#!/usr/local/bin/perl -w

#use strict;
#use warnings;
use DBI;
use Net::MySQL;
use HTTP::Request::Common;
use LWP::UserAgent;
use CGI qw(header -no_debug); 
use XML::Twig;

#==============================database connection================================================
print "trying to connect to database \n";
my $database = '';
my $host = '';
my $user = '';
my $password = '';

my $mysql = Net::MySQL->new(
        hostname => $host,
        database => $database,
        user     => $user,
        password => $password,
    );
    
print "Connection established \n";

#=============================end database connection==================================================


$mysql->query(qq{SELECT accession_code FROM protein});

my $record_set = $mysql->create_record_iterator;

while (my $record = $record_set->each) {
    print "Accession ID: $record->[0] \n";
    
    #For retrieving data from a url post in perl, we will use the LWP module "get" function

    use LWP::Simple; #supports the "get" function

    $baseurl="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
    $eutil="esearch.fcgi?";
    $parameters="db=protein&term=$record->[0]&retmode=xml";        #db=protein&id=gi_id     db=taxonomy&id=tax_id
    $url=$baseurl.$eutil.$parameters;            &nb
sp;              &nb
sp;#term=$record->[0]

    $raw=get($url);
    
    open(FILE, ">$record->[0]");              &n
bsp;     #$record->[0]
    print FILE $raw;
    close FILE;
    
    $xml_file = $record->[0];              &n
bsp;             #$record->[0]
    
    my $twig= XML::Twig->new(
               
 TwigHandlers => {
               
     IdList => \&id_Tag
               
 }
    );
 

    #actually parse the file
    $twig->parsefile($xml_file) or die "cannot parse [$xml_file]: $!";

    
 
     ###########################################
     sub id_Tag {
     ###########################################
       my($t, $idTag)= @_;
         unless($idTag->first_child('Id')->text) {
               print "ID-tag leer\n";
           }
         
         my $id = $idTag->first_child('Id')->text;
           print "GI_ID: ",$id,"\n";
       # Release memory of processed tree up to here
    $t->purge();
    }
    

    unlink($record->[0]);
    
    
}

Can't call method "text" on an undefined value at /home/Hubert/installed/eclipse/workspace/Database_Search/species.pl line 71.
trying to connect to database 
Connection established 
Accession ID: 140U_DROME 
GI_ID: 29427659
Accession ID: 145L_ 
GI_ID: 15078858
Accession ID: 14KD_RHOSH 
GI_ID: 231344
Accession ID: 194K_TRVSY 
GI_ID: 112711
Accession ID: 1A02_PANTR 
GI_ID: 122149
Accession ID: 1A0I_ 
GI_ID: 3114525
Accession ID: 1A0L_A 

unless($idTag->first_child('Id')->text) {
              print "ID-tag leer\n";
          }

unless(defined $idTag->first_child('Id')) {
              print "ID-tag leer\n";
          }

Can't call method "text" on an undefined value

unless(defined $idTag->first_child('Id')) {
             print "ID-tag leer\n";
} else {
             print $idTag->first_child('Id')->text();
}