Metadata: Update values to strings

app/services/samples/metadata/update_service.rb

@@ -24,8 +24,6 @@ def execute # rubocop:disable Metrics/MethodLength
 
         validate_metadata_param
 
-        transform_metadata_keys
-
         @sample.with_lock do
           perform_metadata_update
           @sample.save
@@ -69,14 +67,10 @@ def validate_metadata_param
               I18n.t('services.samples.metadata.empty_metadata', sample_name: @sample.name)
       end
 
-      def transform_metadata_keys
-        # Without transforming and downcasing keys,
-        # issues with overwritting can occur and multiples of the same key can appear
-        @metadata = @metadata.transform_keys { |key| key.to_s.downcase }
-      end
-
       def perform_metadata_update
         @metadata.each do |key, value|
+          key = key.to_s.downcase
+          value = value.to_s # remove data types
           if value.blank?
             if @sample.metadata.key?(key)
               @sample.metadata.delete(key)

db/migrate/20241003193845_update_metadata_values_to_text.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+# Update all metadata values to be text
+class UpdateMetadataValuesToText < ActiveRecord::Migration[7.2]
+  def change
+    reversible do |dir|
+      dir.up do
+        execute <<~SQL.squish
+          UPDATE samples SET metadata = metadata::text::jsonb;
+        SQL
+      end
+    end
+  end
+end

db/seeds.rb

@@ -76,7 +76,7 @@ def seed_namespace_group_links(user, namespace, group, group_access_level)
 def fake_metadata # rubocop:disable Metrics/MethodLength
   indsc_abbr = %w[SRR ERR DRR]
   random_abbr = indsc_abbr.sample
-  random_date = Faker::Date.between(from: 2.years.ago.to_s, to: Time.zone.today)
+  random_date = Faker::Date.between(from: 2.years.ago, to: Time.zone.today)
 
   {
     'WGS_id' => Faker::Number.number(digits: 10),

test/graphql/create_group_mutation_test.rb

@@ -148,7 +148,7 @@ def setup
 
     group = Group.last
     # Top level group
-    assert_equal nil, group.parent
+    assert_nil group.parent
     assert_equal 'new-group-one', group.path
     assert_equal 'new-group-one', group.full_path
   end

test/graphql/update_sample_metadata_test.rb

@@ -283,4 +283,46 @@ def setup
     ]
     assert_equal expected_error, data['errors']
   end
+
+  test 'updateSampleMetadata mutation should convert keys and values to strings and lower case them' do
+    result = IridaSchema.execute(UPDATE_SAMPLE_METADATA_BY_SAMPLE_ID_MUTATION,
+                                 context: { current_user: @user, token: @api_scope_token },
+                                 variables: { sampleId: @sample.to_global_id.to_s,
+                                              metadata: { integer: 1, True_Boolean: true, false_boolean: false,
+                                                          date: Date.parse('2024-03-11'), string: 'A Test', empty: '',
+                                                          nil: nil } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['updateSampleMetadata']
+
+    assert_not_empty data, 'updateSampleMetadata should be populated when no authorization errors'
+    assert_empty data['errors']
+
+    assert_not_empty data['status']
+    assert_not_empty data['status'][:added]
+    assert data['status'][:added].include?('integer')
+    assert data['status'][:added].include?('true_boolean')
+    assert data['status'][:added].include?('false_boolean')
+    assert data['status'][:added].include?('date')
+    assert data['status'][:added].include?('string')
+    assert_not data['status'][:added].include?('empty')
+    assert_not data['status'][:added].include?('nil')
+
+    assert_not_empty data['sample']
+    assert_not_empty data['sample']['metadata']
+    assert_not_empty data['sample']['metadata']['integer']
+    assert data['sample']['metadata'].include?('integer')
+    assert_equal '1', data['sample']['metadata']['integer']
+    assert data['sample']['metadata'].include?('true_boolean')
+    assert_equal 'true', data['sample']['metadata']['true_boolean']
+    assert data['sample']['metadata'].include?('false_boolean')
+    assert_equal 'false', data['sample']['metadata']['false_boolean']
+    assert data['sample']['metadata'].include?('date')
+    assert_equal '2024-03-11', data['sample']['metadata']['date']
+    assert data['sample']['metadata'].include?('string')
+    assert_equal 'A Test', data['sample']['metadata']['string']
+    assert_not data['sample']['metadata'].include?('empty')
+    assert_not data['sample']['metadata'].include?('nil')
+  end
 end

test/services/samples/metadata/file_import_service_test.rb

@@ -139,13 +139,15 @@ def setup
         xls = File.new('test/fixtures/files/metadata/valid.xls', 'r')
         params = { file: xls, sample_id_column: 'sample_name' }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, params).execute
-        assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
+        assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] },
-                       @sample2.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
+                       @sample2.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] } }, response)
-        assert_equal({ 'metadatafield1' => 10, 'metadatafield2' => 20, 'metadatafield3' => 30 },
+        assert_equal({ 'metadatafield1' => '10', 'metadatafield2' => '2024-01-04', 'metadatafield3' => 'true',
+                       'metadatafield4' => 'A Test' },
                      @sample1.reload.metadata)
-        assert_equal({ 'metadatafield1' => 15, 'metadatafield2' => 25, 'metadatafield3' => 35 },
+        assert_equal({ 'metadatafield1' => '15', 'metadatafield2' => '2024-12-31', 'metadatafield3' => 'false',
+                       'metadatafield4' => 'Another Test' },
                      @sample2.reload.metadata)
       end
 
@@ -155,13 +157,15 @@ def setup
         xlsx = File.new('test/fixtures/files/metadata/valid.xlsx', 'r')
         params = { file: xlsx, sample_id_column: 'sample_name' }
         response = Samples::Metadata::FileImportService.new(@project.namespace, @john_doe, params).execute
-        assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
+        assert_equal({ @sample1.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] },
-                       @sample2.name => { added: %w[metadatafield1 metadatafield2 metadatafield3],
+                       @sample2.name => { added: %w[metadatafield1 metadatafield2 metadatafield3 metadatafield4],
                                           updated: [], deleted: [], not_updated: [], unchanged: [] } }, response)
-        assert_equal({ 'metadatafield1' => 10, 'metadatafield2' => 20, 'metadatafield3' => 30 },
+        assert_equal({ 'metadatafield1' => '10', 'metadatafield2' => '2024-01-04', 'metadatafield3' => 'true',
+                       'metadatafield4' => 'A Test' },
                      @sample1.reload.metadata)
-        assert_equal({ 'metadatafield1' => 15, 'metadatafield2' => 25, 'metadatafield3' => 35 },
+        assert_equal({ 'metadatafield1' => '15', 'metadatafield2' => '2024-12-31', 'metadatafield3' => 'false',
+                       'metadatafield4' => 'Another Test' },
                      @sample2.reload.metadata)
       end
 

test/services/workflow_executions/completion_service_test.rb

@@ -350,10 +350,10 @@ def setup # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
                         'organism' => 'the organism' }
       old_metadata2 = { 'metadatafield2' => 'value2',
                         'organism' => 'some organism' }
-      new_metadata1 = { 'number' => 1,
+      new_metadata1 = { 'number' => '1',
                         'metadatafield1' => 'value1',
                         'organism' => 'an organism' }
-      new_metadata2 = { 'number' => 2,
+      new_metadata2 = { 'number' => '2',
                         'metadatafield2' => 'value2',
                         'organism' => 'a different organism' }
       # Test start

test/system/projects/samples_test.rb

@@ -1597,7 +1597,7 @@ class SamplesTest < ApplicationSystemTestCase
         click_on I18n.t('shared.samples.metadata.file_imports.success.ok_button')
       end
 
-      assert_selector 'table thead tr th', count: 9
+      assert_selector 'table thead tr th', count: 10
     end
 
     test 'should not import metadata via invalid file type' do