rbbt-rest 1.6.2 → 1.6.3

data/share/views/entity_partials/entity_map_card.haml

@@ -1,62 +1,54 @@
 - map = card.map
 - map_id = card.map_id
-.entity_map_card(id="#{ map_id.gsub(/\s/,'_') }_card")
+.entity_map_card.very.basic.ui.segment(id="#{ map_id.gsub(/\s/,'_') }_card" data-map=map_id data-type=page_entity_base_type data-column=page_entity_map_column)
 
-  .title
+  .title.ui.header
     .name
       = map.key_field
       Map
     .long_name
       = Misc.humanize map_id
 
-  .card
+  .content
 
-    .sidebar.offcanvas.show
+    .info.ui.compact.segment
       .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, :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}
+        .map_management.ui.buttons
+          = reveal "Rename", nil, :class => 'ui small button' 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/,'')
+            - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
+            %a.ui.small.button(href=url) Pvalue score
+
+          - if Gene == Entity.formats[map.key_field]
+            - if map.key_field != "Ensembl Gene ID"
+              - url = add_GET_param(@fullpath, '_format', 'ensembl')
+              %a.ensembl.ui.small.button(href=url) Ensembl
+            - if map.key_field != "Associated Gene Name"
+              - url = add_GET_param(@fullpath, '_format', 'name')
+              %a.name.ui.small.button(href=url) Name
+          - if "Rank" == map.fields.first
+            - url = add_GET_param(@fullpath, '_format', 'invert_ranks')
+            %a.invert_ranks.ui.small.button(href=url) Invert ranks
+          - else
+            - url = add_GET_param(@fullpath, '_format', 'ranks')
+            %a.ranks.ui.small.button(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)
+            - $page_entity_base_type = page_entity_base_type 
+            - $page_entity_map_column = page_entity_map_column 
+            = reveal :rank_products, nil, :title => "Rank Product", :class => 'ui small button' 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
+        = table :class => 'ui collapsing table' do
           - map
       - if card.action_controller
         .actions

data/share/views/entity_partials/list_container.haml

@@ -1,15 +1,15 @@
-%dl.rbbt_accordion
+.entity_list.ui.styled.accordion
   - container.lists.each do |id, list, text, options|
     - if Proc === list
       = fragment do
         - list = list.call
         - next if list.nil?
-        %dt.next
+        .title
           = list.respond_to?(:list_link) ? list.list_link(:length, id) : list.length
           %span.title
             - title = text || id 
             = title.sub('--', '—').sub('->', '⇨')
-        %dd
+        .content 
           - if (defined? force and force) or list.length < 500
             - if list.respond_to? :link
               = list.link * ", "
@@ -23,18 +23,18 @@
                 = list * ", "
     - else
       - if list.empty?
-        %dt
+        .title
           = 0
           %span.title
             - title = text || id 
             = title.sub('--', '&#8212;').sub('->', '&#8680;')
       - else
-        %dt.next
+        .title
           = list.respond_to?(:list_link) ? list.list_link(:length, id) : list.length
           %span.title
             - title = text || id 
             = title.sub('--', '&#8212;').sub('->', '&#8680;')
-        %dd
+        .content
           - if (defined? force and force) or list.length < 500
             - if list.respond_to? :link
               = list.link * ", "

data/share/views/layout.haml

@@ -1,78 +1,34 @@
-!!!
-/ paulirish.com/2008/conditional-stylesheets-vs-css-hacks-answer-neither/
-/[if lt IE 7 ] <html class=\"ie6\" lang=\"en\">
-/[if IE 7 ]    <html class=\"ie7\" lang=\"en\">
-/[if IE 8 ]    <html class=\"ie8\" lang=\"en\">
-/[if IE 9 ]    <html class=\"ie9\" lang=\"en\">
-/[if (gt IE 9)|!(IE)] <!--> <html lang=\"en\">
+= partial_render('layout/doctype')
 
 %head
-  %meta{ :charset => "utf-8" }/
+  = partial_render('layout/header')
 
-  %meta(name="viewport" content="width=device-width, initial-scale=1.0")
+:sass
 
-  %link{:rel => "icon", :type => "image/gif", :href => "/favicon.gif"}/
-
-  %title= $title
-  
-  // Semantic-ui
-
-  - record_css '/stylesheets/app'
-
-  - record_css '/plugins/foundation-icons/foundation-icons.css'
-  - record_css '/plugins/semantic-ui/dist/semantic.min.css'
-
-  - record_css '/stylesheets/layout'
-  - record_css '/stylesheets/layout'
-  - record_css '/stylesheets/responsive'
-  - record_css '/stylesheets/text'
-  - record_css '/stylesheets/cards'
-  - record_css '/stylesheets/elements'
-  - record_css '/stylesheets/menu'
-  - record_css '/stylesheets/color'
-
-  = serve_css
-
-  // Third party frameworks
-
-  - record_js '/js/defer'
-  - record_js "/plugins/underscore/js/underscore.js"
-
-  = serve_js
-
-  - %w(jquery-2.1.1 jquery.cookie jquery.form).each do |jquery_file|
-    - record_js File.join('/plugins/jquery/js/', jquery_file)
-
-  - record_js '/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js'
-  - record_js '/plugins/jquery.tablesorter/jquery.tablesorter.min.js'
-  - record_js '/plugins/jquery.scrollTo/jquery.scrollTo'
-  - record_js '/plugins/semantic-ui/dist/semantic.min.js'
-
-  - %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
-    - record_js "/js-find/#{ file }"
-
-  - %w(dom_update workflow fragment menu favourites page_type modal reveal actions table list map hide).each do |file|
-    - record_js "/js-find/rbbt/#{ file }"
-
-  - record_js "/js-find/app"
+  .favourite 
+    > .item:empty
+      display: none
+    .dropdown.item  .dropdown.item
+      i.icon.dropdown
+        margin-right: -10px !important
 
 %body.preload
 
   /{{{ TOP MENU
   /------------
-  #top_menu
+  #top_menu.main.ui.menu.fixed
     = partial_render('layout/top_menu')
 
-  /{{{ MODAL
-  /---------
-  #modal
-
   /{{{ CONTENT
   /-----------
-  #content
+  #content.ui.main.container.top.attached
     - @reload_page = false
     = yield
 
+  /{{{ MODAL
+  /---------
+  #modal.ui.modal
+
   /{{{ FOOTER
   /----------
   #footer
@@ -81,4 +37,42 @@
   /{{{ CODA
   /--------
   #coda
+    = link_js "http://cdnjs.cloudflare.com/ajax/libs/mithril/0.1.28/mithril.min.js"
+    -# ["/js-find/rbbt", "/js-find/rbbt.page", "/js-find/rbbt.entity", "/js-find/rbbt.entity_list", "/js-find/rbbt.knowledge_base", "/js-find/rbbt.favourites"].each do |file|
+      - record_js file
     =partial_render('layout/coda')
+  
+
+  :deferjs
+    function gene_name(name){
+      return new Entity({type: "Gene", id: name, name: name, format: "Associated Gene Name", info: { organism: "Hsa/feb2014" }})
+    }
+
+    function entity_link(entity){
+      return m('a', {href: entity.url()}, entity.name)
+    }
+
+    function entity_item(entity){
+      return m('li', entity_link(entity))
+    }
+
+    function entity_list(list){
+      return m('ul.entity_list', list.map(entity_item))
+    }
+
+    function draw_entity_list(list){
+      var content_elem = $('#content')[0]
+      var content = [m("p", {style: 'padding: 3em'}, entity_list(list))]
+      return m.render(content_elem, content)
+    }
+
+    function debug(name){
+      gene = gene_name(name)
+      gene.children("tfacts@genomics").then(draw_entity_list)
+      gene.parents("tfacts@genomics").then(draw_entity_list)
+    }
+
+    require_js(["/js-find/rbbt", "/js-find/rbbt.entity", "/js-find/rbbt.entity_list", "/js-find/rbbt.entity_map", "/js-find/rbbt.knowledge_base", "/js-find/rbbt.page", "/js-find/rbbt.aesthetics", "/js-find/rbbt.favourites"], function(){
+      //debug("TP53")
+    })
+

data/share/views/layout/coda.haml

@@ -1,3 +1,4 @@
+= link_js "http://cdnjs.cloudflare.com/ajax/libs/mithril/0.1.28/mithril.min.js"
 = serve_js
 :javascript
   var main_url = window.location.toString();

data/share/views/layout/doctype.haml

@@ -0,0 +1,8 @@
+!!!
+/ paulirish.com/2008/conditional-stylesheets-vs-css-hacks-answer-neither/
+/[if lt IE 7 ] <html class=\"ie6\" lang=\"en\">
+/[if IE 7 ]    <html class=\"ie7\" lang=\"en\">
+/[if IE 8 ]    <html class=\"ie8\" lang=\"en\">
+/[if IE 9 ]    <html class=\"ie9\" lang=\"en\">
+/[if (gt IE 9)|!(IE)] <!--> <html lang=\"en\">
+

data/share/views/layout/footer.haml

@@ -1,10 +1,36 @@
-.logo
-  %a.image(href="http://www.cnio.es/")
-    %img(src="http://www.cnio.es/img/comunes/header/cnio.gif")
-.address
-  %span.center CNIO. Centro Nacional de Investigaciones Oncologicas (Spanish National Cancer Research Center)
-  %span.group Structural Computational Biology Group
-  %span.address   C/ Melchor Fernandez Almagro, 3, E-28029 Madrid
-.contact
-  %span.who miguel.vazquez
-  %span.where cnio.es
+:sass
+
+  #footer
+    border: none !important
+    padding: 0px !important
+    margin: 0px !important
+    .card
+      width: 100%
+      height: 100%
+    .contact
+      &:before
+        content: "Contact: "
+        font-weight: bold
+      span.where:before
+        content: " at "
+    .image 
+      font-size: 0px
+      img
+        width: 100%
+    .image, .content
+      float: left
+.ui.card
+  .image
+    %a.image(href="http://www.cnio.es/")
+      %img(src="http://www.cnio.es/img/comunes/header/cnio.gif")
+  .content
+    .header
+      CNIO. Centro Nacional de Investigaciones Oncologicas (Spanish National Cancer Research Center)
+    .description
+      %br/
+      %span.group Structural Computational Biology Group
+      %br/
+      %span.address   C/ Melchor Fernandez Almagro, 3, E-28029 Madrid
+    .meta.contact
+      %span.who miguel.vazquez
+      %span.where cnio.es

data/share/views/layout/header.haml

@@ -0,0 +1,47 @@
+%meta{ :charset => "utf-8" }/
+
+%meta(name="viewport" content="width=device-width, initial-scale=1.0")
+
+%link{:rel => "icon", :type => "image/gif", :href => "/favicon.gif"}/
+
+%title= $title
+
+// Semantic-ui
+
+-# record_css '/stylesheets/app'
+
+-# record_css '/plugins/foundation-icons/foundation-icons.css'
+- record_css '/plugins/semantic-ui/dist/semantic.min.css'
+
+-# record_css '/stylesheets/layout'
+-# record_css '/stylesheets/responsive'
+-# record_css '/stylesheets/text'
+-# record_css '/stylesheets/cards'
+-# record_css '/stylesheets/elements'
+-# record_css '/stylesheets/menu'
+-# record_css '/stylesheets/color'
+
+= serve_css
+
+// Third party frameworks
+
+- record_js '/js/defer'
+- record_js "/plugins/underscore/js/underscore.js"
+
+= serve_js
+
+- %w(jquery-2.1.1 jquery.cookie jquery.form).each do |jquery_file|
+  - record_js File.join('/plugins/jquery/js/', jquery_file)
+
+- record_js '/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js'
+- record_js '/plugins/jquery.tablesorter/jquery.tablesorter.min.js'
+- record_js '/plugins/jquery.scrollTo/jquery.scrollTo'
+- record_js '/plugins/semantic-ui/dist/semantic.min.js'
+
+- %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
+  - record_js "/js-find/#{ file }"
+
+- %w(dom_update workflow fragment menu favourites page_type modal reveal actions table list map hide).each do |file|
+  - record_js "/js-find/rbbt/#{ file }"
+
+- record_js "/js-find/app"

data/share/views/layout/top_menu.haml

@@ -1,20 +1,34 @@
-.title
-  %a(href='/')= $title
+%a.title.item(href='/')= $title
 
-.reload
-  %i.general.fi-refresh
+%span.favourite
 
-.container
+%a.item.reload.right(href='#')
+  %i.icon.repeat
 
+%a.item.login.right(href='/login')
+  %i.icon.user
+  - if user
+    = user
 
-- if user
-  .favourites.hide(hide-title="Favs")
-    = partial_render('layout/top_menu/favourites')
+%a.item.right(href='/help') Help
 
-.user.hide(hide-title="User")
-  = partial_render('layout/top_menu/user')
+- if defined? Sinatra::RbbtRESTWorkflow and Sinatra::RbbtRESTWorkflow::WORKFLOWS
+  - expoted_workflows = Sinatra::RbbtRESTWorkflow::WORKFLOWS.collect do |workflow|
+    - next if workflow.asynchronous_exports.empty? and workflow.synchronous_exports.empty? and workflow.exec_exports.empty?
+    - workflow
 
-- if settings.respond_to?(:finder) and settings.finder and settings.finder.instances.any?
-  .find.hide(hide-title="Find")
-    = partial_render('layout/top_menu/finder')
+  - expoted_workflows.compact!
+  - if expoted_workflows.any?
+    .item.right(style='padding:0px')
+      .ui.menu
+        .ui.dropdown.item
+          %i.icon.dropdown
+          Workflows
+          .menu
+            - expoted_workflows.each do |workflow|
+              %a.item(href='#{'/' + workflow.to_s}')= workflow.to_s
 
+- if settings.respond_to?(:finder) and settings.finder and settings.finder.instances.any?
+  .finder.right.item
+    %form.collapse(action='/find' method="POST")
+      %input(type="search" name="term" placeholder='Search')

data/share/views/partials/form.haml

@@ -12,7 +12,7 @@
     =description
   %hr
 
-%form(class=klass action=action method=method id=id enctype=enctype)
+%form.ui.form(class=klass action=action method=method id=id enctype=enctype)
 
   - inputs       = consume_parameter(:inputs, info) || []
   - types        = consume_parameter(:input_types, info) || {}
@@ -24,14 +24,14 @@
   - inputs.each do |input|
     - input_id = id.nil? ? nil : id + "__" << input.to_s
     - hide = (options[input] != nil and options[input][:hide])
-    %div(class="input #{types[input]} #{input} #{hide ? 'hide' : ''}")
+    %div(class="input field #{types[input]} #{input} #{hide ? 'hide' : ''}")
       - input_options = options[input]
       - input_options = input_options.dup unless input_options.nil?
       != form_input(input, types[input], defaults[input], values[input], descriptions[input], input_id, input_options)
 
 
-  .input.submit
-    %input(type="submit")
+  .input.field.submit
+    %input.ui.submit.button(type="submit")
     - if klass =~ /workflow_task/
       %input.jobname(type='text' name='jobname' placeholder='optional job name')
       %select.format(name="_format")