Feature/rmh brca #67
Feature/rmh brca #67
Conversation
|
The |
| teststatus = record.raw_fields['teststatus'] | ||
| if record.raw_fields['variantpathclass'].nil? |
There was a problem hiding this comment.
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
There was a problem hiding this comment.
Changes made in commit 1c81ce7. I checked that the variant counts still match.
| @@ -29,8 +29,8 @@ class RoyalMarsdenHandler < Import::Germline::ProviderHandler | |||
| TEST_TYPE_MAP = { 'affected' => :diagnostic, | |||
| 'unaffected' => :predictive }.freeze | |||
| # 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 | |||
There was a problem hiding this comment.
is that supposed to be separtors ?
There was a problem hiding this comment.
@lauramccluskey1 should this be separators?
There was a problem hiding this comment.
See commit a7f7fa0- tested and counts are still the same
| @@ -45,6 +45,54 @@ def setup | |||
| normal_record.raw_fields['teststatus'] = 'NO PATHOGENIC VARIANT IDENTIFIED' | |||
| @handler.process_teststatus(@genotype, normal_record) | |||
| assert_equal 1, @genotype.attribute_map['teststatus'] | |||
|
|
|||
| non_path_record = build_raw_record('pseudo_id1' => 'bob') | |||
| non_path_record.raw_fields['teststatus'] = 'Ex del' | |||
There was a problem hiding this comment.
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' } )
There was a problem hiding this comment.
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!
There was a problem hiding this comment.
Ah ok, perhaps something for a future PR. It'd be nice for build_raw_record to be able to popluate raw_fields
|
Further |
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.