Merge pull request seek4science#1722 from ELIXIR-Belgium/implement_as…

…say_streams_for_single_page

Implement assay streams for single page

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/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

app/views/assays/_buttons.html.erb

@@ -1,4 +1,12 @@
-<% assay_word = item.is_modelling? ? t('assays.modelling_analysis') : t('assays.assay') %>
+<% assay_word ||=
+  if item.is_assay_stream?
+    t('assays.assay_stream')
+  elsif Seek::Config.isa_json_compliance_enabled && item.is_isa_json_compliant?
+    t('isa_assay')
+  else
+    t("assays.#{item.assay_class.long_key.delete(' ').underscore}")
+  end
+%>
 <%= render :partial => "subscriptions/subscribe", :locals => {:object => item} %>
 
 <% if Seek::Config.project_single_page_enabled %>
@@ -21,10 +29,14 @@
 
 <% if item.can_edit? %>
 	<% if Seek::Config.isa_json_compliance_enabled && item.is_isa_json_compliant? %>
-		<% valid_study = item&.study&.sample_types.present? %>
-		<% valid_assay = item&.sample_type.present? %>
+		<% valid_study = item&.study&.is_isa_json_compliant? %>
+		<% valid_assay = item&.is_isa_json_compliant? %>
 		<% if valid_study && valid_assay %>
-    	<%= button_link_to("Design the next #{t('assay')}", 'new', new_isa_assay_path(source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page])) %>
+      <% if item&.is_assay_stream? %>
+    	  <%= button_link_to("Design #{t('assay')}", 'new', new_isa_assay_path(source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page], assay_stream_id: item.id)) %>
+      <% else %>
+    	  <%= button_link_to("Design the next #{t('assay')}", 'new', new_isa_assay_path(source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page], assay_stream_id: item.assay_stream_id)) %>
+      <% end %>
 		<% end %>
 	<% else %>
     <%= add_new_item_to_dropdown(item) %>
@@ -38,16 +50,20 @@
 <%= item_actions_dropdown do %>
   <% if item.can_edit? %>
     <% if Seek::Config.isa_json_compliance_enabled && item.is_isa_json_compliant? %>
-      <li><%= image_tag_for_key('edit', edit_isa_assay_path(item, source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page]), "Edit #{t('isa_assay')}", nil, "Edit #{t('isa_assay')}") -%></li>
+      <% if item&.is_assay_stream? %>
+        <li><%= image_tag_for_key('edit', edit_isa_assay_path(item, source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page], is_assay_stream: true), "Edit #{assay_word}", nil, "Edit #{assay_word}") -%></li>
+      <% else %>
+        <li><%= image_tag_for_key('edit', edit_isa_assay_path(item, source_assay_id: item.id, study_id: item.study.id, single_page: params[:single_page], assay_stream_id: item.assay_stream_id), "Edit #{assay_word}", nil, "Edit #{assay_word}") -%></li>
+      <% end %>
     <% else %>
       <li><%= image_tag_for_key('edit', edit_assay_path(item), "Edit #{assay_word}", nil, "Edit #{assay_word}") -%></li>
     <% end %>
   <% end %>
 
   <% if item.can_manage? -%>
     <li><%= image_tag_for_key('manage', manage_assay_path(item), "Manage #{assay_word}", nil, "Manage #{assay_word}") -%></li>
-    <%= render :partial => 'snapshots/new_snapshot_link', :locals => {:item => item} %>
+    <%= render partial: 'snapshots/new_snapshot_link', locals: {item: item} %>
   <% end -%>
 
-  <%= delete_icon(item, current_user) %>
+  <%= delete_icon(item, current_user, 'Are you sure?', assay_word) %>
 <% end %>