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Sheffield BRCA new normal genotype str #179

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Merged
shilpigoeldev merged 1 commit into from
Mar 9, 2026
Merged

Sheffield BRCA new normal genotype str #179

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4 changes: 2 additions & 2 deletions lib/import/brca/providers/sheffield/sheffield_handler.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion lib/import/helpers/brca/providers/rcu/rcu_constants.rb
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Expand Up @@ -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
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18 changes: 18 additions & 0 deletions test/lib/import/brca/providers/sheffield/sheffield_handler_test.rb
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Expand Up @@ -277,6 +277,24 @@ 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
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