Merge pull request #2296 from broadinstitute/development

Release 1.101.2

Author: bistline

app/models/cluster_group.rb

@@ -74,6 +74,8 @@ def by_name_and_type(name, type, subsample_threshold=nil)
       'cell_annotations.type' => %w(group numeric)
   }
 
+  before_update :update_cluster_in_study_options
+
   # method to return a single data array of values for a given data array name, annotation name, and annotation value
   # gathers all matching data arrays and orders by index, then concatenates into single array
   # can also load subsample arrays by supplying optional subsample_threshold
@@ -166,6 +168,21 @@ def can_visualize_cell_annotation?(annotation)
     end
   end
 
+  # whenever a cluster is updated, we need to update the study default_options ordering to reflect this
+  def update_cluster_in_study_options
+    return unless name_changed?
+
+    study = self.study
+    list_name = spatial? ? :spatial_order : :cluster_order
+    return unless study.present? && study.default_options[list_name].present?
+
+    old_name, new_name = name_change
+    idx = study.default_options[list_name].index(old_name)
+    idx ? study.default_options[list_name][idx] = new_name : study.default_options[list_name] << new_name
+    study.save(validate: false) # skip validations to avoid circular dependency issues
+    CacheRemovalJob.new(study.accession).delay.perform
+  end
+
   # method used during parsing to generate representative sub-sampled data_arrays for rendering
   #
   # annotation_name: name of annotation to subsample off of

app/models/delete_queue_job.rb

@@ -36,6 +36,7 @@ def perform
       case file_type
       when 'Cluster'
         cluster_group = ClusterGroup.find_by(study:, study_file_id: object.id)
+        study.update_cluster_order(cluster_group, action: :remove)
         delete_differential_expression_results(study:, study_file: object)
         delete_parsed_data(object.id, study.id, ClusterGroup, DataArray)
         delete_dot_plot_data(study.id, query: { cluster_group_id: cluster_group&.id })

app/models/ingest_job.rb

@@ -543,6 +543,7 @@ def set_study_default_options
     when 'Cluster'
       set_default_cluster
       set_default_annotation
+      update_cluster_ordering
     when 'AnnData'
       set_default_cluster
       set_default_annotation
@@ -601,6 +602,12 @@ def set_default_cluster
     end
   end
 
+  # update the study.default_cluster_order after clustering finishes ingesting
+  def update_cluster_ordering
+    cluster = study.cluster_groups.by_name(cluster_name_by_file_type)
+    study.update_cluster_order(cluster, action: :append)
+  end
+
   # set the point count on a cluster group after successful ingest
   #
   # * *yields*

app/models/study.rb

@@ -1324,6 +1324,24 @@ def default_spatial_order
     default_options[:spatial_order] || spatial_cluster_groups.map(&:name)
   end
 
+  # handle updates to the cluster order menus
+  def update_cluster_order(cluster, action:)
+    return nil unless cluster
+
+    list_name = cluster.spatial? ? :spatial_order : :cluster_order
+    case action.to_sym
+    when :append
+      new_list = send("default_#{list_name}").push(cluster.name).uniq
+    when :remove
+      new_list = send("default_#{list_name}").reject { |c| c == cluster.name }
+    else
+      return nil # invalid action
+    end
+    default_options[list_name] = new_list
+    save
+    CacheRemovalJob.new(accession).perform
+  end
+
   ###
   #
   # INSTANCE VALUE SETTERS & GETTERS

test/models/delete_queue_job_test.rb

@@ -287,4 +287,24 @@ class DeleteQueueJobTest < ActiveSupport::TestCase
     study.reload
     assert_empty study.expression_matrix_cells(matrix, matrix_type: 'raw')
   end
+
+  test 'should update cluster order when deleting cluster file' do
+    study = FactoryBot.create(:detached_study,
+                              name_prefix: 'Cluster Order Update Test',
+                              user: @user,
+                              test_array: @@studies_to_clean)
+    cell_input = { x: [1, 2, 3], y: [4, 5, 6], cells: %w[A B C] }
+    1.upto(3) do |i|
+      FactoryBot.create(:cluster_file, name: "cluster_#{i}.txt", study:, cell_input:)
+    end
+    assert_equal 3, study.cluster_groups.count
+    study.default_options[:cluster_order] = study.default_cluster_order
+    study.save!
+
+    file = study.cluster_groups.first.study_file
+    DeleteQueueJob.new(file).perform
+    study.reload
+    assert_equal %w[cluster_2.txt cluster_3.txt], study.default_cluster_order,
+                 'Did not update cluster order after deleting a cluster file'
+  end
 end

test/models/study_test.rb

@@ -252,4 +252,33 @@ class StudyTest < ActiveSupport::TestCase
     study.set_cell_count
     assert_equal 4, study.cell_count
   end
+
+  test 'should update cluster order' do
+    study = FactoryBot.create(:detached_study,
+                              user: @user,
+                              name_prefix: 'Cluster Order Test',
+                              test_array: @@studies_to_clean)
+    assert_empty study.default_cluster_order
+    cell_input = {
+      x: [1, 4, 6],
+      y: [7, 5, 3],
+      cells: %w(A B C)
+    }
+    FactoryBot.create(:cluster_file, name: 'cluster_example.txt', study:, cell_input:)
+    cluster = study.cluster_groups.first
+    study.update_cluster_order(cluster, action: :append)
+    study.reload
+    assert_equal [cluster.name], study.default_cluster_order
+    FactoryBot.create(:cluster_file, name: 'cluster_2_example.txt', study:, cell_input:)
+    new_cluster = study.cluster_groups.last
+    study.update_cluster_order(new_cluster, action: :append)
+    study.reload
+    assert_equal [cluster.name, new_cluster.name], study.default_cluster_order
+
+    # test renaming cluster directly
+    new_name = 'Renamed Cluster'
+    cluster.update(name: new_name)
+    study.reload
+    assert_equal [new_name, new_cluster.name], study.default_cluster_order
+  end
 end