rbbt-views 1.0.0 → 1.0.1

data/share/views/layout.haml

@@ -9,7 +9,7 @@
     - if defined? step and Step === step
       - title = "#{step.task.name} [#{step.status}]"
     - else
-      - title = "Workflow Explorer"
+      - title = $title || "Workflow Explorer"
     %title
       = title
     %link{:rel => "shortcut icon", :type => "image/png", :href => "/favicon.gif"}/
@@ -24,6 +24,7 @@
 
     %script{:src => '/plugins/jquery/js/jquery-1.6.2.min.js', :type => 'text/javascript'}
     %script{:src => '/plugins/jquery/js/jquery.form.js', :type => 'text/javascript'}
+    %script{:src => '/plugins/jquery/js/jquery.cookie.js', :type => 'text/javascript'}
     %script{:src => '/plugins/jmol/Jmol.js', :type => 'text/javascript'}
 
     -# %link{:href=>"/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css", :rel=>"stylesheet", :type=>"text/css"}/
@@ -43,6 +44,8 @@
           - else
             Not logged in
             %a(href="/login") login
+        %span.list_dropdown
+          %a(href='#lists') Loaded Entity Lists
  
     - unless $nomenu
       #menu
@@ -77,6 +80,8 @@
             %a.button(href="#" id="back_details") back
       #details
 
+    #lists
+
 :javascript        
 
   $('h3.workflow_title').click(function(){
@@ -93,3 +98,17 @@
   $('#back_details').click(back_details);
 
   var details_history = [];
+  
+  $('span.list_dropdown > a').click(function(){ $('#lists').toggle(); return false})
+
+  var _saved_lists = saved_lists();
+  if (_saved_lists == null){ _saved_lists = []; }
+
+  update_list_viewer();
+
+  $.each(_saved_lists, function(type, lists){
+    $.each(lists, function(id, list){
+      add_entity_list(type, list)
+    })
+  })
+

data/share/views/partials/_form.haml

@@ -9,6 +9,7 @@
 - action ||= ''
 - klass ||= ''
 - enctype = method == 'post' ? "multipart/form-data" : ""
+- id ||= ""
 
 %form(class=klass action=action method=method id=id enctype=enctype)
   - if inputs.empty?
@@ -20,8 +21,9 @@
     - default = input_defaults[name]
     - value = values[name] || default
     - description = input_descriptions[name]
+    - select_options = defined?(input_options)? input_options[name] : nil
     - hide = hide_inputs.include? name
-    = input(input_type, name, :id => input_id, :value => value, :default => default, :description => description, :default => default, :hide => hide)
+    = input(input_type, name, :id => input_id, :value => value, :default => default, :description => description, :select_options => select_options, :default => default, :hide => hide)
 
   %div.submit_job
     - if jobname

data/share/views/partials/_result_table.haml

@@ -6,8 +6,11 @@
   - header = result.fields
 - else
   - header = result.all_fields
-  - if rows.type == :single
+  - case
+  - when rows.type == :single
     - rows = rows.collect{|k,v| [k, NamedArray.setup([k].push(v), header, k, result.namespace)]}
+  - when rows.type == :flat
+    - rows = rows.collect{|k,v| [k, NamedArray.setup([k].push([v]), header, k, result.namespace)]}
   - else
     - rows = rows.collect{|k,v| [k, NamedArray.setup([k].concat(v), header, k, result.namespace)]}
 

data/share/views/public/plugins/jquery/js/jquery.cookie.js

@@ -0,0 +1,47 @@
+/**
+ * jQuery Cookie plugin
+ *
+ * Copyright (c) 2010 Klaus Hartl (stilbuero.de)
+ * Dual licensed under the MIT and GPL licenses:
+ * http://www.opensource.org/licenses/mit-license.php
+ * http://www.gnu.org/licenses/gpl.html
+ *
+ */
+(function($) {
+    $.cookie = function(key, value, options) {
+
+        // key and at least value given, set cookie...
+        if (arguments.length > 1 && (!/Object/.test(Object.prototype.toString.call(value)) || value === null || value === undefined)) {
+            options = $.extend({}, options);
+
+            if (value === null || value === undefined) {
+                options.expires = -1;
+            }
+
+            if (typeof options.expires === 'number') {
+                var days = options.expires, t = options.expires = new Date();
+                t.setDate(t.getDate() + days);
+            }
+
+            value = String(value);
+
+            return (document.cookie = [
+                encodeURIComponent(key), '=', options.raw ? value : encodeURIComponent(value),
+                options.expires ? '; expires=' + options.expires.toUTCString() : '', // use expires attribute, max-age is not supported by IE
+                options.path    ? '; path=' + options.path : '',
+                options.domain  ? '; domain=' + options.domain : '',
+                options.secure  ? '; secure' : ''
+            ].join(''));
+        }
+
+        // key and possibly options given, get cookie...
+        options = value || {};
+        var decode = options.raw ? function(s) { return s; } : decodeURIComponent;
+
+        var pairs = document.cookie.split('; ');
+        for (var i = 0, pair; pair = pairs[i] && pairs[i].split('='); i++) {
+            if (decode(pair[0]) === key) return decode(pair[1] || ''); // IE saves cookies with empty string as "c; ", e.g. without "=" as opposed to EOMB, thus pair[1] may be undefined
+        }
+        return null;
+    };
+})(jQuery);

data/share/views/user_lists.haml

@@ -0,0 +1,10 @@
+
+%dl
+  - lists.each do |type, lists|
+    %dt= type
+    %dd
+      %ul
+        - lists.each do |list_id|
+          %li
+            %a(href="/entity_list/#{ type }/#{ list_id }")= list_id
+

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-views
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: 
   segments: 
   - 1
   - 0
-  - 0
-  version: 1.0.0
+  - 1
+  version: 1.0.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,8 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-01-13 00:00:00 +01:00
-default_executable: 
+date: 2012-01-31 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sinatra
@@ -127,15 +126,19 @@ files:
 - share/views/compass/main.sass
 - share/views/compass/screen.sass
 - share/views/dependencies.haml
+- share/views/edit_list.haml
 - share/views/entity/GOTerm.haml
 - share/views/entity/Gene.haml
 - share/views/entity/GenomicMutation.haml
 - share/views/entity/KeggPathway.haml
 - share/views/entity/MutatedIsoform.haml
-- share/views/entity/NCIBioCartaPathways.haml
-- share/views/entity/NCINaturePathways.haml
-- share/views/entity/NCIReactomePathways.haml
+- share/views/entity/MutatedIsoform/marked_svg.haml
+- share/views/entity/MutatedIsoform/pdbs.haml
+- share/views/entity/NCIBioCartaPathway.haml
+- share/views/entity/NCINaturePathway.haml
+- share/views/entity/NCIReactomePathway.haml
 - share/views/entity/PfamDomain.haml
+- share/views/entity/Protein.haml
 - share/views/entity_list/Default.haml
 - share/views/error.haml
 - share/views/files.haml
@@ -787,14 +790,15 @@ files:
 - 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.cookie.js
 - share/views/public/plugins/jquery/js/jquery.form.js
 - share/views/result.haml
 - share/views/task_list.haml
+- share/views/user_lists.haml
 - share/views/wait.haml
 - LICENSE
 - test/test_helper.rb
 - test/rbbt/workflow/rest/test_client.rb
-has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt-views
 licenses: []
 
@@ -824,7 +828,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Rest and HTML interface

data/share/views/entity/NCIBioCartaPathways.haml

@@ -1,9 +0,0 @@
-%h3= entity.name
-
-- genes_in_pathway = entity.genes.ensembl
-
-%dl
-
-  %dt All Genes in pathway
-  %dd= genes_in_pathway.link * ", "
-

data/share/views/entity/NCINaturePathways.haml

@@ -1,9 +0,0 @@
-%h3= entity.name
-
-- genes_in_pathway = entity.genes.ensembl
-
-%dl
-
-  %dt All Genes in pathway
-  %dd= genes_in_pathway.link * ", "
-

data/share/views/entity/NCIReactomePathways.haml

@@ -1,9 +0,0 @@
-%h3= entity.name
-
-- genes_in_pathway = entity.genes.ensembl
-
-%dl
-
-  %dt All Genes in pathway
-  %dd= genes_in_pathway.link * ", "
-