Reload failed SequencingExperiment

Author: lmrodriguezr

app/models/genome/external_resources.rb

@@ -51,7 +51,6 @@ def reload_source_json!
   # String (or +nil+)
   def external_sra_to_biosample(acc)
     sr = SequencingExperiment.by_sra(acc)
-    sr.reload_metadata! unless sr.metadata_xml.present?
     ephemeral_report << (sr.try(:ephemeral_report) || 'No SRA experiments')
     sr.try(:biosample_accession)
   end
@@ -67,8 +66,7 @@ def external_biosample_to_sra(acc)
     ng = Nokogiri::XML(body)
     ng.xpath('//result/entries/entry').map do |exp|
       sra_acc = exp['acc'] || exp['id'] or next
-      sr = SequencingExperiment.find_or_create_by(sra_accession: sra_acc)
-      sr.reload_metadata! unless sr.metadata_xml.present?
+      sr = SequencingExperiment.by_sra(sra_acc)
       ephemeral_report << (sr.try(:ephemeral_report) || 'No SRA experiments')
     end
   end

app/models/sequencing_experiment.rb

@@ -10,11 +10,15 @@ class SequencingExperiment < ApplicationRecord
 
   class << self
     def by_biosample(acc)
-      SequencingExperiment.where(biosample_accession: acc)
+      SequencingExperiment
+        .where(biosample_accession: acc)
+        .tap(&:load_and_save_metadata!)
     end
 
     def by_sra(acc)
-      SequencingExperiment.find_or_create_by(sra_accession: acc)
+      SequencingExperiment
+        .find_or_create_by(sra_accession: acc)
+        .tap(&:load_and_save_metadata!)
     end
   end
 
@@ -61,6 +65,13 @@ def amplicon?
     %w[amplicon].include? strategy.downcase
   end
 
+  def load_and_save_metadata!
+    unless metadata_xml.present?
+      reload_metadata!
+      save
+    end
+  end
+
   private
 
   def load_from_sra_accession