[BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.12,1.13
Naohisa Goto
ngoto at dev.open-bio.org
Wed Apr 23 16:48:28 UTC 2008
Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv12456/lib/bio/db/embl
Modified Files:
common.rb
Log Message:
Bug fix: Bio::EMBL#references failed to parse journal name, volume, issue,
pages, and year. In addition, it might failed to parse PubMed ID.
Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** common.rb 5 Apr 2007 23:35:40 -0000 1.12
--- common.rb 23 Apr 2008 16:48:25 -0000 1.13
***************
*** 279,294 ****
hash['title'] = value
when 'RL'
! if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
! hash['journal'] = $1
hash['volume'] = $2
! hash['issue'] = $3
! hash['pages'] = $4
! hash['year'] = $5
else
hash['journal'] = value
end
when 'RX' # PUBMED, MEDLINE
! value.split('.').each {|item|
! tag, xref = item.split(/; /).map {|i| i.strip }
hash[ tag.downcase ] = xref
}
--- 279,294 ----
hash['title'] = value
when 'RL'
! if /(.*) (\d+) *(\(([^\)]+)\))?(\, |\:)([a-zA-Z\d]+\-[a-zA-Z\d]+) *\((\d+)\)\.?\z/ =~ value.to_s
! hash['journal'] = $1.rstrip
hash['volume'] = $2
! hash['issue'] = $4
! hash['pages'] = $6
! hash['year'] = $7
else
hash['journal'] = value
end
when 'RX' # PUBMED, MEDLINE
! value.split(/\. /).each {|item|
! tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
hash[ tag.downcase ] = xref
}
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