Feature/36558/st george old import mising records #123
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…now the FS gene in question
…nt_system into feature/36558/st_george_old_import_mising_records
…nt_system into feature/36558/st_george_old_import_mising_records
shilpigoeldev
requested changes
Jan 27, 2025
lib/import/brca/providers/st_george_old/st_george_handler_old.rb
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shilpigoeldev
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Jan 29, 2025
test/lib/import/brca/providers/st_george_old/st_george_handler_old_test.rb
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LGTM now , but pending Fiona confirmation on QA so can approve and merge once Fiona's approval comes in. Thanks @NImeson !!
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What?
Adding in functionality to import UCS variants add in the test status 10 value when recording the status of variant results. Expanding the regular expressions to account for missing SRIs. Deal with missing SRIs where there is an abornal variant but no gene to assign it to.
Why?
There are 64 records that are not currently being imported from the raw files into MBIS / CASREF. These records are large;ly abnormal results that which we really do want to capture.
Need to broaden the regex that assigns a teststatus as 2. To include fields that contain strings such as 'IVS' or 'Del X 5-7'.
Include functionality to import UCS variants and give them teststatus 10 outcome
Incorpoate functionality to import abnormal variants where the gene is unknown (also create additional empty tests for BRCA1+2 where these are full screen)
How?
Added in method to ctreate BRCA1/2 records as standard when we don't know what the FS gene in question is .
Added in method to handle a variant when we don't know the gene it belongs to
Expanded to exon regex to account for additional variant nomenclatures eg. IVS, DEL X 5-7
Added in functionality to import UCS variants and give them test status 10 value
Testing?
All missing SRIs are now being being imported with the exception of one, which has a 'nil' field (would need more substantial changes to importer). Variants for each missing SRI are being imported to some extent (it's difficult to fully import some as the way they are written conflicts with importer rules).
Variant counts between existing importer and this version show additional SRIs across the board, mostly the expected missing SRIs but also exra ones. Extra counts have been investigated and importer is performing correctly with these records.
Additional QA checks completed looking at number of variant entries across a varierty of metrics.testing has shown that the changes now include more cDNA variants, protein variants, exonintron variants than previously.