Disease ontology improvements

app/controllers/admin_controller.rb

@@ -122,6 +122,8 @@ def update_features_enabled
     Seek::Config.samples_enabled = string_to_boolean params[:samples_enabled]
     Seek::Config.sops_enabled = string_to_boolean params[:sops_enabled]
     Seek::Config.workflows_enabled = string_to_boolean params[:workflows_enabled]
+    Seek::Config.human_diseases_enabled = string_to_boolean params[:human_diseases_enabled]
+    Seek::Config.human_diseases_plot_enabled = string_to_boolean params[:human_diseases_plot_enabled]
 
     Seek::Config.require_cookie_consent = string_to_boolean params[:require_cookie_consent]
 

app/controllers/assays_controller.rb

@@ -86,7 +86,6 @@ def create
     @assay = Assay.new(assay_params)
 
     update_assay_organisms @assay, params
-    update_assay_human_diseases @assay, params
     @assay.contributor = current_person
     update_sharing_policies @assay
     update_annotations(params[:tag_list], @assay)
@@ -132,7 +131,6 @@ def fix_assay_linkage
 
   def update
     update_assay_organisms @assay, params
-    update_assay_human_diseases @assay, params
     update_annotations(params[:tag_list], @assay)
     update_sharing_policies @assay
     update_relationships(@assay, params)
@@ -160,14 +158,6 @@ def update_assay_organisms(assay, params)
     end
   end
 
-  def update_assay_human_diseases(assay, params)
-    human_diseases             = params[:assay_human_disease_ids] || params[:assay][:human_disease_ids] || []
-    assay.assay_human_diseases = []
-    Array(human_diseases).each do |human_disease_id|
-      assay.associate_human_disease(human_disease_id)
-    end
-  end
-
   def show
     respond_to do |format|
       format.html { render(params[:only_content] ? { layout: false } : {}) }
@@ -185,7 +175,7 @@ def assay_params
                                   { samples_attributes: %i[asset_id direction] },
                                   { data_files_attributes: %i[asset_id direction relationship_type_id] },
                                   { placeholders_attributes: %i[asset_id direction relationship_type_id] },
-                                  { publication_ids: [] },
+                                  { publication_ids: [] }, { human_disease_ids: [] },
                                   { extended_metadata_attributes: determine_extended_metadata_keys },
           { discussion_links_attributes:[:id, :url, :label, :_destroy] }
                                   ).tap do |assay_params|

app/controllers/data_files_controller.rb

@@ -381,17 +381,17 @@ def create_metadata
 
     if all_valid
 
-      update_relationships(@data_file, params)      
-      
+      update_relationships(@data_file, params)
+
 
       respond_to do |format|
         flash[:notice] = "#{t('data_file')} was successfully uploaded and saved." if flash.now[:notice].nil?
         # parse the data file if it is with sample data
 
         # the assay_id param can also contain the relationship type
         @data_file.assays << @assay if @create_new_assay
-        format.html { redirect_to params[:single_page] ? 
-          { controller: :single_pages, action: :show, id: params[:single_page] } 
+        format.html { redirect_to params[:single_page] ?
+          { controller: :single_pages, action: :show, id: params[:single_page] }
           : data_file_path(@data_file) }
         format.json { render json: @data_file, include: [params[:include]] }
       end
@@ -469,7 +469,7 @@ def forbid_new_version_if_samples
 
   def data_file_params
     params.require(:data_file).permit(:title, :description, :simulation_data, { project_ids: [] },
-                                      :license, *creator_related_params, { event_ids: [] },
+                                      :license, *creator_related_params, { event_ids: [] }, { human_disease_ids: [] },
                                       { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] },
                                       { assay_assets_attributes: [:assay_id, :relationship_type_id] },
                                       { creator_ids: [] }, { assay_assets_attributes: [:assay_id, :relationship_type_id] },

app/helpers/human_diseases_helper.rb

@@ -58,18 +58,27 @@ def get_transitive_related_resources(resource, limit = nil)
   end
 
   def get_human_diseases_plot_data()
-    Rails.cache.fetch('human_diseases_plot_data', expires_in: 12.hours) do
-      HumanDisease.all.order(:id).map do |c|
-        {
-          id:           c.id.to_s,
-          title:        c.title,
-          parent:       c.parents.first ? c.parents.first.id.to_s : '',
-          projects:     c.projects.count,
-          assays:       c.assays.count,
-          publications: c.publications.count,
-          models:       c.models.count,
-        }
-      end
+    Rails.cache.fetch('human_diseases_data', expires_in: 12.hours) do
+      {
+        tagged:
+          HumanDisease.all.order(:id).map do |c|
+            {
+              id:           c.id.to_s,
+              title:        c.title,
+              parent:       c.parents.first ? c.parents.first.id.to_s : '',
+              projects:     c.projects.count,
+              publications: c.publications.count,
+              models:       c.models.count,
+              data_files:   c.data_files.count,
+            }
+          end,
+        untagged: {
+          projects:     Project.left_outer_joins(:human_diseases).where(human_diseases: { id: nil }).count(),
+          publications: Publication.left_outer_joins(:human_diseases).where(human_diseases: { id: nil }).count(),
+          models:       Model.where(human_disease: nil).count(),
+          data_files:   DataFile.left_outer_joins(:human_diseases).where(human_diseases: { id: nil }).count(),
+        },
+      }
     end
   end
 end

app/models/data_file.rb

@@ -42,8 +42,10 @@ class DataFile < ApplicationRecord
       joins: [:assays]
   )
 
-  explicit_versioning(version_column: 'version', sync_ignore_columns: ['doi', 'file_template_id']) do
+  has_and_belongs_to_many :human_diseases
+  has_filter :human_disease
 
+  explicit_versioning(version_column: 'version', sync_ignore_columns: ['doi', 'file_template_id']) do
     acts_as_doi_mintable(proxy: :parent, type: 'Dataset', general_type: 'Dataset')
     acts_as_versioned_resource
     acts_as_favouritable
@@ -229,6 +231,10 @@ def initialise_assay_from_template
     end
   end
 
+  def human_disease_terms
+    human_diseases.collect(&:searchable_terms).flatten
+  end
+
   has_task :sample_extraction
   has_task :sample_persistence
 end

app/models/human_disease.rb

@@ -17,6 +17,7 @@ class HumanDisease < ApplicationRecord
 
   has_and_belongs_to_many :projects
   has_and_belongs_to_many :publications
+  has_and_belongs_to_many :data_files
 
   has_many :human_disease_parents, foreign_key: 'human_disease_id', class_name: 'HumanDiseaseParent'
   has_many :parents, through: :human_disease_parents, source: :parent, dependent: :destroy
@@ -69,7 +70,7 @@ class HumanDisease < ApplicationRecord
   end
 
   def can_delete?(user = User.current_user)
-    !user.nil? && user.is_admin_or_project_administrator? && models.empty? && assays.empty? && projects.empty? && publications.empty?
+    !user.nil? && user.is_admin_or_project_administrator? && models.empty? && assays.empty? && projects.empty? && publications.empty? && data_files.empty?
   end
 
   def can_manage?(_user = User.current_user)
@@ -114,7 +115,8 @@ def to_node(selected = nil, ignore_count = false)
     ids = projects.pluck(:id).map { |x| 'proj_' + x.to_s } +
       assays.pluck(:id).map { |x| 'ass_' + x.to_s } +
       models.pluck(:id).map { |x| 'mod_' + x.to_s } +
-      publications.pluck(:id).map { |x| 'pub_' + x.to_s }
+      publications.pluck(:id).map { |x| 'pub_' + x.to_s } +
+      data_files.pluck(:id).map { |x| 'data_' + x.to_s }
     child_nodes = []
 
     children.each do |child|

app/models/model.rb

@@ -43,6 +43,11 @@ class Model < ApplicationRecord
       label_field: 'organisms.title',
       includes: [:organism]
   )
+  has_filter human_disease: Seek::Filtering::Filter.new(
+    value_field: 'human_diseases.id',
+    label_field: 'human_diseases.title',
+    includes: [:human_disease]
+  )
 
   has_filter  :model_type, :model_format, :recommended_environment
   has_filter modelling_analysis_type: Seek::Filtering::Filter.new(

app/models/publication.rb

@@ -528,11 +528,6 @@ def related_organism_ids
     joins: [:assays_organisms, :models_organisms]
   )
 
-  # returns a list of related human diseases, related through either the assay or the model
-  def related_human_diseases
-    (assays.collect(&:human_diseases).flatten | models.collect(&:human_disease).flatten).uniq
-  end
-
   def self.subscribers_are_notified_of?(action)
     action == 'create'
   end

app/views/admin/features_enabled.html.erb

@@ -65,6 +65,14 @@
   <%= admin_checkbox_setting(:organisms_enabled, 1, Seek::Config.organisms_enabled,
                              "Organisms enabled", "Whether the users can register organisms in SEEK.") %>
 
+  <%= admin_checkbox_setting(:human_diseases_enabled, 1, Seek::Config.human_diseases_enabled,
+                             "Human diseases enabled", "Whether the users can register human diseases in SEEK.",
+                             :onchange=>toggle_appear_javascript('human_diseases_plot')) %>
+  <div id="human_diseases_plot" class="additional_settings" style="<%= show_or_hide_block Seek::Config.human_diseases_enabled -%>">
+    <%= admin_checkbox_setting(:human_diseases_plot_enabled, 1, Seek::Config.human_diseases_plot_enabled,
+                               "Show plot on SEEK frontpage", "A sunburst plot will be displayed on the frontpage, which contains annotated human diseases and counts.") %>
+  </div>
+
   <%= admin_checkbox_setting(:programmes_enabled, 1, Seek::Config.programmes_enabled,
                              "#{t('programme').pluralize} enabled", "Whether #{t('programme').pluralize} are enabled. #{t('programme').pluralize} allow a collection of #{t('project').pluralize} to be grouped together. This is useful if you have a large number of #{t('project').pluralize} from different initiatives.",onchange: toggle_appear_javascript('programme_details')) %>
   <div id="programme_details" class="additional_settings" style="<%= show_or_hide_block Seek::Config.programmes_enabled -%>">
@@ -126,7 +134,7 @@
 
 
   <%= admin_checkbox_setting(:require_cookie_consent, 1, Seek::Config.require_cookie_consent,
-                             "Add a cookie consent banner and a cookie setting page", "Show a banner asking for consent for the use of cookies. SEEK uses an essential cookie for session handling, and optional cookies for tracking if set below. 
+                             "Add a cookie consent banner and a cookie setting page", "Show a banner asking for consent for the use of cookies. SEEK uses an essential cookie for session handling, and optional cookies for tracking if set below.
                              Some cookies might be also set by embedded content. This banner will offer 3 choices: Only necessary, Embedded content, All.
                              Setting up this option will also add a cookie setting page accessible from the footer.") %>
 

app/views/assays/_form.html.erb

@@ -64,9 +64,7 @@
     <% end %>
 
     <% if Seek::Config.human_diseases_enabled %>
-        <div id="add_human_disease_form">
-          <%= render :partial=>"assays/select_human_diseases" -%>
-        </div>
+      <%= f.fancy_multiselect :human_diseases, { possibilities: HumanDisease.order(:title).all, with_new_link: true, hidden: false } %>
     <% end %>
 
     <%= render partial: 'assets/manage_specific_attributes', locals:{f:f} if show_form_manage_specific_attributes? %>

app/views/assets/_resource_list_item.html.erb

@@ -8,7 +8,7 @@
    avatar_partial = get_list_item_avatar_partial(resource) if avatar_partial.nil?
 
    #dont show JERM avatar for strain without contributor, as there are strains without contributor and are not harvested
-   avatar_partial = nil if (resource.kind_of?(Strain) && resource.contributor.try(:person).nil?) || resource.is_a?(Organism)
+   avatar_partial = nil if (resource.kind_of?(Strain) && resource.contributor.try(:person).nil?) || resource.is_a?(Organism) || resource.is_a?(HumanDisease)
    avatar_content = avatar_partial.blank? ? nil : render(:partial=> avatar_partial,:locals=>{:resource => resource})
 
    access_based_css_class = "list_item"

app/views/data_files/_resource_list_item.html.erb

@@ -3,6 +3,9 @@
 <div class="row">
   <div class="col-sm-6">
     <%= render partial:"assets/resource_list_item_contributor_and_creators",object:resource %>
+    <% if Seek::Config.human_diseases_enabled and !resource.human_diseases.empty? %>
+      <%= list_item_simple_list resource.human_diseases, "Human Diseases" %>
+    <% end %>
     <%= list_item_doi(resource) %>
     <%= @assay ? (list_item_optional_attribute "Relationship type", resource.relationship_type(@assay).try(:title)) : "" %>
   </div>

app/views/data_files/edit.html.erb

@@ -27,11 +27,15 @@
 
       </div>
 
+      <% if Seek::Config.human_diseases_enabled %>
+        <%= f.fancy_multiselect :human_diseases, { possibilities: HumanDisease.order(:title).all, with_new_link: true, hidden: false } %>
+      <% end %>
+
       <% if Seek::Config.file_templates_enabled %>
         <%= render :partial => "assets/select_template", :locals => {:resource => (@data_file ? @data_file : DataFile.new),
 	: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/license_selector', :locals => { :resource => @data_file } %>