NAME
Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server
SYNOPSIS
$fac = Bio::DB::ESoap->new( -util => 'esearch' );
$som = $fac->run( -db => 'prot', -term => 'HIV and gp120' );
$fac->set_parameters( -term => 'HIV2 and gp160' );
# accessors corresponding to valid parameters are also created:
$fac->db('nuccore');
$som = $fac->run;
# more later.DESCRIPTION
ESoap provides a basic SOAP interface to the NCBI Entrez Utilities Web Service (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html). SOAP::Lite handles the SOAP calls. Higher level access, pipelines, BioPerl object I/O and such are provided by Bio::DB::SoapEUtilities.
ESoap complies with Bio::ParameterBaseI. It depends explicitly on NCBI web service description language files to inform the available_parameters() method. WSDLs are parsed by a relative lightweight, Entrez-specific module Bio::DB::ESoap::WSDL.
The run() method returns SOAP::SOM (SOAP Message) objects. No fault checking or other parsing is performed in this module.
SEE ALSO
Bio::DB::EUtilities, Bio::DB::SoapEUtilities, Bio::DB::ESoap::WSDL
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = new Bio::DB::ESoap();
Function: Builds a new Bio::DB::ESoap factory
Returns : an instance of Bio::DB::ESoap
Args :_wsdl()
Title : _wsdl
Usage : $obj->_wsdl($newval)
Function: Bio::DB::ESoap::WSDL object associated with
this factory
Example :
Returns : value of _wsdl (object)
Args : on set, new value (object or undef, optional)_client()
Title : _client
Usage : $obj->_client($newval)
Function: holds a SOAP::Lite object
Example :
Returns : value of _client (a SOAP::Lite object)
Args : on set, new value (a SOAP::Lite object or undef, optional)_operation()
Title : _operation
Alias : util
Usage :
Function: check and convert the requested operation based on the wsdl
Returns :
Args : operation (scalar string)action()
Title : action
Usage :
Function: return the soapAction associated with the factory's utility
Returns : scalar string
Args : nonewsdl_file()
Title : wsdl_file
Usage :
Function: get filename of the local WSDL XML copy
Returns : filename (scalar string)
Args : nonerun()
Title : _run
Usage : $som = $self->_run(@optional_setting_args)
Function: Call the SOAP service with the factory-associated utility
and parameters
Returns : SOAP::SOM (SOAP Message) object
Args : named parameters appropriate for the utility
Note : no fault checking hereBio::ParameterBaseI compliance
parameters_changed()
Title : parameters_changed
Usage : $obj->parameters_changed($newval)
Function: flag to indicate, well, you know
Example :
Returns : value of parameters_changed (a scalar)
Args : on set, new value (a scalar or undef, optional)_init_parameters()
Title : _init_parameters
Usage : $fac->_init_parameters
Function: identify the available input parameters
using the wsdl object
Returns : arrayref of parameter names (scalar strings)
Args : none