fix to how isa-exporter deterimnes whether an attribute is ontology b…

…ased #1632
seek4science · Nov 8, 2023 · 77d78d9 · 77d78d9
1 parent c8bb9ab
commit 77d78d9
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/app/models/sample_attribute.rb b/app/models/sample_attribute.rb
@@ -59,6 +59,11 @@ def linked_custom_metadata_type
     nil
   end
 
+  # whether this attribute is tied to a controlled vocab which has a source ontology
+  def ontology_based?
+    controlled_vocab? && sample_controlled_vocab&.source_ontology.present?
+  end
+
   private
 
   def store_accessor_name

diff --git a/lib/isa_exporter.rb b/lib/isa_exporter.rb
@@ -173,7 +173,7 @@ def convert_ontologies
       sample_types = @investigation.studies.map(&:sample_types) + @investigation.assays.map(&:sample_type)
       sample_types.flatten.each do |sa|
         sa.sample_attributes.each do |atr|
-          source_ontologies << atr.sample_controlled_vocab.source_ontology if atr.sample_attribute_type.ontology?
+          source_ontologies << atr.sample_controlled_vocab.source_ontology if atr.ontology_based?
         end
       end
       source_ontologies.uniq.map { |s| { name: s, file: '', version: '', description: '' } }
@@ -487,7 +487,7 @@ def extract_sample_ids(obj, type)
     end
 
     def get_ontology_details(sample_attribute, label, vocab_term)
-      is_ontology = sample_attribute.sample_attribute_type.ontology?
+      is_ontology = sample_attribute.ontology_based?
       iri = ''
       if is_ontology
         iri =