Feature/rmh brca#67
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| nonpathvarclass = nil | ||
| teststatus = record.raw_fields['teststatus'] | ||
| if record.raw_fields['variantpathclass'].nil? |
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I think you can use safe navigation here
replace
if record.raw_fields['variantpathclass'].nil?
nonpathvarclass = nil
else
nonpathvarclass = record.raw_fields['variantpathclass'].downcase.strip
end
with
nonpathvarclass = record.raw_fields['variantpathclass']&.downcase&.strip
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Changes made in commit 1c81ce7. I checked that the variant counts still match.
| # rubocop:disable Lint/MixedRegexpCaptureTypes | ||
| CDNA_REGEX_PROT = /c\.(?<cdna>.+)(?=(?<separtors>_|;.)p\.(?<impact>.+))/i.freeze | ||
| CDNA_REGEX_NOPROT = /c\.(?<cdna>.+)/i.freeze | ||
| CDNA_REGEX_PROT = /c\.(?<cdna>.+)(?=(?<separtors>_|;.)p\.(?<impact>.+))/i |
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is that supposed to be separtors ?
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See commit a7f7fa0- tested and counts are still the same
| assert_equal 1, @genotype.attribute_map['teststatus'] | ||
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| non_path_record = build_raw_record('pseudo_id1' => 'bob') | ||
| non_path_record.raw_fields['teststatus'] = 'Ex del' |
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Can raw_fields be passed to the build_raw_record method, eg:
broken_record = build_raw_record('pseudo_id1' => 'bob', raw_fields: { 'teststatus' => 'Ex del' } )
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Thanks for the suggestion @ollietulloch ! I have tried that and it doesn't work- I think its because build new record adds the test status field by loading the rawtext_clinical_json. So that needs to be loaded first then we can update the test status afterwards. Let me know if there is another way!
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Ah ok, perhaps something for a future PR. It'd be nice for build_raw_record to be able to popluate raw_fields
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Further |
4 participants
Planio ticket 35297. Updating the Royal Marsden importer to include test status 10.
Variants counts sent as part of QA, and they match the manual counts.