How to extract multiple tags with same name from an XML file in perl

Question

My XML file looks like this:

<eLinkResult>
  <LinkSet>
    <DbFrom>nuccore</DbFrom>
    <IdList>
      <Id>133909243</Id>
    </IdList>
    <LinkSetDb>
      <DbTo>taxonomy</DbTo>
      <LinkName>nuccore_taxonomy</LinkName>
      <Link>
        <Id>417290</Id>
      </Link>
      <Link>
        <Id>417289</Id>
      </Link>
      <Link>
        <Id>405948</Id>
      </Link>
    </LinkSetDb>
  </LinkSet>
</eLinkResult>

I am looking to get all <Id> information, and I know how to extract if there was one <Id> like so:

my $test="Some URL;
      my $Result = get ($test);
      my $Data = $Parser->XMLin($Result);
my $x=0;
if (exists($Data->{LinkSet}{LinkSetDb}->[0]->{Link}{Id})) {
    $TaxId=$Data->{LinkSet}{LinkSetDb}{Link}->[0]->{Id};

or just

if (exists($Data->{LinkSet}{LinkSetDb}{Link}{Id})) {
    $TaxId=$Data->{LinkSet}{LinkSetDb}{Link}{Id};
}

However when i try to use the XML file above I get Not a HASH reference

I also tried

foreach  (@{$Data->{LinkSet}{LinkSetDb}{Link}{Id}}) {
Print $_;
}

But Still I get an error, is there a way so I can get all the <Id> without specifying which one I want?

You need to iterate over all the Link elements, then grab the Id in the loop body. — ikegami
– ikegami, Commented Jun 5, 2013 at 22:12

Birei · Accepted Answer · 2013-06-05 21:29:05Z

2

Try with parser XML::Twig.

Content of script.pl:

#!/usr/bin/env perl

use warnings;
use strict;
use XML::Twig;

my $twig = XML::Twig->new(
    twig_handlers => {
        'LinkSet/LinkSetDb/Link/Id' => sub {
            printf qq|%s\n|, $_->text_only;
        },  
    },  
)->parsefile( shift );

Run it with the xml file as input argument, like:

perl script.pl xmlfile

That yields:

417290
417289
405948

answered Jun 5, 2013 at 21:29

Birei

36.4k3 gold badges80 silver badges84 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

Borodin · Accepted Answer · 2013-06-05 23:21:48Z

XML::Simple is rarely a good choice for processing XML. It does not accurately represent XML data structures, and in my experience it is far from simple to use, because the Perl data structure it creates is difficult to predict and awkward to navigate.

XML::LibXML and XML::Twig are good candidates, and, although XML::Twig can be used to process large XML files piece by piece, there is no reason to use it that way.

This short program uses XML::Twig to read the complete data structure and print the text values of all the Id elements.

use strict;
use warnings;

use XML::Twig;

my $twig = XML::Twig->new;
$twig->parsefile('xml.xml');
print $_->text, "\n" for $twig->findnodes('//Id');

output

Update

If you want only the Id elements from within the LinkSetDb part of the data and not those inside IdList, then change the findnodes call to $twig->findnodes('//Link/Id')

Collectives™ on Stack Overflow

How to extract multiple tags with same name from an XML file in perl

2 Answers 2

Comments

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

Comments

Your Answer

Sign up or log in

Post as a guest

Related