[biomart-users] Phytozome Biomart Perl API issue

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[biomart-users] Phytozome Biomart Perl API issue

Joy Doong
Hi, 

I am having issues connecting to phytozome through perl API and I am wondering if anyone knows how to do it right.

I copied the registry information off this link: https://phytozome.jgi.doe.gov/biomart/martservice?type=registry to make the configuration file.

Then I used script I got off phytozome biomart website:

# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >=  0.5 
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;

my $confFile = "../conf/registryPhytozome.xml";
#
# NB: change action to 'clean' if you wish to start a fresh configuration  
# and to 'cached' if you want to skip configuration step on subsequent runs from the same registry
#

my $action='clean';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');

$query->setDataset("phytozome");
$query->addFilter("gene_name_filter", ["AT1G05210"]);
$query->addAttribute("gene_name1");
$query->addAttribute("transcript_name1");
$query->addAttribute("peptide_sequence");

$query->formatter("FASTA");

my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
# $query->count(1);
# $query_runner->execute($query);
# print $query_runner->getCount();
#####################################################################


############################## GET RESULTS ##########################
# to obtain unique rows only
# $query_runner->uniqueRowsOnly(1);

$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################


This is the error message I got:

Cached Registry Unavailable...

Running Complete Clean...


Connection parameters of [Current Phytozome] [ OK ]

Connection parameters of [Sequences] [ OK ]

Connection parameters of [Genome_Archive] [ OK ]

Connection parameters of [Sequence_Archive] [ OK ]

Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust

               No datasets available with given parameters for Location: phytozome_mart


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust

               No datasets available with given parameters for Location: phytozome_mart


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust


               No datasets available with given parameters for Location: sequence_mart


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust

               No datasets available with given parameters for Location: sequence_mart


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust

               No datasets available with given parameters for Location: phytozome_mart_archive


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust


               No datasets available with given parameters for Location: phytozome_mart_archive


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust


               No datasets available with given parameters for Location: sequence_mart_archive


Problems with the web server: 500 Can't verify SSL peers without knowing which Certificate Authorities to trust


               No datasets available with given parameters for Location: sequence_mart_archive

 Problems with the retrieval of dataset configuration 

               Please check: 

               that your mart Registry files contains correct connection params, 

               that you are using the correct version on XML::Simple, 

               that BioMart  databases contain a populated meta_conf tables and

               that you have set martUser correctly if you are running in restricted data 

               access mode (populated meta_conf__user__dm)

What should I do to make it work?

Thanks!

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