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Add new variable into Sheffield regex #178

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Merged
NImeson merged 2 commits into from
Feb 27, 2026
Merged

Add new variable into Sheffield regex #178

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a616d37
added new variable into regex, reorders process_fullscreen_records to…
NImeson Feb 23, 2026
7cad43c
added aditional normal tes for new variable
NImeson Feb 25, 2026
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8 changes: 5 additions & 3 deletions lib/import/colorectal/providers/sheffield/sheffield_handler_colorectal.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -219,17 +219,19 @@ def no_scope?(genocolorectal)

def process_fullscreen_records(genocolorectal, record, genocolorectals)
genotype_str = record.raw_fields['genotype']
if normal?(genotype_str)
process_normal_full_screen(genocolorectal, genocolorectals)
elsif positive_cdna?(genotype_str) || positive_exonvariant?(genotype_str)
if positive_cdna?(genotype_str) || positive_exonvariant?(genotype_str)
process_variant_fs_records(genocolorectal, record, genocolorectals)
elsif only_protein_impact?(genotype_str)
process_only_protein_rec(genocolorectal, record, genocolorectals)
positive_gene = get_gene(record)
negative_genes = @genes_set - positive_gene
add_other_genes_with_status(negative_genes, genocolorectal, genocolorectals, 1)
elsif normal?(genotype_str)
process_normal_full_screen(genocolorectal, genocolorectals)
elsif genotype_str.scan(/see\sbelow|comments/ix).size.positive?
add_other_genes_with_status(@genes_set, genocolorectal, genocolorectals, 4)
else # else give a test status of 4 (unknown)
add_other_genes_with_status(@genes_set, genocolorectal, genocolorectals, 4)
end
end

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2 changes: 1 addition & 1 deletion lib/import/helpers/colorectal/providers/rcu/constants.rb
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Expand Up @@ -203,7 +203,7 @@ module Constants

# rubocop:disable Lint/MixedRegexpCaptureTypes
NORMAL_VAR_REGEX = %r{(?<not>no|not)[a-z /]+
(?<det>detected|reported|deteected|deteceted|present)+}ix.freeze
(?<det>detected|reported|deteected|deteceted|present|identified)+}ix.freeze

CDNA_REGEX = /c\.\[?(?<cdna>
([0-9]+[+>_-][0-9][+>_-][0-9]+[+>_-][0-9][ACGTdelinsup]+)|
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16 changes: 16 additions & 0 deletions test/lib/import/brca/providers/sheffield/sheffield_handler_test.rb
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Expand Up @@ -78,6 +78,22 @@ def setup
assert_nil genotypes[1].attribute_map['codingdnasequencechange']
end

test 'normal_full_screen_new_variable' do
normal_fs_record = build_raw_record('pseudo_id1' => 'bob')
normal_fs_record.raw_fields['genetictestscope'] = 'Breast & Ovarian cancer panel'
normal_fs_record.raw_fields['karyotypingmethod'] = 'BRCA1 and BRCA2'
normal_fs_record.raw_fields['genotype'] = 'A genetic cause for this individuals clinical presentation has not been identified'
@handler.add_test_scope_from_geno_karyo(@genotype, normal_fs_record)
genotypes = @handler.process_variants_from_record(@genotype, normal_fs_record)
assert_equal 2, genotypes.size
assert_equal 1, genotypes[0].attribute_map['teststatus']
assert_equal 1, genotypes[1].attribute_map['teststatus']
assert_equal 7, genotypes[0].attribute_map['gene']
assert_equal 8, genotypes[1].attribute_map['gene']
assert_nil genotypes[0].attribute_map['proteinimpact']
assert_nil genotypes[1].attribute_map['codingdnasequencechange']
end

test 'failed_full_screen' do
fail_fs_record = build_raw_record('pseudo_id1' => 'bob')
fail_fs_record.raw_fields['genetictestscope'] = 'Breast & Ovarian cancer panel'
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