Merge branch 'main' into digital-research-hub

app/assets/javascripts/controlled_vocabs.js.erb

@@ -30,14 +30,20 @@ var SampleTypeControlledVocab = {
         initialise_rich_text_editors(".rich-text-edit");            
     },
 
+    copyBlankModalForm: function() {
+        // first destroy any select2 elements, which won't survive being cloned. They will be initialised again when reset
+        $j('#cv-modal select[data-role="seek-objectsinput"]').select2('destroy');
+        SampleTypeControlledVocab.blankControlledVocabModelForm=$j('#cv-modal').clone();
+    },
+
     //resets the modal
     resetModalControlledVocabForm: function () {
         $j('#cv-modal').remove();
         $j('#modal-dialogues').append(SampleTypeControlledVocab.blankControlledVocabModelForm.clone());
         CVTerms.init();
+        ObjectsInput.init();
         SampleTypeControlledVocab.bindNewControlledVocabShowEvent();
         SampleTypeControlledVocab.initialise_deferred_rich_editor_modal();
-
     },    
 
     //selected CV item changed

app/controllers/admin_controller.rb

@@ -13,7 +13,7 @@ def index
     respond_to do |format|
       format.html
     end
-  end  
+  end
 
   def update_admins
     # Don't let admin remove themselves or they won't be able to manage roles
@@ -134,6 +134,11 @@ def update_features_enabled
     Seek::Config.piwik_analytics_url = params[:piwik_analytics_url]
     Seek::Config.piwik_analytics_tracking_notice = params[:piwik_analytics_tracking_notice]
 
+    Seek::Config.custom_analytics_snippet_enabled = string_to_boolean params[:custom_analytics_snippet_enabled]
+    Seek::Config.custom_analytics_snippet = params[:custom_analytics_snippet]
+    Seek::Config.custom_analytics_tracking_notice = params[:custom_analytics_tracking_notice]
+    Seek::Config.custom_analytics_name = params[:custom_analytics_name]
+
     Seek::Config.doi_minting_enabled = string_to_boolean params[:doi_minting_enabled]
     Seek::Config.datacite_username = params[:datacite_username]
     Seek::Config.datacite_password = params[:datacite_password]

app/controllers/assays_controller.rb

@@ -70,7 +70,7 @@ def new
     @permitted_params = assay_params if params[:assay]
 
     # jump straight to experimental if modelling analysis is disabled
-    @assay_class ||= 'experimental' unless Seek::Config.modelling_analysis_enabled
+    @assay_class ||= 'EXP' unless Seek::Config.modelling_analysis_enabled
 
     @assay.assay_class = AssayClass.for_type(@assay_class) unless @assay_class.nil?
 
@@ -82,7 +82,7 @@ def edit
   end
 
   def create
-    params[:assay_class_id] ||= AssayClass.for_type('experimental').id
+    params[:assay_class_id] ||= AssayClass.experimental.id
     @assay = Assay.new(assay_params)
 
     update_assay_organisms @assay, params
@@ -117,7 +117,7 @@ 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_assay_sample_type&.id
+    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

app/controllers/isa_assays_controller.rb

@@ -6,14 +6,18 @@ class IsaAssaysController < ApplicationController
   before_action :find_requested_item, only: %i[edit update]
 
   def new
-    @isa_assay = IsaAssay.new
+    if params[:is_assay_stream]
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id } })
+    else
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id } })
+    end
   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
+    @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!')
@@ -27,7 +31,11 @@ def create
 
   def edit
     # let edit the assay if the sample_type is not authorized
-    @isa_assay.sample_type = nil unless requested_item_authorized?(@isa_assay.sample_type)
+    if @isa_assay.assay.is_assay_stream?
+      @isa_assay.sample_type = nil
+    else
+      @isa_assay.sample_type = nil unless requested_item_authorized?(@isa_assay.sample_type)
+    end
 
     respond_to do |format|
       format.html
@@ -38,9 +46,11 @@ def update
     @isa_assay.assay.attributes = isa_assay_params[:assay]
 
     # update the sample_type
-    if requested_item_authorized?(@isa_assay.sample_type)
-      @isa_assay.sample_type.update(isa_assay_params[:sample_type])
-      @isa_assay.sample_type.resolve_inconsistencies
+    unless @isa_assay.assay.is_assay_stream?
+      if requested_item_authorized?(@isa_assay.sample_type)
+        @isa_assay.sample_type.update(isa_assay_params[:sample_type])
+        @isa_assay.sample_type.resolve_inconsistencies
+      end
     end
 
     if @isa_assay.save
@@ -87,10 +97,12 @@ def assay_params
      { data_files_attributes: %i[asset_id direction relationship_type_id] },
      { publication_ids: [] },
      { extended_metadata_attributes: determine_extended_metadata_keys(:assay) },
-     { discussion_links_attributes: %i[id url label _destroy] }]
+     { discussion_links_attributes: %i[id url label _destroy] }, :assay_stream_id]
   end
 
   def sample_type_params(params)
+    return [] unless params[:sample_type]
+
     attributes = params[:sample_type][:sample_attributes]
     if attributes
       params[:sample_type][:sample_attributes_attributes] = []
@@ -128,9 +140,16 @@ def set_up_instance_variable
   end
 
   def find_requested_item
-    @isa_assay = IsaAssay.new
+    if params[:is_assay_stream]
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id } })
+    else
+      @isa_assay = IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id } })
+    end
     @isa_assay.populate(params[:id])
 
+    # Should not deal with sample type if assay has assay_class assay stream
+    return if @isa_assay.assay.is_assay_stream?
+
     if @isa_assay.sample_type.nil? || !requested_item_authorized?(@isa_assay.assay)
       flash[:error] = "You are not authorized to edit this #{t('isa_assay')}"
       flash[:error] = 'Resource not found.' if @isa_assay.sample_type.nil?

app/controllers/workflow_classes_controller.rb

@@ -50,6 +50,10 @@ def edit
 
   def index
     @workflow_classes = WorkflowClass.order(extractor: :desc).all
+    respond_to do |format|
+      format.html
+      format.jsonld { render json: @workflow_classes.map(&:ro_crate_metadata), adapter: :attributes }
+    end
   end
 
   private

app/forms/isa_assay.rb

@@ -3,29 +3,31 @@ class IsaAssay
 
   attr_accessor :assay, :sample_type, :input_sample_type_id
 
-  validates_presence_of :assay, :sample_type, :input_sample_type_id
+  validates_presence_of :assay
   validate :validate_objects
 
   def initialize(params = {})
     @assay = Assay.new(params[:assay] || {})
-    @sample_type = SampleType.new((params[:sample_type] || {}).merge({ project_ids: @assay.project_ids }))
-    @sample_type.sample_attributes.build(is_title: true, required: true) unless params[:sample_type]
-    @assay.sample_type = @sample_type
-    @assay.assay_class = AssayClass.for_type('experimental')
+    unless @assay.is_assay_stream?
+      @sample_type = SampleType.new((params[:sample_type] || {}).merge({ project_ids: @assay.project_ids }))
+      @sample_type.sample_attributes.build(is_title: true, required: true) unless params[:sample_type]
+      @assay.sample_type = @sample_type
+    end
+
     @input_sample_type_id = params[:input_sample_type_id]
   end
 
   def save
     if valid?
-      if @assay.new_record?
+      if @assay.new_record? && !@assay.is_assay_stream?
         # connect the sample type multi link attribute to the last sample type of the assay's study
         input_attribute = @sample_type.sample_attributes.detect(&:seek_sample_multi?)
         input_attribute.linked_sample_type_id = @input_sample_type_id
         title = SampleType.find(@input_sample_type_id).sample_attributes.detect(&:is_title).title
         input_attribute.title = "Input (#{title})"
       end
+      @sample_type.save unless @assay.is_assay_stream?
       @assay.save
-      @sample_type.save
     else
       false
     end
@@ -54,6 +56,12 @@ def populate(id)
   def validate_objects
     @assay.errors.each { |e| errors.add(:base, "[Assay]: #{e.full_message}") } unless @assay.valid?
 
+    return if @assay.is_assay_stream?
+
+    errors.add(:base, '[Assay]: The assay is missing a sample type.') if @sample_type.nil?
+
+    return unless @sample_type
+
     @sample_type.errors.full_messages.each { |e| errors.add(:base, "[Sample type]: #{e}") } unless @sample_type.valid?
 
     unless @sample_type.sample_attributes.any?(&:seek_sample_multi?)
@@ -66,22 +74,22 @@ def validate_objects
 
     unless @sample_type.sample_attributes.select { |a| a.title.include?('Input') && a.isa_tag.nil? }.one?
       errors.add(:base,
-                 "[Sample type]: Should have exactly one attribute with the title 'Input' <u><b>and</b></u> no ISA tag".html_safe)
+                  "[Sample type]: Should have exactly one attribute with the title 'Input' <u><b>and</b></u> no ISA tag".html_safe)
     end
 
     if @sample_type.sample_attributes.select { |a| !a.title.include?('Input') && a.isa_tag.nil? }.any?
       errors.add(:base,
-                 "[Sample type]: All attributes should have an ISA Tag except for the <em>'Input'</em> attribute (hidden)".html_safe)
+                  "[Sample type]: All attributes should have an ISA Tag except for the <em>'Input'</em> attribute (hidden)".html_safe)
     end
 
     assay_sample_or_datafile_attributes = @sample_type.sample_attributes.select do |a|
       a.isa_tag&.isa_other_material? || a.isa_tag&.isa_data_file?
     end
+
     unless assay_sample_or_datafile_attributes.one?
       errors.add(:base,
-                 "[Sample type]: Should have exactly one attribute with the 'data_file' <u><b>or</b></u> 'other_material' ISA tag selected".html_safe)
+                  "[Sample type]: Should have exactly one attribute with the 'data_file' <u><b>or</b></u> 'other_material' ISA tag selected".html_safe)
     end
-
     errors.add(:base, '[Input Assay]: Input Assay is not provided') if @input_sample_type_id.blank?
   end
 end

app/helpers/images_helper.rb

@@ -70,8 +70,8 @@ def append_size_parameter(url, size)
     url
   end
 
-  def delete_icon(model_item, user, confirm_msg='Are you sure?')
-    item_name = text_for_resource model_item
+  def delete_icon(model_item, user, confirm_msg='Are you sure?', alternative_item_name=nil)
+    item_name = alternative_item_name.nil? ? (text_for_resource model_item) : alternative_item_name
     if model_item.can_delete?(user)
       fullURL = url_for(model_item)
 

app/models/assay.rb

@@ -25,6 +25,9 @@ class Assay < ApplicationRecord
 
   belongs_to :sample_type
 
+  has_many :child_assays, class_name: 'Assay', foreign_key: 'assay_stream_id', dependent: :destroy
+  belongs_to :assay_stream, class_name: 'Assay', optional: true
+
   belongs_to :assay_class
   has_many :assay_organisms, dependent: :destroy, inverse_of: :assay
   has_many :organisms, through: :assay_organisms, inverse_of: :assays
@@ -65,19 +68,38 @@ class Assay < ApplicationRecord
 
   enforce_authorization_on_association :study, :view
 
-  def previous_linked_assay_sample_type
-    sample_type.sample_attributes.detect { |sa| sa.isa_tag.nil? && sa.title.include?('Input') }&.linked_sample_type
+  def is_assay_stream?
+    assay_class&.is_assay_stream?
+  end
+
+  def previous_linked_sample_type
+    return unless is_isa_json_compliant?
+
+    if is_assay_stream?
+      study.sample_types.second
+    else
+      sample_type.sample_attributes.detect { |sa| sa.isa_tag.nil? && sa.title.include?('Input') }&.linked_sample_type
+    end
   end
 
   def has_linked_child_assay?
-    sample_type&.linked_sample_attributes&.any?
+    return false unless is_isa_json_compliant?
+
+    if is_assay_stream?
+      child_assays.any?
+    else
+      sample_type&.linked_sample_attributes&.any?
+    end
   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
+  def next_linked_child_assay
+    return unless has_linked_child_assay?
+
+    if is_assay_stream?
+      previous_linked_sample_type&.linked_sample_attributes&.detect { |sa| sa.isa_tag.nil? && sa.title.include?('Input') }&.sample_type&.assays&.first
+    else
+      sample_type.linked_sample_attributes.detect { |sa| sa.isa_tag.nil? && sa.title.include?('Input') }&.sample_type&.assays&.first
+    end
   end
 
   def default_contributor
@@ -95,7 +117,7 @@ def state_allows_delete?(*args)
   end
 
   def is_isa_json_compliant?
-    investigation.is_isa_json_compliant? && !sample_type.nil?
+    investigation.is_isa_json_compliant? && (!sample_type.nil? || is_assay_stream?)
   end
 
   # returns true if this is a modelling class of assay

app/models/assay_class.rb

@@ -1,31 +1,40 @@
 class AssayClass < ApplicationRecord
-
-  #this returns an instance of AssayClass according to one of the types "experimental" or "modelling"
-  #if there is not a match nil is returned
-  def self.for_type type
-    keys={"experimental"=>"EXP","modelling"=>"MODEL"}
-    return AssayClass.find_by(key: keys[type])
+  # this returns an instance of AssayClass according to one of the constants defined in seek/isa/assay_class.rb
+  # if there is not a match nil is returned
+  def self.for_type(type)
+    AssayClass.find_by(key: type)
   end
 
   def self.experimental
-    self.for_type('experimental')
+    for_type('EXP')
   end
 
   def self.modelling
-    self.for_type('modelling')
+    for_type('MODEL')
+
+  end
+
+  def self.assay_stream
+    for_type('STREAM')
   end
 
   def is_modelling?
-    key == "MODEL"
+    key == 'MODEL'
   end
 
   def is_experimental?
     key == 'EXP'
   end
 
+  def is_assay_stream?
+    key == 'STREAM'
+  end
+
+  LONG_KEYS = { 'EXP': 'Experimental Assay', 'MODEL': 'Modelling Analysis', 'STREAM': 'Assay Stream' }.freeze
+
   # for cases where a longer more descriptive key is useful, but can't rely on the title
   #  which may have been changed over time
   def long_key
-    {'EXP'=>'Experimental Assay','MODEL'=>'Modelling Analysis'}[key]
+    LONG_KEYS[key.to_sym]
   end
 end

app/models/study.rb

@@ -36,6 +36,10 @@ class Study < ApplicationRecord
     has_many "related_#{type.pluralize}".to_sym, -> { distinct }, through: :assays, source: type.pluralize.to_sym
   end
 
+  def assay_streams
+    assays.select(&:is_assay_stream?)
+  end
+
   def assets
     related_data_files + related_sops + related_models + related_publications + related_documents
   end