Feature/31243/leeds crc refactor #76
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| @genes_hash = YAML.safe_load(File.open(Rails.root.join(GENES_FILEPATH))) | ||
| @status_hash = YAML.safe_load(File.open(Rails.root.join(STATUS_FILEPATH))) |
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I think these would be better populated in the #initialize method (i.e. once per batch), instead of reloading YAML file for every record. Maybe .freeze the result, if you want to be sure the lookup isn't mutated.
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Thanks @bshand , done in latest commit
| genotype = record.raw_fields['genotype'].downcase.strip | ||
| mtype = record.raw_fields['moleculartestingtype'].downcase.strip | ||
| if genotype.match(/pms2\s-\smlpa\spred\snegative\sc5/i) || | ||
| genotype.match(/pms2\s-\sconf\smlpa\spositive\sc5/i) |
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I can't see this in the rules? Can you send me the updated ones please?
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Have mailed you the rules , and following -
<style> </style>| Raw:genotype | Test Scope |
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| PMS2 - MLPA pred negative C5 | Targeted |
| PMS2 - Conf MLPA positive C5 | Targeted |
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Thank you! This makes sense now
| raw_report = report | ||
| exclude_statements = [ | ||
| 'Screening for mutations in MLH1, MSH2 and MSH6 is now in progress as requested.', | ||
| 'MLPA and MSH2 analysis was not requested.', |
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Would it be good to add these to the constants file instead?
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Done in latest commit .
| @@ -336,7 +340,7 @@ def add_variant_impact(impact) | |||
| end | |||
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| def add_variant_class(variant) | |||
| if variant.is_a?(Integer) && variant >= 1 && variant <= 5 | |||
| if variant.is_a?(Integer) && variant >= 1 && variant <= 7 | |||
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As this is an update to the assigning variant class in the genotype.rb file, have you checked that it won't affect any of the other importers?
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Its extending the range that's allowed to be in variantpathclass and adheres to Zvariantpathclass. If any other importer is able to extract c4/5 pathogenicity values and map upto 7 in future that should be fine.
| end | ||
| end | ||
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| def allocate_genes(_record) |
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record is not being used by the function- can this be removed?
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Done in latest commit
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Can you also add more comments please? |
Added now in latest commit at places and left for methods where name seems self explanatory, thanks @lauramccluskey1 ! |
| populate_and_persist_genotype(record) | ||
| end | ||
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| # populate class variables that can be used over different methods |
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I think these are instance variables, may be worth changing the comment
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Thanks @ollietulloch , done in latest commit .
| end | ||
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| # checks if file has colorectal tests and should be processed under this importer | ||
| def should_process |
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If this only returns true of false, could this be a predicate method?
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Thanks @ollietulloch , done in latest commit .
| def process_variants_from_record(genocolorectal, record) | ||
| genotypes = [] | ||
| allocate_genes | ||
| find_test_status(record) |
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A small thing but naming methods consistently is really helpful regarding readability. allocate_genes and find_test_status do similar things, i.e. setting an instance variable, so perheps calling it allocate_test_status might be more consistent?
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Thanks @ollietulloch , done in latest commit .
| @teststatus | ||
| end | ||
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| def exceptinal_teststatus |
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Should this be exceptional_teststatus?
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Thanks @ollietulloch , done in latest commit .
| @teststatus | ||
| end | ||
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| def exceptinal_teststatus |
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Can you update to "exceptional" please?
| else | ||
| @logger.debug 'Cannot determine test status for : '\ | ||
| "#{record.raw_fields['report']} a priori" | ||
| def process_normal_targ(genocolorectal, _record, genotypes) |
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record is not being used by this function- can it be removed?
| genotypes << genocolorectal | ||
| end | ||
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| def process_abnormal_targ(genocolorectal, _record, genotypes) |
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record is not being used by this function- can it be removed?
| end | ||
| end | ||
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| def process_normal_fs(genocolorectal, _record, genotypes) |
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record is not being used by this function- can it be removed?
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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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If you have "." as one of the options in the square brackets, do you need the rest of the options if "." includes all of the other characters you have listed?
| 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)?| |
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Are lines 60-61 similar to 58-59 but with a few extra optional values- could this be simplified?
| cdna_vars = get_cdna_mutations(report_variants) | ||
| if cdna_vars.size > 1 | ||
| proteins = report_variants.scan(PROTEIN_REGEX).flatten.uniq | ||
| cdna_vars.zip(proteins).each do |cdna_mutation, protein| |
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Is this using an assumption that the the order of the cdna will match the order of the protein in the sentence? What happens there isn't a protein listed for every cdna? Would that mean they get matched incorrectly?
| genotypes << genocolorectal_dup | ||
| end | ||
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| def extract_targeted_genes |
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Check if this method is needed- as discussed on call
What?
I have refactored Leeds CRC importer with latest rules provided by Fiona , as per Planio ticket 35286
Why?
Whole Leeds CRC had to be re-written again as older code wasn't getting the right denominators and counts.
How?
Have re-written Leeds CRC importer as per rules sheet provided by Fiona.
Testing?
QA signed off by Fiona after sharing the counts. Also added handler tests for each kind of case.
Anything Else?
It still has rubocop errors for existing code in parent classes like genocolorectal.rb, which can't be edited in this scope of work as being used across all importers.