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POXML::Smart Parser in Perl
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  1. POXML::Smart Parser in Perl
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    copied!<p>I'm continuing to work out of an outdated <a href="http://books.google.com/books?id=bvY21DGa1OwC&amp;pg=PA549&amp;lpg=PA549&amp;dq=&quot;bioinformatics+programming+using+perl+and+perl+modules&quot;&amp;source=bl&amp;ots=gJZIZVNkpy&amp;sig=AUj2GHbAUDbVlwI4haDYv_rUuv8&amp;hl=en&amp;ei=xb6XS-OOJpK-lAfP6e2UDQ&amp;sa=X&amp;oi=book_result&amp;ct=result&amp;resnum=1&amp;ved=0CAgQ6AEwAA#v=onepage&amp;q=%22bioinformatics%20programming%20using%20perl%20and%20perl%20modules%22&amp;f=false" rel="nofollow noreferrer">bioinformatics book</a> and I'm attempting to use the XML::Smart Module. </p> <p>I suspect the module's methods have changed over the course of 6 years and I'm inexperienced with perl to troubleshoot from <a href="http://search.cpan.org/~gmpassos/XML-Smart-1.6.9/lib/XML/Smart.pm#new_(FILE|DATA|URL_,_PARSER_,_OPTIONS)" rel="nofollow noreferrer">cpan source</a>. The commented out code proves the ncbi.gov query functions, I'm having trouble with the 'new' method - it's not parsing the XML. What am I doing wrong? Thanks! </p> <p><strong>Update</strong> Specifically I'm running into trouble with parsing and displaying the Id array: <code>my @Id = $results-&gt;{eSearchResult}{IdList}{Id}{'@'};</code> I'm running this on OSX terminal and I don't see any Ids when I run this script. I am seeing the proper Count. Thanks!</p> <pre><code>#!/usr/local/bin/perl # use lib "/Users/fogonthedowns/myperllib"; # use LWP::Simple; use XML::Smart; use strict; #Set base URL for all eutils my $utils = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils"; my $db = "Pubmed"; my $query ="Cancer+Prostate"; my $retmax = 10; my $esearch = "$utils/esearch.fcgi?" . "db=$db&amp;retmax=$retmax&amp;term="; # my $esearch_result = get($esearch.$query); # print "ESEARCH RESULT: $esearch_result\n"; # print "Using Query: \n$esearch$query\n"; # print "hello world\n"; my $results = XML::Smart-&gt;new($esearch.$query,"XML::Parser"); my $count = $results-&gt;{eSearchResult}{Count}; my @Id = $results-&gt;{eSearchResult}{IdList}{Id}{'@'}; my $all_Id = join("\n", @Id); print "Count = $count\n"; print "$all_Id\n"; </code></pre>
 

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