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Viewing changes to Bio/Biblio/IO/medline2ref.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/Biblio/IO/medline2ref.pm
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# $Id: medline2ref.pm,v 1.15.4.1 2006/10/02 23:10:13 sendu Exp $
 
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# $Id: medline2ref.pm 15149 2008-12-12 10:52:28Z heikki $
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#
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# BioPerl module Bio::Biblio::IO::medline2ref.pm
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#
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#
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sub _convert_date {
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    my ($date) = @_;
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    return undef unless
 
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    return unless
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        exists $$date{'year'} or
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            exists $$date{'month'} or
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                exists $$date{'day'} or
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        $$person{"_$key"} = $$person{$key};
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        delete $$person{$key};
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    }
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    new Bio::Biblio::Person (%$person);
 
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    Bio::Biblio::Person->new(%$person);
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}
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#
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    # create and populate both a Journal and a resulting Article objects
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    my $from_journal = $$article{'journal'};
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    my $journal = new Bio::Biblio::MedlineJournal;
 
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    my $journal = Bio::Biblio::MedlineJournal->new();
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    $journal->name ($$from_journal{'title'}) if defined $$from_journal{'title'};
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    $journal->issn ($$from_journal{'iSSN'}) if defined $$from_journal{'iSSN'};
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    $journal->abbreviation ($$from_journal{'iSOAbbreviation'}) if defined $$from_journal{'iSOAbbreviation'};
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    # create and populate both book and resulting article objects
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    my $from_book = $$article{'book'};
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    my $book = new Bio::Biblio::MedlineBook;
 
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    my $book = Bio::Biblio::MedlineBook->new();
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    $book->title ($$from_book{'title'}) if defined $$from_book{'title'};
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    $book->volume ($$from_book{'volume'}) if defined $$from_book{'volume'};
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    $book->series ($$from_book{'collectionTitle'}) if defined $$from_book{'collectionTitle'};
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    }
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    if (defined $$from_book{'publisher'}) {
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        my $publisher = new Bio::Biblio::Organisation;
 
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        my $publisher = Bio::Biblio::Organisation->new();
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        $publisher->name ($$from_book{'publisher'});
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        $book->publisher ($publisher);
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    }
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            my $db_name = $$bank{'dataBankName'};
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            if (defined $$bank{'accessionNumbers'}) {
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                foreach my $accn ( @{ $$bank{'accessionNumbers'} } ) {
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                    my $dblink = new Bio::Annotation::DBLink (-primary_id => $accn);
 
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                    my $dblink = Bio::Annotation::DBLink->new(-primary_id => $accn);
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                    $dblink->database ($db_name);   # it does not matter if it is undef
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                    push (@references, $dblink);
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                }
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            my $converted = &_convert_personal_name ($$provider{'personalName'});
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            push (@results, $converted) if defined $converted;
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        } elsif (defined $$provider{'collectiveName'}) {
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            push (@results, new Bio::Biblio::Organisation (-name => $$provider{'collectiveName'}));
 
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            push (@results, Bio::Biblio::Organisation->new(-name => $$provider{'collectiveName'}));
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        } else {
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            new Bio::Biblio::Provider;
 
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            Bio::Biblio::Provider->new();
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        }
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    }
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    return () unless @results;