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1 # $Id: pubmed2ref.pm,v 1.2 2002/10/22 07:45:13 lapp Exp $
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2 #
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3 # BioPerl module Bio::Biblio::IO::pubmed2ref.pm
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4 #
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5 # Cared for by Martin Senger <senger@ebi.ac.uk>
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6 # For copyright and disclaimer see below.
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7
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8 # POD documentation - main docs before the code
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9
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10 =head1 NAME
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11
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12 Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations
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13
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14 =head1 SYNOPSIS
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15
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16 # to be written
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17
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18 =head1 DESCRIPTION
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19
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20 # to be written
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21
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22 =head1 FEEDBACK
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23
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24 =head2 Mailing Lists
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25
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26 User feedback is an integral part of the evolution of this and other
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27 Bioperl modules. Send your comments and suggestions preferably to
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28 the Bioperl mailing list. Your participation is much appreciated.
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29
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30 bioperl-l@bioperl.org - General discussion
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31 http://bioperl.org/MailList.shtml - About the mailing lists
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32
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33 =head2 Reporting Bugs
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34
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35 Report bugs to the Bioperl bug tracking system to help us keep track
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36 of the bugs and their resolution. Bug reports can be submitted via
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37 email or the web:
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38
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39 bioperl-bugs@bioperl.org
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40 http://bugzilla.bioperl.org/
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41
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42 =head1 AUTHOR
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43
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44 Martin Senger (senger@ebi.ac.uk)
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45
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46 =head1 COPYRIGHT
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47
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48 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
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49
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50 This module is free software; you can redistribute it and/or modify
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51 it under the same terms as Perl itself.
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52
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53 =head1 DISCLAIMER
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54
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55 This software is provided "as is" without warranty of any kind.
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56
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57 =head1 APPENDIX
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58
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59 Here is the rest of the object methods. Internal methods are preceded
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60 with an underscore _.
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61
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62 =cut
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63
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64
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65 # Let the code begin...
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66
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67
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68 package Bio::Biblio::IO::pubmed2ref;
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69
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70 use strict;
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71 use vars qw(@ISA $VERSION $Revision);
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72
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73 use Bio::Biblio::IO::medline2ref;
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74 @ISA = qw(Bio::Biblio::IO::medline2ref);
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75
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76 BEGIN {
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77 # set the version for version checking
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78 $VERSION = do { my @r = (q$Revision: 1.2 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
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79 $Revision = q$Id: pubmed2ref.pm,v 1.2 2002/10/22 07:45:13 lapp Exp $;
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80 }
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81
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82 # ---------------------------------------------------------------------
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83 #
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84 # Here is the core...
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85 #
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86 # ---------------------------------------------------------------------
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87
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88 sub _load_instance {
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89 my ($self, $source) = @_;
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90
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91 my $result;
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92 my $article = $$source{'article'};
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93 if (defined $article) {
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94 if (defined $$article{'journal'}) {
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95 $result = $self->_new_instance ('Bio::Biblio::PubmedJournalArticle');
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96 $result->type ('JournalArticle');
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97 } elsif (defined $$article{'book'}) {
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98 $result = $self->_new_instance ('Bio::Biblio::PubmedBookArticle');
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99 $result->type ('BookArticle');
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100 } else {
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101 $result->type ('PubmedArticle');
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102 }
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103 }
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104 $result = $self->_new_instance ('Bio::Biblio::Ref') unless defined $result;
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105 return $result;
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106 }
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107
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108 sub convert {
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109 my ($self, $source) = @_;
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110 my $result = $self->SUPER::convert ($source->{'Citation'});
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111
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112 # here we do PUBMED's specific stuff
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113 my $pubmed_data = $$source{'PubmedData'};
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114 if (defined $pubmed_data) {
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115
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116 # ... just take it (perhaps rename it)
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117 $result->pubmed_status ($$pubmed_data{'publicationStatus'}) if defined $$pubmed_data{'publicationStatus'};
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118 $result->pubmed_provider_id ($$pubmed_data{'providerId'}) if defined $$pubmed_data{'providerId'};
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119 $result->pubmed_article_id_list ($$pubmed_data{'pubmedArticleIds'}) if defined $$pubmed_data{'pubmedArticleIds'};
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120 $result->pubmed_url_list ($$pubmed_data{'pubmedURLs'}) if defined $$pubmed_data{'pubmedURLs'};
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121
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122 # ... put all dates from all 'histories' into one array
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123 if (defined $$pubmed_data{'histories'}) {
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124 my @history_list;
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125 foreach my $history ( @{ $$pubmed_data{'histories'} } ) {
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126 my $ra_pub_dates = $$history{'pubDates'};
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127 foreach my $pub_date ( @{ $ra_pub_dates } ) {
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128 my %history = ();
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129 my $converted_date = &Bio::Biblio::IO::medline2ref::_convert_date ($pub_date);
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130 $history{'date'} = $converted_date if defined $converted_date;
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131 $history{'pub_status'} = $$pub_date{'pubStatus'} if defined $$pub_date{'pubStatus'};
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132 push (@history_list, \%history);
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133 }
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134 }
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135 $result->pubmed_history_list (\@history_list);
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136 }
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137 }
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138
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139 # Done!
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140 return $result;
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141 }
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142
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143 1;
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144 __END__
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