rbbt-rest 1.8.45 → 1.8.46

data/lib/rbbt/rest/helpers.rb

@@ -47,5 +47,17 @@ module Sinatra
       clean_name = parts * "_"
       "<span class='name' jobname='#{ name }'>#{ clean_name }</span> <span class='hash'>#{ hash }</span>"
     end
+
+    def values2d3(data)
+      data = data.to_single if data.respond_to? :to_single and not data.type == :single
+
+      values = []
+      data.each do |key, value|
+        name = key.respond_to?(:name) ? key.name || key : key
+        values << {:label => name, :value => value}
+      end
+
+      values
+    end
   end
 end

data/share/views/compass/app.sass

@@ -3,6 +3,7 @@
 @import 'layout'
 @import 'card_templates'
 @import 'tab_menu'
+@import 'documentation'
 @import 'misc'
 
 
@@ -64,3 +65,62 @@ table > caption
   &.small > a
     padding: .78571429em !important
     display: inline-block
+
+body, html
+  font-size: 16px 
+
+#modal
+  & > .header
+    font-size: 2em
+  
+.entity_card, .entity_list_card, .entity_map_card
+  width: calc(100% + 2rem)
+  .card_sidebar_open
+    margin-left: -1em !important
+    padding-left: 2em !important
+  .card_sidebar
+    min-width: 400px
+    transition: margin-left 0.3s, margin-right 0.3s, max-height 0.3s, min-width 0.5s
+    & + .column
+      transition: width 0.1s
+      max-width: calc(100% - 400px)
+    &.hidden
+      overflow: hidden
+      margin-left: calc(-25% - 32px) !important
+      margin-right: 32px !important
+      min-width: 25% !important
+      max-height: 500px
+    &.hidden + .column
+      //min-width: 100% !important
+      transition: width 0.3s, max-width 0.5s
+      max-width: 100% !important
+      width: 100% !important
+      margin: 0px
+
+  .card_sidebar
+    .sub.item
+      margin-left: 2em
+
+  .card_actions
+    width: 100% !important
+
+  @media only screen and (max-width: 600px)
+    .card_sidebar:not(.hidden) + .column
+      max-width: calc(100% + 400px) !important
+      margin-right: -500px !important
+
+.table.loading 
+  tfoot
+    display: none !important
+  &:after
+    content: "Loading..."
+    line-height: 60px
+    padding-left: 2em
+    display: inline-block
+    color: red
+    font-size: 1.5em
+
+dl > dd
+  margin-left: 1em
+
+

data/share/views/compass/card_templates.sass

@@ -24,6 +24,7 @@
   .action_controller > .action_menu 
     & > .button 
       max-width: 25%
+      min-width: 150px
 
 
 .entity_card, .entity_list_card, .action_card

data/share/views/compass/documentation.sass

@@ -0,0 +1,11 @@
+
+.documented.segment
+  .hidden.documentation
+    display: none
+  .help.label
+    opacity: 0.1
+    i
+      margin: 0 !important
+  &:hover > .help.label
+    opacity: 1
+

data/share/views/compass/layout.sass

@@ -55,6 +55,9 @@ body
     form input
       width: calc(100% - 16px)
 
+  .ui.modal
+    width: 75%
+    margin: 0 0 0 -37%
   .entity_card, .entity_list_card
     > .content
       > .info
@@ -79,7 +82,6 @@ body
     margin-right: 10%
     float: left
 
-
 #footer
   clear: both
 

data/share/views/compass/tab_menu.sass

@@ -41,9 +41,11 @@ $jiffy: 0.14s
 +keyframes(grow-down)
   0%
     max-height: 0px
-    padding-top: 0px
-    padding-bottom: 0px
-    +opacity(0.2)
+    padding-top: 0px !important
+    padding-bottom: 0px !important
+    margin-top: 0px !important
+    margin-bottom: 0px !important
+    //+opacity(0.2)
 
   100%
     max-height: 500px
@@ -100,10 +102,15 @@ dl.rbbt_tabs
     padding: 1em
     display: inline-block
     min-width: 20%
+    background: white
     &.active
       font-weight: bold
+      border-bottom: none
+      padding-bottom: calc(1em + 12px)
+      margin-bottom: -13px
+      z-index: 10
     border: 1px solid #D4D4D5
-    &:hover
+    &:not(.active):hover
       border: 1px solid darken(#D4D4D5,30)
   dd
     font-size: 14px
@@ -113,6 +120,7 @@ dl.rbbt_tabs
     overflow-y: auto
     min-width: calc(100% - 16px)
     padding: 1em
+    background: white
 
     &:not(.show)
       +animation(shrink-up $jiffy forwards)

data/share/views/documented_section.haml

@@ -0,0 +1,10 @@
+.ui.very.basic.documented.segment
+
+  = yield
+
+  %a.ui.floating.teal.circular.help.label
+    %i.help.icon
+  .ui.very.basic.hidden.documentation
+    - require 'kramdown'
+    = Kramdown::Document.new(markdown).to_html
+

data/share/views/entity_partials/action_card.haml

@@ -1,50 +1,55 @@
-.action_card.ui.very.basic.segment
-  .title.ui.header
-    .name
-      - case page_type
-      - when 'entity_action'
-        = @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
+:sass
+  .action_card > .content
+    width: 100%
+    //& > .action_parameters, & > .action_content
+      width: 100%
+.action_card.ui.grid
+  .ui.basic.segment.content
+    .ui.header.basic.segment
+      %h1.name
+        - case page_type
+        - when 'entity_action'
+          = @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
+      %p.long_name
+        = Misc.humanize page_action if page_action
 
-  - if card.description
-    .action_description.ui.basic.segment
+    - if card.description
       - case card.description
       - when String
-        = card.description
+        %p= card.description
       - when Proc
         = capture_haml &card.description
       - else
         - raise "Unknown description: #{fff card.description}"
 
-  - if card.action_parameters
-    = action_parameters &card.action_parameters
+    - if card.action_parameters
+      = action_parameters &card.action_parameters
 
-  - exception_html = nil
-  - require_parameters = false
-  - card.requires.each do |input|
-    - if Array === input
-      - inputs, input_block = input
-      - if inputs.select{|input| @params[input.to_s].nil? }.any?
-        - require_parameters = true
-        - exception_html = capture_haml  &input_block
-        - break
+    - exception_html = nil
+    - require_parameters = false
+    - card.requires.each do |input|
+      - if Array === input
+        - inputs, input_block = input
+        - if inputs.select{|input| @params[input.to_s].nil? }.any?
+          - require_parameters = true
+          - exception_html = capture_haml  &input_block
+          - break
 
-    - else
-      - if @params[input.to_s].nil?
-        - require_parameters = true
-        - break
+      - else
+        - if @params[input.to_s].nil?
+          - require_parameters = true
+          - break
 
-  - if exception_html
-    = exception_html
+    - if exception_html
+      = exception_html
 
-  .action_content
-    - if require_parameters
-      %p Please configure the parameters to execute the action
-    - else
-      = capture_haml &block
+    .action_content
+      - if require_parameters
+        %p Please configure the parameters to execute the action
+      - else
+        = capture_haml &block
 

data/share/views/entity_partials/action_controller.haml

@@ -1,6 +1,6 @@
 - entity = controller.entity
 - if controller.actions.any?
-  .card_actions.ui.segment
+  .card_actions.ui.segment#entity_actions
     .action_controller
       .ui.buttons.controls
         %a.item.reload.ui.icon.disabled.button(href="#" title="Refresh action")

data/share/views/entity_partials/entity_card.haml

@@ -1,72 +1,91 @@
 - entity = card.entity
 - entity_id = "entity__" + entity.id
 - default = entity.respond_to?(:default)? entity.default || entity.to_s : entity.to_s
-.entity_card.ui.very.basic.segment(data-entity=entity data-entity-id=default data-entity-type="#{entity.base_type}" data-entity-format="#{entity.respond_to?(:format) ? entity.format : ""}" data-entity-info="#{entity.info.to_json}")
-  /-- title --
-  .ui.header.title
-    .name
-      - case card.name
-      - when nil
-        = entity.respond_to?(:name) ? entity.name || entity : entity
-      - when String
-        = card.name
-      - when Proc
-        = fragment :name, &card.name
 
-    .long_name
-      - case card.long_name
-      - when nil
-        = entity.respond_to?(:long_name) ? entity.long_name : nil
-      - when String
-        = card.long_name
-      - when Proc
-        = fragment :long_name, &card.long_name
+      
+.entity_card.ui.grid(data-entity=entity data-entity-id=default data-entity-type="#{entity.base_type}" data-entity-format="#{entity.respond_to?(:format) ? entity.format : ""}" data-entity-info="#{entity.info.to_json}")
+  /-- card_sidebar --
+  .ui.four.wide.column.vertical.card_sidebar.menu.hidden
+    - if card.sections.any?
+      %h3 Sections
+      - card.sections.each do |name,section|
+        %a.item(href="##{Misc.snake_case(name)}")= Misc.humanize(name)
+      %a.item(href="#entity_actions") Entity actions
 
-  .content
-    - info = entity.info.dup
-    - info.delete :annotated_array
-    - info.delete :annotation_types
+    - info = card.entity.info
     - if info.any? or card.meta or card.list_container
-      /-- sidebar --
-      .info.ui.compact.segment
-        .meta
-          - if info.any?
-            .entity_info
-              = hash2dl(info)
+      %h3 Meta data
+      .meta
+        - if info.any?
+          .entity_info
+            = hash2dl(info)
 
-          - case card.meta
-          - when nil
-          - when Hash
-            = hash2dl(card.meta)
-          - when Proc
-            = fragment :meta, &card.meta
+        - case card.meta
+        - when nil
+        - when Hash
+          = hash2dl(card.meta)
+        - when Proc
+          = fragment :meta, &card.meta
+
+    - if card.list_container
+      %h3 Related lists
+      .list_container
+        = list_container_render(card.list_container)
 
-          - if card.list_container
-            = list_container_render(card.list_container)
 
+  .ui.twelve.wide.column.content
+    .ui.header.basic.segment
+      .content
+        %h1.header.name
+          - case card.name
+          - when nil
+            = entity.respond_to?(:name) ? entity.name || entity : entity
+          - when String
+            = card.name
+          - when Proc
+            = fragment :name, &card.name
+        %p.long_name
+          - case card.long_name
+          - when nil
+            = entity.respond_to?(:long_name) ? entity.long_name : entity.base_type.to_s
+          - when String
+            = card.long_name
+          - when Proc
+            = fragment :long_name, &card.long_name
 
+    .ui.basic.segment.controls.buttons
+      .ui.icon.button.card_sidebar_open
+        %i.bars.icon
 
-    /-- content --
-    - case card.description
-    - when nil
-      - if entity.respond_to?(:description) and entity.description
+    .ui.basic.segment(id='description')
+      /-- content --
+      - case card.description
+      - when nil
+        - if entity.respond_to?(:description) and entity.description
+          /-- description --
+          .description.ui.very.basic.segment<
+            %p= entity.description
+      - when String
+        /-- description --
+        .description.ui.very.basic.segment<
+          :documentation
+            #{card.description}
+      - when Proc
         /-- description --
-        .description.ui.compact.basic.segment<
-          %p= entity.description
-    - when String
-      /-- description --
-      .description.ui.compact.basic.segment<
-        :documentation
-          #{card.description}
-    - when Proc
-      /-- description --
-      .description.ui.compact.basic.segment<
-        = fragment :description, &card.description
+        .description.ui.very.basic.segment<
+          = fragment :description, &card.description
+
+      - if defined? block and block
+        /-- description block --
+        .description.ui.basic.segment<
+          = capture_haml &block
 
-    - if defined? block and block
-      /-- content block --
-      .description.ui.compact.basic.segment<
-        = capture_haml &block
+      - card.sections.each do |name,section_block|
+        .ui.very.basic.segment(id="#{Misc.snake_case(name)}")
+          %h2.header
+            = Misc.humanize(name)
+          .content
+            = fragment name, &section_block
 
     - if card.action_controller
       /-- actions --

data/share/views/entity_partials/entity_list_card.haml

@@ -1,6 +1,113 @@
 - list = card.list
 - list_id = card.list_id
-.entity_list_card.ui.very.basic.segment(id="#{ list_id.gsub(/\s/,'_') }_card" data-list=list_id data-list-type="#{list.base_type}")
+
+.entity_list_card.ui.grid(id="#{ list_id.gsub(/\s/,'_') }_card" data-list=list_id data-list-type="#{list.base_type}")
+  .ui.four.wide.column.vertical.card_sidebar.menu.hidden
+    - if card.sections.any?
+      %h3 Sections
+      - card.sections.each do |name,section|
+        %a.item(href="##{Misc.snake_case(name)}")= Misc.humanize(name)
+
+    .list_management.ui.small.buttons.flex-wrap
+      %a.compare_list.ui.button(href="#" data-reveal-id='modal1') Compare
+      %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"}") As Name
+
+      - if list.respond_to? :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
+
+    - info = card.list.info
+    - if info.any? or card.meta or card.list_container
+      /-- sidebar --
+      %h3 Meta data
+      .meta
+        - if info.any?
+          .entity_info
+            = hash2dl(info)
+
+        - case card.meta
+        - when nil
+        - when Hash
+          = hash2dl(card.meta)
+        - when Proc
+          = fragment :meta, &card.meta
+
+    .entities
+      %h3 Entities
+      %p #{list.length} entities
+      - if (defined? force and force) or list.length < 500
+        %ul.entity_list.clean_list
+          - list = list.sort_by{|g| g.name || "Z" << g} if list.respond_to? :name
+          - list.link.each do |link|
+            %li= link
+      - else
+        %p
+          = 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.clean_list
+                - list.link.each do |link|
+                  %li= link
+ 
+    - if card.list_container
+      %h3 Related lists
+      .list_container
+        = list_container_render(card.list_container)
+
+  .ui.twelve.wide.column.content
+    .ui.header.basic.segment
+      .content
+        %h1.name
+          = Misc.humanize list_id
+        %p.type
+          = list.base_type
+          List
+
+    .ui.basic.segment.controls.buttons
+      .ui.icon.button.card_sidebar_open
+        %i.bars.icon
+
+    .ui.basic.segment(id='description')
+      /-- content --
+      - case card.description
+      - when nil
+        - if entity.respond_to?(:description) and entity.description
+          /-- description --
+          .description.ui.very.basic.segment<
+            %p= entity.description
+      - when String
+        /-- description --
+        .description.ui.very.basic.segment<
+          :documentation
+            #{card.description}
+      - when Proc
+        /-- description --
+        .description.ui.very.basic.segment<
+          = fragment :description, &card.description
+
+      - if defined? block and block
+        /-- description block --
+        .description.ui.basic.segment<
+          = capture_haml &block
+
+      - card.sections.each do |name,section_block|
+        .ui.very.basic.segment(id="#{Misc.snake_case(name)}")
+          %h2.header
+            = Misc.humanize(name)
+          .content
+            = fragment name, &section_block
+
+    - if card.action_controller
+      /-- actions --
+      = action_controller_render(card.action_controller)
+
+// LIIIIIIIIIII
+-#.entity_list_card.ui.very.basic.segment(id="#{ list_id.gsub(/\s/,'_') }_card" data-list=list_id data-list-type="#{list.base_type}")
 
   /-- title --
   .title.ui.header
@@ -78,3 +185,4 @@
     - if card.action_controller
       /-- actions --
       = action_controller_render(card.action_controller)
+