Hi All,
I am getting the timeout error,
"Problems with the web server: 500 Can't connect to
www.sanger.ac.uk:80<http://www.sanger.ac.uk/>(connect: timeout)"
most of the time. Here is my Registry file;
<?xml version="1.0" encoding="UTF-8"?>
<!-- <!DOCTYPE MartRegistry> -->
<MartRegistry>
<MartURLLocation
database="cosp"
default="1"
displayName="COSMIC (SANGER UK)"
host="www.sanger.ac.uk"
includeDatasets=""
martUser=""
name="CosmicMart"
path="/genetics/CGP/cosmic/biomart/martservice"
port="80"
redirect="1"
serverVirtualSchema="default"
visible="1"
/>
</MartRegistry>
Here is my code
#!/usr/local/bin/perl
use strict;
use lib '/home/manjula/biomart-perl/lib';
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile ="/home/manjula/TestMart/cosmicRegistry.xml";
print "Starting API\n";
print "using cached registry build\n";
my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);
my $registry = $initializer->getRegistry;
my $query =
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->setDataset("COSMIC54");
$query->addFilter("samp_gene_mutated", ["y"]);
$query->addFilter("site_primary", ["liver"]);
$query->addFilter("tumour_source", ["recurrent"]);
$query->addAttribute("sample_name");
$query->addAttribute("sample_source");
$query->addAttribute("tumour_source");
$query->addAttribute("gene_name");
$query->addAttribute("accession_number");
$query->addAttribute("site_primary");
$query->addAttribute("hist_primary");
$query->addAttribute("pubmed_pmid");
$query->formatter("TSV");
my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
$query->count(1);
$query_runner->execute($query);
#my $resultNo=
print $query_runner->getCount();
#if ($resultNo>0) {
#print "Count is $resultNo\n";
#} else {
#print "No results\n";
#}
#####################################################################
############################## GET RESULTS ##########################
# to obtain unique rows only
print "Getting unique rows\n";
$query_runner->uniqueRowsOnly(1);
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################
Strange thing is that, I get the timeout error when I use a clean registry
build. When I use the cached registry I get this error,
1Getting unique rows
Can't call method "getDisplayNames" on an undefined value at
/home/manjula/biomart-perl/lib/BioMart/QueryRunner.pm line 281.
Here 1 is the number of rows, then my print, after that the error. But I do
not get it all the time. Only getting it most of the time.
How can make this more reliable
Any help is greatly appreciated.
Thanking in advance
Manjula
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