Updates to catch new genotype str (#179)

Author: shilpigoeldev

lib/import/brca/providers/sheffield/sheffield_handler.rb

@@ -391,12 +391,12 @@ def process_fullscreen_records(genotype, record, genotypes)
             genotype_str = record.raw_fields['genotype']
             if mlpa_fail?(record)
               process_mlpa_fail_full_screen(genotype, record, genotypes)
+            elsif positive_cdna?(genotype_str) || positive_exonvariant?(genotype_str)
+              process_variant_fs_records(genotype, record, genotypes)
             elsif normal?(record)
               process_normal_full_screen(genotype, record, genotypes)
             elsif failed_test?(record)
               process_failed_full_screen(genotype, record, genotypes)
-            elsif positive_cdna?(genotype_str) || positive_exonvariant?(genotype_str)
-              process_variant_fs_records(genotype, record, genotypes)
             else
               # else give a test status of 4 (unknown)
               add_other_genes_with_status(@genes_set, genotype, genotypes, 4)

lib/import/helpers/brca/providers/rcu/rcu_constants.rb

@@ -246,7 +246,7 @@ module RcuConstants
                                   ([a-z\s]+(?<mutationtype>del(etion)?|duplicati?on|dup(licated)?))?/ix
 
             NORMAL_VAR_REGEX = %r{(?<not>no|not)[a-z /]+
-                                  (?<det>detect|report|detet|mutation)+}ix
+                                  (?<det>detect|report|detet|mutation|identified)+}ix
             # rubocop:enable Lint/MixedRegexpCaptureTypes
           end
         end

test/lib/import/brca/providers/sheffield/sheffield_handler_test.rb

@@ -293,6 +293,24 @@ def setup
     assert_equal 'Targeted BRCA mutation test', genotypes[0].attribute_map['genetictestscope']
   end
 
+  test 'normal_full_screen_not_identified_case' do
+    normal_fs_not_identfied_record = build_raw_record('pseudo_id1' => 'bob')
+    normal_fs_not_identfied_record.raw_fields['genetictestscope'] = 'R208 :: BRCA1 and BRCA2 testing at high familial risk'
+    normal_fs_not_identfied_record.raw_fields['karyotypingmethod'] = 'R208.1 :: NGS in Leeds'
+    normal_fs_not_identfied_record.raw_fields['genotype'] = 'A hereditary (germline) genetic cause for this individual’s cancer has not been identified;'
+    @handler.add_test_scope_from_geno_karyo(@genotype, normal_fs_not_identfied_record)
+    genotypes = @handler.process_variants_from_record(@genotype, normal_fs_not_identfied_record)
+    assert_equal 3, genotypes.size
+    assert_equal 1, genotypes[0].attribute_map['teststatus']
+    assert_equal 1, genotypes[1].attribute_map['teststatus']
+    assert_equal 1, genotypes[2].attribute_map['teststatus']
+    assert_equal 7, genotypes[0].attribute_map['gene']
+    assert_equal 8, genotypes[1].attribute_map['gene']
+    assert_equal 3186, genotypes[2].attribute_map['gene']
+    assert_nil  genotypes[0].attribute_map['proteinimpact']
+    assert_nil  genotypes[1].attribute_map['codingdnasequencechange']
+  end
+
   private
 
   def clinical_json