XML parsing issue in Perl

Question

I am trying to parse the abstract part from the XML file. I am using forcearray. I wrote the code but its just working when the abstract is in array and not working when array is not present. This is because when in an array I also use {content} and when not in array the {content} is missing. The code is as follows

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

open (FH, ">:utf8","xmlparsed2.txt");

my $db1 = "pubmed";
my $query  = "9915366";
my $q = 16404398;
my $xml = new XML::Simple;

$urlxml = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=$db1&id=$q&retmode=xml&rettype=abstract";
$dataxml = get($urlxml);
$data = $xml->XMLin("$dataxml", ForceArray => [qw( MeshHeading Author AbstractText )], ForceContent => 1);
print FH Dumper($data);

print FH "Abstract: ".join "\n", map {join ":",($_->{NlmCategory},$_->{content})} @{$data->{PubmedArticle}->{MedlineCitation}->{Article}->{Abstract}->{AbstractText}};
print FH "\n";
print FH "Title: "."$data->{PubmedArticle}->{MedlineCitation}->{Article}->{ArticleTitle}\n";
print FH "\n";
print FH "MeSH: ".join '$$', map $_->{DescriptorName}{content}, @{$data->{PubmedArticle}->{MedlineCitation}->{MeshHeadingList}->{MeshHeading}};
print FH "\n";
print FH "Authors: ".join '$$', map {join " ",($_->{LastName},$_->{ForeName})} @{$data->{PubmedArticle}{MedlineCitation}{Article}{AuthorList}{Author}};

Well, when in array(replcae $q in $urlxml by $query) I want the abstract with its NlmCategory like Objective: To determine if the long....... For the above code it is giving me the desired output but with hash at the end as follows:

METHODS:Tertiary care outpatient and inpatient rehabilitation center directly attached to a university hospital.:HASH(0x69d0810).

And for the abstract where it is not an array($q in $urlxml) this code doesn't seem to work, probably because there is not content term(I found this in data dumper). I played a bit and it sort of worked if I do something like just $_ for the array but also prints the two ::. In short I want my code to work for both $query and $q. Can you help?

ikegami · Accepted Answer · 2011-07-24 00:21:04Z

4

Use ForceContent => 1.

Or:

use strict;
use warnings;
use feature qw( say );

use LWP::Simple qw( get );
use XML::LibXML qw( );
use URI         qw( );

binmode STDOUT, ':encoding(UTF-8)';

my $db = "pubmed";
my $id = $ARGV[0] || '9915366';

my $url = URI->new('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi');
$url->query_form(
   db      => $db,
   id      => $id,
   retmode => 'xml',
   rettype => 'abstract',
);

my $xml = get($url);

my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($xml);
my $root = $doc->documentElement();

for my $node ($root->findnodes('PubmedArticle/MedlineCitation/Article/Abstract/AbstractText')) {
   say join ':', $node->getAttribute('NlmCategory') // '', $node->textContent();
}

edited Jul 24, 2011 at 0:21

answered Jul 24, 2011 at 0:10

ikegami

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5 Comments

smandape Over a year ago

Ooppss..nice to see you here. Well, I am trying to put questions in right sense now. Thank you for your help. Okay, thank you for the code but I already have a code which has other things included in it to extract along with abstract. To be frank I am a beginner,it really takes me long to understand the basic things about the code. And I just don't want to do it because I am doing it, I want to learn things. So, I understood this code a bit but then I will start looking for few things in it and then modify my original code which will take long time. So, I will go with your first answer.

smandape Over a year ago

I tired using forceconten=>1 as edited in the code above but then I am also trying to extract other things which is also edited in the code above. When I use forcecontent my other things are messed up which are not coming through content. Also, I am going to loop this code for the set of all the ids I have. I hope I am clear.

ikegami Over a year ago

@smandape, So add ->{content} where needed, as shown by the dump you create.

ikegami Over a year ago

@smandape, By the way, I showed an alternative to XML::Simple because XML::Simple is the most difficult XML parser to use correctly.

smandape Over a year ago

I thank you for your help. This really worked. Well, I will also try the alternative way for XML::Simple. Thank you for your help. Thank you a lot.

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