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

…nt_template_make_over

Merge main branch in experiment_template_make_over.

app/controllers/assays_controller.rb

@@ -114,6 +114,7 @@ def create
 
   def delete_linked_sample_types
     return unless is_single_page_assay?
+    return if @assay.sample_type.nil?
 
     @assay.sample_type.destroy
   end

app/controllers/studies_controller.rb

@@ -90,6 +90,7 @@ def update
 
   def delete_linked_sample_types
     return unless is_single_page_study?
+    return if @study.sample_types.empty?
 
     # The study sample types must be destroyed in reversed order
     # otherwise the first sample type won't be removed becaused it is linked from the second

app/models/sample.rb

@@ -93,14 +93,6 @@ def extracted?
     !!originating_data_file
   end
 
-  def projects
-    extracted? ? originating_data_file.projects : super
-  end
-
-  def project_ids
-    extracted? ? originating_data_file.project_ids : super
-  end
-
   def creators
     extracted? ? originating_data_file.creators : super
   end

app/views/projects/guided_create/_programme_details.html.erb

@@ -3,6 +3,9 @@
 <% else %>
   <div id='programme-details' style="display:none;">
 <% end %>
+<div class="help-block">
+  Specify a title for a new <%= t('programme') %>, which your new <%= t('project') %> will be associated with.
+</div>
 <%= label_tag :programme_title, "Title" %><span class="required">*</span>
 <%= text_field_tag 'programme[title]', '', class: 'form-control' %>
 </div>

db/migrate/20230928124148_rename_custom_metadata_attribute_to_extended_metadata_attribute.rb

@@ -1,6 +1,6 @@
 class RenameCustomMetadataAttributeToExtendedMetadataAttribute < ActiveRecord::Migration[6.1]
     def change
-      rename_table :extended_metadata_attributes, :extended_metadata_attributes
+      rename_table :custom_metadata_attributes, :extended_metadata_attributes
 
       rename_column :extended_metadata_attributes, :custom_metadata_type_id, :extended_metadata_type_id
       rename_column :extended_metadata_attributes, :linked_custom_metadata_type_id, :linked_extended_metadata_type_id

lib/seek/samples/extractor.rb

@@ -30,6 +30,7 @@ def persist
 
             last_id = Sample.last.try(:id) || 0
             sample_type = samples.first.sample_type
+            project_ids = samples.first.project_ids
             disable_authorization_checks { Sample.import(samples, validate: false, batch_size: 2000) }
             SampleTypeUpdateJob.new(sample_type, false).queue_job
 
@@ -38,6 +39,9 @@ def persist
             samples = Sample.where(sample_type: sample_type, title: samples.collect(&:title), contributor: contributor).where(
               'id > ?', last_id
             )
+            samples.each do |sample|
+              sample.project_ids = project_ids
+            end
             ReindexingQueue.enqueue(samples)
             AuthLookupUpdateQueue.enqueue(samples)
           end

lib/tasks/seek_upgrades.rake

@@ -9,6 +9,7 @@ namespace :seek do
   task upgrade_version_tasks: %i[
     environment
     decouple_extracted_samples_policies
+    decouple_extracted_samples_projects
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -61,6 +62,28 @@ namespace :seek do
     puts " ... finished creating independent policies of #{decoupled.to_s} extracted samples"
   end
 
+  task(decouple_extracted_samples_projects: [:environment]) do
+    puts '... copying project ids for extracted samples...'
+    decoupled = 0
+    hash_array = []
+    disable_authorization_checks do
+      Sample.find_each do |sample|
+        # check if the sample was extracted from a datafile and their projects are linked
+        if sample.extracted? && sample.project_ids.empty?
+          sample.originating_data_file.project_ids.each do |project_id|
+            hash_array << { project_id: project_id, sample_id: sample.id }
+          end
+          decoupled += 1
+        end
+      end
+      unless hash_array.empty?
+        class ProjectsSample < ActiveRecord::Base; end;
+        ProjectsSample.insert_all(hash_array)
+      end
+    end
+    puts " ... finished copying project ids of #{decoupled.to_s} extracted samples"
+  end
+
   private
 
   ##

test/unit/jobs/sample_data_persist_job_test.rb

@@ -6,13 +6,15 @@ def setup
     @person = FactoryBot.create(:project_administrator)
     User.current_user = @person.user
 
+    @project_id = @person.projects.first.id
+
     @data_file = FactoryBot.create :data_file, content_blob: FactoryBot.create(:sample_type_populated_template_content_blob),
                                      policy: FactoryBot.create(:private_policy), contributor: @person
     refute @data_file.sample_template?
     assert_empty @data_file.possible_sample_types
 
     @sample_type = SampleType.new title: 'from template', uploaded_template: true,
-                                  project_ids: [@person.projects.first.id], contributor: @person
+                                  project_ids: [@project_id], contributor: @person
     @sample_type.content_blob = FactoryBot.create(:sample_type_template_content_blob)
     @sample_type.build_attributes_from_template
     # this is to force the full name to be 2 words, so that one row fails
@@ -47,6 +49,7 @@ def setup
     assert_equal 3, @data_file.extracted_samples.count
     assert_equal @sample_type, @data_file.extracted_samples.first.sample_type
     assert_equal @person, @data_file.extracted_samples.first.contributor
+    assert_equal [@project_id], @data_file.extracted_samples.first.project_ids
   end
 
   test 'persists samples and associate with assay' do

test/unit/sample_test.rb

@@ -746,7 +746,7 @@ class SampleTest < ActiveSupport::TestCase
     refute sample2.can_view?(nil)
   end
 
-  test 'extracted samples inherit projects from data file' do
+  test 'extracted samples copy projects from data file' do
     person = FactoryBot.create(:person)
     create_sample_attribute_type
     data_file = FactoryBot.create :data_file, content_blob: FactoryBot.create(:sample_type_populated_template_content_blob),
@@ -769,9 +769,9 @@ class SampleTest < ActiveSupport::TestCase
       data_file.save!
     end
 
-    assert_equal new_projects.sort, sample.projects.sort
-    assert_equal sample.projects.sort, data_file.projects.sort
-    assert_equal sample.project_ids.sort, data_file.project_ids.sort
+    assert_not_equal new_projects.sort, sample.projects.sort
+    assert_not_equal sample.projects.sort, data_file.projects.sort
+    assert_not_equal sample.project_ids.sort, data_file.project_ids.sort
   end
 
   test 'extracted samples inherit creators from data file' do