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examples/caBIOtest.pl  view on Meta::CPAN

#!/usr/bin/perl -w

# works with Axis 1.2

use strict;

use LWP::UserAgent;
use HTTP::Request::Common;
use CaCORE::ApplicationService;
use CaCORE::CaBIO;
use CaCORE::Security;
use CaCORE::CaDSR;

#
# ApplicationService is a utility classs that encapsulates webservice invocation to caCORE server.
# ApplicationService object follows the Singleton pattern, in that each program will ONLY contain one instance
# of such class.
# The URL being passed to the intance method is the service endpoint of the caCORE webservice.
# If no such URL is provided in the program, it will default to the caCORE production server, "http://cabio.nci.nih.gov/cacore30/ws/caCOREService"
#
my $appsvc = CaCORE::ApplicationService->instance("http://cabio.nci.nih.gov/cacore32/ws/caCOREService");

# test CaBIO 1: use ApplicationService
# 
# This test retrieves all Chromosomes whoses associated genes have a symbol of "NAT2" using the direct
# and basic search function of ApplicationService->queryObject
#
print "test CaBIO 1: use ApplicationService to search Gene given a gene symbol attribute\n";

# instantiate a Gene domain object and sets the value of symbol attribute to NAT2.
my $gene = new CaCORE::CaBIO::Gene;
$gene->setSymbol("NAT2");

my @chromos;
# the eval...warn... construct is recommended, if error is encountered during webservice call, this will
# trap the exception and allows for error handling, and prevent the program from exiting.
eval{
	#
	# This call encapsulates the webservice invocation to the caCORE server, and converts
	# the returned XML into list of Chromosome objects
	# Parameter 1 indicates target class, Chromosome, to be retrieved
	# Parameter 2 indicates search criteria. In this case, is the genes associated with the chromosome.
	#
	@chromos = $appsvc->queryObject("CaCORE::CaBIO::Chromosome", $gene);
};
warn "Test CaBIO 1 failed. Error:\n" . $@ if $@; # some exception handling

# iterate thru results
foreach my $chromo (@chromos){
	print "id= " . $chromo->getId . "  number=" . $chromo->getNumber . "\n";
}

# test CaBIO 2: use association: many to one
# 
# This test retrieves the Taxon object that is associated with a Chromosome object via a get method
#
print "test CaBIO 2: navigation by association: many to one\n";
print "\tSearch for the associated taxon given a chromosome object.\n";

# Our starting point is a chromosome object obtained from test 1
my $chromo1 = $chromos[0];
print "start chromosome id=" . $chromo1->getId . "\n";
my $taxon;
eval{
	#
	# The Taxon is associated with Chromosome via a one to many relationship
	# i.e., one taxon is associated with many chromosomes
	# The Chromosome->getTaxon is implemented as a ApplicationService->queryObject as in test 1