| Bio::DB::ESoap(3pm) | User Contributed Perl Documentation | Bio::DB::ESoap(3pm) |
Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server
$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.
"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.
Bio::DB::EUtilities, Bio::DB::SoapEUtilities, Bio::DB::ESoap::WSDL
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 lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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/
Email maj -at- fortinbras -dot- us
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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)
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)
Title : _operation Alias : util Usage : Function: check and convert the requested operation based on the wsdl Returns : Args : operation (scalar string)
Title : action Usage : Function: return the soapAction associated with the factory's utility Returns : scalar string Args : none
Title : wsdl_file Usage : Function: get filename of the local WSDL XML copy Returns : filename (scalar string) Args : none
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
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)
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
| 2023-01-22 | perl v5.36.0 |