rbbt-views 1.0.1 → 2.0.0

data/share/views/result.haml

@@ -1,6 +1,11 @@
 - if locals.include? :jobname or locals.include? "jobname"
   = workflow_partial("partials/_job_control", workflow, task, locals)
 
+
+- result = locals[:result] = step.run unless not defined? step or defined? result
+
+- result_type = locals[:result_type] = workflow.tasks[task][:result_type] unless defined? result_type or not defined? workflow or not defined? task
+
 - result_type = result_type.to_sym if String === result_type
 - case result_type
 - when :string
@@ -21,7 +26,7 @@
 - when :boolean
   = result.to_s
 
-- when :array
+- when :array, :annotations
   %ul
     - if locals.include? :result_description and defined? Entity and Entity.respond_to? :formats and Entity.formats.include? locals[:result_description] and Entity.formats[locals[:result_description]].include? Entity::REST
       - if Entity.formats[locals[:result_description]].annotations.first == :format

data/share/views/step_error.haml

@@ -0,0 +1,5 @@
+%header.error Error
+%ul.messages
+  - step.messages.reverse.each do |line|
+    %li.message= escape_html line
+

data/share/views/user_lists.haml

@@ -1,10 +1,11 @@
 
-%dl
-  - lists.each do |type, lists|
-    %dt= type
+%dl.user_lists
+  - lists.each do |entity_type, lists|
+    %dt= entity_type
     %dd
-      %ul
+      %ul.user_list
         - lists.each do |list_id|
-          %li
-            %a(href="/entity_list/#{ type }/#{ list_id }")= list_id
-
+          - target_id = "user_list_" + list_id.gsub(/\s/,'_')
+          %li(id=target_id)
+            %a(class="entity_list #{entity_type.to_s.sub(' ','_')}"href="/entity_list/#{ entity_type }/#{ list_id }" target_id=target_id)= list_id
+            = workflow_partial('partials/_list_control', workflow, task, :saved_already => true, :entity_type => entity_type, :format => nil, :id => list_id)

data/share/views/wait.haml

@@ -1,2 +1,40 @@
-%span.status= step.status
-%span.message= step.messages.last
+%h3
+  Status:
+  %span.status= step.status
+%ul.messages
+  - step.messages.reverse.each do |message|
+    %li.message= message
+
+- if step.status == "done"
+  :javascript
+    alert("Actualy done");
+    window.location = remove_parameter(remove_parameter(remove_parameter(window.location.to_s, "_"), "_layout"), "_update");
+- else
+  :javascript
+    deffer(function(){ 
+      var url = window.location.toString();
+
+      url=remove_parameter(url, "_update");
+      url=add_parameters(url, "_layout=true");
+
+      function reload(){
+        $.ajax({url: url, cache:false, 
+        success: function(data, stat, req){
+          if (req.status == 202){
+            $('#main').html(data)
+          }else{
+            window.location = remove_parameter(url, "_layout");
+          }
+        },
+        error:function(jqXHR, status, thrownError){
+          if (undefined === jqXHR.responseText || jqXHR.responseText == ''){
+            $('#main').html('No response. Server down?')
+          }else{
+            $('#main').html($(jqXHR.responseText).find('#main').html())
+          }
+        }})
+      }
+
+      window.setTimeout(reload, 7000);
+    })
+

metadata

@@ -1,130 +1,215 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rbbt-views
-version: !ruby/object:Gem::Version 
-  hash: 21
+version: !ruby/object:Gem::Version
+  version: 2.0.0
   prerelease: 
-  segments: 
-  - 1
-  - 0
-  - 1
-  version: 1.0.1
 platform: ruby
-authors: 
+authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-01-31 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-12-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: sinatra
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: compass
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: compass
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: json
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: haml
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: haml
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rest-client
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: sinatra-authorization
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sinatra-cross_origin
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: RedCloth
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: BlueCloth
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yui-compressor
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id006
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Rest and HTML interface
 email: miguel.vazquez@cnio.es
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
-files: 
+files:
 - lib/rbbt/workflow/rest.rb
 - lib/rbbt/workflow/rest/auth.rb
 - lib/rbbt/workflow/rest/client.rb
 - lib/rbbt/workflow/rest/email.rb
 - lib/rbbt/workflow/rest/entity.rb
+- lib/rbbt/workflow/rest/finder.rb
 - lib/rbbt/workflow/rest/helpers.rb
+- lib/rbbt/workflow/rest/notes.rb
 - lib/rbbt/workflow/rest/render.rb
 - lib/rbbt/workflow/rest/util.rb
 - share/views/compass/_base.sass
 - share/views/compass/app.sass
+- share/views/compass/colors.sass
+- share/views/compass/colors/ventana_azul.sass
 - share/views/compass/compass.config
+- share/views/compass/details.sass
+- share/views/compass/dom.sass
+- share/views/compass/embedded.sass
+- share/views/compass/entities.sass
+- share/views/compass/error.sass
+- share/views/compass/finder.sass
+- share/views/compass/fonts.sass
 - share/views/compass/form.sass
+- share/views/compass/header.sass
+- share/views/compass/helpers.sass
 - share/views/compass/layout.sass
-- share/views/compass/main.sass
-- share/views/compass/screen.sass
+- share/views/compass/lists.sass
+- share/views/compass/menu.sass
+- share/views/compass/notes.sass
+- share/views/compass/sizes.sass
+- share/views/compass/tables.sass
+- share/views/compass/wait.sass
 - share/views/dependencies.haml
 - share/views/edit_list.haml
 - share/views/entity/GOTerm.haml
@@ -139,22 +224,76 @@ files:
 - share/views/entity/NCIReactomePathway.haml
 - share/views/entity/PfamDomain.haml
 - share/views/entity/Protein.haml
+- share/views/entity/Transcript.haml
 - share/views/entity_list/Default.haml
+- share/views/entity_list/Default/compare_to_other_lists.haml
+- share/views/entity_list/Default/entity_links.haml
+- share/views/entity_list/Default/find_in_other_lists.haml
 - share/views/error.haml
 - share/views/files.haml
+- share/views/find.haml
 - share/views/form.haml
 - share/views/front.haml
 - share/views/info.haml
 - share/views/job_list.haml
+- share/views/js/_action_setup.js
+- share/views/js/_basic.js
+- share/views/js/_cytoscape.js
+- share/views/js/_details.js
+- share/views/js/_dom_updates.js
+- share/views/js/_embedded.js
+- share/views/js/_images.js
+- share/views/js/_layout.js
+- share/views/js/_lists.js
+- share/views/js/_table.js
+- share/views/js/_workflow.js
 - share/views/js/app.js
+- share/views/js/fix_tablesorter_scientific.js
+- share/views/js/json2.js
 - share/views/layout.haml
+- share/views/notes.haml
 - share/views/partials/_context_control.haml
 - share/views/partials/_form.haml
 - share/views/partials/_job_control.haml
+- share/views/partials/_list_control.haml
+- share/views/partials/_list_header.haml
+- share/views/partials/_note_list.haml
 - share/views/partials/_result_table.haml
 - share/views/partials/_result_table_controls.haml
 - share/views/partials/_table.haml
+- share/views/partials/layout/_coda.haml
+- share/views/partials/layout/_details.haml
+- share/views/partials/layout/_head.haml
+- share/views/partials/layout/_header.haml
+- share/views/partials/layout/_menu.haml
+- share/views/partials/layout/_resources.haml
+- share/views/public/background.png
 - share/views/public/favicon.gif
+- share/views/public/plugins/cytoscape-web/LICENSE.txt
+- share/views/public/plugins/cytoscape-web/README.txt
+- share/views/public/plugins/cytoscape-web/js/AC_OETags.js
+- share/views/public/plugins/cytoscape-web/js/cytoscapeweb.js
+- share/views/public/plugins/cytoscape-web/js/json2.js
+- share/views/public/plugins/cytoscape-web/swf/CytoscapeWeb.swf
+- share/views/public/plugins/cytoscape-web/swf/playerProductInstall.swf
+- share/views/public/plugins/fancybox/CHANGELOG.md
+- share/views/public/plugins/fancybox/README.md
+- share/views/public/plugins/fancybox/css/blank.gif
+- share/views/public/plugins/fancybox/css/fancybox_loading.gif
+- share/views/public/plugins/fancybox/css/fancybox_sprite.png
+- share/views/public/plugins/fancybox/css/jquery.fancybox.css
+- share/views/public/plugins/fancybox/helpers/fancybox_buttons.png
+- share/views/public/plugins/fancybox/helpers/jquery.fancybox-buttons.css
+- share/views/public/plugins/fancybox/helpers/jquery.fancybox-buttons.js
+- share/views/public/plugins/fancybox/helpers/jquery.fancybox-media.js
+- share/views/public/plugins/fancybox/helpers/jquery.fancybox-thumbs.css
+- share/views/public/plugins/fancybox/helpers/jquery.fancybox-thumbs.js
+- share/views/public/plugins/fancybox/js/jquery.fancybox.js
+- share/views/public/plugins/fancybox/js/jquery.mousewheel-3.0.6.pack.js
+- share/views/public/plugins/fancybox/lib/jquery-1.7.2.min.js
+- share/views/public/plugins/featuredimagezoomer/css/featuredimagezoomer.css
+- share/views/public/plugins/featuredimagezoomer/images/spinningred.gif
+- share/views/public/plugins/featuredimagezoomer/js/featuredimagezoomer.js
 - share/views/public/plugins/jmol/CHANGES.txt
 - share/views/public/plugins/jmol/COPYRIGHT.txt
 - share/views/public/plugins/jmol/ChimeToJmol.jar
@@ -380,6 +519,7 @@ files:
 - share/views/public/plugins/jqgrid/src/jqDnR.js
 - share/views/public/plugins/jqgrid/src/jqModal.js
 - share/views/public/plugins/jqgrid/src/jquery.fmatter.js
+- share/views/public/plugins/jquery-ui.hitarea.js
 - share/views/public/plugins/jquery-ui/css/custom-theme/images/ui-bg_flat_0_aaaaaa_40x100.png
 - share/views/public/plugins/jquery-ui/css/custom-theme/images/ui-bg_glass_55_fbf9ee_1x400.png
 - share/views/public/plugins/jquery-ui/css/custom-theme/images/ui-bg_glass_65_ffffff_1x400.png
@@ -789,10 +929,75 @@ files:
 - share/views/public/plugins/jquery-ui/index.html
 - share/views/public/plugins/jquery-ui/js/jquery-1.5.1.min.js
 - share/views/public/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js
-- share/views/public/plugins/jquery/js/jquery-1.6.2.min.js
+- share/views/public/plugins/jquery/js/jquery-1.8.0.min.js
 - share/views/public/plugins/jquery/js/jquery.cookie.js
 - share/views/public/plugins/jquery/js/jquery.form.js
+- share/views/public/plugins/tablesorter/addons/pager/jquery.tablesorter.pager.css
+- share/views/public/plugins/tablesorter/addons/pager/jquery.tablesorter.pager.js
+- share/views/public/plugins/tablesorter/build.xml
+- share/views/public/plugins/tablesorter/build/ParseMaster.js
+- share/views/public/plugins/tablesorter/build/js.jar
+- share/views/public/plugins/tablesorter/build/jsmin.js
+- share/views/public/plugins/tablesorter/build/min.js
+- share/views/public/plugins/tablesorter/build/pack.js
+- share/views/public/plugins/tablesorter/build/packer.js
+- share/views/public/plugins/tablesorter/build/writeFile.js
+- share/views/public/plugins/tablesorter/changelog
+- share/views/public/plugins/tablesorter/docs/assets/ajax-content.html
+- share/views/public/plugins/tablesorter/docs/css/jq.css
+- share/views/public/plugins/tablesorter/docs/example-ajax.html
+- share/views/public/plugins/tablesorter/docs/example-empty-table.html
+- share/views/public/plugins/tablesorter/docs/example-extending-defaults.html
+- share/views/public/plugins/tablesorter/docs/example-meta-headers.html
+- share/views/public/plugins/tablesorter/docs/example-meta-parsers.html
+- share/views/public/plugins/tablesorter/docs/example-meta-sort-list.html
+- share/views/public/plugins/tablesorter/docs/example-option-debug.html
+- share/views/public/plugins/tablesorter/docs/example-option-digits.html
+- share/views/public/plugins/tablesorter/docs/example-option-sort-force.html
+- share/views/public/plugins/tablesorter/docs/example-option-sort-key.html
+- share/views/public/plugins/tablesorter/docs/example-option-sort-list.html
+- share/views/public/plugins/tablesorter/docs/example-option-sort-order.html
+- share/views/public/plugins/tablesorter/docs/example-option-text-extraction.html
+- share/views/public/plugins/tablesorter/docs/example-options-headers.html
+- share/views/public/plugins/tablesorter/docs/example-pager.html
+- share/views/public/plugins/tablesorter/docs/example-parsers.html
+- share/views/public/plugins/tablesorter/docs/example-trigger-sort.html
+- share/views/public/plugins/tablesorter/docs/example-triggers.html
+- share/views/public/plugins/tablesorter/docs/example-update-cell.html
+- share/views/public/plugins/tablesorter/docs/example-widgets.html
+- share/views/public/plugins/tablesorter/docs/img/external.png
+- share/views/public/plugins/tablesorter/docs/index.html
+- share/views/public/plugins/tablesorter/docs/js/docs.js
+- share/views/public/plugins/tablesorter/docs/js/examples.js
+- share/views/public/plugins/tablesorter/jquery-latest.js
+- share/views/public/plugins/tablesorter/jquery.metadata.js
+- share/views/public/plugins/tablesorter/jquery.tablesorter.js
+- share/views/public/plugins/tablesorter/jquery.tablesorter.min.js
+- share/views/public/plugins/tablesorter/tests/assets/ajax-content.html
+- share/views/public/plugins/tablesorter/tests/cell.metadata.html
+- share/views/public/plugins/tablesorter/tests/checkbox.html
+- share/views/public/plugins/tablesorter/tests/colspan.html
+- share/views/public/plugins/tablesorter/tests/demo.html
+- share/views/public/plugins/tablesorter/tests/index.html
+- share/views/public/plugins/tablesorter/tests/large.html
+- share/views/public/plugins/tablesorter/tests/lockedOrder.html
+- share/views/public/plugins/tablesorter/tests/metadata.html
+- share/views/public/plugins/tablesorter/tests/multiple-headers.html
+- share/views/public/plugins/tablesorter/tests/pager.html
+- share/views/public/plugins/tablesorter/themes/blue/asc.gif
+- share/views/public/plugins/tablesorter/themes/blue/bg.gif
+- share/views/public/plugins/tablesorter/themes/blue/blue.zip
+- share/views/public/plugins/tablesorter/themes/blue/desc.gif
+- share/views/public/plugins/tablesorter/themes/blue/style.css
+- share/views/public/plugins/tablesorter/themes/green/asc.png
+- share/views/public/plugins/tablesorter/themes/green/bg.png
+- share/views/public/plugins/tablesorter/themes/green/desc.png
+- share/views/public/plugins/tablesorter/themes/green/green.zip
+- share/views/public/plugins/tablesorter/themes/green/style.css
+- share/views/public/plugins/wz_jsgraphics.js
+- share/views/public/tmp/foo
 - share/views/result.haml
+- share/views/step_error.haml
 - share/views/task_list.haml
 - share/views/user_lists.haml
 - share/views/wait.haml
@@ -801,37 +1006,28 @@ files:
 - test/rbbt/workflow/rest/test_client.rb
 homepage: http://github.com/mikisvaz/rbbt-views
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Rest and HTML interface
-test_files: 
+test_files:
 - test/test_helper.rb
 - test/rbbt/workflow/rest/test_client.rb