Merge branch 'seek-1.15' into main

app/controllers/single_pages_controller.rb

@@ -47,7 +47,7 @@ def dynamic_table_data
   rescue Exception => e
     render json: { status: :unprocessable_entity, error: e.message }
   end
-  
+
   def download_samples_excel
     sample_ids, sample_type_id, study_id, assay_id = Rails.cache.read(params[:uuid]).values_at(:sample_ids, :sample_type_id,
                                                                                                :study_id, :assay_id)
@@ -94,7 +94,10 @@ def download_samples_excel
   rescue StandardError => e
     flash[:error] = e.message
     respond_to do |format|
-      format.html { redirect_to single_page_path(@project.id) }
+      format.html do
+        redirect_to single_page_path(id: @project.id, item_type: @assay.nil? ? 'study' : 'assay',
+                                     item_id: @assay.nil? ? @study.id : @assay.id)
+      end
       format.json do
         render json: { parameters: { sample_ids:, sample_type_id:, study_id: }, errors: e }, status: :bad_request
       end
@@ -244,7 +247,7 @@ def get_spreadsheet_data(samples_sheet)
       next if sample_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
 
       sample_cells.map do |cell|
-        cell&.value
+        cell&.value unless cell&.value == ''
       end.drop(1)
     end.compact
 
@@ -334,7 +337,7 @@ def separate_unauthorized_samples(existing_excel_samples, db_samples, authorized
       is_changed = false
 
       db_sample.map do |k, v|
-        unless ees[k] == v
+        unless ees[k] == v || %w[id uuid].include?(k)
           is_changed = true
           break
         end

app/models/sample_attribute.rb

@@ -11,7 +11,7 @@ class SampleAttribute < ApplicationRecord
 
   auto_strip_attributes :pid
   validates :sample_type, presence: true
-  validates :pid, format: { with: URI::regexp, allow_blank: true, allow_nil: true, message: 'not a valid URI' }
+  validates :pid, format: { with: URI::ABS_URI, allow_blank: true, allow_nil: true, message: 'not a valid URI' }
   validate :validate_against_editing_constraints, if: -> { sample_type.present? }
 
   before_save :store_accessor_name
@@ -64,7 +64,14 @@ def template_column_definition
 
   def short_pid
     return '' unless pid.present?
-    URI.parse(pid).fragment || pid.gsub(/.*\//,'') || pid
+    begin
+      URI.parse(pid).fragment || pid.gsub(/.*\//,'') || pid
+    rescue URI::InvalidURIError
+      # likely a space that managed to pass through earlier uri validation
+      fixed_pid = pid.gsub(' ','-')
+      URI.parse(fixed_pid).fragment || fixed_pid.gsub(/.*\//,'') || fixed_pid
+    end
+
   end
 
   def linked_extended_metadata_type

app/views/assets/_asset_buttons.html.erb

@@ -33,7 +33,7 @@
   <% if can_download_asset?(asset, params[:code]) -%>
     <% if asset.is_a?(Workflow) %>
       <% if display_asset.is_git_versioned? || asset.content_blob&.file_exists? %>
-        <%= button_link_to('Download RO Crate', 'ro_crate_file', ro_crate_workflow_path(asset, version: version, code: params[:code]),
+        <%= button_link_to('Download RO-Crate', 'ro_crate_file', ro_crate_workflow_path(asset, version: version, code: params[:code]),
                            'data-tooltip' => tooltip("The Workflow RO-Crate is a package containing the workflow definition, its metadata and supporting resources like test data")) %>
         <% if asset.can_run? %>
           <%= button_link_to("Run on Galaxy", 'run_galaxy', display_asset.run_url) %>

app/views/single_pages/_duplicate_samples_panel.html.erb

@@ -1,8 +1,9 @@
 <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
-  <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"},
-                  :help_text => "These new samples have been matched to already existing samples.") do %>
+  <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => { :id => "duplicate-samples-panel-content" },
+                    :help_text => "These new samples have been matched to already existing samples.") do %>
     <div class="table-responsive">
       <table id="duplicate-samples-table" class="table">
+        <thead>
         <tr>
           <th></th>
           <% for key in @possible_duplicates[0].keys %>
@@ -11,56 +12,64 @@
             <% end %>
           <% end %>
         </tr>
+        </thead>
+        <tbody>
         <% for dupl_sample in @possible_duplicates %>
-          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-            <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
-          <% dupl_sample.map do |key, val| %>
-            <% val = '<new>' if key =='id' %>
-            <% unless %w[uuid duplicate].include?(key) %>
-              <% if @multiple_input_fields.include?(key)%>
-                <td>
-                  <% val.each do |sub_sample| %>
-                    <span class="badge", title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
-                  <% end %>
-                </td>
-              <% elsif @cv_list_fields.include?(key) %>
-                <td>
-                  <% val.each do |cv_term| %>
-                    <span class="label label-default", title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
-                  <% end %>
-                </td>
-              <% elsif @registered_sample_fields.include?(key) %>
-                <td><span class="badge", title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span></td>
-              <% else %>
-                <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>'>
+            <td rowspan=2>
+              <button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="btn glyphicon glyphicon-trash danger
+              " style="background-color:#d9534f;color:white;"
+              onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+            <% dupl_sample.map do |key, val| %>
+              <% val = '<new>' if key == 'id' %>
+              <% unless %w[uuid duplicate].include?(key) %>
+                <% if @multiple_input_fields.include?(key) %>
+                  <td>
+                    <% val.each do |sub_sample| %>
+                      <span class="badge" , title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% elsif @cv_list_fields.include?(key) %>
+                  <td>
+                    <% val.each do |cv_term| %>
+                      <span class="label label-default" , title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
+                    <% end %>
+                  </td>
+                <% elsif @registered_sample_fields.include?(key) %>
+                  <td>
+                    <span class="badge" , title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span>
+                  </td>
+                <% else %>
+                  <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>'><%= val %></td>
+                <% end %>
               <% end %>
             <% end %>
-          <% end %>
             <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
               <% dupl_sample['duplicate'].map do |key, val| %>
                 <% unless %w[uuid duplicate].include?(key) %>
-                  <% if @multiple_input_fields.include?(key)%>
+                  <% if @multiple_input_fields.include?(key) %>
                     <td>
                       <% val.each do |sub_sample| %>
-                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                        <span class="badge" , title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
                       <% end %>
                     </td>
                   <% elsif @cv_list_fields.include?(key) %>
                     <td>
                       <% val.each do |cv_term| %>
-                        <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
+                        <span class="label label-default" , title='<%= cv_term %>'><%= cv_term %></span>
                       <% end %>
                     </td>
                   <% elsif @registered_sample_fields.include?(key) %>
-                    <td><span class="badge", title='<%= val['id'] %>'><%= val['title'] %></span></td>
+                    <td><span class="badge" , title='<%= val['id'] %>'><%= val['title'] %></span></td>
                   <% else %>
-                    <td><%= val%></td>
+                    <td><%= val %></td>
                   <% end %>
                 <% end %>
               <% end %>
             </tr>
-          </tr>
+            </tr>
         <% end %>
+        </tbody>
       </table>
     </div>
   <% end %>

app/views/single_pages/_new_samples_panel.html.erb

@@ -1,8 +1,9 @@
 <% unless @new_samples.nil? or @new_samples.compact.none? %>
-  <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
-  :help_text => "These samples have been detected as new samples and will be created.") do %>
+  <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => { :id => "new-samples-panel-content" },
+                    :help_text => "These samples have been detected as new samples and will be created.") do %>
     <div class="table-responsive">
       <table id="create-samples-table" class="table">
+        <thead>
         <tr>
           <th></th>
           <% for key in @new_samples[0].keys %>
@@ -11,36 +12,42 @@
             <% end %>
           <% end %>
         </tr>
+        </thead>
+        <tbody>
         <% for new_sample in @new_samples %>
           <% new_sample_id = UUID.generate %>
           <tr id='<%= "new-sample-#{new_sample_id}" %>'>
-            <td><button id=<%= "remove-#{new_sample_id}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
-              <% new_sample.map do |key, val| %>
-                <% val = '<new>' if key =='id' %>
+            <td>
+              <button id=<%= "remove-#{new_sample_id}" %> class="btn glyphicon glyphicon-trash danger
+              " style="background-color:#d9534f;color:white;"
+              onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+            <% new_sample.map do |key, val| %>
+              <% val = '<new>' if key == 'id' %>
               <% unless key == 'uuid' %>
-                <% if @multiple_input_fields.include?(key)%>
-                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
+                <% if @multiple_input_fields.include?(key) %>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>'>
                     <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
+                      <span class="badge" , title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
                     <% end %>
                   </td>
                 <% elsif @cv_list_fields.include?(key) %>
-                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>'>
                     <% val.each do |cv_term| %>
-                      <span class="label label-default", title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
+                      <span class="label label-default" , title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
                     <% end %>
                   </td>
                 <% elsif @registered_sample_fields.include?(key) %>
-                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
-                    <span class="badge", title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>'>
+                    <span class="badge" , title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span>
                   </td>
                 <% else %>
-                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>'><%= val %></td>
                 <% end %>
               <% end %>
             <% end %>
           </tr>
         <% end %>
+        </tbody>
       </table>
     </div>
   <% end %>

app/views/single_pages/_unauthorized_samples_panel.html.erb

@@ -1,30 +1,34 @@
 <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
   <% @can_upload = false %>
   <% errors.append("There are unauthorized samples present in the spreadsheet.") %>
-  <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"},
-                :help_text => "Sample the current user does not have permission to edit them.") do %>
+  <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => { :id => "unauthorized-samples-panel-content" },
+                    :help_text => "Sample the current user does not have permission to edit them.") do %>
     <div>
       <p>
-        <b>You don't have permission to edit the samples listed below. Please contact the submitter of these samples or revert the changes in the spreadsheet to its original values.</b>
+        <b>You don't have permission to edit the samples listed below. Please contact the submitter of these samples or
+          revert the changes in the spreadsheet to its original values.</b>
       </p>
     </div>
     <div class="table-responsive">
       <table id="unauthorized-samples-table" class="table">
+        <thead>
         <tr>
           <% for key in @unauthorized_samples[0].keys %>
             <% unless key == 'uuid' %>
               <th><%= key %></th>
             <% end %>
           <% end %>
         </tr>
+        </thead>
+        <tbody>
         <% for unauthorized_sample in @unauthorized_samples %>
           <tr id='<%= "unauthorized-sample-#{unauthorized_sample['id']}" %>' class="">
             <% unauthorized_sample.map do |key, val| %>
               <% unless key == 'uuid' %>
                 <% if @multiple_input_fields.include?(key) %>
                   <td>
                     <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <span class="badge" , title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
                     <% end %>
                   </td>
                 <% else %>
@@ -34,6 +38,7 @@
             <% end %>
           </tr>
         <% end %>
+        </tbody>
       </table>
     </div>
   <% end %>