Merge pull request #2150 from broadinstitute/jb-anndata-ux-reference-…

…file Don't create default cluster fragment for reference AnnData files (SCP-5825)
broadinstitute · Oct 7, 2024 · 7c49585 · 7c49585
2 parents 381701f + ca12d1d
commit 7c49585
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/app/models/ann_data_file_info.rb b/app/models/ann_data_file_info.rb
@@ -193,7 +193,7 @@ def sanitize_fragments!
 
   # create the default cluster data_fragment entries
   def set_default_cluster_fragments!
-    return false if fragments_by_type(:cluster).any?
+    return false if fragments_by_type(:cluster).any? || reference_file
 
     default_obsm_keys = AnnDataIngestParameters::PARAM_DEFAULTS[:obsm_keys]
     default_obsm_keys.each do |obsm_key_name|

diff --git a/app/models/ingest_job.rb b/app/models/ingest_job.rb
@@ -350,7 +350,7 @@ def poll_for_completion(run_at: 1.minute.from_now)
     if done? && !failed?
       Rails.logger.info "IngestJob poller: #{pipeline_name} is done!"
       Rails.logger.info "IngestJob poller: #{pipeline_name} status: #{current_status}"
-      unless special_action? || action == :ingest_anndata
+      unless special_action? || (action == :ingest_anndata && study_file.is_viz_anndata?)
         study_file.update(parse_status: 'parsed')
         study_file.bundled_files.each { |sf| sf.update(parse_status: 'parsed') }
       end

diff --git a/test/models/ann_data_file_info_test.rb b/test/models/ann_data_file_info_test.rb
@@ -127,14 +127,19 @@ def generate_id
   end
 
   test 'should set default cluster fragments' do
-    ann_data_info = AnnDataFileInfo.new
+    ann_data_info = AnnDataFileInfo.new(reference_file: false)
     assert ann_data_info.valid?
     default_keys = AnnDataIngestParameters::PARAM_DEFAULTS[:obsm_keys]
     default_keys.each do |obsm_key_name|
       name = obsm_key_name.delete_prefix('X_')
       matcher = { data_type: :cluster, name:, obsm_key_name: }.with_indifferent_access
       assert ann_data_info.find_fragment(**matcher).present?
     end
+    # ensure non-parseable AnnData files don't create fragment
+    reference_anndata = AnnDataFileInfo.new
+    assert reference_anndata.valid?
+    assert_empty reference_anndata.data_fragments
+    assert_empty reference_anndata.obsm_key_names
   end
 
   test 'should validate data fragments' do