| Subject: | Variable scope and TwigHandlers |
Debian 3.1
Kernel 2.6.10
Package libxml-twig-perl 3.17
I'm using a TwigHandler to loop through the many children of the root of an XML file, and write certain parts to a database. I can't pass parameters into the handler function (can I?) so I'm creating the $dbh with global scope like in the examples. I'm also creating a simple counter with global scope and incrementing it inside the handler.
In the first loop of the handler the counter appears to be undef. However, in subsequent loops it increments properly. A database handle initialized in the main program also appears undef inside the handler. I've had to put a nasty condition in the handler to check if these vars are defined, to take care of the first call.
This code reproduces the problem:
#!/usr/bin/perl -w
use strict;
use XML::Twig;
use DBD::mysql;
my $twig= new XML::Twig(TwigHandlers => {entry => \&entry,});
$twig->parsefile("uniprot_sprot.xml");
my $entry_id = 1; # Need these to be global
my $dbh = dbconnect();
sub dbconnect
{
my $database = "";
my $host = "";
my $user = "";
my $password = "";
my $dsn = "DBI:mysql:$database:$host";
my $dbh = DBI->connect($dsn,$user,$password,{AutoCommit => 0, PrintError => 1}) or die "No database handle\n";
return $dbh;
}
sub entry
{
my ($twig,$entry) = @_;
$entry_id = 1 if (!defined $entry_id); # These lines are needed to get these
$dbh = dbconnect() if (!defined $dbh); # vars to be defined in the first call
# without the above lines I get the error shown at the bottom
# Otherwise it works fine
my $organism = $entry->first_child('organism');
my $taxid = organism($organism) if (defined $organism);
my $sql = "insert into entry (entry_id, taxonomy_id) values ($entry_id,$taxid)";
print STDERR $sql;
print STDERR "\n";
my $sth = $dbh->prepare($sql);
$sth->execute();
$sth->finish();
$entry_id++;
$twig->purge;
}
$twig->purge;
sub organism
{
my $organism = shift;
my $dbreference = $organism->first_child('dbReference');
my $taxid = $dbreference->{'att'}->{'id'};
return $taxid;
}
Use of uninitialized value in concatenation (.) or string at parser.pl line 35.
insert into entry (entry_id, taxonomy_id) values (,5875)
Can't call method "prepare" on an undefined value at parser.pl line 38.