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Feature/31243/leeds crc refactor (#76)
* Initial commit to new Leeds CRC code * Leeds CRC refactoring QA final code * rubocop fixes * rubocop fixes * corrected script command * Review comment , moved batch level code * PR review comments changes * More comments added * PR review comments changes
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lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb
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lib/import/helpers/colorectal/providers/rr8/constants.rb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| module Import | ||
| module Helpers | ||
| module Colorectal | ||
| module Providers | ||
| module Rr8 | ||
| # Constants used by Leeds Colorectal | ||
| module Constants | ||
| TEST_SCOPE_MAP_COLO = { 'carrier test' => :targeted_mutation, | ||
| 'confirmation' => :targeted_mutation, | ||
| 'diagnostic' => :full_screen, | ||
| 'diagnostic; fap' => :full_screen, | ||
| 'diagnostic; lynch' => :full_screen, | ||
| 'diagnostic; pms2' => :full_screen, | ||
| 'predictive' => :targeted_mutation, | ||
| 'predictive test' => :targeted_mutation, | ||
| 'r209.1' => :full_screen, | ||
| 'r209.2' => :full_screen, | ||
| 'r210.5' => :full_screen, | ||
| 'r210.2' => :full_screen, | ||
| 'r211.1' => :full_screen, | ||
| 'r211.2' => :full_screen, | ||
| 'familial' => :targeted_mutation }.freeze | ||
|
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| TEST_TYPE_MAP_COLO = { 'carrier test' => :carrier, | ||
| 'diagnostic' => :diagnostic, | ||
| 'diagnostic; fap' => :diagnostic, | ||
| 'diagnostic; lynch' => :diagnostic, | ||
| 'confirmation' => :diagnostic, | ||
| 'predictive' => :predictive, | ||
| 'predictive test' => :predictive, | ||
| 'familial' => :predictive }.freeze | ||
|
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||
| PASS_THROUGH_FIELDS = %w[age consultantcode | ||
| providercode | ||
| receiveddate | ||
| authoriseddate | ||
| requesteddate | ||
| servicereportidentifier | ||
| organisationcode_testresult | ||
| specimentype].freeze | ||
| FIELD_NAME_MAPPINGS = { 'consultantcode' => 'practitionercode', | ||
| 'instigated_date' => 'requesteddate' }.freeze | ||
|
|
||
| GENES = 'APC|ATM|BAP1|BMPR1A|BRCA1|BRCA2|CHEK2|EPCAM|FH|FLCN|GREM1|MET| | ||
| MLH1|MSH2|MSH6|MUTYH|NTHL1|PALB2|PMS2|POLD1|POLE|PTEN|RAD51C|RAD51D| | ||
| RNF43|SDHB|SMAD4|STK11|TP53|VHL'.freeze | ||
|
|
||
| # rubocop:disable Lint/MixedRegexpCaptureTypes | ||
| MMR_GENE_REGEX = /APC|BMPR1A|EPCAM|GREM1|MLH1|MSH2|MSH6|MUTYH|NTHL1|PMS2|POLD1| | ||
| POLE|PTEN|SMAD4|STK11/ix | ||
| CDNA_REGEX = /c\.(?<cdna>[\w+>*\-]+)?/ix | ||
| PROTEIN_REGEX = /\(?p\.\(?(?<impact>\w+)\)?/ix | ||
| EXON_REGEX = /(?<exon>exon(s)?[\s\-\d]+)/ix | ||
| GENE_FAIL_REGEX = /(?=(?<gene>#{GENES})[\w\s]+fail)/ix | ||
| NOPATH_REGEX = /.No pathogenic variant was identified./i | ||
| EXON_VARIANT_REGEX = /(?<variant>del|dup|ins).+ex(on)?s?\s? | ||
| (?<exons>[0-9]+(-[0-9]+)?)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+(-[0-9]+)?)\s? | ||
| (?<variant>del|dup|ins)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+\s?(\s?-\s?[0-9]+)?)\s? | ||
| (?<variant>del|dup|ins)?| | ||
| (?<variant>del|dup|ins)\s?(?<exons>[0-9]+(?<dgs>-[0-9]+)?)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+(\sto\s[0-9]+)?)\s | ||
| (?<variant>del|dup|ins)| | ||
| x(?<exons>[0-9+-? ]+)+(?<variant>del|dup|ins)| | ||
| ex(on)?s?[\s\w,]+(?<variant>del|dup|ins)| | ||
| (?<variant>del|dup|ins)[\s\w]+gene/ix | ||
|
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| COLORECTAL_GENES_REGEX = /(?<colorectal>#{GENES})/x | ||
|
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||
| VARIANT_REPORT_REGEX = /(?<report>(hetero|homo)zygo[\w\s\-.>():=,'+]+)+/ix | ||
|
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| EXONIC_REPORT_REGEX = /(?<report>(#{GENES})\sexon(s)?[\w\s\-.>():=,&]+)/ix | ||
|
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| PATHOGENIC_REPORT_REGEX = /(?<report>pathogenic\s(#{GENES})[\w\s\-.>():=,&]+)/ix | ||
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| TARG_GENE_REGEX = /(?<report>(#{GENES})[\w\s]+(c\.[\w\s\-.>():=,']+))/ix | ||
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| ABSENT_REGEX = /is absent in this patient/i | ||
| NO_DEL_REGEX = /this patient does not have the deletion/i | ||
| PATHOGENIC_REGEX = /(?<pathogenic>likely\snon-pathogenic|likely\spathogenic| | ||
| likely\s(to\sbe\s)?pathogenic|pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)/ix | ||
| PATHOGENIC_GENES_REGEX = /(?<pathogenic>likely\snon-pathogenic|likely\spathogenic| | ||
| pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)[\w\s\W]*(?<assocgene>#{GENES})/ix | ||
| GENE_PATH_REGEX = /(?<assocgene>#{GENES})[\w\s\W]*(?<pathogenic>likely\snon-pathogenic| | ||
| likely\spathogenic|pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)/ix | ||
| # rubocop:enable Lint/MixedRegexpCaptureTypes | ||
|
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||
| GENES_FILEPATH = 'lib/import/helpers/colorectal/providers/rr8/genes.yml'.freeze | ||
| STATUS_FILEPATH = 'lib/import/helpers/colorectal/providers/rr8/status.yml'.freeze | ||
|
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||
| GENES_PANEL = { | ||
| 'apc' => %w[APC], | ||
| 'epcam' => %w[EPCAM], | ||
| 'mlh1' => %w[MLH1], | ||
| 'mlh1_msh2' => %w[MLH1 MSH2], | ||
| 'mlh1_msh2_msh6' => %w[MLH1 MSH2 MSH6], | ||
| 'mlh1_pms2' => %w[MLH1 PMS2], | ||
| 'pms2_mutyh' => %w[MUTYH PMS2], | ||
| 'msh2' => %w[MSH2], | ||
| 'msh6' => %w[MSH6], | ||
| 'mutyh' => %w[MUTYH], | ||
| 'pms2' => %w[PMS2] | ||
| }.freeze | ||
|
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||
| STATUS_PANEL = { | ||
| 'unknown' => 4, | ||
| 'normal' => 1, | ||
| 'abnormal' => 2, | ||
| 'normal_var' => 10, | ||
| 'fail' => 9 | ||
| }.freeze | ||
|
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||
| VARIANT_CLASS_5 = [ | ||
| 'conf mlpa +ve', | ||
| 'mlh1 confirmation +ve', | ||
| 'mlpa del confirmation +ve', | ||
| 'msh2 confirmation +ve', | ||
| 'mlpa +ve(large exon deletion) + seq -ve', | ||
| 'mlpa multi-exon deletion (with seq)', | ||
| 'ngs class m', | ||
| 'sequencing positive', | ||
| 'pred mlpa epcam del +ve', | ||
| 'pred mlpa msh2 del +ve', | ||
| 'pred mlpa msh2 dup +ve', | ||
| 'pred mlpa msh6 del +ve', | ||
| 'pred seq mlh1 +ve', | ||
| 'pred seq msh2 +ve', | ||
| 'pred seq msh6 +ve', | ||
| 'confirmation_seq_positive', | ||
| 'diagnostic apc +ve', | ||
| 'predictive_seq_positive', | ||
| 'seq mutation +ve', | ||
| 'biallelic pred positive', | ||
| 'mlpa pred positive', | ||
| 'pred complex mut +ve', | ||
| 'r802x homozygote (diag)', | ||
| 'seq pred positive', | ||
| 'apc - conf mlpa +ve', | ||
| 'fap diagn mutyh het.', | ||
| 'conf seq +ve (apc)', | ||
| 'conf seq +ve (mutyh)', | ||
| 'fap conf-pred +ve (apc)', | ||
| 'fap diagn +ve (apc)', | ||
| 'fap diagn +ve (mutyh c.het)', | ||
| 'fap diagn +ve (mutyh homoz)', | ||
| 'fap diagn mutyh het.', | ||
| '(v2) mutyh het.', | ||
| 'apc - conf seq +ve' | ||
| ].freeze | ||
|
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||
| VARIANT_CLASS_7 = [ | ||
| 'conf seq +ve', | ||
| 'mlpa -ve + seq (splice site mutation)', | ||
| 'mlpa -ve + seq +ve (nonsense/frameshift)', | ||
| 'ngs mlh1 truncating/frameshift', | ||
| 'ngs msh2 truncating/frameshift', | ||
| 'ngs multiple exon mlpa del', | ||
| 'pred mlpa +ve', | ||
| 'mlpa positive', | ||
| 'mlpa positive (diag)', | ||
| 'pred (other) positive', | ||
| 'generic c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'generic c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'r210_c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'generic c4/5' | ||
| ].freeze | ||
|
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||
| NON_PATH_VARCLASS = [ | ||
| 'likely benign', | ||
| 'likely to be benign', | ||
| 'non-pathological variant', | ||
| 'likely non-pathogenic', | ||
| 'benign' | ||
| ].freeze | ||
|
|
||
| EXCLUDE_STATEMENTS = [ | ||
| 'Screening for mutations in MLH1, MSH2 and MSH6 is now in progress as requested.', | ||
| 'MLPA and MSH2 analysis was not requested.', | ||
| 'MLPA and MSH2 analysis were not requested.', | ||
| 'if MSH2 and MSH6 data analysis is required.', | ||
| 'No further screening for mutations in MLH1, MSH2 or MSH6 has been performed.', | ||
| 'developing further MSH2-related cancers', | ||
| 'developing MSH2-associated cancer' | ||
| ].freeze | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end |
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