Capture metadata from VCF header #136
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kenny-lee-1
reviewed
Dec 11, 2024
lib/ndr_import/file/vcf.rb
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| file_metadata_hash = {} | ||
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| ::File.read(@filename).each_line do |line| | ||
| next unless line =~ /^##/ |
kenny-lee-1
reviewed
Dec 11, 2024
lib/ndr_import/file/vcf.rb
Outdated
| next unless line =~ /^##/ | ||
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| vcf_file_metadata.each do |attribute, pattern| | ||
| file_metadata_hash[attribute] = line.match(pattern)[1].presence if line =~ pattern |
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match? unless you don't think the regex security concern can be triggered here
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match? will also convert pattern to a Regexp
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This PR allows storage of VCF metadata at the
Fileand thenTablelevel.Config in table mappings tells the file handler identifies metadata and what to label it as. The File handler then passes the metadata to the
Table, where it can be accessed downstream.