Fixed issue with taxon assignment during isolate import.

Gemfile.lock

@@ -484,6 +484,7 @@ GEM
     yard (0.9.34)
 
 PLATFORMS
+  ruby
   x86_64-linux
 
 DEPENDENCIES

app/models/isolate.rb

@@ -108,11 +108,22 @@ def self.import(file_path, project_id)
       collection ||= Collection.find_by(acronym: row['Collection'])
       individual.collection = collection if collection
 
+      if row['Family']
+        family = Taxon.find_or_create_by(scientific_name: row['Family'], taxonomic_rank: :is_family) if row['Family']
+        taxon = family
+      end
+
       if row['Genus'] && row['Species']
+        species = Taxon.find_or_create_by(scientific_name: [row['Genus'], row['Species']].join(' '),
+                                          taxonomic_rank: :is_species)
+        species.update(parent: family)
+
+        taxon = species
+
         if row['Subspecies']
-          taxon = Taxon.find_or_create_by(scientific_name: [row['Genus'], row['Species'], row['Subspecies']].join(' '))
-        else
-          taxon = Taxon.find_or_create_by(scientific_name: [row['Genus'], row['Species']].join(' '))
+          taxon = Taxon.find_or_create_by(scientific_name: [row['Genus'], row['Species'], row['Subspecies']].join(' '),
+                                          taxonomic_rank: :is_subspecies)
+          taxon.update(parent: species)
         end
       end
 

app/models/ngs_run.rb

@@ -185,7 +185,7 @@ def import(results_path)
           # Download result file
           sftp.download!(results_path, "#{Rails.root}/#{self.name}_out.zip")
 
-          #TODO: Maybe add possibility to use AWS copy here in case of a reimport of data at a later point
+          #TODO: Maybe add possibility to use local/AWS copy here in case of a reimport of data at a later point
 
           # Unzip results
           Zip::File.open("#{Rails.root}/#{self.name}_out.zip") do |zip_file|