Reference

Bio::DB::ESoap(3pm)

Client for the NCBI Entrez EUtilities SOAP server

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.

  [email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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    : none

wsdl_file()

 Title   : wsdl_file
 Usage   : 
 Function: get filename of the local WSDL XML copy
 Returns : filename (scalar string)
 Args    : none

run()

 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 here

Bio::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

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