields.first] or (map.entity_templates[map.fields.first] and map.entity_templates[map.fields.first].annotation_types.include? NumericValue)
+              %li
+                - $page_entity_base_type = page_entity_base_type 
+                - $page_entity_map_column = page_entity_map_column 
+                = reveal :rank_products 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}
+
+
+
+    .content
+      .description
+        = table do
+          - map
+      - if card.action_controller
+        .actions
+          = action_controller_render(card.action_controller)
+

data/share/views/entity_partials/list_container.haml

@@ -26,5 +26,6 @@
             - if (defined? force and force) or list.length < 500
               = list.link * ", "
             - else
-              = modal_fragment "Too many entities to list" do
-                = list.link * ", "
+              = reveal "Too many entities to list" do
+                = fragment do
+                  = list.link * ", "

data/share/views/error.haml

@@ -1,12 +1,16 @@
 .row
   .column.small-12
-  %h5 Error processing #{File.basename(job.name)}
-  - if job.messages and job.messages.any?
-    %span.error_message= job.messages[-2]
-  - backtrace = job.info[:backtrace]
-  - if backtrace and backtrace.any?
-    .row
-      .column.twelve
-        %ul.error_backtrace
-          - backtrace.each do |line|
-            %li= line
+    %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
+
+- if backtrace and backtrace.any?
+  .row
+    .column.twelve
+      %ul.error_backtrace.clean_list
+        - backtrace.each do |line|
+          %li= line

data/share/views/help.haml

@@ -0,0 +1,34 @@
+.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.
+
+    %a(href='/help/entity' class="help") Entity subsystem
+    %a(href='/help/workflow' class="help") Workflow subsystem

data/share/views/help/entity.haml

@@ -0,0 +1,193 @@
+.row.help
+  .column.small-12
+    :markdown
+
+      The Entity subsystem
+      =================
+
+      ### Introduction: Entities and Entity Lists
+
+      This is the operation mode that regular users most like use. Its
+      organized quite different than other applications you might know.  The
+      objective is to provide a simple abstraction to organize and interconnect
+      functionalities and background information. Everything is built around
+      the idea of Entities. An Entity is anything that can be the subject of
+      investigation: 
+
+        * genes
+        * proteins
+        * transcripts
+        * drugs
+        * SNPs
+        * samples
+        * studies
+        * pathways
+        * chromosomal ranges
+        * ...
+
+      Each type of entity has associated a number of reports. There is an
+      *Entity Report*, which displays information about an entity. If the
+      entity is a gene, then the report will contain the description of the
+      gene, its isoforms, functional information, and many other things. There
+      is also an *Entity List Report*, which covers not a single entity, but a
+      list of entities. For instance, the report for a list of genomic
+      mutations includes the types of mutations (transversions, transitions,
+      etc), the genes affected, damage predictions, etc. 
+      
+      Each report links to other reports. For instance, a gene report will
+      include links to reports for its isoforms, the pathways it is associated
+      with, etc.  This offers a way to navigate the information and pursue
+      interesting leads.
+
+      In addition to reports, there are also *Actions* associated to Entities
+      and Entity Lists. These Actions are accessible from each report page.
+      The Actions allow the user to issue analysis jobs centered on the current
+      Entity or Entity List. For instance, when viewing the report for a gene
+      lists, which may contain for example all genes mutated recurrently in a
+      cohort, the Actions available include performing enrichment analysis,
+      examining the mutation frequencies of the genes in COSMIC or examining
+      the mutational status of these genes on other genotyping studies that you
+      may have access to.
+
+      Both Entities and Entity Lists can be marked as *Favourites*, this will
+      include a link in the menu on the top of the page. Favourite Lists have
+      some special features, they can be *flagged* any link that points to an
+      entity in the list will be highlighted. This provides a fast an easy way
+      to track a list of interest throughout your explorations.  Additionally
+      some Actions may take Entity Lists as inputs, and will allow the user to
+      choose among her Favourite Lists. 
+
+      There is a third type of report, the *Entity Map Report*. Its meant as
+      additional way to connect functionalities and is less important right
+      now. They will cover this on the section on *Tables* and ignore them until
+      then.
+
+      All reports are unambiguously identified from its URL, including Actions,
+      which allows to bookmark or share anything with your collaborators.
+
+      #### A simple example
+
+      A common place to start using the application is from a *Study Report*.
+      The Study entity represents a collection of datasets, for instance a
+      cohort of exome sequenced samples for the ICGC CLL study. The report
+      includes a link to all the genes that have mutations altering their
+      protein isoforms in at least two samples; clicking on that link takes as
+      to the *Gene List Report* for the list with name "Recurrently mutated
+      genes in CLL".  From the Gene List Report we can access the Action
+      "Enrichment", where we are presented with the option of performing an
+      hypergeometric-based enrichment analysis for functional annotations that
+      include Kegg, The Gene Ontology, Pfam domains, Reactome, and several
+      other functional information databases.
+
+      #### A very important note
+
+      The system must be able to unambiguously and precisely identify the
+      entities. For instance the string "TP53" may seem to clearly identify a
+      gene, yet this is not entirely true. First we need to know the organism
+      it refers to, in this case Human. Consider now that we ask for the
+      genomic coordinates of the gene, this question cannot be answered until
+      we known the version of the build we need to use. By default the system
+      will try the most recent version of the genome in Ensembl, but other
+      builds can be specified. The complete way to specify the organism will be
+      "Hsa/may2009" for the hg18 build or "Hsa/jan2013" for the latest hg19
+      build. This system downloads all data consistently from Ensembl using the
+      builds. Using an explicit version of the build (Hsa/jan2013) instead of
+      just the organism (Hsa) will prevent problems with inconsistencies that
+      could result from downloading different files at different times, where
+      there may have being some updates. The organism codes follow the convention of Kegg, one
+      letter from the *genus*, two from the *species*; Examples: Homo sapiens
+      -- Hsa; Mus musculus -- Mmu. The dates that specify the builds represent
+      the different archives of Ensembl, which is the corner stone of all our
+      genomic data.
+      
+      Additionally, there are several ways to refer to the same gene; for
+      instance "TP53" can also be expressed as "ENSG00000141510". So, when
+      asking the system for a gene, the information on the format of the
+      identifier must also be provided. Fortunately, the system will take care
+      of transparently translating identifiers between different formats to
+      match the formats in different resources. It will also propagate the
+      information about the organism across different reports.
+
+      Last but by all means not least: This system is *CASE-SENSITIVE* almost
+      all over the place. TP53 is a Human gene, Tp53 is a Mouse gene, no wiggle
+      room allowed! It might take a little getting used to, but
+      case-insensitive behaviour has been avoided almost all over the system
+      for performance issues. Again, the user should not have to worry about
+      this most of the time, as the system will take care of most details, but
+      its very important to know.
+      
+      ### User Interface: Basics
+ 
+      Before we continue let us see how the user interface is organized. The
+      top bar contains the application title, which links to he main page,
+      the *Reload* button, the *Start* button, the *Favourite* menus, and 
+      the *Search* box. 
+
+      When a report is first requested the result is saved for further use,
+      even if there was an error producing it.  This is true for entities,
+      lists, actions, and almost everything else. Clicking the reload button
+      on the browser will just render the saved result. To force regenerating
+      the report you need to use the Reload button on the top of the page.
+      An exception to this are Actions. These can be opened in separate windows,
+      in which case it works as usual, but are more often opened from the 
+      *Action Section* of the report, which will be covered bellow. The Action 
+      Section has its own Reload button.
+
+      To Star button toggles the favourite status of the current Entity or
+      Entity List. It only works for Entities, Entity Lists, and Entity.  It
+      has no effect on Actions, for the time being. The Favourite Menus are
+      updated when the Star button is clicked. If a Favourite is made on a
+      different browser tab or window, the current Favourite Menus can be
+      updated by reloading the page using the browser button (the page should
+      already be saved), or by clicking on the Star button, which also updates
+      the current menus. Input forms and actions that have Entity Lists as
+      inputs will also be updated this way.
+
+      Some parts of the page will be loaded in the background. These include
+      portions of the report that are more costly to compute, or particular
+      processes that are issues by the user interacting with the page. To make
+      the user aware of these, the little number on the far right of the top
+      bar displays the number of processes communicating with the server on
+      background.
+
+      On small devices (tablets and phones), the top-bar will be collapsed and
+      some elements hidden. To display these elements, click on the "Menu"
+      button on the top right.
+
+
+      ### User Interface: Report template
+
+      Reports may have any type of content, however, they are usually based on
+      a common template. It has a title on the top row, a side bar on the left,
+      a description on the right, at the top, and the Actions Section bellow
+      it.  Note that, depending on the particular report, the description may
+      be empty or there might not be any actions associated to it.
+
+      In general, the sidebar is used to display technical information about
+      the Entity at hand. For a Gene Report, for instance, the sidebar is used
+      to display the format used to specify the gene (such as Ensembl Gene ID),
+      and the organism it refers to. In the case of gene reports, the basic
+      identification information is followed with additional information about
+      isoforms, functional annotations, PubMed articles, etc. On small devices
+      (tablets and phones), the sidebar will hide on the right of the screen,
+      and will be displayed on clicking the blue button on the title section.
+
+
+      ### User Interface: Actions
+
+      Entities and Entity Lists may have associated Actions, depending on the
+      type of Entity. When Actions are available for a Report, they are displayed
+      in the Actions Section. This section is composed on an horizontal bar
+      with a button for each each action. When a button is clicked the action
+      is displayed bellow the bar. If the action takes some time, a 'Loading...'
+      message will appear. The bar includes a button to reload an action that
+      has already been computed. If the action accepts parameters, the user
+      will be required to set them. To set the parameters click on the button
+      with a gear; this will display the parameter section. Of course, if the
+      parameters of an action are changed, a new report will be generated; 
+      Actions are saved separately for each combination of parameters. 
+
+      For actions with large reports, it may be better to open them in a separate
+      window. You can do this using the mouse-right-click, just like any regular
+      link.
+