Merge pull request #80 from emrojo/bugfix_uuids_as_data_not_supported

Quotes sample information when the data is a uuid but it does not refer

Author: emrojo

app/models/assets/import.rb

@@ -247,11 +247,11 @@ def annotate_container(asset, remote_asset, fact_changes)
         if remote_asset.try(:aliquots)
           remote_asset.aliquots.each do |aliquot|
             updates.replace_remote(asset, 'sample_tube', asset)
-            updates.replace_remote(asset, 'sanger_sample_id', aliquot&.sample&.sanger_sample_id)
+            updates.replace_remote(asset, 'sanger_sample_id', TokenUtil.quote_if_uuid(aliquot&.sample&.sanger_sample_id))
             updates.replace_remote(asset, 'sample_uuid', TokenUtil.quote(aliquot&.sample&.uuid), literal: true)
-            updates.replace_remote(asset, 'sanger_sample_name', aliquot&.sample&.name)
-            updates.replace_remote(asset, 'supplier_sample_name', aliquot&.sample&.sample_metadata&.supplier_name)
-            updates.replace_remote(asset, 'sample_common_name', aliquot&.sample&.sample_metadata&.sample_common_name)
+            updates.replace_remote(asset, 'sanger_sample_name', TokenUtil.quote_if_uuid(aliquot&.sample&.name))
+            updates.replace_remote(asset, 'supplier_sample_name', TokenUtil.quote_if_uuid(aliquot&.sample&.sample_metadata&.supplier_name))
+            updates.replace_remote(asset, 'sample_common_name', TokenUtil.quote_if_uuid(aliquot&.sample&.sample_metadata&.sample_common_name))
           end
         end
       end
@@ -265,6 +265,7 @@ def _annotate_container(asset, remote_asset, fact_changes)
             updates.replace_remote(asset, 'sanger_sample_id', aliquot&.sample&.sanger&.sample_id)
             updates.replace_remote(asset, 'sample_uuid', TokenUtil.quote(aliquot&.sample&.sanger&.sample_uuid), literal: true)
             updates.replace_remote(asset, 'sanger_sample_name', aliquot&.sample&.sanger&.name)
+
             updates.replace_remote(asset, 'supplier_sample_name', aliquot&.sample&.supplier&.sample_name)
           end
         end

lib/token_util.rb

@@ -19,6 +19,11 @@ def self.is_uuid?(str)
     str.kind_of?(String) && !str.match(TokenUtil.UUID_REGEXP).nil?
   end
 
+  def self.quote_if_uuid(str)
+    return quote(str) if is_uuid?(str)
+    return str
+  end
+
   def self.is_valid_fluidx_barcode?(barcode)
     barcode.to_s.starts_with?(fluidx_barcode_prefix)
   end

spec/lib/token_util_spec.rb

@@ -72,6 +72,18 @@
     end
   end
 
+  context '#quote_if_uuid' do
+    it 'quotes the string if is an uuid' do
+      expect(TokenUtil.quote_if_uuid(uuid)).to eq("\"#{uuid}\"")
+    end
+    it 'does not quote the string if is not an uuid' do
+      expect(TokenUtil.quote_if_uuid("text")).to eq("text")
+    end
+    it 'returns nil if the string is nil' do
+      expect(TokenUtil.quote_if_uuid(nil)).to eq(nil)
+    end
+  end
+
   context '#kind_of_asset_id?' do
     it 'detects when an argument is a uuid' do
       expect(TokenUtil.kind_of_asset_id?(uuid)).to eq(true)