merge with seek-1.15

app/assets/javascripts/sample_types.js

@@ -96,6 +96,16 @@ var SampleTypes = {
         else {
             seek_sample_element.hide();
         }
+    },
+
+    expandIRI: function () {
+        var termIRI = $j(this).next('.term-iri');
+        termIRI.toggleClass('visible');
     }
 
 };
+
+
+$j(document).ready(function() {
+    $j('.term-label').on('click', SampleTypes.expandIRI);
+});

app/assets/javascripts/upload.js

@@ -69,6 +69,7 @@ $j(document).ready(function () {
                 filenameInput.val('');
                 $j('[data-role="seek-url-checker-msg-success"]', field).hide();
                 $j('[data-role="seek-url-checker-msg-too-big"]', field).hide();
+                $j('[role="seek-url-checker-remind-to-add-file"]',field).hide();
                 pending.append(HandlebarsTemplates['upload/remote_file'](remoteFile));
             }
         };
@@ -92,6 +93,7 @@ $j(document).ready(function () {
         var result = field.find('[data-role="seek-url-checker-result"]');
         var copyDialog = $j('[data-role="seek-url-checker-msg-success"]', field);
         var tooBig = $j('[data-role="seek-url-checker-msg-too-big"]', field);
+        var addReminder = $j('[role="seek-url-checker-remind-to-add-file"]',field);
 
         var submitUrl = function () {
             result.html('').spinner('add');
@@ -111,6 +113,7 @@ $j(document).ready(function () {
                     checker.trigger('urlChecked', [info]);
                     if (info.allow_copy) {
                         copyDialog.show();
+                        addReminder.show();
                     } else {
                         tooBig.show();
                     }

app/assets/stylesheets/linked_extended_metadata.css

@@ -1,3 +1,21 @@
+.term-label {
+    font-weight: normal;
+    text-decoration: underline;
+}
+
+.term-iri {
+    display: none;
+    background-color: rgba(177, 183, 187, 0.47);
+    color: black;
+    font-weight: normal;
+}
+
+.term-iri.visible {
+    display: inline;
+    opacity: 1;
+    margin-left: 10px;
+}
+
 .linked_extended_metdata .panel-default .panel-heading {
     font-weight: bold;
     color: #333;

app/controllers/samples_controller.rb

@@ -220,31 +220,45 @@ def typeahead
 
   def query
     project_ids = params[:project_ids]&.map(&:to_i)
-
+    attribute_filter_value = params[:template_attribute_value]&.downcase
     @result = params[:template_id].present? ?
       Template.find(params[:template_id]).sample_types.map(&:samples).flatten : []
 
-    if params[:template_attribute_id].present? && params[:template_attribute_value].present?
-      attribute_title = TemplateAttribute.find(params[:template_attribute_id]).title
-      @result = @result.select { |s| s.get_attribute_value(attribute_title)&.include?(params[:template_attribute_value]) }
+    if params[:template_attribute_id].present? && attribute_filter_value.present?
+      template_attribute = TemplateAttribute.find(params[:template_attribute_id])
+      @result = @result.select do |s|
+        sample_attribute = s.sample_type.sample_attributes.detect { |sa| template_attribute.sample_attributes.include? sa }
+        sample_attribute_title = sample_attribute&.title
+        if sample_attribute&.sample_attribute_type&.seek_sample_multi?
+          attr_value = s.get_attribute_value(sample_attribute_title)
+          attr_value&.any? { |v| v[:title].downcase.include?(attribute_filter_value) }
+        elsif sample_attribute&.sample_attribute_type&.seek_sample?
+          s.get_attribute_value(sample_attribute_title)[:title]&.downcase&.include?(attribute_filter_value)
+        elsif sample_attribute&.sample_attribute_type&.seek_cv_list?
+          attr_value = s.get_attribute_value(sample_attribute_title)
+          attr_value&.any? { |v| v.downcase.include?(attribute_filter_value) }
+        else
+          s.get_attribute_value(sample_attribute_title)&.downcase&.include?(attribute_filter_value)
+        end
+      end
     end
 
     if params[:input_template_id].present? # linked
-      title =
-        TemplateAttribute.find(params[:input_attribute_id]).title if params[:input_attribute_id].present?
-      @result = find_samples(@result, :linked_samples,
-        { attribute_id: params[:input_attribute_id],
+      input_template_attribute =
+        TemplateAttribute.find(params[:input_attribute_id])
+      @result = filter_linked_samples(@result, :linked_samples,
+                                      { attribute_id: params[:input_attribute_id],
           attribute_value: params[:input_attribute_value],
-          template_id: params[:input_template_id] }, title)
+          template_id: params[:input_template_id] }, input_template_attribute)
     end
 
     if params[:output_template_id].present? # linking
-      title =
-        TemplateAttribute.find(params[:output_attribute_id]).title if params[:output_attribute_id].present?
-      @result = find_samples(@result, :linking_samples,
-        { attribute_id: params[:output_attribute_id],
+      output_template_attribute =
+        TemplateAttribute.find(params[:output_attribute_id])
+      @result = filter_linked_samples(@result, :linking_samples,
+                                      { attribute_id: params[:output_attribute_id],
           attribute_value: params[:output_attribute_value],
-          template_id: params[:output_template_id] }, title)
+          template_id: params[:output_template_id] }, output_template_attribute)
     end
 
     @result = @result.select { |s| (project_ids & s.project_ids).any? } if project_ids.present?
@@ -318,16 +332,36 @@ def find_index_assets
     end
   end
 
-  def find_samples(samples, link, options, title)
+  # Filters linked samples based on the provided options and template attribute title.
+  #
+  # @param samples [Array<Sample>] the list of samples to filter
+  # @param link [Symbol] the method to call on each sample to get the linked samples (:linked_samples or :linking_samples)
+  # @param options [Hash] the options for filtering
+  # @option options [Integer] :template_id the ID of the template to filter by
+  # @option options [String] :attribute_value the value of the attribute to filter by
+  # @option options [Integer] :attribute_id the ID of the attribute to filter by
+  # @param template_attribute_title [String] the title of the template attribute to filter by
+  # @return [Array<Sample>] the filtered list of samples
+  def filter_linked_samples(samples, link, options, template_attribute)
+    raise ArgumentError, "Invalid linking method provided. '#{link.to_s}' is not allowed!" unless %i[linked_samples linking_samples].include? link
+
+    template_attribute_title = template_attribute&.title
     samples.select do |s|
       s.send(link).any? do |x|
         selected = x.sample_type.template_id == options[:template_id].to_i
-        selected = x.get_attribute_value(title)&.include?(options[:attribute_value]) if title.present? && selected
-        selected || find_samples([x], link, options, title).present?
+        if template_attribute.sample_attribute_type.seek_sample_multi?
+          selected = x.get_attribute_value(template_attribute_title)&.any? { |v| v[:title].downcase.include?(options[:attribute_value]) } if template_attribute.present? && selected
+        elsif  template_attribute.sample_attribute_type.seek_sample?
+          selected = x.get_attribute_value(template_attribute_title)&[:title].downcase&.include?(options[:attribute_value]) if template_attribute.present? && selected
+        elsif template_attribute.sample_attribute_type.seek_cv_list?
+          selected = x.get_attribute_value(template_attribute_title)&.any? { |v| v.downcase.include?(options[:attribute_value]) } if template_attribute.present? && selected
+        else
+          selected = x.get_attribute_value(template_attribute_title)&.downcase&.include?(options[:attribute_value]&.downcase) if template_attribute.present? && selected
+        end
+        selected || filter_linked_samples([x], link, options, template_attribute).present?
       end
     end
   end
-
   def templates_enabled?
     unless Seek::Config.isa_json_compliance_enabled
       flash[:error] = 'Not available'

app/controllers/templates_controller.rb

@@ -94,7 +94,7 @@ def populate_template
     dir = Seek::Config.append_filestore_path('source_types')
 
     if Dir.exist?(dir)
-      `rm #{dir}/*`
+      FileUtils.rm_f(Dir.glob("#{dir}/*"))
     else
       FileUtils.mkdir_p(dir)
     end
@@ -116,7 +116,7 @@ def populate_template
   # post
   def template_attributes
     template = Template.find(params[:id])
-    items = template.template_attributes.map { |a| { id: a.id, title: a.title } }
+    items = template.template_attributes.map { |a| { id: a.id, title: a.title.sanitize } }
     respond_to do |format|
       format.json { render json: items.to_json }
     end
@@ -172,7 +172,7 @@ def set_status
     elsif File.exist?(resultfile)
       res = File.read(resultfile)
       @status = res
-      `rm #{resultfile}`
+      FileUtils.rm_f(resultfile)
     else
       @status = 'not_started'
     end
@@ -187,12 +187,12 @@ def resultfile
   end
 
   def running!
-    `touch #{lockfile}`
+    FileUtils.touch(lockfile)
     set_status
   end
 
   def done!
-    `rm -f #{lockfile}`
+    FileUtils.rm_f(lockfile)
   end
 
   def running?

app/helpers/samples_helper.rb

@@ -143,7 +143,9 @@ def display_attribute_value(value, attribute, options = {})
       when Seek::Samples::BaseType::CV
         seek_cv_attribute_display(value, attribute)
       when Seek::Samples::BaseType::CV_LIST
-        value.each{|v| seek_cv_attribute_display(v, attribute) }.join(', ')
+        value.map do |v|
+          seek_cv_attribute_display(v, attribute)
+        end.join(', ').html_safe
       when Seek::Samples::BaseType::LINKED_EXTENDED_METADATA
         linked_extended_metadata_attribute_display(value, attribute)
       when Seek::Samples::BaseType::LINKED_EXTENDED_METADATA_MULTI
@@ -171,12 +173,15 @@ def select_cv_source_ontology(sample_controlled_vocab)
   end
 
   def seek_cv_attribute_display(value, attribute)
-    term = attribute.sample_controlled_vocab.sample_controlled_vocab_terms.where(label:value).last
-    content = value
+    term = attribute.sample_controlled_vocab.sample_controlled_vocab_terms.where(label: value).last
     if term && term.iri.present?
-      content << " (#{term.iri}) "
+      iri_content = term.iri.match?(/^https?:\/\//) ? link_to(term.iri, term.iri, target: '_blank') : term.iri
+      label_tag = content_tag(:label, term.label, class: 'term-label')
+      iri_tag = content_tag(:label, iri_content, class: 'term-iri badge')
+      "#{label_tag}#{iri_tag}".html_safe
+    else
+      term.label
     end
-    content
   end
 
   def linked_extended_metadata_attribute_display(value, attribute)

app/helpers/templates_helper.rb

@@ -17,12 +17,12 @@ def template_attribute_details(template_attribute)
   def load_templates
     privilege = Seek::Permissions::Translator.translate('view')
     Template.order(:group, :group_order).select { |t| t.can_perform?(privilege) }.map do |item|
-      { title: item.title,
-        group: item.group,
-        level: item.level,
-        organism: item.organism,
+      { title: item.title&.sanitize,
+        group: item.group&.sanitize,
+        level: item.level&.sanitize,
+        organism: item.organism&.sanitize,
         template_id: item.id,
-        description: item.description,
+        description: item.description&.sanitize,
         group_order: item.group_order,
         attributes: item.template_attributes.order(:pos).map { |a| map_template_attributes(a) } }
     end
@@ -77,19 +77,19 @@ def template_attribute_type_link(template_attribute)
   def map_template_attributes(attribute)
     {
       attribute_type_id: attribute.sample_attribute_type_id,
-      data_type: SampleAttributeType.find(attribute.sample_attribute_type_id)&.title,
+      data_type: SampleAttributeType.find(attribute.sample_attribute_type_id)&.title&.sanitize,
       cv_id: attribute.sample_controlled_vocab_id,
       allow_cv_free_text: attribute.allow_cv_free_text,
-      title: attribute.title,
+      title: attribute.title&.sanitize,
       is_title: attribute.is_title,
-      short_name: attribute.short_name,
-      description: attribute.description,
-      pid: attribute.pid,
+      short_name: attribute.short_name&.sanitize,
+      description: attribute.description&.sanitize,
+      pid: attribute.pid&.sanitize,
       required: attribute.required,
       unit_id: attribute.unit_id,
       pos: attribute.pos,
       isa_tag_id: attribute.isa_tag_id,
-      isa_tag_title: attribute.isa_tag&.title,
+      isa_tag_title: attribute.isa_tag&.title&.sanitize,
       linked_sample_type_id: attribute.linked_sample_type_id,
       template_attribute_id: attribute.id
     }

app/models/sample_type.rb

@@ -60,6 +60,30 @@ class SampleType < ApplicationRecord
 
   has_annotation_type :sample_type_tag, method_name: :tags
 
+  # Creates sample attributes from an ISA template.
+  # @param template [Template] The ISA template to create sample attributes from.
+  # @param linked_sample_type [SampleType, nil] The linked sample type, if any.
+  def create_sample_attributes_from_isa_template(template, linked_sample_type = nil)
+    self.sample_attributes = template.template_attributes.map do |temp_attr|
+      has_seek_samples = temp_attr.sample_attribute_type.seek_sample? || temp_attr.sample_attribute_type.seek_sample_multi?
+      has_linked_st = linked_sample_type && has_seek_samples
+
+      SampleAttribute.new(
+        title: temp_attr.title,
+        description: temp_attr.description,
+        sample_attribute_type_id: temp_attr.sample_attribute_type_id,
+        required: temp_attr.required,
+        unit_id: temp_attr.unit_id,
+        is_title: temp_attr.is_title,
+        sample_controlled_vocab_id: temp_attr.sample_controlled_vocab_id,
+        linked_sample_type_id: has_linked_st ? linked_sample_type&.id : nil,
+        isa_tag_id: temp_attr.isa_tag_id,
+        allow_cv_free_text: temp_attr.allow_cv_free_text,
+        template_attribute_id: temp_attr.id
+      )
+    end
+  end
+
   def level
     isa_template&.level
   end

app/views/assets/_upload.html.erb

@@ -85,7 +85,11 @@
 
       <% if batch %>
         <div class="form-group">
-          <%= button_link_to 'Add', 'new', '#', 'data-role' => 'seek-upload-field-add-remote' %>
+
+          <div>
+            <div class='alert alert-warning' role='seek-url-checker-remind-to-add-file' style='display:none'>
+              Please click on "<b>Add</b>" button to confirm adding this Remote URL to <%= Seek::Config.instance_name %> !</div></div>
+            <%= button_link_to 'Add', 'new', '#', 'data-role' => 'seek-upload-field-add-remote' %>
         </div>
         <%= content_tag :script,
                         existing_objects.map { |o| { text: "#{o.url.blank? ? o.original_filename : o.url} (original)", id: o.id } }.to_json.html_safe,

app/views/extended_metadata/_single_row.html.erb

@@ -15,7 +15,7 @@
       <div class="form-group single-attr-row">
         <% attr_element_name = "#{element_name}[#{index}][#{attr.title}]" %>
         <%= attribute_form_element(attr, value ? value[attr.title] : nil, attr_element_name, element_class) %>
-        <% unless attribute.description.nil? %>
+        <% unless attr.description.nil? %>
           <%= extended_metadata_attribute_description(attr.description) %>
         <% end %>
       </div>

app/views/general/_item_title.html.erb

@@ -29,7 +29,7 @@ gatekeeper_status_bar = item.is_asset? && item.can_manage? && (item.is_waiting_a
                 <ul class="dropdown-menu" role="menu">
                   <% visible_versions.reverse.each do |v| %>
                       <li>
-                        <%= link_to({:version => v.version}, :method => request.request_method) do -%>
+                        <%= link_to({:version => v.version, :code => params[:code]}, :method => request.request_method) do -%>
                             <%= v.name %> <%= item.describe_version(v.version) -%><br/>
                         <% end %>
                       </li>

app/views/models/simulate.html.erb

@@ -1,4 +1,4 @@
-<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(@model,:version=>@display_model.version)) } %>
+<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(@model,:version=>@display_model.version, :code=>params[:code])) } %>
 
 <%= render :partial => "general/item_title",:locals=>{:item=>@model,:title_postfix=>" - JWS Online #{t('model')} Simulation"} %>
 

app/views/samples/_attribute_values.html.erb

@@ -3,4 +3,4 @@
       <label><%= sample_attribute_display_title(attribute) %> : </label>
       <%= display_attribute(sample, attribute, link: true) %>
     </p>
-<% end %>
+<% end %>

app/views/samples/query_form.html.erb

@@ -17,7 +17,7 @@
 			<label>Select Project(s)</label>
 			<select id="projects" class="form-control select2" multiple="multiple">
 				<% projects.each do |p| %>
-					<option value='<%= p[:id] %>'><%= p[:title] %></option>
+					<option value='<%= p[:id] %>'><%= p[:title].sanitize %></option>
 				<% end %>
 			</select>
 		</div>
@@ -31,7 +31,7 @@
 				<% templates.pluck(:group).uniq.each do |group_name| %>
 					<optgroup label='<%= group_name %>'>
 						<% templates.select{|t| t[:group]==group_name}.each do |t| %>
-							<option value='<%= t[:template_id] %>'><%=t[:title]%></option>
+							<option value='<%= t[:template_id] %>'><%=t[:title].sanitize%></option>
 						<% end %>
 					</optgroup>
 				<% end %>
@@ -66,7 +66,7 @@
 					<% templates.pluck(:group).uniq.each do |group_name| %>
 						<optgroup label='<%= group_name %>'>
 							<% templates.select{|t| t[:group]==group_name}.each do |t| %>
-								<option value='<%= t[:template_id] %>'><%= t[:title] %></option>
+								<option value='<%= t[:template_id] %>'><%= t[:title].sanitize %></option>
 							<% end %>
 						</optgroup>
 					<% end %>
@@ -99,7 +99,7 @@
 					<% templates.pluck(:group).uniq.each do |group_name| %>
 						<optgroup label='<%= group_name %>'>
 							<% templates.select{|t| t[:group]==group_name}.each do |t| %>
-								<option value='<%= t[:template_id] %>'><%= t[:title] %></option>
+								<option value='<%= t[:template_id] %>'><%= t[:title].sanitize %></option>
 							<% end %>
 						</optgroup>
 					<% end %>

config/version.yml

@@ -9,4 +9,4 @@
 
 major:        1
 minor:        16
-patch:        0-main 
+patch:        0-main