Merge branch 'seek_ena_upload' of github.com:ELIXIR-Belgium/seek into…

… fairdom_test

Pulling in latest commits from 'seek_ena_upload' branch

app/assets/stylesheets/application.css

@@ -45,5 +45,5 @@
 *= require jquery.splitter/jquery.splitter
 *= require select2.min
 *= require select2.bootstrap.min
-*= require linked_custom_metadata
+*= require linked_extended_metadata
 */

app/assets/stylesheets/linked_custom_metadata.css → app/assets/stylesheets/linked_extended_metadata.css

@@ -1,57 +1,57 @@
-.linked_custom_metdata .panel-default .panel-heading {
+.linked_extended_metdata .panel-default .panel-heading {
     font-weight: bold;
     color: #333;
     background-color: #ffffff;
     border: 0;
     padding-left:0px;
 }
 
-.linked_custom_metdata .panel-body {
+.linked_extended_metdata .panel-body {
     background-color: rgb(248,248,248);
     padding: 10px 15px;
     border-radius: 5px;
 }
 
 
-.linked_custom_metdata .panel {
+.linked_extended_metdata .panel {
    border: 0;
 }
 
-.linked_custom_metdata_even {
+.linked_extended_metdata_even {
     background-color: rgb(248,248,248);
     padding: 10px 15px 10px 15px;
     border-radius: 5px;
 }
 
-.linked_custom_metdata_odd {
+.linked_extended_metdata_odd {
     background-color: rgb(224,224,224);
 
     padding: 10px 15px 10px 15px;
     border-radius: 5px;
 }
 
-.multi_linked_custom_metdata {
+.multi_linked_extended_metdata {
     background-color: rgb(246, 246, 246);
     padding: 10px 15px 10px 15px;
     border-radius: 5px;
     margin-bottom: 15px;
 }
 
-.linked_custom_metdata_display .panel-default .panel-heading {
+.linked_extended_metdata_display .panel-default .panel-heading {
     font-weight: bold;
     border: none;
     background-color: #ffffff;
     padding: 0px 0px;
 }
 
 
-.linked_custom_metdata_display .panel {
+.linked_extended_metdata_display .panel {
     border: none;
     box-shadow: none;
     margin-bottom: 0px;
 }
 
-.linked_custom_metdata_display .panel-body {
+.linked_extended_metdata_display .panel-body {
     padding: 0px 0px;
     border-radius: 5px;
 }

app/controllers/application_controller.rb

@@ -596,29 +596,29 @@ def relationify_collection(collection)
     end
   end
 
-  def determine_custom_metadata_keys(asset = nil)
+  def determine_extended_metadata_keys(asset = nil)
     keys = []
     if asset
-      type_id = params.dig(controller_name.singularize.to_sym, asset, :custom_metadata_attributes, :custom_metadata_type_id)
+      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, :custom_metadata_attributes, :custom_metadata_type_id)
+      type_id = params.dig(controller_name.singularize.to_sym, :extended_metadata_attributes, :extended_metadata_type_id)
     end
     if type_id.present?
-      metadata_type = CustomMetadataType.find(type_id)
-      keys = [:custom_metadata_type_id, :id, data: recursive_determine_custom_metadata_keys(metadata_type)]
+      metadata_type = ExtendedMetadataType.find(type_id)
+      keys = [:extended_metadata_type_id, :id, data: recursive_determine_extended_metadata_keys(metadata_type)]
     end
     keys
   end
 
-  def recursive_determine_custom_metadata_keys(metadata_type)
+  def recursive_determine_extended_metadata_keys(metadata_type)
     keys = []
-    metadata_type.custom_metadata_attributes.each do |attr|
+    metadata_type.extended_metadata_attributes.each do |attr|
       key = attr.title.to_sym
       if attr.sample_attribute_type.controlled_vocab? || attr.sample_attribute_type.seek_sample_multi? || attr.sample_attribute_type.seek_sample?
         keys << key
         keys << { key => [] }
-      elsif attr.linked_custom_metadata? || attr.linked_custom_metadata_multi?
-        keys << { key => recursive_determine_custom_metadata_keys(attr.linked_custom_metadata_type) }
+      elsif attr.linked_extended_metadata? || attr.linked_extended_metadata_multi?
+        keys << { key => recursive_determine_extended_metadata_keys(attr.linked_extended_metadata_type) }
       else
         keys << key
       end

app/controllers/assays_controller.rb

@@ -176,7 +176,7 @@ def assay_params
                                   { data_files_attributes: [:asset_id, :direction, :relationship_type_id] },
                                   { placeholders_attributes: [:asset_id, :direction, :relationship_type_id] },
                                   { publication_ids: [] },
-                                  { custom_metadata_attributes: determine_custom_metadata_keys },
+                                  { extended_metadata_attributes: determine_extended_metadata_keys },
           { discussion_links_attributes:[:id, :url, :label, :_destroy] }
                                   ).tap do |assay_params|
       assay_params[:document_ids].select! { |id| Document.find_by_id(id).try(:can_view?) } if assay_params.key?(:document_ids)

app/controllers/extended_metadata_types_controller.rb

@@ -0,0 +1,37 @@
+class ExtendedMetadataTypesController < ApplicationController
+  respond_to :json
+
+  before_action :find_extended_metadata_type, only: [:show]
+
+  # 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: '' }
+      else
+        cm = ExtendedMetadataType.find(id)
+        resource = safe_class_lookup(cm.supported_type).new
+        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:, parent_resource: }
+        end
+      end
+    end
+  end
+
+  def show
+     respond_to do |format|
+        format.json {render json: @extended_metadata_type}
+      end
+  end
+
+  private
+
+  def find_extended_metadata_type
+    @extended_metadata_type = ExtendedMetadataType.find(params[:id])
+  end
+
+end

app/controllers/investigations_controller.rb

@@ -141,7 +141,7 @@ def investigation_params
     params.require(:investigation).permit(:title, :description, { project_ids: [] }, *creator_related_params,
                                           :position, { publication_ids: [] },
                                           { discussion_links_attributes:[:id, :url, :label, :_destroy] },
-                                          { custom_metadata_attributes: determine_custom_metadata_keys })
+                                          { extended_metadata_attributes: determine_extended_metadata_keys })
   end
 
   def check_studies_are_for_this_investigation

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: [] },
-     { custom_metadata_attributes: determine_custom_metadata_keys(:assay) },
+     { 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] },
-     { custom_metadata_attributes: determine_custom_metadata_keys(:study) }]
+     { extended_metadata_attributes: determine_extended_metadata_keys(:study) }]
   end
 
   def sample_type_params(params, field)

app/controllers/studies_controller.rb

@@ -201,7 +201,7 @@ def batch_create
     # e.g: Study.new(title: 'title', investigation: investigations(:metabolomics_investigation), policy: FactoryBot.create(:private_policy))
     # study.policy = Policy.create(name: 'default policy', access_type: 1)
     # render plain: params[:studies].inspect
-    metadata_types = CustomMetadataType.where(title: 'MIAPPE metadata', supported_type: 'Study').last
+    metadata_types = ExtendedMetadataType.where(title: 'MIAPPE metadata', supported_type: 'Study').last
     studies_length = params[:studies][:title].length
     studies_uploaded = false
     data_file_uploaded = false
@@ -211,14 +211,14 @@ def batch_create
         title: params[:studies][:title][index],
         description: params[:studies][:description][index],
         investigation_id: params[:study][:investigation_id],
-        custom_metadata: CustomMetadata.new(
-          custom_metadata_type: metadata_types,
+        extended_metadata: ExtendedMetadata.new(
+          extended_metadata_type: metadata_types,
           data: metadata
         )
       }
       @study = Study.new(study_params)
       StudyBatchUpload.check_study_is_MIAPPE_compliant(@study, metadata)
-      if @study.valid? && @study.save! && @study.custom_metadata.valid?
+      if @study.valid? && @study.save! && @study.extended_metadata.valid?
         studies_uploaded = true if @study.save
       end
       data_file_uploaded = create_batch_assay_asset(params, index)
@@ -262,7 +262,7 @@ def create_batch_assay_asset(params, index)
     data_file_names.length.times do |data_file_index|
 
       study_metadata_id = params[:studies][:id][index]
-      study_id = CustomMetadata.where('json_metadata LIKE ?', "%\"id\":\"#{study_metadata_id}\"%").last.item_id
+      study_id = ExtendedMetadata.where('json_metadata LIKE ?', "%\"id\":\"#{study_metadata_id}\"%").last.item_id
       assay_class_id = AssayClass.where(title: 'Experimental assay').first.id
       data_file_description = params[:studies][:data_file_description][index].remove(' ').split(',')
       assay_params = {
@@ -343,7 +343,7 @@ def remove_existing_studies(studies)
       metadata_id = JSON.parse(study.gsub("=>",":"))["metadata_id"].to_i
 
       Study.where(id: study_id).delete_all
-      CustomMetadata.where(id: metadata_id).delete_all
+      ExtendedMetadata.where(id: metadata_id).delete_all
       assays = Assay.where(study_id: study_id)
       assays.each do |assay|
         AssayAsset.where(assay_id: assay.id).delete_all
@@ -357,7 +357,7 @@ def study_params
     params.require(:study).permit(:title, :description, :experimentalists, :investigation_id,
                                   *creator_related_params, :position, { publication_ids: [] },
                                   { discussion_links_attributes:[:id, :url, :label, :_destroy] },
-                                  { custom_metadata_attributes: determine_custom_metadata_keys })
+                                  { extended_metadata_attributes: determine_extended_metadata_keys })
   end
 end
 

app/helpers/extended_metadata_helper.rb

@@ -0,0 +1,50 @@
+module ExtendedMetadataHelper
+  include SamplesHelper
+
+  def extended_metadata_form_field_for_attribute(attribute, resource, parent_resource = nil)
+    element_class = "extended_metadata_attribute_#{attribute.sample_attribute_type.base_type.downcase}"
+
+    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
+        folding_panel(attribute.label, false, id:attribute.title) do
+            attribute_form_element(attribute, resource.extended_metadata.get_attribute_value(attribute.title), element_name, element_class)
+        end
+      end
+    else
+      content_tag(:label,attribute.label, class: attribute.required? ? 'required' : '') +
+        attribute_form_element(attribute, resource.extended_metadata.get_attribute_value(attribute.title), element_name, element_class)
+    end
+  end
+
+  def extended_metadata_attribute_description(description)
+    html = '<p class="help-block">'
+    html += '<small>'+description+'</small>'
+    html += '</p>'
+    html.html_safe
+  end
+
+    def render_extended_metadata_value(attribute, resource)
+
+      if resource.extended_metadata.data[attribute.title].blank?
+        return '' # Return an empty string if the extended metadata is blank.
+      end
+
+      content_tag(:div, class: 'extended_metadata') do
+        if attribute.linked_extended_metadata? || attribute.linked_extended_metadata_multi?
+          content_tag(:span, class: 'linked_extended_metdata_display') do
+            folding_panel(attribute.label, true, id: attribute.title) do
+              display_attribute(resource.extended_metadata, attribute, link: true)
+            end
+          end
+        else
+          label_tag("#{attribute.label} : ") + " " + display_attribute(resource.extended_metadata, attribute, link: true)
+        end
+      end
+    end
+end

app/helpers/sample_types_helper.rb

@@ -91,7 +91,7 @@ def sample_attribute_pid_help_icon
   private
 
   def displayed_sample_attribute_types
-    SampleAttributeType.all.reject{ |x|x.linked_custom_metadata? || x.linked_custom_metadata_multi? }
+    SampleAttributeType.all.reject{ |x|x.linked_extended_metadata? || x.linked_extended_metadata_multi? }
   end
 
   def attribute_type_link(sample_type_attribute)