XML parsing Help..

[bioswami]

Dear All, I am using XML::Simple to parse some simple xml files. However I ran into a problem with this particular example. Here is what the data dumper gives me:

          'reaction' => [
                        {
                          'substrate' => {
                                         'name' => 'cpd:C00084'
                                       },
                          'name' => 'rn:R00710',
                          'product' => {
                                       'name' => 'cpd:C00033'
                                     },
                          'type' => 'reversible'
                        },                       {
                          'substrate' => [
                                         {
                                           'name' => 'cpd:C00068'
                                         },
                                         {
                                           'name' => 'cpd:C00022'
                                         }
                                       ],
                          'name' => 'rn:R00014',
                          'product' => {
                                       'name' => 'cpd:C05125'
                                     },
                          'type' => 'irreversible'
                        },

What I want to do is get to each product and substrate name for a given reaction and print it out. Here is what I would like to do:

$data = $xml->XMLin($input_file);

foreach $g (@{$data->{reaction}})
{
        foreach $h ($g->{substrate}){
                $temp1 = $h->{name};
                foreach $i ($g->{product}->{name}){
                      $temp2 = $i->{name}
                      print "$temp1 -- $temp2\n";
                }
        ]
}

It works for the first product and substrate, but for the second one, since there are now TWO substrates, it doesn't seem to pick it up. The fact that this doesn't work tells me that I am wrong somewhere, but I can't for the life of me figure it out. The error I get is: Bad index while coercing array into hash Any help will be much appreciated!! Thanks in advance. Cheers, Bioswami

[davorg]

You need to look at the "ForceArray" option in the XML::Simple documentation.

[bioswami]

Thanks davorg. That does help. For someone else who comes here looking for an answer to this same Q, here is what I did:

$xml = new XML::Simple (KeyAttr=>[],ForceArray=>['substrate','product'
+]);

So I specifically made all "substrate" and "product" elements into arrays. I then had to figure out the number of elements in that array. And this I did by:

foreach $g (@{$data->{reaction}}){
        $length = scalar @{$g->{substrate}};
        print " $g->{name}, len = $length\n";
}

Thanks for all your help! Cheers, Bioswami

[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}},