CaCORE::ApplicationService is a utility class 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 instance 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";. The ApplicationService class exposes two methods: queryObject and query for search. The ApplicationService is the fundamental class that all other search methods utilizes.
my $appsvc = CaCORE::ApplicationService->instance("http://cabio.nci.nih.gov/cacore31/ws/caCOREService");
my $gene = new CaCORE::CaBIO::Gene;
$gene->setSymbol("NAT2");
my @chromos = $appsvc->queryObject("CaCORE::CaBIO::Chromosome", $gene);
The following methods are supported in CaCORE::ApplicationService:
instance(url): returns the ApplicationService instance. "url" is the service endpoint to a caCORE server. Example url: "http://cabio.nci.nih.gov/cacore30/ws/caCOREService".
queryObject(targetPath, sourceObject): invoke caCORE server to search for domain objects. This method returns at most 1000 objects because caCORE webservice automatically trims the result set to 1000 if actual result set is greater than 1000.
query(targetPath, sourceObject, startIndex, requestSize): invoke caCORE server to search for domain objects. Allows for specifying the return result set.
Description of parameters used in the above functions:
url: the service endpoint to a caCORE server. Example url: "http://cabio.nci.nih.gov/cacore30/ws/caCOREService".
targetPath: can be either a fully qualified target object name, such as "CaCORE::CaBIO::Gene"; or a series of comma separated fully qualified object names indicating a navigational path, such as "CaCORE::CaBIO::Taxon,CaCORE::CaBIO::Chromosome". This navigational path specifies the relationship to traverse when retrieving the target objects.
sourceObject: is the search criteria that specifies the search starting point.
startIndex (for method "query" only): allows for control of the starting index of the result set. When presented, requestSize must also be present.
requestSize (for method "query" only): defines the requested size. Server trims the return result to the requested size before returns. If the result set is smaller than the requested size, the result set is returned without trimming.
This following example retrieves all Chromosomes whose associated genes have a symbol of "NAT2" using the direct and basic search function of ApplicationService->queryObject(). This queryObject() function 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 gene associated with the chromosome.
use CaCORE::ApplicationService;
use CaCORE::CaBIO;
my $gene = new CaCORE::CaBIO::Gene;
$gene->setSymbol("NAT2");
my $appsvc = CaCORE::ApplicationService->instance("http://cabio.nci.nih.gov/cacore31/ws/caCOREService");
my @chromos = $appsvc->queryObject("CaCORE::CaBIO::Chromosome", $gene);
The first parameter in the search method can be constructed as a "navigation path" that reflects how these objects are related to the target object. This example retrieves all the Taxons related to the Chromosomes that are related to a Gene object:
my @taxons = $appsvc->queryObject("CaCORE::CaBIO::Taxon,CaCORE::CaBIO::Chromosome", $gene);
foreach my $tx (@taxons){
print "id= " . $tx->getId . " scientificName=" . $tx->getScientificName ."\n";
}
Depending on the search criteria, a search may yield a large result set, which cause slower response time and increase the likelihood of failure. A throttle mechanism is provided by:
ApplicationService->query(targetClassName, knownSourceObject, startingIndex, requestedSize)
In the following example:
Parameter 1 indicates name of the target object, Gene, to be retrieved
Parameter 2 indicates search criteria. In this case, is the chromosome associated with the genes.
Parameter 3 indicates the requested start index, 10
Parameter 4 indicates the requested size, 20
my @geneSet = $appsvc->query("CaCORE::CaBIO::Gene", $chromo1, 10, 20);
This will retrieve related Gene objects from a Chromosome object, the result set starts from index number 10, and contains up to 20 Gene objects.
By default, when calling ApplicationService->queryObject, the caCORE server automatically trim the resultset to 1000 objects if the there more than 1000. So in reality, if you want to retrieve anything beyond 1000, you must use ApplicationService->query.