caGRID::CQL1 - Construct a CQL XML request
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);
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.
Jason Zhang, Brian Osborne
Email jason@bioteam.net, briano@bioteam.net
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").
This caBIG(r) Software License (the "License") is between caBIG(r) Participant and You. "You" (or "Your") shall mean a person or an entity, and all other entities that control, are controlled by, or are under common control with the entity. "Control" for purposes of this definition means (i) the direct or indirect power to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.
License. Provided that You agree to the conditions described below, caBIG(r) Participant grants You a non-exclusive, worldwide, perpetual, fully-paid-up, no-charge, irrevocable, transferable and royalty-free right and license in its rights in the caBIG(r) Software, including any copyright or patent rights therein, to (i) use, install, disclose, access, operate, execute, reproduce, copy, modify, translate, market, publicly display, publicly perform, and prepare derivative works of the caBIG(r) Software in any manner and for any purpose, and to have or permit others to do so; (ii) make, have made, use, practice, sell, and offer for sale, import, and/or otherwise dispose of caBIG(r) Software (or portions thereof); (iii) distribute and have distributed to and by third parties the caBIG(r) Software and any modifications and derivative works thereof; and (iv) sublicense the foregoing rights set out in (i), (ii) and (iii) to third parties, including the right to license such rights to further third parties. For sake of clarity, and not by way of limitation, caBIG(r) Participant shall have no right of accounting or right of payment from You or Your sublicensees for the rights granted under this License. This License is granted at no charge to You. Your downloading, copying, modifying, displaying, distributing or use of caBIG(r) Software constitutes acceptance of all of the terms and conditions of this Agreement. If you do not agree to such terms and conditions, you have no right to download, copy, modify, display, distribute or use the caBIG(r) Software.
1. Your redistributions of the source code for the caBIG(r) Software must retain the above copyright notice, this list of conditions and the disclaimer and limitation of liability of Article 6 below. Your redistributions in object code form must reproduce the above copyright notice, this list of conditions and the disclaimer of Article 6 in the documentation and/or other materials provided with the distribution, if any.
2. Your end-user documentation included with the redistribution, if any, must include the following acknowledgment: "This product includes software developed by the Ohio State University Research Foundation ("OSURF"), Argonne National Laboratory ("ANL"), SemanticBits LLC ("SemanticBits"), and Ekagra Software Technologies Ltd. ("Ekagra")." If You do not include such end-user documentation, You shall include this acknowledgment in the caBIG(r) Software itself, wherever such third-party acknowledgments normally appear.
3. You may not use the names "The Ohio State University Research Foundation", "OSURF", "Argonne National Laboratory", "ANL", "SemanticBits LLC", "SemanticBits", "Ekagra Software Technologies Ltd.", "Ekagra", "The National Cancer Institute", "NCI", "Cancer Biomedical Informatics Grid" or "caBIG(r)" to endorse or promote products derived from this caBIG(r) Software. This License does not authorize You to use any trademarks, service marks, trade names, logos or product names of either caBIG(r) Participant, NCI or caBIG(r), except as required to comply with the terms of this License.
4. For sake of clarity, and not by way of limitation, You may incorporate this caBIG(r) Software into Your proprietary programs and into any third party proprietary programs. However, if You incorporate the caBIG(r) Software into third party proprietary programs, You agree that You are solely responsible for obtaining any permission from such third parties required to incorporate the caBIG(r) Software into such third party proprietary programs and for informing Your sublicensees, including without limitation Your end-users, of their obligation to secure any required permissions from such third parties before incorporating the caBIG(r) Software into such third party proprietary software programs. In the event that You fail to obtain such permissions, You agree to indemnify caBIG(r) Participant for any claims against caBIG(r) Participant by such third parties, except to the extent prohibited by law, resulting from Your failure to obtain such permissions.
5. For sake of clarity, and not by way of limitation, You may add Your own copyright statement to Your modifications and to the derivative works, and You may provide additional or different license terms and conditions in Your sublicenses of modifications of the caBIG(r) Software, or any derivative works of the caBIG(r) Software as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
6. THIS caBIG(r) SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED WARRANTIES (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN NO EVENT SHALL THE OHIO STATE UNIVERSITY RESEARCH FOUNDATION ("OSURF"), ARGONNE NATIONAL LABORTORY ("ANL"), SEMANTICBITS LLC ("SEMANTICBITS"), AND EKAGRA SOFTWARE TECHNOLOGIES LTD. ("EKAGRA") OR ITS AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS caBIG(r) SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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.
Title : new Usage : Function: Create a caGRID::CQL1 object Example : $obj = caGRID::CQL1->new() or @proxy = ('http','http://proxy.sn.no:8001/'); $cql = caGRID::CQL1->new(-proxy => \@proxy); 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, -proxy => $proxy
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 modifier
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 object
Title : getCount Usage : Function: Return the count value Example : Returns : Args : An instance of XML::LibXML::Reader
Title : getTargetClass Usage : Function: Return the targetClass from query result Example : Returns : Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollection
Title : getAttributeResultAsHashRef Usage : Function: Return all the AttributeResult as a hash reference Example : Returns : Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollection
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 element
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 element
Title : getAttributeResultAsArrayRef Usage : Function: Return all the AttributeResult as array reference Example : Returns : Args : An instance of XML::LibXML::Reader positioned to CQLQueryResultCollection
Title : toXML Usage : Function: Private method to write CQL XML Example : Returns : CQL XML Args : A Target and any QueryModifier
Title : printObjChildren Usage : Function: Print any Association, Attribute, or Group objects Example : Returns : Args : An XML Writer, an Object
Title : printAttr Usage : Function: Print any Attribute objects Example : Returns : Args : An XML Writer, an Attribute
Title : printAssoc Usage : Function: Print any Association objects Example : Returns : Args : An XML Writer, an Association object
Title : printGroup Usage : Function: Print any Group objects Example : Returns : Args : An XML Writer, a Group object
Title : extractFault Usage : Function: Example : Returns : Error string Args :
Title : _rearrange Usage : Function: Initialize with arguments to new() Example : Returns : Args : Optional, parameters with -
To install caGRID::CQL1, copy and paste the appropriate command in to your terminal.
cpanm
cpanm caGRID::CQL1
CPAN shell
perl -MCPAN -e shell install caGRID::CQL1
For more information on module installation, please visit the detailed CPAN module installation guide.