Merge branch 'main' into digital-research-hub

Gemfile

@@ -52,7 +52,7 @@ gem 'will_paginate', '~> 3.1'
 gem 'yaml_db'
 gem 'rails_autolink'
 gem 'rfc-822'
-gem 'nokogiri', '~> 1.14.3'
+gem 'nokogiri', '~> 1.16.2'
 #necessary for newer hashie dependency, original api_smith is no longer active
 gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
 gem 'rdf-virtuoso', '>= 0.2.0'

Gemfile.lock

@@ -460,7 +460,7 @@ GEM
       nokogiri (~> 1)
       rake
     mini_mime (1.1.5)
-    mini_portile2 (2.8.4)
+    mini_portile2 (2.8.5)
     minitest (5.20.0)
     minitest-reporters (1.5.0)
       ansi
@@ -492,8 +492,8 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.0)
-    nokogiri (1.14.5)
-      mini_portile2 (~> 2.8.0)
+    nokogiri (1.16.2)
+      mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     nori (1.1.5)
     oauth2 (2.0.9)
@@ -566,7 +566,7 @@ GEM
     puma (5.6.8)
       nio4r (~> 2.0)
     pyu-ruby-sasl (0.0.3.3)
-    racc (1.7.1)
+    racc (1.7.3)
     rack (2.2.8)
     rack-attack (6.6.0)
       rack (>= 1.0, < 3)
@@ -1029,7 +1029,7 @@ DEPENDENCIES
   my_responds_to_parent!
   mysql2
   net-ftp
-  nokogiri (~> 1.14.3)
+  nokogiri (~> 1.16.2)
   omniauth (~> 2.1.0)
   omniauth-github
   omniauth-rails_csrf_protection

app/assets/javascripts/controlled_vocabs.js.erb

@@ -137,7 +137,7 @@ CVTerms = {
             dataType: "html",
             data: {
                 source_ontology_id: $j('select#sample_controlled_vocab_source_ontology').val(),
-                root_uri: $j('#sample_controlled_vocab_ols_root_term_uri').val(),
+                root_uris: $j('#sample_controlled_vocab_ols_root_term_uris').val(),
                 include_root_term: $j('#include_root_term:checked').val()
             },
             success: function (resp) {
@@ -179,7 +179,7 @@ CVTerms = {
         $j('select#sample_controlled_vocab_source_ontology').on('change', function () {
             var selected = this.selectedOptions[0];
             if (selected.value == "") {
-                $j('#sample_controlled_vocab_ols_root_term_uri').val('');
+                $j('#sample_controlled_vocab_ols_root_term_uris').val('');
                 $j('#ontology-root-uri').hide();
             } else {
                 $j('#ontology-root-uri').show();

app/controllers/assays_controller.rb

@@ -6,13 +6,19 @@ class AssaysController < ApplicationController
   before_action :find_assets, only: [:index]
   before_action :find_and_authorize_requested_item,
                 only: %i[edit update destroy manage manage_update show new_object_based_on_existing_one]
-  before_action :fix_assay_linkage, only: [:destroy]
-  before_action :delete_linked_sample_types, only: [:destroy]
 
   # project_membership_required_appended is an alias to project_membership_required, but is necessary to include the actions
   # defined in the application controller
   before_action :project_membership_required_appended, only: [:new_object_based_on_existing_one]
 
+  # Only for ISA JSON compliant assays
+  # => Fix sample type linkage
+  before_action :fix_assay_linkage_when_deleting_assays, only: :destroy
+  # => Delete sample type of deleted assay
+  before_action :delete_linked_sample_types, only: :destroy
+  # => Rearrange positions
+  after_action :rearrange_assay_positions_at_destroy, only: :destroy
+
   include Seek::Publishing::PublishingCommon
 
   include Seek::IsaGraphExtensions
@@ -106,30 +112,6 @@ def create
     end
   end
 
-  def delete_linked_sample_types
-    return unless is_single_page_assay?
-    return if @assay.sample_type.nil?
-
-    @assay.sample_type.destroy
-  end
-
-  def fix_assay_linkage
-    return unless is_single_page_assay?
-    return unless @assay.has_linked_child_assay?
-
-    previous_assay_linked_st_id = @assay.previous_linked_sample_type&.id
-
-    next_assay = Assay.all.detect do |a|
-      a.sample_type&.sample_attributes&.first&.linked_sample_type_id == @assay.sample_type_id
-    end
-
-    next_assay_st_attr = next_assay.sample_type&.sample_attributes&.first
-
-    return unless next_assay && previous_assay_linked_st_id && next_assay_st_attr
-
-    next_assay_st_attr.update(linked_sample_type_id: previous_assay_linked_st_id)
-  end
-
   def update
     update_assay_organisms @assay, params
     update_assay_human_diseases @assay, params
@@ -178,6 +160,32 @@ def show
 
   private
 
+  def delete_linked_sample_types
+    return unless @assay.is_isa_json_compliant?
+    return if @assay.sample_type.nil?
+
+    @assay.sample_type.destroy
+  end
+
+  def fix_assay_linkage_when_deleting_assays
+    return unless @assay.is_isa_json_compliant?
+    return unless @assay.has_linked_child_assay?
+
+    previous_assay_linked_st_id = @assay.previous_linked_sample_type&.id
+
+    next_assay = @assay.next_linked_child_assay
+
+    next_assay_st_attr = next_assay.sample_type&.sample_attributes&.detect(&:input_attribute?)
+
+    return unless next_assay && previous_assay_linked_st_id && next_assay_st_attr
+
+    next_assay_st_attr.update(linked_sample_type_id: previous_assay_linked_st_id)
+  end
+
+  def rearrange_assay_positions_at_destroy
+    rearrange_assay_positions(@assay.assay_stream)
+  end
+
   def assay_params
     params.require(:assay).permit(:title, :description, :study_id, :assay_class_id, :assay_type_uri, :technology_type_uri,
                                   :license, *creator_related_params, :position, { document_ids: [] },
@@ -194,10 +202,4 @@ def assay_params
       assay_params[:model_ids].select! { |id| Model.find_by_id(id).try(:can_view?) } if assay_params.key?(:model_ids)
     end
   end
-
-  def is_single_page_assay?
-    return false unless params.key?(:return_to)
-
-    params[:return_to].start_with? '/single_pages/'
-  end
 end

app/controllers/git_controller.rb

@@ -8,7 +8,6 @@ class GitController < ApplicationController
   before_action :fetch_git_version
   before_action :get_tree, only: [:tree]
   before_action :get_blob, only: [:blob, :download, :raw]
-  before_action :coerce_format
 
   user_content_actions :raw
 
@@ -17,6 +16,11 @@ class GitController < ApplicationController
   rescue_from Git::InvalidPathException, with: :render_invalid_path_error
   rescue_from URI::InvalidURIError, with: :render_invalid_url_error
 
+  # See: config/initializers/action_dispatch_http_mime_negotiation.rb
+  def self.ignore_format_from_extension
+    true
+  end
+
   def browse
     respond_to do |format|
       format.html
@@ -25,12 +29,12 @@ def browse
 
   def tree
     respond_to do |format|
-      format.json { render json: @tree, adapter: :attributes, root: '' }
       if request.xhr?
         format.html { render partial: 'tree' }
       else
         format.html
       end
+      format.json { render json: @tree, adapter: :attributes, root: '' }
     end
   end
 
@@ -40,12 +44,12 @@ def download
 
   def blob
     respond_to do |format|
-      format.json { render json: @blob, adapter: :attributes, root: '' }
       if request.xhr?
         format.html { render partial: 'blob' }
       else
         format.html
       end
+      format.json { render json: @blob, adapter: :attributes, root: '' }
     end
   end
 
@@ -118,7 +122,6 @@ def update
 
   def operation_response(notice = nil, status: 200)
     respond_to do |format|
-      format.json { render json: { }, status: status, adapter: :attributes, root: '' }
       format.html do
         if request.xhr?
           render partial: 'files', locals: { resource: @parent_resource, git_version: @git_version }, status: status
@@ -127,6 +130,7 @@ def operation_response(notice = nil, status: 200)
           redirect_to polymorphic_path(@parent_resource, tab: 'files')
         end
       end
+      format.json { render json: { }, status: status, adapter: :attributes, root: '' }
     end
   end
 
@@ -226,17 +230,6 @@ def add_remote_file
     @git_version.save!
   end
 
-  def coerce_format
-    # I have to do this because Rails doesn't seem to be behaving as expected.
-    # In routes.rb, the git routes are scoped with "format: false", so Rails should disregard the extension
-    # (e.g. /git/1/blob/my_file.yml) when determining the response format.
-    # However this results in an UnknownFormat error when trying to load the HTML view, as Rails still seems to be
-    # looking for an e.g. application/yaml view.
-    # You can fix this by adding { defaults: { format: :html } }, but then it is not possible to request JSON,
-    # even with an explicit `Accept: application/json` header! -Finn
-    request.format = :html unless json_api_request?
-  end
-
   def file_content
     file_params.key?(:content) ? StringIO.new(Base64.decode64(file_params[:content])) : file_params[:data]
   end

app/controllers/isa_assays_controller.rb

@@ -4,6 +4,9 @@ class IsaAssaysController < ApplicationController
 
   before_action :set_up_instance_variable
   before_action :find_requested_item, only: %i[edit update]
+  before_action :initialize_isa_assay, only: :create
+  before_action :fix_assay_linkage_for_new_assays, only: :create
+  after_action :rearrange_assay_positions_create_isa_assay, only: :create
 
   def new
     if params[:is_assay_stream]
@@ -14,10 +17,6 @@ def new
   end
 
   def create
-    @isa_assay = IsaAssay.new(isa_assay_params)
-    update_sharing_policies @isa_assay.assay
-    @isa_assay.assay.contributor = current_person
-    @isa_assay.sample_type.contributor = User.current_user.person if isa_assay_params[:sample_type]
     if @isa_assay.save
       redirect_to single_page_path(id: @isa_assay.assay.projects.first, item_type: 'assay',
                                    item_id: @isa_assay.assay, notice: 'The ISA assay was created successfully!')
@@ -66,6 +65,42 @@ def update
 
   private
 
+  def fix_assay_linkage_for_new_assays
+    return unless @isa_assay.assay.is_isa_json_compliant?
+    return if @isa_assay.assay.is_assay_stream? # Should not fix anything when creating an assay stream
+
+    previous_sample_type = SampleType.find(params[:isa_assay][:input_sample_type_id])
+    previous_assay = previous_sample_type.assays.first
+
+    # In case an assay is inserted right at the beginning of an assay stream,
+    # the next assay is the current first one in the assay stream.
+    next_assay = previous_assay.nil? ? @isa_assay.assay.assay_stream.next_linked_child_assay : previous_assay.next_linked_child_assay
+
+    # In case no next assay (an assay was appended to the end of the stream), assay linkage does not have to be fixed.
+    return unless next_assay
+
+    next_assay_input_attribute_id = next_assay.sample_type.sample_attributes.detect(&:input_attribute?).id
+    return unless next_assay_input_attribute_id
+
+    # Add link of next assay sample type to currently created assay sample type
+    updated_lsai = @isa_assay.assay.sample_type.linked_sample_attribute_ids.push(next_assay_input_attribute_id)
+    @isa_assay.assay.sample_type.update(linked_sample_attribute_ids: updated_lsai)
+  end
+
+  def rearrange_assay_positions_create_isa_assay
+    return if @isa_assay.assay.is_assay_stream?
+    return unless @isa_assay.assay.is_isa_json_compliant?
+
+    rearrange_assay_positions(@isa_assay.assay.assay_stream)
+  end
+
+  def initialize_isa_assay
+    @isa_assay = IsaAssay.new(isa_assay_params)
+    update_sharing_policies @isa_assay.assay
+    @isa_assay.assay.contributor = current_person
+    @isa_assay.sample_type.contributor = User.current_user.person if isa_assay_params[:sample_type]
+  end
+
   def isa_assay_params
     # TODO: get the params from a shared module
     isa_assay_params = params.require(:isa_assay).permit(

app/controllers/sample_controlled_vocabs_controller.rb

@@ -6,7 +6,6 @@ class SampleControlledVocabsController < ApplicationController
 
   before_action :samples_enabled?, except: :typeahead
   before_action :login_required, except: %i[show index]
-  before_action :is_user_admin_auth, only: %i[destroy update]
   before_action :find_and_authorize_requested_item, except: %i[index new create]
   before_action :find_assets, only: :index
   before_action :auth_to_create, only: %i[new create]
@@ -89,13 +88,16 @@ def fetch_ols_terms_html
     error_msg = nil
     begin
       source_ontology = params[:source_ontology_id]
-      root_uri = params[:root_uri]
-
-      raise 'No root URI provided' if root_uri.blank?
+      root_uris = params[:root_uris]
 
+      raise 'No root URI provided' if root_uris.blank?
+      @terms = []
       client = Ebi::OlsClient.new
-      @terms = client.all_descendants(source_ontology, root_uri)
-      @terms.reject! { |t| t[:iri] == root_uri } unless params[:include_root_term] == '1'
+      root_uris.split(',').collect(&:strip).reject(&:blank?).each do |uri|
+        terms = client.all_descendants(source_ontology, uri)
+        terms.reject! { |t| t[:iri] == uri } unless params[:include_root_term] == '1'
+        @terms = @terms | terms
+      end
       error_msg = "There are no descendant terms to populate the list." unless @terms.present?
     rescue StandardError => e
       error_msg = e.message
@@ -129,7 +131,7 @@ def typeahead
   private
 
   def cv_params
-    params.require(:sample_controlled_vocab).permit(:title, :description, :group, :source_ontology, :ols_root_term_uri,
+    params.require(:sample_controlled_vocab).permit(:title, :description, :group, :source_ontology, :ols_root_term_uris,
                                                     :required, :short_name,
                                                     { sample_controlled_vocab_terms_attributes: %i[id _destroy label
                                                                                                    iri parent_iri] })

app/controllers/studies_controller.rb

@@ -89,7 +89,7 @@ def update
   end
 
   def delete_linked_sample_types
-    return unless is_single_page_study?
+    return unless @study.is_isa_json_compliant?
     return if @study.sample_types.empty?
 
     # The study sample types must be destroyed in reversed order
@@ -361,9 +361,3 @@ def study_params
                                   { extended_metadata_attributes: determine_extended_metadata_keys })
   end
 end
-
-def is_single_page_study?
-  return false unless params.key?(:return_to)
-
-  params[:return_to].start_with? '/single_pages/'
-end

app/forms/isa_assay.rb

@@ -56,6 +56,12 @@ def populate(id)
   def validate_objects
     @assay.errors.each { |e| errors.add(:base, "[Assay]: #{e.full_message}") } unless @assay.valid?
 
+    if @assay.new_record? && @assay.next_linked_child_assay&.sample_type&.samples&.any?
+      next_assay_id = @assay.next_linked_child_assay.id
+      next_assay_title = @assay.next_linked_child_assay.title
+      errors.add(:base, "[Assay]: Not allowed to create an assay before assay '#{next_assay_id} - #{next_assay_title}'. It has samples linked to it.")
+    end
+
     return if @assay.is_assay_stream?
 
     errors.add(:base, '[Assay]: The assay is missing a sample type.') if @sample_type.nil?

app/helpers/dynamic_table_helper.rb

@@ -22,7 +22,7 @@ def dt_aggregated(study, assay = nil)
   # Links all sample_types in a sequence of sample_types
   def link_sequence(sample_type)
     sequence = [sample_type]
-    while link = sample_type.sample_attributes.detect(&:seek_sample_multi?)&.linked_sample_type
+    while link = sample_type.previous_linked_sample_type
       sequence << link
       sample_type = link
     end
@@ -96,8 +96,8 @@ def dt_cols(sample_type)
       is_seek_multi_sample = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI
       is_cv_list = a.sample_attribute_type.base_type == Seek::Samples::BaseType::CV_LIST
       cv_allows_free_text =  a.allow_cv_free_text
-      attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type.id }) if is_seek_multi_sample
-      attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample
+      attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type_id }) if is_seek_multi_sample
+      attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type_id }) if is_seek_sample
       attribute.merge!({is_cv_list: , cv_allows_free_text:}) if is_cv_list
       attribute
     end