rbbt-rest 1.4.10 → 1.4.11

data/share/views/compass/app.sass

@@ -1,17 +1 @@
-@import "_normalize"
-@import "_rbbt"
-
-@import "style"
-
-@import "user"
-@import "entity_card"
-@import "workflow"
-@import "finder"
-@import "favourites"
-@import "actions"
-@import "top_menu"
-@import "help"
-@import "figure"
-@import "monitor"
-@import "layout"
-
+@import "_app"

data/share/views/compass/finder.sass

@@ -1,8 +1,10 @@
 li.find
   @media #{$only-large}
+    width: 5em
+    margin-left: $indent / 2
+    margin-right: $indent / 2
+  @media #{$only-very-large}
     width: 10em
-    margin-left: $indent
-    margin-right: $indent
   @media #{$not-large}
     width: 50%
     margin: 0 
@@ -17,13 +19,11 @@ li.find
     padding: 0
     input[type=text]
       width: 100%
-      height: 2em
-      padding-right: $width_finder_button
+      height: 1.96em
     button[type=submit]
       width: $width_finder_button
-      display: inline-block
-      @media #{$not-large}
-        display: none
+      //display: inline-block
+      display: none
       position: absolute
       top: 0px
       right: 0

data/share/views/compass/grid_system.sass

@@ -8,15 +8,7 @@ $legacy-support-for-ie6: false !default
 
 $breakpoint: 1024px
 
-$small-screen: 1024px
-$medium-screen: 1280px 
-$large-screen: 1440px 
-
-$not-small: "only screen and (min-width: #{$small-screen})" 
-$only-small: "only screen and (max-width: #{$small-screen})" 
-
-$only-large: "only screen and (min-width: #{$small-screen})" 
-$not-large: "only screen and (max-width: #{$small-screen})" 
+@import 'screen_sizes'
 
 $row-width: auto 
 $column-gutter: 30px

data/share/views/compass/layout.sass

@@ -113,7 +113,7 @@ ul.list_comparison
     input
       width: 100%
 
-.wait
+.wait, .error
   ul.step_messages
     li
       color: darken($color_main, 30)
@@ -134,7 +134,7 @@ ul.list_comparison
 .action_loader
   min-height: 500px
 
-@media #{$not-large} 
+@media #{$only-very-small} 
   table.wide, table.flip
     +responsive_table
 

data/share/views/compass/rbbt/table.sass

@@ -2,6 +2,7 @@ $triglecolor: rgba(0,0,0,0.15)
 $margin_table_actions: 7px
 $padding_table: 5px 7px
 $color_table_border: darken($table_color, 45)
+
 =rbbt_table()
   min-width: 300px
 

data/share/views/compass/screen_sizes.sass

@@ -0,0 +1,16 @@
+$very-small-screen: 500px
+$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/top_menu.sass

@@ -21,6 +21,7 @@ $padding_top_menu: 5px
   box-shadow: 0px 3px -4px 4px rgba(0, 0, 0, 0.1)
   padding-left: 0px
   & > ul
+    margin: 0
     +grid_row()
     +clean_list
     +clear_fix

data/share/views/entity_partials/action_card.haml

@@ -1,6 +1,8 @@
 .action_card
   .title
     .name
+      = Misc.humanize page_action if page_action
+    .long_name
       - case page_type
       - when 'entity_action'
         = @entity.respond_to?(:name) ? @entity.name || @entity : @entity
@@ -8,8 +10,6 @@
         = Misc.humanize page_entity_list
       - when 'entity_map_action'
         = Misc.humanize page_entity_map
-    .long_name
-      = Misc.humanize page_action if page_action
 
   - if card.description
     .action_description

data/share/views/entity_partials/entity_card.haml

@@ -22,7 +22,6 @@
         = fragment :long_name, &card.long_name
 
   .card
-
     - info = entity.info.dup
     - info.delete :annotated_array
     - info.delete :annotation_types
@@ -32,6 +31,7 @@
         .meta
           .entity_info
             = hash2dl(info)
+
           - case card.meta
           - when nil
           - when Hash
@@ -45,22 +45,28 @@
 
 
     /-- content --
-    .content
+    .content<
       - case card.description
       - when nil
         - if entity.respond_to?(:description) and entity.description
+          /-- description --
           .description
             %p= entity.description
       - when String
+        /-- description --
         .description
-          %p= card.description
+          :documentation
+            #{card.description}
       - when Proc
+        /-- description --
         = fragment :description, &card.description
 
       - if defined? block and block
+        /-- content block --
         = capture_haml &block
 
       - if card.action_controller
-        .actions
+        /-- actions --
+        .actions.togglable_hide(hide-title='Actions')<
           = action_controller_render(card.action_controller)
 

data/share/views/entity_partials/entity_list_card.haml

@@ -2,6 +2,7 @@
 - list_id = card.list_id
 .entity_list_card(id="#{ list_id.gsub(/\s/,'_') }_card")
 
+  /-- title --
   .title
     .name
       = list.base_type
@@ -11,6 +12,7 @@
 
   .card
 
+    /-- sidebar --
     .sidebar.offcanvas
       .meta
         .list_management
@@ -69,8 +71,10 @@
 
 
 
+    /-- content --
     .content
-      .description
+      /-- description --
+      .description<
         - case card.description
         - when nil
           - if list.length == list.uniq.length
@@ -83,5 +87,6 @@
           = capture_haml &card.description
 
       - if card.action_controller
-        .actions
+        /-- actions --
+        .actions.togglable_hide(hide-title="Actions")<
           = action_controller_render(card.action_controller)

data/share/views/entity_partials/entity_map_card.haml

@@ -11,7 +11,7 @@
 
   .card
 
-    .sidebar.offcanvas
+    .sidebar.offcanvas.show
       .meta
         .map_management
           %ul

data/share/views/error.haml

@@ -1,14 +1,18 @@
-%h5 Error processing #{File.basename(job.name)}
-- if job.messages and job.messages.any?
-  %span.error_message
-    %pre= CGI.escapeHTML(job.messages[-1] || "")
-- backtrace = job.info[:backtrace]
+.error
+  %h5 Error on #{format_name File.basename(job.name)}
+  - if job.messages and job.messages.any?
+    %span.error_message
+      %pre= CGI.escapeHTML(job.messages[-1] || "")
+  - backtrace = job.info[:backtrace]
 
-%hr
+  - clean_url = add_GET_param(request.env["REQUEST_URI"], "_update", "clean")
+  %a(href=clean_url) Clean
 
-- if backtrace and backtrace.any?
-  .row
-    .column.twelve
-      %ul.error_backtrace.clean_list
-        - backtrace.each do |line|
-          %li= line
+  %hr
+
+  - if backtrace and backtrace.any?
+    .row
+      .column.twelve
+        %ul.error_backtrace.clean_list
+          - backtrace.each do |line|
+            %li= line

data/share/views/form.haml

@@ -21,7 +21,7 @@
   - if workflow.libdir.examples[task.to_s].exists?
     .examples
 
-      Click the links bellow to load example data:
+      Click below to load example data:
         
       :javascript
         example_inputs = [];
@@ -37,7 +37,7 @@
             %a.load_example(href="#" task=task name=name)= name
 
       :javascript
-        deffer(function(){
+        defer(function(){
           var form = $('.workflow_task[id=#{id}] > .form > form')
 
           $("a.load_example").click(function(){

data/share/views/help.haml

@@ -1,4 +1,4 @@
-:markdown
+:documentation
 
   ##Overview
 
@@ -36,12 +36,12 @@
   another. This web site is 'responsive', meaning that it adapts to the size
   of the device you are using: computer, tablet, or phone. On small devices many
   of the layout elements shift around or get hidden behind toggle buttons to
-  accommodate themselves better to the screen size. The examples bellow are taken
+  accommodate themselves better to the screen size. The examples below are taken
   from a computer screen.
 
 =partial_render('help/UI') 
 
-:markdown
+:documentation
   ##Workflows
 
   In addition to exploring entity reports, this site servers collections of

data/share/views/help/UI.haml

@@ -2,32 +2,31 @@
 
   %dt.next.active.show Report structure
   %dd.show
-    .description
-      :markdown
-
-        This application presents reports for individual entities, lists of
-        entities, and entity maps. Each type of entity (gene, study, pathway, etc.)
-        has its own report template, and they are prepared on-demand.
-        
-        All reports have the same overall structure; the images show a report
-        for a genotyping study from the ICGC project. The top-bar is always
-        there and provides a placeholder for several functionalities, most
-        importantly the control of `favourites`. 
-        
-        Bellow the top-bar comes the report itself. It consists of a title, a
-        side-bar, a description, and an `action controller`. In general the
-        side-bar is used to show general meta-data about the entity and the
-        description to show a brief overview. 
-        
-        The action controller offers access to `actions`, which are like
-        sub-reports. Each type of entity has its own actions. If the entity
-        type in particular does not have any action defined then the action
-        controller will not be displayed. When an action is selected, it will
-        be displayed below, in the area called action loader. 
-
-        Actions can also be opened in their own page, clicking the
-        middle-button like any link. These pages are like reports but with no
-        action controller or side-bar
+    :documentation
+
+      This application presents reports for individual entities, lists of
+      entities, and entity maps. Each type of entity (gene, study, pathway, etc.)
+      has its own report template, and they are prepared on-demand.
+      
+      All reports have the same overall structure; the images show a report
+      for a genotyping study from the ICGC project. The top-bar is always
+      there and provides a placeholder for several functionalities, most
+      importantly the control of `favourites`. 
+      
+      Bellow the top-bar comes the report itself. It consists of a title, a
+      side-bar, a description, and an `action controller`. In general the
+      side-bar is used to show general meta-data about the entity and the
+      description to show a brief overview. 
+      
+      The action controller offers access to `actions`, which are like
+      sub-reports. Each type of entity has its own actions. If the entity
+      type in particular does not have any action defined then the action
+      controller will not be displayed. When an action is selected, it will
+      be displayed below, in the area called action loader. 
+
+      Actions can also be opened in their own page, clicking the
+      middle-button like any link. These pages are like reports but with no
+      action controller or side-bar
         
     .images
       %dl.tabs.active.show
@@ -42,27 +41,26 @@
 
   %dt.next Top-bar
   %dd
-    .description
-      :markdown
-
-        The top-bar provides access to several functionalities. Clicking on the
-        title of the application will link to its front-page.  Next to it is
-        the reload-button, which is used to force the server to recalculate a
-        report, otherwise the report will be taken from a cache.  This is
-        useful when a report has given an error or when when it was updated
-        somehow. *Note:* After a reload of the report, the browser might still
-        try to get the file from its own cache, so you might need to use the
-        reload button in the browser as well; I'm planning to fix this.
-
-        Next is the `favourites` controls, which we will discuss shortly. After
-        that there might be a search box, if the server was started with that
-        functionality. This search box can be configured to identify any type
-        of entity, but generally it is only genes.
-
-        The final component of the top-bar, which I label "User", has the user
-        controls, which allows to login or logout, and the job bookmarks, where
-        bookmarked actions are kept. Also this help page. Will discuss
-        bookmarking actions latter.
+    :documentation
+
+      The top-bar provides access to several functionalities. Clicking on the
+      title of the application will link to its front-page.  Next to it is
+      the reload-button, which is used to force the server to recalculate a
+      report, otherwise the report will be taken from a cache.  This is
+      useful when a report has given an error or when when it was updated
+      somehow. *Note:* After a reload of the report, the browser might still
+      try to get the file from its own cache, so you might need to use the
+      reload button in the browser as well; I'm planning to fix this.
+
+      Next is the `favourites` controls, which we will discuss shortly. After
+      that there might be a search box, if the server was started with that
+      functionality. This search box can be configured to identify any type
+      of entity, but generally it is only genes.
+
+      The final component of the top-bar, which I label "User", has the user
+      controls, which allows to login or logout, and the job bookmarks, where
+      bookmarked actions are kept. Also this help page. Will discuss
+      bookmarking actions latter.
 
     .images
       %dl.tabs.active.show
@@ -77,28 +75,27 @@
 
   %dt.next Favourites
   %dd
-    .description
-      :markdown
-
-        As we said before, we have reports for entities, lists, and maps.
-        Clicking the star on the favourites control makes a favourite out of
-        what-ever we are viewing: an entity, like a study; a list of entities,
-        such as the genes mutated in the study; or a map, which could for
-        instance map genes to the ratio of mutations per amino-acid in the
-        COSMIC database.
-
-        Favourites are used not only to track our interests, but as a means to
-        communicate between different functionalities or parts of the
-        application. We could for instance make a list of genes a favourite and
-        then go to a study report, open the "Gene list in study" action, select
-        our list from all the favourites and see a report of how these genes
-        are affected in the study
-
-        The favourite controls have an option to create a new list of entities
-        from scratch. This allows a user, for instance, to make a list with her
-        genes of interest instead of having to browse the application to find
-        it. *Note:* New lists are not made favourite be default, you still need to
-        click on the star once the report is shown.
+    :documentation
+
+      As we said before, we have reports for entities, lists, and maps.
+      Clicking the star on the favourites control makes a favourite out of
+      what-ever we are viewing: an entity, like a study; a list of entities,
+      such as the genes mutated in the study; or a map, which could for
+      instance map genes to the ratio of mutations per amino-acid in the
+      COSMIC database.
+
+      Favourites are used not only to track our interests, but as a means to
+      communicate between different functionalities or parts of the
+      application. We could for instance make a list of genes a favourite and
+      then go to a study report, open the "Gene list in study" action, select
+      our list from all the favourites and see a report of how these genes
+      are affected in the study
+
+      The favourite controls have an option to create a new list of entities
+      from scratch. This allows a user, for instance, to make a list with her
+      genes of interest instead of having to browse the application to find
+      it. *Note:* New lists are not made favourite be default, you still need to
+      click on the star once the report is shown.
 
     .images
       %dl.tabs.active.show
@@ -112,48 +109,46 @@
 
   %dt.next Actions
   %dd
-    .description
-      :markdown
-
-        Actions are the primary way to integrate data and functionalities.
-        Some actions are defined globally, but most commonly they are defined
-        inside workflows; when a report is produced, all workflows are
-        interrogated to see if they provide actions for it. The great majority
-        of the actions are defined in the `Genomics` workflow.
-
-        When an action is selected, it loads bellow the action controller. An
-        action report consists of the content of the action, and optionally,
-        parameter controls and an action description. When the action is loaded
-        inside a report the parameter controls and description are hidden, but
-        they can be shown using the action control buttons in the top left of
-        the action controller. Actions can also be opened in their own report
-        by right/middle clicking on its button.
-
-        As with all reports, they are executed the first time they are
-        requested and the result is cached for further access. The action
-        control buttons can be used to reload the action, just like the reload
-        button in the top-bar does for the complete report. The actions will
-        of-course be recomputed for each configuration of parameters. The
-        parameters of the action can be favourites from the user, lists or
-        maps. These are presented to the user using an input `select`, and are
-        synchronized with the user current favourites.
-
-        If an action is used often with a particular combination of parameters.
-        For instance the "Enrichment" action of gene lists performs an
-        over-representation based analysis of functional classes. The
-        functional classes include several pathway databases, protein domains,
-        gene ages, etc. If we where interested primarily in performing enrichment
-        analysis using GO biological process terms, we can use the paperclip
-        button to set that configuration of parameters as default, so that it
-        always uses it initially.
-
-        Some actions may require a significant amount of time to compute. The
-        action controller tries to reload the action periodically until it is
-        completed (after a while it will stop insisting to not overload the
-        server). Instead of having to wait on that page for it to finish, the
-        user can click on the bookmark button, which will place a link in the
-        "jobs" tab on the "Extra" menu of the top-bar, and come back to it
-        later.
+    :documentation
+
+      Actions are the primary way to integrate data and functionalities.
+      Some actions are defined globally, but most commonly they are defined
+      inside workflows; when a report is produced, all workflows are
+      interrogated to see if they provide actions for it. The great majority
+      of the actions are defined in the `Genomics` workflow.
+
+      When an action is selected, it loads below the action controller. An
+      action report consists of the content of the action, and optionally,
+      documentation a report the parameter controls and description are
+      hidden, but they can be shown using the action control buttons in the top
+      left of the action controller. Actions can also be opened in their own
+      report by right/middle clicking on its button.
+
+      As with all reports, they are executed the first time they are
+      requested and the result is cached for further access. The action
+      control buttons can be used to reload the action, just like the reload
+      button in the top-bar does for the complete report. The actions will
+      of-course be recomputed for each configuration of parameters. The
+      parameters of the action can be favourites from the user, lists or
+      maps. These are presented to the user using an input `select`, and are
+      synchronized with the user current favourites.
+
+      If an action is used often with a particular combination of parameters.
+      For instance the "Enrichment" action of gene lists performs an
+      over-representation based analysis of functional classes. The
+      functional classes include several pathway databases, protein domains,
+      gene ages, etc. If we where interested primarily in performing enrichment
+      analysis using GO biological process terms, we can use the paperclip
+      button to set that configuration of parameters as default, so that it
+      always uses it initially.
+
+      Some actions may require a significant amount of time to compute. The
+      action controller tries to reload the action periodically until it is
+      completed (after a while it will stop insisting to not overload the
+      server). Instead of having to wait on that page for it to finish, the
+      user can click on the bookmark button, which will place a link in the
+      "jobs" tab on the "Extra" menu of the top-bar, and come back to it
+      later.
 
     .images
       %dl.tabs.active.show
@@ -177,41 +172,40 @@
 
   %dt.next Tables
   %dd
-    .description
-      :markdown
-
-        Tables in this application come enhanced with several functionalities.
-        The rows can be sort by the values of any column. 
-        
-        The values of the columns can also be used to filter the rows of the
-        table through the `filter` button. The filters are defined per-column,
-        and can contain exact strings, regular expressions like
-        `/(COMPLETE|PARTIAL) RESPONSE/i`, statements such as `> \< ==` or `!=`.
-        And columns containing entities they can be prefixed with the term
-        `name:` to force the filtering to work over the human readible text of
-        the entities e.g. `name:/SF3B\d+/` for a column containing 'Ensembl
-        Gene ID'.
-
-        When a column contains entities, these are usualy listed in the table
-        using some identifier like 'Ensembl Gene ID' for genes or 'GO Term
-        IDs', etc. When displaying the table, it automatically substitutes
-        these identifiers with links to their corresponding reports, and lists
-        them by name. Additionally the `column` button allows the user to
-        report the list of entities of any column or, if the first column is
-        itselve an entity, it allows the user to report the `map` between the
-        entities in this column and the values of any other column.  Maps are
-        generally used as inputs to actions and tools, but may have actions as
-        well; gene maps have an action that performs a rank-based enrichment
-        analysis (provided the Enrichment workflow is loaded in the
-        server).
-
-        The content of the table can be downloaded in two forms, as TSV files,
-        which is the original source of the table, or as Excel files. When
-        downloding as Excel files, since are generally intended to be read by
-        people, all entities listed that can be translated to a more human
-        readible identifier are translated automatically. This includes change
-        genes identifiers from `Ensembl Gene ID` to `Associated Gene Name`, or
-        changing KEGG pathway ids to their descriptive name.
+    :documentation
+
+      Tables in this application come enhanced with several functionalities.
+      The rows can be sort by the values of any column. 
+      
+      The values of the columns can also be used to filter the rows of the
+      table through the `filter` button. The filters are defined per-column,
+      and can contain exact strings, regular expressions like
+      `/(COMPLETE|PARTIAL) RESPONSE/i`, statements such as `> \< ==` or `!=`.
+      And columns containing entities they can be prefixed with the term
+      `name:` to force the filtering to work over the human readible text of
+      the entities e.g. `name:/SF3B\d+/` for a column containing 'Ensembl
+      Gene ID'.
+
+      When a column contains entities, these are usualy listed in the table
+      using some identifier like 'Ensembl Gene ID' for genes or 'GO Term
+      IDs', etc. When displaying the table, it automatically substitutes
+      these identifiers with links to their corresponding reports, and lists
+      them by name. Additionally the `column` button allows the user to
+      report the list of entities of any column or, if the first column is
+      itselve an entity, it allows the user to report the `map` between the
+      entities in this column and the values of any other column.  Maps are
+      generally used as inputs to actions and tools, but may have actions as
+      well; gene maps have an action that performs a rank-based enrichment
+      analysis (provided the Enrichment workflow is loaded in the
+      server).
+
+      The content of the table can be downloaded in two forms, as TSV files,
+      which is the original source of the table, or as Excel files. When
+      downloding as Excel files, since are generally intended to be read by
+      people, all entities listed that can be translated to a more human
+      readible identifier are translated automatically. This includes change
+      genes identifiers from `Ensembl Gene ID` to `Associated Gene Name`, or
+      changing KEGG pathway ids to their descriptive name.
 
     .images
       %img(src="/img/UI/table.png")
@@ -219,23 +213,22 @@
 
   %dt.next Tools
   %dd
-    .description
-      :markdown
-
-        Some workflows implement `tools`, which provide special interactive
-        visualization for different types of data. For instance: the `Graph`
-        workflow implements the `cytoscape` tool, which is used to display
-        different kinds of entities connected through databases or analitical
-        results (defined as `knowledge_bases`, but that is a subject for
-        another discussion); the `Structure` `jmol` tool displays mutations in
-        the secondary and tertiary structures and complexes; and the `D3Js`
-        workflow that implements a tool to display `d3js` interactive SVG
-        figures. Alternative R is used through a native interface in Rbbt to
-        display plots using `ggplot2`.
-
-        These tools are used by different reports and actions. The `Graph`
-        workflow for instance redefines the template for `Gene` lists to
-        include a cytoscape plot to the description section of the report.
+    :documentation
+
+      Some workflows implement `tools`, which provide special interactive
+      visualization for different types of data. For instance: the `Graph`
+      workflow implements the `cytoscape` tool, which is used to display
+      different kinds of entities connected through databases or analitical
+      results (defined as `knowledge_bases`, but that is a subject for
+      another discussion); the `Structure` `jmol` tool displays mutations in
+      the secondary and tertiary structures and complexes; and the `D3Js`
+      workflow that implements a tool to display `d3js` interactive SVG
+      figures. Alternative R is used through a native interface in Rbbt to
+      display plots using `ggplot2`.
+
+      These tools are used by different reports and actions. The `Graph`
+      workflow for instance redefines the template for `Gene` lists to
+      include a cytoscape plot to the description section of the report.
 
     .images
       %dl.tabs.active.show