test coverage, removing frozen_string_literal re: callback errors

Author: bistline

app/lib/dot_plot_service.rb

@@ -1,10 +1,7 @@
-# frozen_string_literal: true
-
 # service that handles preprocessing expression/annotation data to speed up dot plot rendering
 class DotPlotService
   # main handler for launching ingest job to process expression data into DotPlotGene objects
-  # since the study can have only one processed matrix, this will only run if the study is eligible
-  # and we do not need to specify which matrix/metadata file to process
+  # since the study can have only one processed matrix/metadata file, this will only run if the study is eligible
   #
   # * *params*
   #   - +study+ (Study) => the study that owns the data
@@ -40,35 +37,37 @@ def self.run_process_dot_plot_genes(study, cluster_group, user)
   # * *returns*
   #   - (DotPlotGeneIngestParameters) => a parameters object with the necessary file paths and metadata
   def self.create_params_object(cluster_group, expression_file, metadata_file)
-    params = DotPlotGeneIngestParameters.new(
+    params = {
       cluster_group_id: cluster_group.id,
-      cluster_file: RequestUtils.cluster_file_url(cluster_group),
-      matrix_file_type: expression_file.file_type == 'Expression Matrix' ? 'dense' : 'mtx'
-    )
+      cluster_file: RequestUtils.cluster_file_url(cluster_group)
+    }
     case expression_file.file_type
     when 'Expression Matrix'
-      params.matrix_file_path = expression_file.gs_url
-      params.cell_metadata_file = metadata_file.gs_url
+      params[:matrix_file_type] = 'dense'
+      params[:matrix_file_path] = expression_file.gs_url
+      params[:cell_metadata_file] = metadata_file.gs_url
     when 'MM Coordinate Matrix'
+      params[:matrix_file_type] = 'mtx'
       genes_file = expression_file.bundled_files.detect { |f| f.file_type == '10X Genes File' }
       barcodes_file = expression_file.bundled_files.detect { |f| f.file_type == '10X Barcodes File' }
-      params.matrix_file_path = expression_file.gs_url
-      params.cell_metadata_file = metadata_file.gs_url
-      params.gene_file = genes_file.gs_url
-      params.barcode_file = barcodes_file.gs_url
+      params[:matrix_file_path] = expression_file.gs_url
+      params[:cell_metadata_file] = metadata_file.gs_url
+      params[:gene_file] = genes_file.gs_url
+      params[:barcode_file] = barcodes_file.gs_url
     when 'AnnData'
-      params.cell_metadata_file = RequestUtils.data_fragment_url(metadata_file, 'metadata')
-      params.matrix_file_path = RequestUtils.data_fragment_url(
+      params[:matrix_file_type] = 'mtx' # extracted expression for AnnData is in MTX format
+      params[:cell_metadata_file] = RequestUtils.data_fragment_url(metadata_file, 'metadata')
+      params[:matrix_file_path] = RequestUtils.data_fragment_url(
         expression_file, 'matrix', file_type_detail: 'processed'
       )
-      params.gene_file = RequestUtils.data_fragment_url(
+      params[:gene_file] = RequestUtils.data_fragment_url(
         expression_file, 'features', file_type_detail: 'processed'
       )
-      params.barcode_file = RequestUtils.data_fragment_url(
+      params[:barcode_file] = RequestUtils.data_fragment_url(
         expression_file, 'barcodes', file_type_detail: 'processed'
       )
     end
-    params
+    DotPlotGeneIngestParameters.new(**params)
   end
 
   # determine study eligibility - can only have one processed matrix and be able to visualize clusters

app/models/dot_plot_gene_ingest_parameters.rb

@@ -1,5 +1,3 @@
-# frozen_string_literal: true
-
 # class to hold parameters specific to ingest job for computing dot plot gene metrics
 class DotPlotGeneIngestParameters
   include ActiveModel::Model

test/models/dot_plot_gene_ingest_parameters_test.rb

@@ -0,0 +1,66 @@
+require 'test_helper'
+
+class DotPlotGeneIngestParametersTest < ActiveSupport::TestCase
+  before(:all) do
+    cluster_group_id = BSON::ObjectId.new
+    @dense_options = {
+      cell_metadata_file: 'gs://test_bucket/metadata.tsv',
+      cluster_file: 'gs://test_bucket/cluster.tsv',
+      cluster_group_id:,
+      matrix_file_path: 'gs://test_bucket/dense.tsv',
+      matrix_file_type: 'dense',
+    }
+
+    @sparse_options = {
+      cell_metadata_file: 'gs://test_bucket/metadata.tsv',
+      cluster_file: 'gs://test_bucket/cluster.tsv',
+      cluster_group_id:,
+      matrix_file_path: 'gs://test_bucket/sparse.tsv',
+      matrix_file_type: 'mtx',
+      gene_file: 'gs://test_bucket/genes.tsv',
+      barcode_file: 'gs://test_bucket/barcodes.tsv'
+    }
+
+    @anndata_options = {
+      cell_metadata_file: 'gs://test_bucket/metadata.tsv',
+      cluster_file: 'gs://test_bucket/cluster.tsv',
+      cluster_group_id:,
+      matrix_file_path: 'gs://test_bucket/matrix.h5ad',
+      matrix_file_type: 'mtx',
+      gene_file: 'gs://test_bucket/genes.tsv',
+      barcode_file: 'gs://test_bucket/barcodes.tsv'
+    }
+  end
+
+  test 'should create and validate parameters' do
+    [@dense_options, @sparse_options, @anndata_options].each do |options|
+      params = DotPlotGeneIngestParameters.new(**options)
+      assert params.valid?
+      assert_equal DotPlotGeneIngestParameters::PARAM_DEFAULTS[:machine_type], params.machine_type
+      if options[:matrix_file_type] == 'mtx'
+        assert params.gene_file.present?
+        assert params.barcode_file.present?
+      else
+        assert params.gene_file.nil?
+        assert params.barcode_file.nil?
+      end
+    end
+  end
+
+  test 'should find associated cluster group' do
+    user = FactoryBot.create(:user, test_array: @@users_to_clean)
+    study = FactoryBot.create(:detached_study,
+                              name_prefix: 'DotPlotGeneIngestParameters Test',
+                              user:,
+                              test_array: @@studies_to_clean)
+    FactoryBot.create(:cluster_file,
+                      name: 'cluster.txt',
+                      study:,
+                      cell_input: { x: [1, 4, 6], y: [7, 5, 3], cells: %w[A B C] }
+    )
+    cluster_group = ClusterGroup.find_by(study:)
+    new_options = @dense_options.dup.merge(cluster_group_id: cluster_group.id)
+    params = DotPlotGeneIngestParameters.new(**new_options)
+    assert_equal cluster_group, params.cluster_group
+  end
+end