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# $Id: generic_tagval_parser.pm,v 1.3 2007/02/02 05:54:11 cmungall Exp $
#
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::Parsers::generic_tagval_parser;
=head1 NAME
GO::Parsers::generic_tagval_parser - syntax parsing of GO .def flat files
=head1 SYNOPSIS
do not use this class directly; use GO::Parser
=cut
=head1 DESCRIPTION
This generates Stag event streams from one of the various GO flat file
formats (ontology, defs, xref, associations). See GO::Parser for details
Examples of these files can be found at http://www.geneontology.org
A description of the event streams generated follows; Stag or an XML
handler can be used to catch these events
=head1 GO DEFINITION FILES
These have a suffix .defs or .definitions
=head1 AUTHOR
=cut
use Exporter;
use base qw(GO::Parsers::base_parser);
use GO::Parsers::ParserEventNames; # declare XML constants
use Carp;
use FileHandle;
use strict qw(subs vars refs);
sub dtd {
'generic_tagval-parser-events.dtd';
}
sub _class { 'generic' }
sub _id_column {}
sub _map_property_type { shift;@_ }
sub parse_fh {
my ($self, $fh) = @_;
my $file = $self->file;
$self->start_event(OBO);
my $lnum = 0;
my $in_record=0;
my $class = $self->_class;
my $id_column = $self->_id_column;
while (my $line = <$fh>) {
chomp $line;
++$lnum;
next if $line =~ /^\!/;
$line =~ s/^\s+$//;
if (!$line) {
$self->pop_stack_to_depth(1);
$in_record = 0;
next;
}
if ($line =~ /^(\S+):\s+(.*)/) {
my ($t,$v) = ($1,$2);
if (!$in_record) {
$self->start_event(INSTANCE);
$self->event(instance_of=>$class);
if (!$id_column) {
$t = 'id';
}
$in_record = 1;
}
if ($id_column && $t eq $id_column) {
$t = 'id';
}
if ($t eq 'id') {
$self->event(ID, $v);
}
else {
my $dt = 'xsd:string';
if ($v =~ /^http:/) {
$dt = 'xsd:anyURI';
}
$self->event(PROPERTY_VALUE,
[[TYPE,$self->_map_property_type($t)],
[VALUE,$v],
[DATATYPE,$dt]]);
}
}
elsif ($line =~ /^(\S+):\s*$/) {
}
else {
# $self->parse_err("cannot parse:\"$line\"");
}
}
$self->pop_stack_to_depth(0); # end event obo
}
1;
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