rbbt-rest 1.6.13 → 1.6.14

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: 1cad835d033ab9fca42bd52a27122111995dd683
-  data.tar.gz: f70095e18c441c99cf03aaa6e91cdc7759957243
+  metadata.gz: 96f5e042d8f089b55dcbd883dd14ccbad0820d80
+  data.tar.gz: 0ab035fcfdf2838540047d8943c03ad0aa03ea6e
 SHA512:
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-  data.tar.gz: 19169e9f980ad14a8e38c267465fc27b22628b23e8a8ab1b730fb9d58b2ca5a3d96099f0ee1dafff7f35da2ce56d73436b1eb1b4c9aad146c5f391b2323f7c0c
+  metadata.gz: f7a7be6a47e7b15131ac8abaf3cd303d00f5d77c791321f68ac54d1af6c1299b865793c93964fc0ead18bc9d3021cadcac9572d8d20e436cc6e4c470c6e6dd0c
+  data.tar.gz: ad2e577ef5ecd4e50f08512784311395e62b9767d0c765cb91fc83f59efb4e7cab1de7d3b59e83ee1d1eed06762c59c4ac7a5cdac712b71a0d11332a77ac2844

data/lib/rbbt/rest/common/misc.rb

@@ -279,3 +279,4 @@ module Haml::Filters::Documentation
   end
 
 end
+

data/lib/rbbt/rest/main.rb

@@ -1,6 +1,7 @@
 require 'rbbt/rest/common/locate'
 require 'rbbt/rest/common/resources'
 require 'rbbt/rest/common/users'
+require 'rbbt/rest/common/misc'
 require 'ruby-prof'
 
 require 'sinatra/base'
@@ -13,11 +14,12 @@ module Sinatra
     def self.add_resource_path(path, priority_templates = false)
       Log.low "Adding resource path: #{Misc.fingerprint path}"
       KnowledgeBaseRESTHelpers.association_resources.unshift path
-      EntityRESTHelpers.entity_resources.unshift path
 
       if priority_templates
+        EntityRESTHelpers.entity_resources.unshift path if defined? EntityRESTHelpers
         RbbtRESTHelpers.template_resources.unshift path 
       else
+        EntityRESTHelpers.entity_resources.push path if defined? EntityRESTHelpers
         RbbtRESTHelpers.template_resources.push path 
       end
 

data/lib/rbbt/rest/workflow.rb

@@ -20,11 +20,11 @@ module Sinatra
     WORKFLOWS = []
 
 
-    def add_workflow_resource(workflow, add_templates = false)
+    def add_workflow_resource(workflow, priority_templates = false)
       views_dir = workflow.respond_to?(:libdir)? workflow.libdir.www.views.find(:lib) : nil
       if views_dir and views_dir.exists?
-        Log.debug "Registering views for #{ workflow }: #{ views_dir.find }"
-        RbbtRESTMain.add_resource_path(views_dir, add_templates)
+        Log.debug "Registering views for #{ workflow }: #{ views_dir.find } - priority #{priority_templates}"
+        RbbtRESTMain.add_resource_path(views_dir, priority_templates)
       end
     end
 
@@ -34,7 +34,7 @@ module Sinatra
 
       Log.debug "Adding #{ workflow } to REST server" 
 
-      add_workflow_resource(workflow, add_resource == :all) if add_resource
+      add_workflow_resource(workflow, add_resource == :priority) if add_resource
       workflow.documentation
 
 

data/lib/rbbt/rest/workflow/jobs.rb

@@ -108,7 +108,8 @@ module WorkflowRESTHelpers
       halt 200, tsv2html(job.path, :url => "/" << [workflow.to_s, task, job.name] * "/")
     when :entities
       tsv = tsv_process(load_tsv(job.path).first)
-      list = tsv.values.flatten
+      list = tsv.column_values(tsv.fields.first).flatten
+      iif list
       if not AnnotatedArray === list and Annotated === list.first
         list.first.annotate list 
         list.extend AnnotatedArray

data/share/views/compass/app.sass

@@ -10,8 +10,12 @@
 
 $subtle-font: rgba(0,0,0,0.30)
 
+body
+  background: none repeat scroll 0% 0% #F7F7F7
+
 #content
   padding: 64px 16px 0 32px
+  width: 100%
 
 #top_menu
   z-index: 100
@@ -113,9 +117,6 @@ $subtle-font: rgba(0,0,0,0.30)
 @media #{$not-large}
   +small_screen
 
-#modal
-  +small_screen
-
 .action_parameters, .filter_controls
   form
     &:after
@@ -294,7 +295,9 @@ span.bullet
   &.green
     color: green
   &+a
-    margin-left: 2em
+    color: red
+    font-style:italic
+    margin-left: 2em !important
     padding-left: 0em
     width: calc(100% - 2em) !important
 
@@ -312,3 +315,11 @@ label[title]
 
 .examples
   clear: both
+
+#modal
+  +small_screen
+  .ui.icon.button.close
+    float: right
+  &.error
+    .header
+      color: red

data/share/views/layout.haml

@@ -16,8 +16,7 @@
 
   /{{{ TOP MENU
   /------------
-  #top_menu.main.ui.menu.fixed
-    = partial_render('layout/top_menu')
+  = partial_render('layout/top_menu')
 
   /{{{ CONTENT
   /-----------

data/share/views/layout/coda.haml

@@ -11,8 +11,6 @@
 
   var known_types = #{Entity::REST::REST_ENTITIES.collect{|m| m.to_s}.to_json}
 
-  if (user != 'none') fav_module.update()
-
   function gene_name(name){
     return new Entity({type: "Gene", id: name, name: name, format: "Associated Gene Name", info: { organism: "Hsa/feb2014" }})
   }

data/share/views/layout/footer.haml

@@ -1,6 +1,8 @@
 :sass
 
   #footer
+    clear: both
+
     border: none !important
     padding: 0px !important
     margin: 0px !important
@@ -15,16 +17,27 @@
         content: " at "
     .image 
       font-size: 0px
-      img
-        width: 100%
+      width: 241px 
+    .content
+      width: calc(100% - 241px -8px)
     .image, .content
-      float: left
-.ui.card
+      //float: left
+      display: inline-block
+      margin-left: 8px
+
+    .ui.segment
+      &:after
+        content: " "
+        display:inline-block
+        float:left
+        clear:both
+
+.ui.segment
   .image
-    %a.image(href="http://www.cnio.es/")
-      %img(src="http://www.cnio.es/img/comunes/header/cnio.gif")
+    %a(href="http://www.cnio.es/")
+      %img(src="http://www.cnio.es/img/comunes/header/cnio.gif" height='115px' width='241px')
   .content
-    .header
+    .ui.header
       CNIO. Centro Nacional de Investigaciones Oncologicas (Spanish National Cancer Research Center)
     .description
       %br/

data/share/views/layout/header.haml

@@ -10,11 +10,8 @@
 
 
 - record_css '/plugins/semantic-ui/dist/semantic.min.css'
-
-- record_css '/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css'
-
+-# record_css '/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css'
 - record_css '/stylesheets/app'
-
 = serve_css
 
 // Third party frameworks
@@ -48,13 +45,11 @@
 - %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 }"
-
-- %w(dom_update workflow fragment menu favourites page_type modal reveal actions table list map hide).each do |file|
+-# %w(dom_update workflow fragment menu favourites page_type modal reveal actions table list map hide).each do |file|
+- %w(dom_update fragment actions table list map reveal).each do |file|
   - record_js "/js-find/rbbt/#{ file }"
 
-- %w(rbbt rbbt.basic rbbt.job rbbt.page rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.knowledge_base rbbt.aesthetics rbbt.modal).each do |file|
+- %w(rbbt rbbt.basic rbbt.exception rbbt.job rbbt.page rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.knowledge_base rbbt.aesthetics rbbt.modal).each do |file|
   - record_js "/js-find/#{ file }"
 
 - record_js "/js-find/app"

data/share/views/layout/top_menu.haml

@@ -1,32 +1,44 @@
-%a.title.item(href='/')= $title
-
-%span.favourite
-
-%a.item.reload.right(href='#')
-  %i.icon.repeat
-
-%a.item.login.right(href='/login')
-  %i.icon.user
-  - if user
-    = user
-
-%a.item.right(href='/help') Help
-
-- 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
-
-  - expoted_workflows.compact!
-  - if expoted_workflows.any?
-    .ui.dropdown.item.right
-      %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')
+:sass
+  #top_menu
+    & > .dropdown
+      display: inline-block !important
+      min-width: 10em
+    & > .favourite > .dropdown, & > .favourite > .item.pointer
+      display: inline-block !important
+    .favourite
+      width: 100%
+#top_menu.ui.fixed.menu
+  %a.header.item(href='/')= $title
+
+  %span.favourite
+
+
+  - 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
+
+    - expoted_workflows.compact!
+    - if expoted_workflows.any?
+      .ui.dropdown.item.right
+        %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')
+
+  %a.item.login.right(href='/login')
+    %i.icon.user
+    - if user
+      = user
+
+  %a.item.right(href='/help') Help
+
+  %a.item.reload(href='#')
+    %i.icon.repeat
+

data/share/views/public/js/app.js

@@ -1,22 +1,23 @@
 function fit_content(){
  var height = window.innerHeight - $('footer').outerHeight(true);
- $('#content').css('min-height', height)
+ var top_offset = $('#content').get()[0].offsetTop
+ $('#content').css('min-height', height - top_offset)
  $('#top_menu dl.rbbt_menu').css('max-height', height - 100)
 }
 
 function update_rbbt(){
  update_dom()
 
- $('.rbbt_reveal_trigger').reveal()
  $('table').table()
- //$('table.tablesorter').tablesorter()
- $('body > #modal').modal()
  $('.action_controller').action_controller()
- $('#top_menu .favourites').favourites('update_list_selects').favourites('update_map_selects')
- $('#top_bar .favourites').favourites('update_list_selects').favourites('update_map_selects')
-
  $('.ui.accordion').accordion();
  $('.ui.checkbox').checkbox();
+
+ $('.rbbt_reveal_trigger').reveal()
+ //$('table.tablesorter').tablesorter()
+ //$('body > #modal').modal()
+ //$('#top_menu .favourites').favourites('update_list_selects').favourites('update_map_selects')
+ //$('#top_bar .favourites').favourites('update_list_selects').favourites('update_map_selects')
  //$('select:not(.favourite_lists)').dropdown();
  //$('.selection.dropdown').find('.item:not([data-value])').removeClass('item').addClass('header');
 
@@ -24,8 +25,6 @@ function update_rbbt(){
  fit_content()
  $('.preload').removeClass('preload');
 
- if (undefined !== rbbt.favourites && user != 'none') rbbt.favourites.update()
-
  if (undefined !== rbbt.aesthetics){
    rbbt.aesthetics.load()
    rbbt.aesthetics.apply()
@@ -57,7 +56,7 @@ $(function(){
   })
  })
 
- $('#top_menu .favourites').favourites()
+ if (undefined !== rbbt.favourites && user != 'none') rbbt.favourites.update()
 
  update_rbbt()
 })

data/share/views/public/js/defer.js

@@ -17,7 +17,7 @@ function start_deferred(){
     if (typeof(func) == 'object'){
       require_js(func[0], func[1]);
     }else{
-      func.call();
+      rbbt.try(func).call()
     }
   })
   deferred_execution = [];

data/share/views/public/js/helpers.js

@@ -123,3 +123,17 @@ function uniqBy(ary, key) {
   return (seen[k] === 1) ? 0 : seen[k] = 1;
  })
 }
+
+
+function unique(arrayName) {
+  var newArray=new Array();
+  label:for(var i=0; i<arrayName.length;i++ ){  
+    for(var j=0; j<newArray.length;j++ ){ 
+    if(newArray[j]==arrayName[i]) 
+      continue label;
+    }
+    newArray[newArray.length] = arrayName[i];
+  }
+  return newArray;
+}
+

data/share/views/public/js/rbbt.aesthetics.js

@@ -54,6 +54,3 @@ aes_module.apply = function(aesthetic){
 }
 
 aes_module.load()
-//aes_module.add(Object.keys(fav_module.entities.types()["Gene"]), 'color', 'red')
-//aes_module.store()
-//aes_module.apply()

data/share/views/public/js/rbbt.exception.js

@@ -0,0 +1,21 @@
+rbbt.exception = {}
+
+rbbt.exception.null = function(variable, text){
+  if (variable == null) throw(text)
+}
+
+rbbt.exception.report = function(err){
+  rbbt.modal.controller().error(err, "Application Error")
+}
+
+rbbt.try = function(func){
+  var f = function(){
+    try {
+      return func.apply(this, arguments)
+    }catch(err){
+      rbbt.exception.report(err)
+    }
+  }
+  return f
+}
+

data/share/views/public/js/rbbt.favourites.js

@@ -37,6 +37,8 @@ fav_module.isFavourite_map = function(map){
 
 fav_module.toggleFavourite_entity = function(){
  var entity = rbbt.page.entity();
+ console.log(entity)
+ console.log(entity.code)
 
  if (fav_module.isFavourite_entity(entity)){
   rbbt.post({url: '/remove_favourite_entity/' + entity.type + '/' + clean_element(entity.code)}).then(fav_module.update)
@@ -86,11 +88,11 @@ fav_module.star_view = function(){
    if (! rbbt.page.map())
     return
    else
-    return m('i.icon.star', {class: (fav_module.isFavourite_map(rbbt.page.map()) ? 'favourite' : 'not_favourite')})
+    return m('.item.pointer', {onclick: fav_module.toggleFavourite},  m('i.icon.star', {class: (fav_module.isFavourite_map(rbbt.page.map()) ? 'favourite' : 'not_favourite')}))
   else
-   return m('i.icon.star', {class: (fav_module.isFavourite_list(rbbt.page.list()) ? 'favourite' : 'not_favourite')})
+   return m('.item.pointer', {onclick: fav_module.toggleFavourite}, m('i.icon.star', {class: (fav_module.isFavourite_list(rbbt.page.list()) ? 'favourite' : 'not_favourite')}))
  else
-  return m('i.icon.star', {class: (fav_module.isFavourite_entity(rbbt.page.entity()) ? 'favourite' : 'not_favourite')})
+  return m('.item.pointer', {onclick: fav_module.toggleFavourite}, m('i.icon.star', {class: (fav_module.isFavourite_entity(rbbt.page.entity()) ? 'favourite' : 'not_favourite')}))
 }
 
 fav_module.draw_favourite_menu = function(){
@@ -102,11 +104,13 @@ fav_module.draw_favourite_menu = function(){
              var _type = favourites[type]
              var entities = Object.keys(_type)
 
-             return m('.ui.dropdown.item', [
-               m('i.icon.dropdown'), 
-               type,
-               m('.menu', entities.map(function(entity, index){ url = _type[entity].url(); return m('a.item', {href: url}, _type[entity].name) }))
-             ]);
+             var type_items = entities.map(function(entity, index){ url = _type[entity].url(); return m('a.item', {href: url}, _type[entity].name) })
+             return rbbt.mview.dropdown(type, type_items)
+             //return m('.ui.dropdown.item', [
+             //  m('i.icon.dropdown'), 
+             //  type,
+             //  m('.menu', entities.map(function(entity, index){ url = _type[entity].url(); return m('a.item', {href: url}, _type[entity].name) }))
+             //]);
            })))
 }
 
@@ -157,11 +161,17 @@ fav_module.draw_favourite_map_menu = function(){
 }
 
 fav_module.view = function(){
-  m.render($('#top_menu > .favourite')[0], [
-    m('.item.pointer', {onclick: fav_module.toggleFavourite}, fav_module.star_view()), 
-    m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_menu()),
-    m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_list_menu()),
-    m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_map_menu())
+  //m.render($('#top_menu .favourite')[0], [
+  //  m('.item.pointer', {onclick: fav_module.toggleFavourite}, fav_module.star_view()), 
+  //  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_menu()),
+  //  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_list_menu()),
+  //  m('.item', {style: 'padding: 0px'}, fav_module.draw_favourite_map_menu())
+  //])
+  m.render($('#top_menu .favourite')[0], [
+    fav_module.star_view(), 
+    fav_module.draw_favourite_menu(),
+    fav_module.draw_favourite_list_menu(),
+    fav_module.draw_favourite_map_menu()
   ])
 }
 
@@ -261,7 +271,7 @@ fav_module.highlight = function(){
 }
 
 fav_module.new_list = function(type){
-  rbbt.modal.controller.show_url('/entity_list/' + type + '/new/?_layout=false')
+  rbbt.modal.controller.show_url('/entity_list/' + type + '/new/?_layout=false', "New " + type + " list")
 }
 
 fav_module.hooks = function(){