Merge pull request #1663 from seek4science/1407-add-cm-to-other-resou…

…rces

1407 add "Extended Metadata" to other resources in SEEK

app/controllers/collections_controller.rb

@@ -46,6 +46,7 @@ def collection_params
     params.require(:collection).permit(:title, :description, { project_ids: [] }, :license, *creator_related_params,
                                        { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                        { publication_ids: [] },
+                                       { extended_metadata_attributes: determine_extended_metadata_keys },
                                        { items_attributes: [:id, :asset_type, :asset_id, :order, :comment, :_destroy]})
   end
 

app/controllers/data_files_controller.rb

@@ -462,6 +462,7 @@ def data_file_params
                                       :file_template_id,
                                       { data_format_annotations: [] }, { data_type_annotations: [] },
                                       { publication_ids: [] }, { workflow_ids: [] },
+                                      { extended_metadata_attributes: determine_extended_metadata_keys },
                                       { workflow_data_files_attributes:[:id, :workflow_id, :workflow_data_file_relationship_id, :_destroy] },
                                       discussion_links_attributes:[:id, :url, :label, :_destroy])
   end

app/controllers/documents_controller.rb

@@ -61,7 +61,8 @@ def document_params
                                 { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                 { assay_assets_attributes: [:assay_id] },
                                 { publication_ids: [] }, { event_ids: [] }, { workflow_ids: [] },
-                                discussion_links_attributes:[:id, :url, :label, :_destroy])
+                                     { extended_metadata_attributes: determine_extended_metadata_keys },
+                                     discussion_links_attributes:[:id, :url, :label, :_destroy])
   end
 
   alias_method :asset_params, :document_params

app/controllers/events_controller.rb

@@ -55,6 +55,6 @@ def event_params
     params.require(:event).permit(:title, :description, :start_date, :end_date, :url, :address, :city, :country, :time_zone,
                                   { project_ids: [] }, { publication_ids: [] }, { presentation_ids: [] },
                                   { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
-                                  { data_file_ids: [] },{document_ids: []}, { publication_ids: [] })
+                                  { data_file_ids: [] },{document_ids: []}, { publication_ids: [] }, { extended_metadata_attributes: determine_extended_metadata_keys } )
   end
 end

app/controllers/models_controller.rb

@@ -153,6 +153,7 @@ def model_params
                                   *creator_related_params,
                                   { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                   { assay_assets_attributes: [:assay_id] }, { publication_ids: [] },
+                                  { extended_metadata_attributes: determine_extended_metadata_keys },
                                   discussion_links_attributes:[:id, :url, :label, :_destroy])
   end
 

app/controllers/presentations_controller.rb

@@ -74,6 +74,7 @@ def presentation_params
                                          { event_ids: [] }, { project_ids: [] },
                                          { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                          { publication_ids: [] }, { workflow_ids: [] },
+                                         { extended_metadata_attributes: determine_extended_metadata_keys },
                                          discussion_links_attributes:[:id, :url, :label, :_destroy])
   end
 

app/controllers/projects_controller.rb

@@ -668,7 +668,7 @@ def project_params
     permitted_params = [:title, :web_page, :wiki_page, :description, { organism_ids: [] }, :parent_id, :start_date,
                         :end_date,
                         { funding_codes: [] }, { human_disease_ids: [] }, topic_annotations: [],
-                        discussion_links_attributes:[:id, :url, :label, :_destroy]]
+                        discussion_links_attributes:[:id, :url, :label, :_destroy], extended_metadata_attributes: determine_extended_metadata_keys ]
 
     if User.admin_logged_in?
       permitted_params += [:site_root_uri, :site_username, :site_password, :nels_enabled]

app/controllers/sops_controller.rb

@@ -62,6 +62,7 @@ def sop_params
                                 { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                 { assay_assets_attributes: [:assay_id] },
                                 { publication_ids: [] }, {workflow_ids: []},
+                                { extended_metadata_attributes: determine_extended_metadata_keys },
                                 discussion_links_attributes:[:id, :url, :label, :_destroy])
   end
 

app/models/event.rb

@@ -23,6 +23,7 @@ class Event < ApplicationRecord
   acts_as_authorized
   acts_as_uniquely_identifiable
   acts_as_favouritable
+  has_extended_metadata
 
   # load the configuration for the pagination
   grouped_pagination

app/models/project.rb

@@ -5,6 +5,7 @@ class Project < ApplicationRecord
 
   acts_as_yellow_pages
   title_trimmer
+  has_extended_metadata
 
   has_and_belongs_to_many :investigations
   has_many :studies, through: :investigations

app/views/collections/edit.html.erb

@@ -14,6 +14,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: {f: f, resource: @collection } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: {f: f, resource: @collection } %>
+
       <%= panel('Items') do %>
         <p class="help-block">Items can be re-arranged by clicking and dragging the button on the left-hand side of each row.</p>
         <table class="table" id="items-table">

app/views/collections/new.html.erb

@@ -18,6 +18,11 @@
         <%= text_area_tag 'collection[description]', collection_description_value, :class=>"form-control rich-text-edit" -%>
       </div>
 
+      <%= fields_for(@collection) do |collection_fields| %>
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: collection_fields, resource: @collection } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: collection_fields, resource: @collection } %>
+      <% end %>
+
       <%= render :partial => "projects/project_selector", :locals => { :resource => @collection } %>
 
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @collection } %>

app/views/collections/show.html.erb

@@ -19,6 +19,8 @@
           </div>
         </div>
 
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @collection } %>
+
         <div class="row">
           <div class="col-md-12">
             <%= panel('Items') do %>

app/views/data_files/edit.html.erb

@@ -15,6 +15,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @data_file } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @data_file } %>
+
       <div class="form-group">
         <div class='help-block'>Check this box if this data is the result of a model simulation</div>
         <label>
@@ -29,7 +32,7 @@
 	:templates => authorised_assets(FileTemplate, nil, 'edit') } %>
       <% end %>
 
-      <%= render partial: 'assets/controlled_vocab_annotations_form_properties', :locals => { :resource => (@data_file ? @data_file : DataFile.new) } -%>
+      <%= render :partial => 'assets/controlled_vocab_annotations_form_properties', :locals => { :resource => (@data_file ? @data_file : DataFile.new) } -%>
 
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @data_file } %>
 

app/views/data_files/multi-steps/_basic_metadata.html.erb

@@ -13,6 +13,10 @@
       <label>Description</label>
       <%= f.text_area :description, :class => 'form-control rich-text-edit', :rows => 5 -%>
     </div>
+
+    <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @data_file } %>
+    <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @data_file } %>
+
     <div class='form-group'>
       <div class='help-block'>Check this box if this data is the result of a model simulation</div>
       <label>

app/views/data_files/show.html.erb

@@ -29,7 +29,9 @@
 
             <%= render :partial => "assets/asset_doi", :locals => {:displayed_resource=>@display_data_file} %>
 
-            <%= render partial: 'nels/data_sheet', locals: { displayed_resource: @display_data_file } if @data_file.nels? %>
+            <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @data_file } %>
+
+            <%= render :partial => 'nels/data_sheet', locals: { displayed_resource: @display_data_file } if @data_file.nels? %>
           </div>
         </div>
         <%= render :partial=>"general/isa_graph", :locals => {:root_item => @data_file, :deep => true, :include_parents => true} %>

app/views/documents/edit.html.erb

@@ -15,6 +15,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @document } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @document } %>
+
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @document } %>
 
       <%= render :partial=> "assets/discussion_links_form", :locals=>{:resource => @document} -%>

app/views/documents/new.html.erb

@@ -20,6 +20,12 @@
         <%= text_area_tag 'document[description]', document_description_value, :class=>"form-control rich-text-edit" -%>
       </div>
 
+      <%= fields_for(@document) do |document_fields| %>
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: document_fields, resource: @document } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: document_fields, resource: @document } %>
+      <% end %>
+
+
       <%= render :partial => "projects/project_selector", :locals => { :resource => @document } %>
 
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @document } %>

app/views/documents/show.html.erb

@@ -22,6 +22,8 @@
             <%= render :partial => "assets/asset_doi", :locals => {:displayed_resource=>@display_document} %>
           </div>
         </div>
+
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @document } %>
         <%= render :partial=>"general/isa_graph", :locals => {:root_item => @document, :deep => true, :include_parents => true} %>
       </div>
 

app/views/events/_form.html.erb

@@ -61,6 +61,11 @@
         <%= f.country_select :country, { include_blank: 'Please select...' }, class: 'form-control' -%>
       </div>
 
+      <div class="form-group">
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @event } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @event } %>
+      </div>
+
       <% if show_form_manage_specific_attributes? && @event.can_manage? %>
           <%= render :partial => "projects/project_selector", locals: {resource: @event } -%>
       <% end %>

app/views/events/show.html.erb

@@ -57,6 +57,9 @@
         </p>
       </div>
     </div>
+
+    <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @event } %>
+
     <%= render :partial=>"general/isa_graph", :locals => {:root_item => @event, :deep => true, :include_parents => true} %>
 
     <%= render :partial => "assets/special_auth_code_display", :locals => {:resource => @event}%>

app/views/models/edit.html.erb

@@ -16,6 +16,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @model } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @model } %>
+
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @model } %>
 
       <%= render :partial=> "assets/discussion_links_form", :locals=>{:resource => @model} -%>

app/views/models/new.html.erb

@@ -32,6 +32,11 @@
         <%= text_area_tag 'model[description]', model_description_value, :class=>"form-control rich-text-edit" -%>
       </div>
 
+      <%= fields_for(@model) do |model_fields| %>
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: model_fields, resource: @model } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: model_fields, resource: @model } %>
+      <% end %>
+
       <%= render partial: "projects/project_selector", locals: { resource: @model } -%>
 
       <%= render partial: 'assets/license_selector', locals: { resource: @model } %>

app/views/models/show.html.erb

@@ -80,6 +80,7 @@
         <%= render :partial => "model_visualisation" -%>
 
         <%= render :partial => "import_details", :object => @display_model %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @model } %>
 
         <%= render :partial => "general/isa_graph", :locals => { :root_item => @model, :deep => true, :include_parents => true } %>
       </div>

app/views/presentations/edit.html.erb

@@ -14,6 +14,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @presentation } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @presentation } %>
+
       <%# only the owner should get to see this option (ability to reload defaults remain in 'edit' action, but project selector is disabled) -%>
       <% if @presentation.can_manage? -%>
           <%= render :partial => "projects/project_selector", :locals => { :resource => @presentation } -%>

app/views/presentations/new.html.erb

@@ -20,6 +20,11 @@
         <%= text_area_tag "presentation[description]", presentation_description_value,:class=>"form-control rich-text-edit" -%>
       </div>
 
+      <%= fields_for(@presentation) do |presentation_fields| %>
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: presentation_fields, resource: @presentation } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: presentation_fields, resource: @presentation } %>
+      <% end %>
+
       <%= render :partial => "projects/project_selector", :locals => { :resource => @presentation } -%>
 
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @presentation } %>

app/views/presentations/show.html.erb

@@ -22,6 +22,8 @@
 
         <%= rendered_asset_view(@display_presentation) %>
 
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @presentation } %>
+
         <%= render :partial => "general/isa_graph", :locals => { :root_item => @presentation, :deep => true, :include_parents => true } %>
       </div>
 

app/views/projects/_form.html.erb

@@ -12,6 +12,10 @@
   <%= f.text_area :description, :rows => 5, :class=>"form-control rich-text-edit" -%>
 </div>
 
+<%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: {f: f, resource: @project } %>
+<%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: {f: f, resource: @project } %>
+
+
 <%= render partial: 'assets/controlled_vocab_annotations_form_properties', locals: { resource: @project } %>
 
 <div class="form-group">

app/views/projects/show.html.erb

@@ -98,6 +98,10 @@
           </div>
         </div>
 
+        <div class="form-group">
+          <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @project } %>
+        </div>
+
       </div>
 
       <div class="col-md-3 col-sm-4">

app/views/sops/edit.html.erb

@@ -15,6 +15,9 @@
         <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%>
       </div>
 
+      <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @sop } %>
+      <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @sop } %>
+
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @sop } %>
 
       <%= render :partial=> "assets/discussion_links_form", :locals=>{:resource => @sop} -%>

app/views/sops/new.html.erb

@@ -20,6 +20,11 @@
         <%= text_area_tag 'sop[description]', sop_description_value, :class=>"form-control rich-text-edit" -%>
       </div>
 
+      <%= fields_for(@sop) do |sop_fields| %>
+        <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: sop_fields, resource: @sop } %>
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: sop_fields, resource: @sop } %>
+      <% end %>
+
       <%= render :partial => "projects/project_selector", :locals => { :resource => @sop } %>
 
       <%= render :partial => 'assets/license_selector', :locals => { :resource => @sop } %>

app/views/sops/show.html.erb

@@ -22,6 +22,9 @@
             <%= render :partial => "assets/asset_doi", :locals => {:displayed_resource=>@display_sop} %>
           </div>
         </div>
+
+        <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @sop } %>
+
         <%= render :partial=>"general/isa_graph", :locals => {:root_item => @sop, :deep => true, :include_parents => true} %>
       </div>
 

lib/seek/acts_as_asset.rb

@@ -38,6 +38,7 @@ def acts_as_asset
         acts_as_discussable
         grouped_pagination
         title_trimmer
+        has_extended_metadata
 
         attr_writer :original_filename, :content_type
 

lib/seek/samples/attribute_type_handlers/integer_attribute_type_handler.rb

@@ -6,6 +6,12 @@ def test_value(value)
           raise 'Not an integer' unless Integer(value.to_f) # the to_f is to allow "1.0" type numbers
           raise 'Not an integer' unless (Float(value) % 1).zero?
         end
+
+        def convert(value)
+          int_value = Integer(value, exception: false) if value.is_a?(String)
+          int_value.nil? ? value : int_value
+        end
+
       end
     end
   end

test/factories/extended_metadata_types.rb

@@ -70,6 +70,46 @@
     supported_type { 'Assay' }
   end
 
+  factory(:simple_document_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple document extended metadata type' }
+    supported_type { 'Document' }
+  end
+
+  factory(:simple_model_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple model extended metadata type' }
+    supported_type { 'Model' }
+    end
+
+  factory(:simple_data_file_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple data file extended metadata type' }
+    supported_type { 'DataFile' }
+  end
+
+  factory(:simple_collection_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple collection extended metadata type' }
+    supported_type { 'Collection' }
+  end
+
+  factory(:simple_sop_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple sop extended metadata type' }
+    supported_type { 'Sop' }
+  end
+
+  factory(:simple_presentation_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple presentation extended metadata type' }
+    supported_type { 'Presentation' }
+  end
+
+  factory(:simple_project_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple project extended metadata type' }
+    supported_type { 'Project' }
+  end
+
+  factory(:simple_event_extended_metadata_type, parent: :simple_investigation_extended_metadata_type) do
+    title { 'simple event extended metadata type' }
+    supported_type { 'Event' }
+  end
+
   factory(:study_extended_metadata_type_with_spaces, class: ExtendedMetadataType) do
     title { 'study extended metadata type with spaces' }
     supported_type { 'Study' }