Bugfix/regexp column names

CHANGELOG.md

@@ -1,5 +1,8 @@
 ## [Unreleased]
-* no unreleased changes
+
+### Fixed
+* Fix bug in VCF metadata
+* Fix bug where table columns are mutated by a regexp column
 
 ## 11.3.0/ 2025-02-11
 ### Fixed

lib/ndr_import/table.rb

@@ -34,6 +34,8 @@ def initialize(options = {})
       end
 
       @row_index = 0
+      # Keep a copy of the original column mappings for use later if columns are mutated
+      @original_columns = @columns.deep_dup
     end
 
     def match(filename, tablename)
@@ -51,12 +53,18 @@ def transform(lines, &block)
       @header_valid = false
       @header_best_guess = nil
       @notifier.try(:started)
-
       last_col = last_column_to_transform
       skip_footer_lines(lines, footer_lines).each do |line|
         line.is_a?(Array) ? process_line(line[0..last_col], &block) : process_line(line, &block)
       end
 
+      # @columns may have been mutated where column is a regular expression.
+      # We want to restore `@columns` back to its original state, so the column regexp
+      # will work on the next file
+      @columns = @original_columns
+      # Also ensure that @masked_mappings are recalculated
+      @masked_mappings = nil
+
       @notifier.try(:finished)
     end
 

lib/ndr_import/vcf/table.rb

@@ -5,10 +5,14 @@ module Vcf
     # Syntatic sugar to ensure `header_lines` and `footer_lines` are 1 and 0 respectively.
     # All other Table logic is inherited from `NdrImport::Table`
     class Table < ::NdrImport::Table
+      VCF_OPTIONS = %w[vcf_file_metadata].freeze
+
       def self.all_valid_options
-        super - %w[delimiter header_lines footer_lines] + %w[vcf_file_metadata]
+        super - %w[delimiter header_lines footer_lines] + VCF_OPTIONS
       end
 
+      attr_reader(*VCF_OPTIONS)
+
       def header_lines
         1
       end

test/universal_importer_helper_test.rb

@@ -222,6 +222,30 @@ def setup
     assert_equal 4, table_enums.first.last.count
   end
 
+  test 'mutated columns get reset' do
+    table_mappings = [
+      NdrImport::Table.new(filename_pattern: /\.csv\z/i,
+                           canonical_name: 'a_table',
+                           header_lines: 1,
+                           footer_lines: 0,
+                           klass: 'SomeTestClass',
+                           columns: [{ 'column' => 'one' },
+                                     { 'column' => 'two' },
+                                     { 'column' => /\A[AB]\d{3}\z/i }])
+    ]
+    source_file = @permanent_test_files.join('regex_column_names.zip')
+    @test_importer.stubs(:get_table_mapping).returns(table_mappings.first)
+    mapped_rows = []
+    @test_importer.extract(source_file) { |table, rows| mapped_rows << table.transform(rows).to_a }
+
+    expected_mapped_data = [
+      [['SomeTestClass', { rawtext: { 'one' => '2', 'two' => '2', 'b456' => '2' } }, 1]],
+      [['SomeTestClass', { rawtext: { 'one' => '1', 'two' => '1', 'a123' => '1' } }, 1]]
+    ]
+
+    assert_equal expected_mapped_data, mapped_rows
+  end
+
   test 'get_notifier' do
     class TestImporterWithoutNotifier
       include NdrImport::UniversalImporterHelper