rbbt-rest 1.6.8 → 1.6.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 07494c877ee9a075de3fce9b8aef3eb6dcc3e656
-  data.tar.gz: a1c87e5660c3a48564a4f370674df4e8115e37a6
+  metadata.gz: 05c447d083fa7c7d20eb9ec6b35fd40def102fac
+  data.tar.gz: 223225ff89f70995dc1f0adef68da27519513630
 SHA512:
-  metadata.gz: cb8234dbc93b45f713bc20988a50c613e317b2d7356be78dbd9b0ee7c5c0034d00985dace331c8b53b54350e2734d53f67d28b699e5d68d04a34e0fa621f96f5
-  data.tar.gz: d56098eb977c566fa52734ae424944f4e23c3071fe9beb2f91bb8ab3f3279f97dabd499d1ba73f5b684be85ea47803fe01981500ca2a93e97722099dece7774f
+  metadata.gz: 45eb8f221717d239d99e2d55b8952c02c13e16a973d7a2e1fb2a2cd9ea90f95bad7fb7f86e7f2930717d1742742e52be5f4a0f768d487cda3de6c870f760bdb9
+  data.tar.gz: 80ca57f493f3d6460053c4a5f775658b6d7bac446c8b95a3023b7d7451e070d234e3c4077ad7012f7f3eec5c2cd40b106ccb0ce5351d7410eee19044c5ab8fde

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

@@ -160,17 +160,23 @@ module RbbtRESTHelpers
 
         else
           # check for problems
-          if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
-            Log.debug{ "Checking on #{step.info_file}" }
-            running = (not step.done?) and step.running?
-            if FalseClass === running
-              Log.debug{ "Aborting zombie #{step.info_file}" }
-              step.abort unless step.done?
-              raise RbbtRESTHelpers::Retry
-            end
-            FileUtils.touch(step.info_file)
+          begin
+            check_step step
+          rescue Aborted
+            raise RbbtRESTHelpers::Retry
           end
 
+          #if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
+          #  Log.debug{ "Checking on #{step.info_file}" }
+          #  running = (not step.done?) and step.running?
+          #  if FalseClass === running
+          #    Log.debug{ "Aborting zombie #{step.info_file}" }
+          #    step.abort unless step.done?
+          #    raise RbbtRESTHelpers::Retry
+          #  end
+          #  FileUtils.touch(step.info_file)
+          #end
+
           wait_on step, false
         end
       end

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

@@ -3,6 +3,23 @@ require 'rbbt/util/misc'
 module RbbtRESTHelpers
   class Retry < Exception; end
 
+  def check_step(step)
+    if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
+      Log.debug{ "Checking on #{step.info_file}" }
+      running = (not step.done?) and step.running?
+      if FalseClass === running
+        if step.done?
+          Log.debug{ "Not aborting zombie #{step.info_file}: it is done" }
+        else
+          Log.debug{ "Aborting zombie #{step.info_file}" }
+          step.abort 
+          raise Aborted, "Zombie job aborted"
+        end
+      end
+      FileUtils.touch(step.info_file)
+    end
+  end
+
   PAGE_SIZE = 20
 
   def log(status, message = nil)
@@ -259,4 +276,5 @@ module Haml::Filters::Documentation
 
     Haml::Engine.new(doc_text).to_html  
   end
+
 end

data/lib/rbbt/rest/entity/rest.rb

@@ -5,7 +5,7 @@ module Entity
   module REST
     USE_ENSEMBL = true
 
-    REST_ENTITIES = []
+    REST_ENTITIES = Set.new
 
     def self.included(base)
       REST_ENTITIES << base

data/lib/rbbt/rest/workflow.rb

@@ -172,6 +172,11 @@ module Sinatra
 
         job = workflow.load_id(File.join(task, job))
 
+        begin
+          check_step job
+        rescue Aborted
+        end
+
         case format
         when :html
           workflow_render('job_info', workflow, task, :info => job.info)

data/share/views/compass/app.sass

@@ -65,8 +65,29 @@ $subtle-font: rgba(0,0,0,0.30)
     float: left
 
 =small_screen
+  form.workflow_task
+    .input.field.submit
+      input, select
+        width: 100% !important
+      select
+        float: left
+  span.file_or_text_area
+    display: block
+    clear: both
+  #top_menu
+    position: relative !important
+    > .favourite
+      display: block
+      width: 100%
+      clear: both
+    > .item
+      float: left
+
+  .dropdown.item .dropdown.item > .menu
+    max-height: 300px
+
   #content
-    padding: 64px 4px
+    padding: 64px 8px
 
   .entity_card, .entity_list_card
     > .content
@@ -258,9 +279,9 @@ span.bullet
   @extend .pointer
   &:hover
     border: 1px solid rgba(0,0,0,0.12)
-  width: 1.5em
-  height: 1.5em
-  margin-top: 0.5em
+  width: 2em
+  height: 2.5em
+  line-height: 2.5em
   text-align: center
   position: absolute
   left: 0
@@ -268,6 +289,14 @@ span.bullet
     color: red
   &.green
     color: green
+  &+a
+    margin-left: 2em
+    padding-left: 0em
+    width: calc(100% - 2em) !important
+
+.dropdown.item .dropdown.item > .menu
+  overflow-y: auto
+  max-height: 500px
 
 label[title]
   cursor: help
@@ -276,3 +305,10 @@ label[title]
   margin-top: 8px
 .progress.ui.message:empty
   display: none
+
+table
+  caption
+    width: 100%
+
+.examples
+  clear: both

data/share/views/layout.haml

@@ -37,42 +37,9 @@
   /{{{ CODA
   /--------
   #coda
-    = link_js "http://cdnjs.cloudflare.com/ajax/libs/mithril/0.1.28/mithril.min.js"
+    //= 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

@@ -1,19 +1,51 @@
 = serve_js
 
 :javascript
-  var user = #{user ? '"' + user + '"' : '"none"'}
-  var main_url = window.location.toString();
-  var production = #{production? ? "true" : "false"};
   $('.offcanvas').click(function(e){ 
     if( e.target !== this ) 
       return;
     $(this).toggleClass('show') 
   })
 
-  requirejs.config({baseUrl: '/js-find'})
-
   start_deferred()
 
+  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" }})
+  }
+
+  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")
+  //})
+
+
 - if @reload_page 
   :javascript
     var wait_timeout = 2000;

data/share/views/layout/header.haml

@@ -13,25 +13,27 @@
 
 - record_css '/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.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'
-
 - record_css '/stylesheets/app'
 
 = serve_css
 
 // Third party frameworks
 
-- record_js '/plugins/mithril/js/mithril.js'
-- record_js "/plugins/requirejs/js/require.js"
+:javascript
+  var user = #{user ? '"' + user + '"' : '"none"'}
+  var main_url = window.location.toString();
+  var production = #{production? ? "true" : "false"};
+
+-#= link_js "http://cdnjs.cloudflare.com/ajax/libs/mithril/0.1.28/mithril.min.js"
+
 - record_js '/js/defer'
+- record_js "/plugins/mithril/js/mithril.js"
+- record_js "/plugins/requirejs/js/require.js"
 = serve_js
 
+:javascript
+  requirejs.config({baseUrl: '/js-find'})
+
 
 - %w(jquery-2.1.1 jquery.cookie jquery.form).each do |jquery_file|
   - record_js File.join('/plugins/jquery/js/', jquery_file)
@@ -41,6 +43,7 @@
 - record_js '/plugins/jquery.scrollTo/jquery.scrollTo'
 - record_js '/plugins/semantic-ui/dist/semantic.min.js'
 - record_js '/plugins/FileSaver/js/FileSaver.js'
+- record_js '/plugins/color-js/color.js'
 
 - %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
   - record_js "/js-find/#{ file }"
@@ -48,4 +51,10 @@
 - %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|
+  - 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|
+  - record_js "/js-find/#{ file }"
+
 - record_js "/js-find/app"

data/share/views/layout/top_menu.haml

@@ -19,14 +19,12 @@
 
   - 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
+    .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

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

@@ -1,5 +1,3 @@
-var rbbt = {}
-
 function fit_content(){
  var height = window.innerHeight - $('footer').outerHeight(true);
  $('#content').css('min-height', height)
@@ -26,7 +24,7 @@ function update_rbbt(){
  fit_content()
  $('.preload').removeClass('preload');
 
- if (undefined !== rbbt.favourites) rbbt.favourites.update()
+ if (undefined !== rbbt.favourites && user != 'none') rbbt.favourites.update()
 
  if (undefined !== rbbt.aesthetics){
    rbbt.aesthetics.load()
@@ -64,5 +62,3 @@ $(function(){
  update_rbbt()
 })
 
-// Activate tools
-

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

@@ -13,13 +13,20 @@ aes_module.store = function(){
 }
 
 aes_module.add = function(selector, aes, value){
- this.aesthetics.push({selector: selector, aes: aes, value: value})
+  var mod = this
+  if (typeof selector == 'function'){ 
+    return selector.then(function(_selector){
+      mod.aesthetics.push({selector: _selector, aes: aes, value: value})
+    })
+  }else{
+    this.aesthetics.push({selector: selector, aes: aes, value: value})
+  }
 }
 
 aes_module.clear_aesthetic = function(aes){
- var data_key = 'data-aes-' + aesthetic.aes
+  var data_key = 'data-aes-' + aesthetic.aes
 
- $('[' + data_key + ']').attr(data_key, 'none')
+  $('[' + data_key + ']').attr(data_key, 'none')
 }
 
 aes_module.apply_aesthetic = function(aesthetic){
@@ -28,6 +35,7 @@ aes_module.apply_aesthetic = function(aesthetic){
   targets = $(aesthetic.selector)
  }else{
   var items = aesthetic.selector
+  if (typeof items[0] == 'object') items = $.map(items, function(i){return i.id})
   targets = $('.entity').filter(function(index){ 
    var id = $(this).attr('data-entity-id')
    return items.indexOf(id) >= 0
@@ -40,7 +48,7 @@ aes_module.apply_aesthetic = function(aesthetic){
 
 aes_module.apply = function(aesthetic){
  if (undefined === aesthetic)
-  this.aesthetics.map(aes_module.apply_aesthetic)
+  aes_module.aesthetics.map(aes_module.apply_aesthetic)
  else
   aes_module.apply_aesthetic(aesthetic)
 }

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

@@ -0,0 +1,51 @@
+
+rbbt.mlog = function(data){
+  console.log(data)
+}
+
+rbbt.insist_request = function(params, deferred, timeout, missing){
+  if (undefined === deferred) deferred = m.deferred()
+  if (undefined === timeout) timeout = 1000
+  if (timeout > 20000) timeout = 20000
+
+  params.extract = function(xhr, xhrOptions){
+    if (xhr.status != '200') throw(xhr)
+    return xhr.responseText
+  }
+
+  m.request(params).then(
+    function(res){
+      deferred.resolve(res)
+    }, 
+    function(xhr){ 
+      m.redraw()
+      if (xhr.status == '202'){ 
+        if (xhr.responseURL != params.url) params = $.extend(params, {url: xhr.responseURL, method: 'GET', data: params.data})
+        if (params.data !== undefined && params.data['_update'] !== undefined) params.data['_update'] = undefined
+          setTimeout(function(){ m.redraw(); rbbt.insist_request(params, deferred,timeout*2.5) }, timeout)
+      }else{ 
+        deferred.reject(new Error(xhr.statusText))
+      }
+    }
+  )
+
+  return deferred.promise
+}
+
+// LocalStorage
+
+rbbt.LS = {}
+
+rbbt.LS.load = function(key){
+ var content = localStorage[key]
+ if (content === undefined)
+  return undefined
+ else
+  return JSON.parse(content)
+}
+
+rbbt.LS.store = function(key, value){
+ localStorage[key] = JSON.stringify(value)
+}
+
+