NAME
caGRID::CQL1 - Construct and send a CQL XML request
SYNOPSIS
use caGRID::CQL1;
use caGRID::CQL1::Object;
use caGRID::CQL1::Group;
use caGRID::CQL1::Attribute;
use caGRID::CQL1::Association;
use caGRID::CQL1::QueryModifier;
$url = 'http://141.161.25.20:8080/wsrf/services/cagrid/GridPIR';
# construct the query
$obj = new caGRID::CQL1::Object();
$obj->name("edu.georgetown.pir.domain.ProteinSequence");
$assoc = new caGRID::CQL1::Association();
$assoc->name("edu.georgetown.pir.domain.Protein");
$assoc->rolename("protein");
my $attr1 = new caGRID::CQL1::Attribute();
$attr1->name("uniprotkbPrimaryAccession");
$attr1->value("P05067");
$attr1->predicate($caGRID::CQL1::Attribute::_EQUAL_TO);
$assoc->attribute($attr1);
$attr2 = new caGRID::CQL1::Attribute();
$attr2->name("id");
$attr2->value("P05067");
$attr2->predicate($caGRID::CQL1::Attribute::_EQUAL_TO);
$grp = new caGRID::CQL1::Group();
$grp->op($caGRID::CQL1::Group::_LOGIC_OR);
$grp->operands($assoc, $attr2);
$obj->group($grp);
$mod = new caGRID::CQL1::QueryModifier();
$mod->attributeNames("length");
$mod->attributeNames("id");
$mod->attributeNames("value");
# send the request, receive the data
$cql = caGRID::CQL1->new;
$response = $cql->request($url, $obj, $mod);DESCRIPTION
caGrid is a service-oriented platform that supports cutting-edge collaborative science by providing the tools for organizations to integrate data silos, securely share data and compose analysis pipelines. caGrid supports e-Science initiatives in basic, translational, and clinical research. A major focus of caGRID at the moment is cancer research, and the publicly available data offered by caGRID currently is concerned with proteins and genes and experiments on proteins and genes as they relate to cancer.
The modules in caGRID-CQL1 are dedicated to constructing, validating, and sending CQL queries to the public Services in caGRID. CQL is the structured XML query language used in caGRID. For more information please see http://cagrid.org.
AUTHOR
Jason Zhang, Brian Osborne
Email jason@bioteam.net, briano@bioteam.net
COPYRIGHT and LICENSE
caBIG(r) Open Source Software License caGrid 1.3
Copyright 2010 The Ohio State University Research Foundation ("OSURF"), Argonne National Laboratory ("ANL"), SemanticBits LLC ("SemanticBits"), and Ekagra Software Technologies Ltd. ("Ekagra") ("caBIG(r) Participant"). The caGrid 1.3 software was created with NCI funding and is part of the caBIG(r) initiative. The software subject to this notice and license includes both human readable source code form and machine readable, binary, object code form (the "caBIG(r) Software").
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SEE ALSO
caGRID::CQL1::Association, caGRID::CQL1::Attribute, caGRID::CQL1::Group, caGRID::CQL1::Object, caGRID::CQL1::QueryModifier, caGRID::CQL1::Validator, caGRID::CQL1::Schema, caGRID::Net::Request, caGRID::Net::Util, caGRID::Transfer::Client, caGRID::CQL1.
new
Title : new
Usage :
Function: Create a caGRID::CQL1 object
Example : my $obj = caGRID::CQL1->new()
Returns : A caGRID::CQL1 object
Args : -debug => 1: if debug is true, the requested XML is printed to console,
-timeout => 5: timeout query if the request did not return in 5 seconds request
Title : request
Usage :
Function: Send the query the server. If the HTTP request fails this method dies with a
HTTP error message
Example :
Returns : SOAP XML from server
Args : 1st parameter: service URL, 2nd parameter: target object (instance of
CQL1::Object), optional 3nd parameter: a Query modifiergetResultCollection
Title : getResultCollection
Usage :
Function: Position the parser to the CQLQueryResultCollection element
Die with error message if the CQLQueryResultCollection element can
not be found
Example :
Returns : Return the positioned reader
Args : A XML::LibXML::Reader objectgetCount
Title : getCount
Usage :
Function: Return the count value
Example :
Returns :
Args : An instance of XML::LibXML::ReadergetTargetClass
Title : getTargetClass
Usage :
Function: Return the targetClass from query result
Example :
Returns :
Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollectiongetAttributeResultAsHashRef
Title : getAttributeResultAsHashRef
Usage :
Function: Return all the AttributeResult as a hash reference
Example :
Returns :
Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollectiongetElementAttributesAsHashRef
Title : getElementAttributesAsHashRef
Usage :
Function: Return the all attributes for an XML element as a reference
Example :
Returns : Hash reference
Args : An instance of XML::LibXML::Reader positioned to an XML elementgetFirstChildElement
Title : getFirstChildElement
Usage :
Function: Position reader to the first child XML element
Example :
Returns :
Args : An instance of XML::LibXML::Reader positioned to an XML elementgetAttributeResultAsArrayRef
Title : getAttributeResultAsArrayRef
Usage :
Function: Return all the AttributeResult as array reference
Example :
Returns :
Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollectiontoXML
Title : toXML
Usage :
Function: Private method to write CQL XML
Example :
Returns : CQL XML
Args : A Target and any QueryModifierprintObjChildren
Title : printObjChildren
Usage :
Function: Print any Association, Attribute, or Group objects
Example :
Returns :
Args : An XML Writer, an ObjectprintAttr
Title : printAttr
Usage :
Function: Print any Attribute objects
Example :
Returns :
Args : An XML Writer, an AttributeprintAssoc
Title : printAssoc
Usage :
Function: Print any Association objects
Example :
Returns :
Args : An XML Writer, an Association objectprintGroup
Title : printGroup
Usage :
Function: Print any Group objects
Example :
Returns :
Args : An XML Writer, a Group objectextractFault
Title : extractFault
Usage :
Function:
Example :
Returns : Error string
Args :_rearrange
Title : _rearrange
Usage :
Function: Initialize with arguments to new()
Example :
Returns :
Args : Optional, parameters with -