[Bioperl-l] SOAP::Lite and bioperl

[Al Park]

Hello everyone,

I have been stumped for the past two days trying to figure out why I can't get the following code to work properly.  I get an error telling me that it "Can't call method "run" on undefined value".  Any help or suggestions for what I'm doing wrong?

Thanks in advance.
Al

######Soap::lite server code
#!/usr/bin/perl
use lib '/var/www/MODs';
use SOAP::Transport::HTTP;
use testpms;

my $server = SOAP::Transport::HTTP::CGI
   ->on_action(sub{return})
   ->dispatch_to('testpms::runTool');
$server->serializer->maptype->{SOAPStruct} = 'xsd1';
$server->handle;

######testpms.pm code
package testpms;

use strict;
use lib '/var/www/MODs';
use SoapExSeq;
use EmbossTools;

sub runTool{
    my ($class,$program,$ids,$chain) = @_;

    my ($dbh,$rc) = SoapExSeq::connectDB();
    my $file = SoapExSeq::getSeq($dbh,$rc,$ids,$chain);
    SoapExSeq::disconnectDB($dbh,$rc);

    my $emboss = new EmbossTools;
    my $hashRef = $emboss->eTools($program,$file);

    my @val;
    my %hash = %$hashRef;
    foreach my $x (keys %hash){
	if($x =~ /^\d+/){
	    my $value = $hash{$x};
	    my $item = SOAP::Data
		->type("SOAPStruct")
		->value({"isolate" => $x,
			 "value" => $value});
	    push(@val, $item);
	}
     }
     return SOAP::Data->name("results" => \@val);
}
1;

#######EmbossTools.pm code
package EmbossTools;
use strict;
use Bio::Factory::EMBOSS;

BEGIN {
    $ENV{EMBOSSDIR} = '/usr/local/bin/emboss/';
}

sub new{
    my $class = shift;
    my $self = {};
    bless ($self, $class);
    return $self;
}

sub eTools{
    my $self = shift;
    my ($program,$seq_to_test) = @_;
    my (%hash);

    my $outfile = sprintf "/var/www/tmp/out.%s.$program", time;

    my $factory = new Bio::Factory::EMBOSS;
    my $application = $factory->program($program);

    if($program eq "iep"){ #handles fasta file	
		$application->run({ '-sequencea' => $seq_to_test,
				'-graph'     => 'none',
				'-outfile'   => $outfile});
    }

    my @all;
    if($outfile){
	if($outfile =~ /iep/){
	    my($isolate,$iep_value);
	    open(FH, "$outfile");
	    while(<FH>){
		chomp;
		if($_ =~ /IEP/){
		    ($isolate = $_) =~ s/\w+\s\w+\s(.+)\sfrom.+$/$1/g;
		}
		if($_ =~ /Isoelectric/){
		    ($iep_value = $_) =~ s/\w+\s\w+\s\=\s(.+)/$1/g;
		    $hash{$isolate} = $iep_value;
		    push(@all, $isolate, $iep_value);
		}
    	   }
    	   close FH;
	}
    return (\%hash);
}
1;