Seek ena upload

app/controllers/application_controller.rb

@@ -596,9 +596,13 @@ def relationify_collection(collection)
     end
   end
 
-  def determine_extended_metadata_keys
+  def determine_extended_metadata_keys(asset = nil)
     keys = []
-    type_id = params.dig(controller_name.singularize.to_sym, :extended_metadata_attributes, :extended_metadata_type_id)
+    if asset
+      type_id = params.dig(controller_name.singularize.to_sym, asset, :extended_metadata_attributes, :extended_metadata_type_id)
+    else
+      type_id = params.dig(controller_name.singularize.to_sym, :extended_metadata_attributes, :extended_metadata_type_id)
+    end
     if type_id.present?
       metadata_type = ExtendedMetadataType.find(type_id)
       keys = [:extended_metadata_type_id, :id, data: recursive_determine_extended_metadata_keys(metadata_type)]

app/controllers/extended_metadata_types_controller.rb

@@ -6,6 +6,7 @@ class ExtendedMetadataTypesController < ApplicationController
   # generated for form, to display fields for selected metadata type
   def form_fields
     id = params[:id]
+    parent_resource = params[:parentResource] unless params[:parentResource]&.empty?
     respond_to do |format|
       if id.blank?
         format.html { render html: '' }
@@ -15,7 +16,7 @@ def form_fields
         resource.extended_metadata = ExtendedMetadata.new(extended_metadata_type: cm)
         format.html do
           render partial: 'extended_metadata/extended_metadata_fields',
-                 locals: { extended_metadata_type: cm, resource: resource }
+                 locals: { extended_metadata_type: cm, resource:, parent_resource: }
         end
       end
     end

app/controllers/isa_assays_controller.rb

@@ -86,7 +86,7 @@ def assay_params
      { samples_attributes: %i[asset_id direction] },
      { data_files_attributes: %i[asset_id direction relationship_type_id] },
      { publication_ids: [] },
-     { extended_metadata_attributes: determine_extended_metadata_keys },
+     { extended_metadata_attributes: determine_extended_metadata_keys(:assay) },
      { discussion_links_attributes: %i[id url label _destroy] }]
   end
 

app/controllers/isa_studies_controller.rb

@@ -88,7 +88,7 @@ def study_params
     [:title, :description, :experimentalists, :investigation_id, { sop_ids: [] },
      *creator_related_params, :position, { scales: [] }, { publication_ids: [] },
      { discussion_links_attributes: %i[id url label _destroy] },
-     { extended_metadata_attributes: determine_extended_metadata_keys }]
+     { extended_metadata_attributes: determine_extended_metadata_keys(:study) }]
   end
 
   def sample_type_params(params, field)

app/helpers/extended_metadata_helper.rb

@@ -1,9 +1,14 @@
 module ExtendedMetadataHelper
   include SamplesHelper
 
-  def extended_metadata_form_field_for_attribute(attribute, resource)
+  def extended_metadata_form_field_for_attribute(attribute, resource, parent_resource=nil)
     element_class = "extended_metadata_attribute_#{attribute.sample_attribute_type.base_type.downcase}"
-    element_name = "#{resource.class.name.underscore}[extended_metadata_attributes][data][#{attribute.title}]"
+
+    if parent_resource
+      element_name = "#{parent_resource}[#{resource.class.name.underscore}][extended_metadata_attributes][data][#{attribute.title}]"
+    else
+      element_name = "#{resource.class.name.underscore}[extended_metadata_attributes][data][#{attribute.title}]"
+    end
 
     if attribute.linked_extended_metadata? || attribute.linked_extended_metadata_multi?
       content_tag(:span, class: 'linked_extended_metdata') do

app/models/assay.rb

@@ -73,6 +73,13 @@ def has_linked_child_assay?
     sample_type&.linked_sample_attributes&.any?
   end
 
+  # Fetches the assay which is linked through linked_sample_attributes (Single Page specific method)
+  def linked_assay
+    sample_type.linked_sample_attributes
+               .select { |lsa| lsa.isa_tag.nil? && lsa.title.include?('Input') }
+               .first&.sample_type&.assays&.first
+  end
+
   def default_contributor
     User.current_user.try :person
   end

app/views/extended_metadata/_extended_metadata_attribute_input.html.erb

@@ -1,12 +1,13 @@
 <%
   panel_label ||= 'Extended metadata'
   panel_style = resource.extended_metadata.try(:extended_metadata_type) ? '' : 'display:none'
-%>
+  parent_resource ||= parent_resource
+  %>
 
 <%= folding_panel(panel_label, false, style:panel_style,id:'extended_metadata_attribute_panel') do %>
   <div id="extended_attributes">
     <% if resource.extended_metadata.try(:extended_metadata_type) %>
-      <%= render partial: 'extended_metadata/extended_metadata_fields', locals: { extended_metadata_type: resource.extended_metadata.extended_metadata_type, resource: resource } %>
+      <%= render partial: 'extended_metadata/extended_metadata_fields', locals: { extended_metadata_type: resource.extended_metadata.extended_metadata_type, resource:, parent_resource: } %>
     <% end %>
   </div>
 <% end %>
@@ -15,6 +16,8 @@
 
     $j(document).ready(function () {
 
+        const parentResourceData = "<%= local_assigns.has_key?(:parent_resource) ? parent_resource : nil %>"
+
         $j('#extended_metadata_attributes_extended_metadata_type_id').change(function() {
             if (this.value) {
                 $j('#extended_metadata_attribute_panel').show();
@@ -24,7 +27,7 @@
             $j.ajax({
                 url: "<%= form_fields_extended_metadata_types_path %>",
                 type: "get",
-                data: {'id':this.value},
+                data: {'id':this.value, 'parentResource': parentResourceData},
                 dataType: 'html',
                 beforeSend: function() {
                     $j('#extended_attributes').html('<div class="spinner"></div>');
@@ -48,4 +51,4 @@
         });
     });
 
-</script>
+</script>

app/views/extended_metadata/_extended_metadata_fields.html.erb

@@ -1,8 +1,8 @@
 <% extended_metadata_type.extended_metadata_attributes.each do |attribute| %>
   <div class="form-group">
-    <%= extended_metadata_form_field_for_attribute(attribute,resource) %>
+    <%= extended_metadata_form_field_for_attribute(attribute,resource, parent_resource) %>
     <% unless attribute.description.nil? %>
       <%= extended_metadata_attribute_description(attribute.description) %>
     <% end %>
   </div>
-<% end %>
+<% end %>

app/views/isa_assays/_form.html.erb

@@ -3,12 +3,31 @@
 <%
 input_sample_type_id = params[:isa_assay][:input_sample_type_id] if params.dig(:isa_assay, :input_sample_type_id)
 source_assay = Assay.find(params[:source_assay_id]) if params[:source_assay_id]
-input_sample_type_id ||= 
+
+if !@isa_assay.assay.new_record?
+  assay_position = source_assay.position
+elsif params[:source_assay_id]
+  assay_position = source_assay.position + 1
+else
+  assay_position = 0
+end
+
+# assay_position = params[:source_assay_id] ? source_assay.position + 1 : 0
+input_sample_type_id ||=
   if params[:is_source]
     study.sample_types.second.id
   else
     source_assay.sample_type.id if params[:source_assay_id]
   end
+
+show_extended_metadata =
+  if params[:is_source]
+    true
+  elsif source_assay&.position&.zero? && !@isa_assay.assay.new_record?
+    true # Custom metadata should be shown in edit as well if assay position is 0.
+  else
+    false
+  end
 %>
 
 <%= error_messages_for :isa_assay %>
@@ -25,16 +44,18 @@ input_sample_type_id ||=
     <%= assay_fields.text_area :description, :rows => 5, :class=>"form-control rich-text-edit"  -%>
   </div>
 
-  <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:assay_fields, resource:@isa_assay.assay} %>
-  <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:assay_fields,resource:@isa_assay.assay} %>
+  <% if show_extended_metadata %>
+    <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:assay_fields, resource:@isa_assay.assay} %>
+    <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:assay_fields,resource:@isa_assay.assay, parent_resource: "isa_assay"} %>
+  <% end %>
 
   <div class="form-group hidden"  >
     <label class="required"><%= t('study') -%></label>
     <%= assay_study_selection('isa_assay[assay][study_id]',@isa_assay.assay.study) %>
   </div>
 
   <div class="hidden">
-    <%= assay_fields.number_field :position, value: source_assay&.position || study.assays.length -%>
+    <%= assay_fields.number_field :position, value: assay_position || study.assays.length -%>
   </div>
 
   <%= assay_fields.hidden_field :assay_class_id -%>
@@ -48,7 +69,7 @@ input_sample_type_id ||=
 
   <%= render :partial=> "assets/discussion_links_form", :locals=>{:resource => @isa_assay.assay} -%>
 
-<% end -%> 
+<% end -%>
 
 <%= f.hidden_field :input_sample_type_id, value: input_sample_type_id  -%>
 
@@ -57,7 +78,7 @@ input_sample_type_id ||=
     <%= render partial: 'isa_studies/sample_types_form', locals: {f: f, sample_type: @isa_assay.sample_type, id_suffix: "_sample_type", isa_element: "assay", action: action} %>
   <% end %>
 <% end %>
- 
+
 <%= form_submit_buttons(@isa_assay.assay) %>
 
 
@@ -75,15 +96,15 @@ input_sample_type_id ||=
       showTemplateModal()
     }
 
-    $j(document).ready(function () {   
+    $j(document).ready(function () {
       const urlSearchParams = new URLSearchParams(window.location.search);
       const params = Object.fromEntries(urlSearchParams.entries());
       const study_id = params["study_id"]
       $j("option:enabled", "#isa_assay_input_sample_type_id").prop('selected', true);
       // Prevent setting the hidden field on redirect (query string parameters are missing)
-      if(study_id) 
-        $j("#isa_assay_assay_study_id").val(study_id).change(); 
+      if(study_id)
+        $j("#isa_assay_assay_study_id").val(study_id).change();
 
-      Templates.init($j('#template-attributes'));   
-    }); 
+      Templates.init($j('#template-attributes'));
+    });
 </script>

app/views/isa_studies/_form.html.erb

@@ -13,7 +13,8 @@
       <%= study_fields.text_area :description, :rows=>5, :class=>"form-control rich-text-edit" %>
     </div>
 
-    <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:f, resource:@isa_study.study} %>
+    <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:study_fields, resource:@isa_study.study} %>
+    <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:study_fields,resource:@isa_study.study, parent_resource: "isa_study"} %>
 
     <% unless @isa_study.study.experimentalists.blank? %>
       <div class="form-group">
@@ -31,8 +32,6 @@
       <%= study_fields.number_field :position, :rows => 5, :class=>"form-control"  -%>
     </div>
 
-    <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:f,resource:@isa_study.study} %>
-
     <%= render partial: 'assets/manage_specific_attributes', locals: { f: study_fields } if show_form_manage_specific_attributes? %>
 
     <%= study_fields.fancy_multiselect :publications, { other_projects_checkbox: true, name: "isa_study[study][publication_ids]" } %>

db/seeds/007_sample_attribute_types.seeds.rb

@@ -52,6 +52,12 @@
                              resolution:'http://identifiers.org/inchi/\\0')
 
 
+# Custom Date dataType tailored to what ENA expects => combination of regex and controlled vocabulary
+ena_iso_date_type = SampleAttributeType.find_or_initialize_by(title: 'ENA collection date')
+ena_iso_date_type.update(base_type: Seek::Samples::BaseType::STRING,
+                         regexp: '^(?:[12]\d{3}(?:-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12]\d|3[01]))?)?(?:T\d{2}:\d{2}(?::\d{2})?Z?(?:[+-]\d{1,2})?)?(?:\/\d{4}-(?:\d{2}-(?:\d{2}(?:T\d{2}:\d{2}(?::\d{2})?Z?(?:[+-]\d{1,2})?)?)?)?)?)?$|^not collected$|^not provided$|^restricted access$|^missing: control sample$|^missing: sample group$|^missing: synthetic construct$|^missing: lab stock$|^missing: third party data$|^missing: data agreement established pre-2023$|^missing: endangered species$|^missing: human-identifiable$',
+                         placeholder: '2015 or 2015-01 or 2015-01-01')
+
 bool_type = SampleAttributeType.find_or_initialize_by(title:'Boolean')
 bool_type.update(base_type: Seek::Samples::BaseType::BOOLEAN)