Re: XML parsing Help..

[Hofmator]

The problem seems to be solved already ... but I liked playing around with it a bit. To ease this for fellow monks who might feel likewise - here is my code, showing similar behaviour to what bioswami wanted to achieve originally.

use strict;
use warnings;

use XML::Simple;
use Data::Dumper;

local $/; # slurp

my $data = XMLin(<DATA>, KeyAttr => [], ForceArray => [qw/substrate pr
+oduct/]);

for my $reaction (@{$data->{reaction}}) {
    print $reaction->{name}, ' (', $reaction->{type}, "):\n";
    for my $substrate (@{$reaction->{substrate}}) {
        foreach my $product (@{$reaction->{product}}) {
            print "\t", $substrate->{name}, " -- ", $product->{name}, 
+"\n";
        }
    }
}

__DATA__
<root>
    <reaction name="rn:R00710" type="reversible">
        <substrate name="cpd:C00084"/>
        <product name="cpd:C00033"/>
    </reaction>
    <reaction name="rn:R00014" type="irreversible">
        <substrate name="cpd:C00068"/>
        <substrate name="cpd:C00022"/>
        <product name="cpd:C05125"/>
    </reaction>
</root>

[Jenda]

Just in case anyone is interested, here are two implementations using XML::Rules. The first one prints the reactions as it parses through the XML, the other builds a more simplified data structure.

use strict;
use warnings;

use XML::Rules;
use Data::Dumper;

my $parser = XML::Rules->new(
    rules => [
        substrate => sub {return '@substrates' => $_[1]->{name}},
        product => sub {return '@products' => $_[1]->{name}},
        reaction => sub {
            print "$_[1]->{name} ($_[1]->{type}):\n";
            print "\tSubstrates: ", join(", ", @{$_[1]->{substrates}})
+, "\n";
            print "\tProducts:   ", join(", ", @{$_[1]->{products}}), 
+"\n\n";
            return;
        },
    ],
);

$parser->parse(\*DATA);

__DATA__
<root>
    <reaction name="rn:R00710" type="reversible">
        <substrate name="cpd:C00084"/>
        <product name="cpd:C00033"/>
    </reaction>
    <reaction name="rn:R00014" type="irreversible">
        <substrate name="cpd:C00068"/>
        <substrate name="cpd:C00022"/>
        <product name="cpd:C05125"/>
    </reaction>
</root>

and

use strict;
use warnings;

use XML::Rules;
use Data::Dumper;

my $parser = XML::Rules->new(
    rules => [
        substrate => sub {return '@substrates' => $_[1]->{name}},
        product => sub {return '@products' => $_[1]->{name}},
        reaction => sub {
            my $name = delete($_[1]->{name});
            delete($_[1]->{_content});
            return $name => $_[1];
        },
        root => 'pass no content',
    ],
);

my $result = $parser->parse(\*DATA);
print Dumper($result);

while (my ($reaction, $data) = each(%$result)) {
    print "$reaction ($data->{type})\n";
    print "\tSubstrates: ", join(", ", @{$data->{substrates}}), "\n";
    print "\tProducts:   ", join(", ", @{$data->{products}}), "\n\n";
}

__DATA__
<root>
    <reaction name="rn:R00710" type="reversible">
        <substrate name="cpd:C00084"/>
        <product name="cpd:C00033"/>
    </reaction>
    <reaction name="rn:R00014" type="irreversible">
        <substrate name="cpd:C00068"/>
        <substrate name="cpd:C00022"/>
        <product name="cpd:C05125"/>
    </reaction>
</root>

The substrate and product rules could be rewriten like this:

 'substrate,product' => sub {return '@'.$_[0].'s' => $_[1]->{name}},