WebPAC/Input/ISI.pm

package WebPAC::Input::ISI;

use warnings;
use strict;

use WebPAC::Input;
use base qw/WebPAC::Common/;

use Data::Dump qw/dump/;

=head1 NAME

WebPAC::Input::ISI - support for ISI Export Format

=cut

our $VERSION = '0.03';

=head1 SYNOPSIS

Open file in ISI export fromat

 my $input = new WebPAC::Input::ISI(
        path => '/path/to/ISI/records.txt',
 );

=head1 FUNCTIONS

=head2 new

Returns new low-level input API object

  my $input = new WebPAC::Input::ISI(
        path => '/path/to/ISI/records.txt'
        filter => sub {
                my ($l,$field_nr) = @_;
                # do something with $l which is line of input file
                return $l;
        },
  }

Options:

=over 4

=item path

path to ISI export file

=back

=cut

my $subfields = {
        'CR' => sub {
                my $full_cr = shift;
                my @v = split(/, /, $full_cr);
                my $f = { full => $full_cr };
                foreach ( qw/author year reference volume page doi/ ) {
                        if ( my $tmp = shift @v ) {
                                $f->{$_} = $tmp;
                        }
                }
                if ( $f->{author} =~ /^\*(.+)/ ) {
                        delete $f->{author};
                        $f->{institution} = $1;
                }
                $f->{doi} =~ s{DOI\s+}{} if $f->{doi}; # strip DOI prefix
                return $f;
        },
};

sub new {
        my $class = shift;
        my $self = {@_};
        bless($self, $class);

        my $arg = {@_};

        my $log = $self->_get_logger();

        open( my $fh, '<', $arg->{path} ) || $log->logconfess("can't open $arg->{path}: $!");

        my ( $format, $version );

        my $line = <$fh>;
        chomp($line);
        if ( $line =~ /^FN\s(.+)$/) {
                $format = $1;
        } else {
                $log->logdie("first line of $arg->{path} has to be FN, but is: $line");
        }

        $line = <$fh>;
        chomp($line);
        if ( $line =~ /^VR\s(.+)$/) {
                $version = $1;
        } else {
                $log->logdie("second line of $arg->{path} has to be VN, but is: $line");
        }

        $log->info("opening $format $version database '$arg->{path}'");

        my $tag;
        my $rec;

        my $offset = $self->{offset} || 0;
        my $limit  = $self->{limit}  || 0;

        my $file_pos = 0;
        my $end_pos  = 0;
        $end_pos = $offset + $limit if $limit;

        $self->{_rec} = [];
        
        warn "# offset: $offset limit: $limit end: $end_pos";

        while( $line = <$fh> ) {
                chomp($line);
                my $v;

                if ( $line eq 'EF' ) {
                        last;
                } elsif ( $line eq 'ER' ) {
                        $file_pos++;
                        last if $end_pos && $file_pos > $end_pos;

                        if ( ! $offset || $file_pos > $offset ) {

                                # join tags
                                foreach ( qw/AB DE ID TI SO RP SC FU FX PA JI/ ) {
                                        $rec->{$_} = join(' ', @{ $rec->{$_} }) if defined $rec->{$_};
                                }
                                # split on ;
                                foreach ( qw/ID SC DE/ ) {
                                        $rec->{$_} = [ split(/;\s/, $rec->{$_}) ] if defined $rec->{$_};
                                }
                                $rec->{'000'} = [ $file_pos ];
                                push @{ $self->{_rec} }, $rec;
                        }

                        $rec = {};
                        $line = <$fh>;
                        chomp $line;
                        $log->logdie("expected blank like in ",$arg->{path}, " +$.: $line") unless ( $line eq '' );
                } elsif ( $offset && $file_pos < $offset ) {
                        next;
                } elsif ( $line =~ /^(\S\S)\s(.+)$/ ) {
                        $tag = $1;
                        $v = $2;
                } elsif ( $line =~ /^\s{3}(.+)$/ ) {
                        $v = $1;
                        if ( $tag eq 'CR' && $v =~ m{DOI$} ) {
                                my $doi = <$fh>;
                                chomp($doi);
                                $doi =~ s{^\s{3}}{ } || die "can't find DOI in: $doi";
                                $v .= $doi;
                        }
                } elsif ( $line =~ m{^(\S\S)\s*$} ) {
                        warn "# $arg->{path} +$. empty |$line|\n";
                } else {
                        $log->logdie("can't parse +$. $arg->{path} |$line|");
                }

                if ( defined $v ) {
                        $v = $subfields->{$tag}->($v) if defined $subfields->{$tag};

                        $log->debug("$tag: ", sub { dump( $v ) });
                        push @{ $rec->{$tag} }, $v;
                }

        }
        $log->debug("loaded ", $self->size, " records");

        $self ? return $self : return undef;
}

=head2 fetch_rec

Return record with ID C<$mfn> from database

  my $rec = $input->fetch_rec( $mfn, $filter_coderef );

=cut

sub fetch_rec {
        my $self = shift;

        my ( $mfn, $filter_coderef ) = @_;

        $mfn -= $self->{offset} if $self->{offset};
        return $self->{_rec}->[$mfn-1];
}


=head2 size

Return number of records in database

  my $size = $input->size;

=cut

sub size {
        my $self = shift;
        $#{ $self->{_rec} } + 1;
}

=head1 SEE ALSO

L<http://isibasic.com/help/helpprn.html> is only sane source of document format which Google could find...
 
=head1 AUTHOR

Dobrica Pavlinusic, C<< <dpavlin@rot13.org> >>

=head1 COPYRIGHT & LICENSE

Copyright 2007 Dobrica Pavlinusic, All Rights Reserved.

This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.

=cut

1; # End of WebPAC::Input::ISI
1	dpavlin	898	package WebPAC::Input::ISI;
2
3			use warnings;
4			use strict;
5
6			use WebPAC::Input;
7			use base qw/WebPAC::Common/;
8
9	dpavlin	904	use Data::Dump qw/dump/;
10
11	dpavlin	898	=head1 NAME
12
13			WebPAC::Input::ISI - support for ISI Export Format
14
15			=cut
16
17	dpavlin	1209	our $VERSION = '0.03';
18	dpavlin	898
19			=head1 SYNOPSIS
20
21			Open file in ISI export fromat
22
23			my $input = new WebPAC::Input::ISI(
24			path => '/path/to/ISI/records.txt',
25			);
26
27			=head1 FUNCTIONS
28
29			=head2 new
30
31			Returns new low-level input API object
32
33			my $input = new WebPAC::Input::ISI(
34			path => '/path/to/ISI/records.txt'
35			filter => sub {
36			my ($l,$field_nr) = @_;
37			# do something with $l which is line of input file
38			return $l;
39			},
40			}
41
42			Options:
43
44			=over 4
45
46			=item path
47
48			path to ISI export file
49
50			=back
51
52			=cut
53
54	dpavlin	901	my $subfields = {
55			'CR' => sub {
56	dpavlin	1194	my $full_cr = shift;
57			my @v = split(/, /, $full_cr);
58			my $f = { full => $full_cr };
59	dpavlin	1209	foreach ( qw/author year reference volume page doi/ ) {
60	dpavlin	901	if ( my $tmp = shift @v ) {
61			$f->{$_} = $tmp;
62			}
63			}
64			if ( $f->{author} =~ /^\*(.+)/ ) {
65			delete $f->{author};
66			$f->{institution} = $1;
67			}
68	dpavlin	1209	$f->{doi} =~ s{DOI\s+}{} if $f->{doi}; # strip DOI prefix
69	dpavlin	901	return $f;
70			},
71			};
72
73	dpavlin	898	sub new {
74			my $class = shift;
75			my $self = {@_};
76			bless($self, $class);
77
78			my $arg = {@_};
79
80			my $log = $self->_get_logger();
81
82			open( my $fh, '<', $arg->{path} ) \|\| $log->logconfess("can't open $arg->{path}: $!");
83
84			my ( $format, $version );
85
86			my $line = <$fh>;
87			chomp($line);
88			if ( $line =~ /^FN\s(.+)$/) {
89			$format = $1;
90			} else {
91			$log->logdie("first line of $arg->{path} has to be FN, but is: $line");
92			}
93
94			$line = <$fh>;
95			chomp($line);
96			if ( $line =~ /^VR\s(.+)$/) {
97			$version = $1;
98			} else {
99			$log->logdie("second line of $arg->{path} has to be VN, but is: $line");
100			}
101
102			$log->info("opening $format $version database '$arg->{path}'");
103
104	dpavlin	899	my $tag;
105			my $rec;
106
107	dpavlin	1303	my $offset = $self->{offset} \|\| 0;
108	dpavlin	1305	my $limit = $self->{limit} \|\| 0;
109	dpavlin	1077
110	dpavlin	1305	my $file_pos = 0;
111			my $end_pos = 0;
112			$end_pos = $offset + $limit if $limit;
113	dpavlin	1287
114	dpavlin	1305	$self->{_rec} = [];
115
116			warn "# offset: $offset limit: $limit end: $end_pos";
117
118	dpavlin	899	while( $line = <$fh> ) {
119			chomp($line);
120			my $v;
121
122	dpavlin	1303	if ( $line eq 'EF' ) {
123			last;
124	dpavlin	899	} elsif ( $line eq 'ER' ) {
125	dpavlin	1305	$file_pos++;
126			last if $end_pos && $file_pos > $end_pos;
127	dpavlin	1303
128	dpavlin	1305	if ( ! $offset \|\| $file_pos > $offset ) {
129
130			# join tags
131			foreach ( qw/AB DE ID TI SO RP SC FU FX PA JI/ ) {
132			$rec->{$_} = join(' ', @{ $rec->{$_} }) if defined $rec->{$_};
133			}
134			# split on ;
135			foreach ( qw/ID SC DE/ ) {
136			$rec->{$_} = [ split(/;\s/, $rec->{$_}) ] if defined $rec->{$_};
137			}
138			$rec->{'000'} = [ $file_pos ];
139			push @{ $self->{_rec} }, $rec;
140	dpavlin	901	}
141	dpavlin	1287
142	dpavlin	899	$rec = {};
143			$line = <$fh>;
144			chomp $line;
145			$log->logdie("expected blank like in ",$arg->{path}, " +$.: $line") unless ( $line eq '' );
146	dpavlin	1305	} elsif ( $offset && $file_pos < $offset ) {
147	dpavlin	1303	next;
148			} elsif ( $line =~ /^(\S\S)\s(.+)$/ ) {
149	dpavlin	1305	$tag = $1;
150			$v = $2;
151	dpavlin	1303	} elsif ( $line =~ /^\s{3}(.+)$/ ) {
152	dpavlin	1305	$v = $1;
153			if ( $tag eq 'CR' && $v =~ m{DOI$} ) {
154			my $doi = <$fh>;
155			chomp($doi);
156			$doi =~ s{^\s{3}}{ } \|\| die "can't find DOI in: $doi";
157			$v .= $doi;
158			}
159	dpavlin	1302	} elsif ( $line =~ m{^(\S\S)\s*$} ) {
160			warn "# $arg->{path} +$. empty \|$line\|\n";
161	dpavlin	899	} else {
162	dpavlin	1302	$log->logdie("can't parse +$. $arg->{path} \|$line\|");
163	dpavlin	899	}
164
165	dpavlin	904	if ( defined $v ) {
166			$v = $subfields->{$tag}->($v) if defined $subfields->{$tag};
167	dpavlin	901
168	dpavlin	904	$log->debug("$tag: ", sub { dump( $v ) });
169			push @{ $rec->{$tag} }, $v;
170			}
171	dpavlin	899
172			}
173			$log->debug("loaded ", $self->size, " records");
174
175	dpavlin	898	$self ? return $self : return undef;
176			}
177
178			=head2 fetch_rec
179
180			Return record with ID C<$mfn> from database
181
182	dpavlin	899	my $rec = $input->fetch_rec( $mfn, $filter_coderef );
183	dpavlin	898
184			=cut
185
186			sub fetch_rec {
187			my $self = shift;
188
189	dpavlin	899	my ( $mfn, $filter_coderef ) = @_;
190	dpavlin	898
191	dpavlin	1305	$mfn -= $self->{offset} if $self->{offset};
192	dpavlin	899	return $self->{_rec}->[$mfn-1];
193	dpavlin	898	}
194
195
196			=head2 size
197
198			Return number of records in database
199
200			my $size = $input->size;
201
202			=cut
203
204			sub size {
205			my $self = shift;
206	dpavlin	1305	$#{ $self->{_rec} } + 1;
207	dpavlin	898	}
208
209	dpavlin	900	=head1 SEE ALSO
210
211			L<http://isibasic.com/help/helpprn.html> is only sane source of document format which Google could find...
212	dpavlin	901
213	dpavlin	898	=head1 AUTHOR
214
215			Dobrica Pavlinusic, C<< <dpavlin@rot13.org> >>
216
217			=head1 COPYRIGHT & LICENSE
218
219			Copyright 2007 Dobrica Pavlinusic, All Rights Reserved.
220
221			This program is free software; you can redistribute it and/or modify it
222			under the same terms as Perl itself.
223
224			=cut
225
226			1; # End of WebPAC::Input::ISI