rbbt-rest 1.1.0

data/share/views/compass/topbar.sass

@@ -0,0 +1,19 @@
+#header
+  nav.top-bar
+    margin-bottom: 0 !important
+
+    li#top-add-favourite
+      cursor: pointer
+    li.search
+      width: auto
+      //@include grid-row(nest-collapse)
+      input, button
+        display: inline-block
+      input
+        width: 70%
+      button
+        width: 28%
+        left: -5px
+        @media #{$not_small}
+          top: 9
+      

data/share/views/compass/web-fonts.sass

@@ -0,0 +1,77 @@
+/*
+ * This is a fairly big mixin.
+ * The reason for this is that at the time of writing (09/01/2013),
+ * Sass does not include functions for substring or find/replace in string.
+ * Chris Eppstein sent a Pull Request to Sass with the str-extract (substring) function back in June,
+ * but it still has not been merged, due to lack of minor comments.
+ * That was five months ago.
+
+=web-font($fonts, $variants: (), $subsets: (), $text: "", $effects: ())
+  $url: "//fonts.googleapis.com/css?family="
+  $i: 0
+  // Add the family argument to the URL string.
+  // We can assume that the user will always specify at least one font.
+  @each $font in $fonts
+    $i: $i + 1
+    // Add the name of the font.
+    $j: 0
+    @each $word in $font
+      $j: $j + 1
+      $url: $url + $word
+      // Add a plus symbol between words.
+      @if $j < length($font)
+        $url: $url + "+"
+    // If there is/are font variant(s) for this font, add them.
+    @if $j <= length($variants)
+      $url: $url + ":"
+      $k: 0
+      @each $variant in nth($variants, $j)
+        $k: $k + 1
+        $url: $url + $variant
+        // Add a comma between variants.
+        // For some reason length($variant) doesn't work. Weird!
+        @if $k < length(nth($variants, $j))
+          $url: $url + ","
+    // Add a pipe between words.
+    // It would seem that a pipe isn't a valid URL character in its unescaped form,
+    // but Google reccommend using it anyway.
+    @if $i < length($fonts)
+      $url: $url + "|"
+  // Add the subset argument to the URL string, if it exists.
+  @if length($subsets) > 0
+    $url: $url + "&subset="
+    $i: 0
+    @each $subset in $subsets
+      $i: $i + 1
+      $url: $url + $subset
+      // Add a comma between subsets.
+      @if $i < length($subsets)
+        $url: $url + ","
+  // Add the text argument to the URL string, if it exists.
+  // $text does not actually need to be enclosed in brackets.
+  @if length($text) > 0 and $text != ""
+    // To save the user the hassle of adding a space character every time they want
+    // to use a web font, we add one automatically.
+    $url: $url + "&text=%20#{$text}"
+  // Add the effect argument to the URL string, if it exists.
+  @if length($effects) > 0
+    $url: $url + "&effect="
+    $i: 0
+    @each $effect in $effects
+      $i: $i + 1
+      // Add the name of the font.
+      $j: 0
+      @each $word in $effect
+        $j: $j + 1
+        $url: $url + $word
+        // Add a hyphen between words.
+        // A hyphen can actually be used to seperate words instead of a space,
+        // in which case the words will be counted as one and no extra hyphens will be added.
+        // Again, a string replacement function would make this a lot easier…
+        @if $j < length($effect)
+          $url: $url + "-"
+      // Add a pipe between effects.
+      @if $i < length($effects)
+        $url: $url + "|"
+  // Finally!
+  @import url(#{$url})

data/share/views/compass/workflow.sass

@@ -0,0 +1,33 @@
+
+.workflow_task
+  @include grid-row()
+
+  .title
+    @include grid-column(12)
+    @extend h4
+    span.workflow
+      font-weight: 600
+
+    span.task
+      font-weight: 300
+      font-size: 0.8em
+      color: lighter(#000, 20%)
+      margin-left: 2em
+
+  .form
+    @include grid-column(12)
+
+dd.job_control
+  ul
+    @include inline-list()
+    @include button-group-container()
+    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/Default.haml

@@ -0,0 +1,20 @@
+- entity_card = EntityCard.new entity
+- name = entity.respond_to?(:name)? entity.name || entity : entity
+
+- if not entity.respond_to?(:long_name)
+  - if entity.respond_to?(:name)
+    - entity_card.name = [entity.base_type, entity] * ": "
+  - else
+    - entity_card.name = entity.base_type
+  - entity_card.long_name = name
+
+- if entity.respond_to? :genes
+  - genes = entity.genes
+  - list_container = ListContainer.new
+  - list_container.add "Genes for #{[entity.base_type, name] * ": "}", genes
+  - entity_card.list_container = list_container
+
+- entity_card.action_controller = default_action_controller entity
+
+= entity_card_render entity_card
+

data/share/views/entity_list/Default.haml

@@ -0,0 +1,7 @@
+- entity_list_card = EntityListCard.new list, list_id
+
+- entity_list_card.action_controller = default_action_controller list, list_id
+
+= entity_list_card_render entity_list_card
+
+

data/share/views/entity_list/Default/edit.haml

@@ -0,0 +1,9 @@
+.edit_list(attr-entity_type="#{page_entity_type.split(":").first}")
+  = action_parameters do
+    - input :list_id, :string, "New list ID", "Copy of #{ list_id }"
+    - list.info.each do |key, value|
+      - next if key.to_sym == :annotation_types or key.to_sym == :annotated_array
+      - input key, :string, "Entity annotation #{ key }", value
+    - input :entities, :array, "Entities", list * "\n", :label => "entities"
+ 
+

data/share/views/entity_list/Default/new.haml

@@ -0,0 +1,9 @@
+.edit_list(attr-entity_type=entity_type)
+  = action_parameters do
+    - input :list_id, :string, "New list ID", list_id
+    - list.info.each do |key, value|
+      - next if key.to_sym == :annotation_types or key.to_sym == :annotated_array
+      - input key, :string, "Entity annotation #{ key }", value
+    - input :entities, :array, "Entities", list * "\n", :label => "entities"
+ 
+

data/share/views/entity_partials/action_card.haml

@@ -0,0 +1,38 @@
+.action_card
+  .title
+    .name
+      - case page_type
+      - when 'entity_action'
+        = @entity.respond_to?(:name) ? @entity.name || @entity : @entity
+      - when 'entity_list_action'
+        = Misc.humanize page_entity_list
+    .long_name
+      = Misc.humanize page_action if page_action
+
+  - 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
+
+    - else
+      - if @params[input.to_s].nil?
+        - require_parameters = true
+        - break
+
+  - if exception_html
+    = exception_html
+
+  .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

@@ -0,0 +1,31 @@
+- entity = controller.entity
+- if controller.actions.any?
+
+  .action_controller
+    %ul.controls
+
+      %li.reload
+        %a.reload_action(href="#")
+          %i.general.foundicon-refresh
+
+      %li.parameters
+        %a(href="#")
+          %i.general.foundicon-settings
+
+    %ul.actions
+      %li.select
+        %a(href="#")
+          %i.general.foundicon-plus
+
+      - 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
+            - id = params.delete :id if Hash === params
+            - id = controller.id if id.nil?
+            = entity.list_action_link action, text, id, params.merge(:reuse => true)
+          - else
+            = entity.action_link action, text, params
+        - last_resource = resource
+
+  .action_loader

data/share/views/entity_partials/entity_card.haml

@@ -0,0 +1,55 @@
+- entity = card.entity
+- entity_id = "entity__" + entity.id
+.entity_card(id=entity_id)
+  .title
+    .name
+      - case card.name
+      - when nil
+        = entity.respond_to?(:name) ? entity.name || entity : entity
+      - when String
+        = card.name
+      - when Proc
+        = capture_haml &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
+        = capture_haml &card.long_name
+
+  .card
+    .sidebar.offcanvas
+      .meta
+        .entity_info
+          - info = entity.info.dup
+          - info.delete :annotated_array
+          - info.delete :annotation_types
+          = hash2dl(info)
+        - case card.meta
+        - when nil
+        - when Hash
+          = hash2dl(card.meta)
+        - when Proc
+          = capture_haml &card.meta 
+        - if card.list_container
+          .entity_lists
+            = list_container_render(card.list_container)
+
+    .content
+      .description
+        - case card.description
+        - when nil
+          %p= entity.respond_to?(:description) ? entity.description : nil
+        - when String
+          %p= card.description
+        - when Proc
+          = capture_haml &card.description
+
+      - if card.action_controller
+        .actions
+          = action_controller_render(card.action_controller)
+
+

data/share/views/entity_partials/entity_list.haml

@@ -0,0 +1,8 @@
+
+- 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

data/share/views/entity_partials/entity_list_card.haml

@@ -0,0 +1,75 @@
+- list = card.list
+- list_id = card.list_id
+.entity_list_card(id="#{ list_id.gsub(/\s/,'_') }_card")
+
+  .title
+    .name
+      = list.base_type
+      List
+    .long_name
+      = Misc.humanize list_id
+
+  .card
+    .sidebar.offcanvas
+      .meta
+        .list_management
+
+          %ul
+
+            %li
+              %a.compare_list(href="#" data-reveal-id='modal1') Compare
+              %a.list_list(href="#{request.path_info + "?_format=list"}") List
+              - if list.respond_to? :name
+                %a.name_list(href="#{request.path_info + "?_format=name"}") Name
+              - 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
+
+        .entity_info
+          - info = list.info.dup
+          - info.delete :annotated_array
+          - info.delete :annotation_types
+          = hash2dl(info)
+        - case card.meta
+        - when nil
+        - when Hash
+          = hash2dl(card.meta)
+        - when Proc
+          = capture_haml &card.meta 
+
+        .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
+              - list.link.each do |link|
+                %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
+ 
+        - if card.list_container
+          .entity_lists
+            = list_container_render(card.list_container)
+
+    .content
+      .description
+        - case card.description
+        - when nil
+          - if list.length == list.uniq.length
+            %p== #{ list.length } elements
+          - else
+            %p== #{ list.length } elements (#{list.uniq.length} unique)
+        - when String
+          %p= card.description
+        - when Proc
+          = capture_haml &card.description
+
+      - if card.action_controller
+        .actions
+          = action_controller_render(card.action_controller)
+

data/share/views/entity_partials/list_container.haml

@@ -0,0 +1,30 @@
+%dl.list_container
+  - 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
+          = 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 * ", "

data/share/views/error.haml

@@ -0,0 +1,12 @@
+.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