Bio::DB::ESoap::WSDL(3pm)

NAME

Bio::DB::ESoap::WSDL - WSDL parsing for Entrez SOAP EUtilities

SYNOPSIS

Used by Bio::DB::ESoap

 # url
 $wsdl = Bio::DB::ESoap::WSDL->new(
    -url => "http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl"
  );
 # local copy
 $wsdl = Bio::DB::ESoap::WSDL->new(
    -wsdl => "local/eutils.wsdl"
  );
  %opns = %{ $wsdl->operations };

DESCRIPTION

This module is a lightweight parser and container for WSDL XML files associated with the NCBI EUtilities SOAP server. XML facilities are provided by XML::Twig.

The following accessors provide names and structures useful for creating SOAP messages using SOAP::Lite (e.g.):

 service()    : the URL of the SOAP service
 operations() : hashref of the form {.., $operation_name => $soapAction, ...}
 request_parameters($operation) : 
    request field names and namelists as an array of hashes
 result_parameters($operation)  : 
    result field names and namelists as an array of hashes

The following accessors provide XML::Twig::Elt objects pointing at key locations in the WSDL:

 root            : the root of the WSDL docment
 _types_elt      : the <types> element
 _portType_elt   : the <portType> element
 _binding_elt    : the <binding> element
 _service_elt    : the <service> element
 _message_elts   : an array of all top-level <message> elements
 _operation_elts : an array of all <operation> elements contained in <binding>

Parsing occurs lazily (on first read, not on construction); all information is cached. To clear the cache and force re-parsing, run

 $wsdl->clear_cache;

The globals $NCBI_BASEURL, $NCBI_ADAPTOR, and %WSDL are exported.

 $NCBI_ADAPTOR : the soap service cgi

To construct a URL for a WSDL:

 $wsdl_eutils = $NCBI_BASEURL.$WSDL{'eutils'}
 $wsdl_efetch_omim = $NCBI_BASEURL.$WSDL{'f_omim'}
 # etc.

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::WSDL();
 Function: Builds a new Bio::DB::ESoap::WSDL object
 Returns : an instance of Bio::DB::ESoap::WSDL
 Args    : named args:
           -URL => $url_of_desired_wsdl -OR-
           -WSDL => $filename_of_local_wsdl_copy
           ( -WSDL will take precedence if both specified )

Getters

request_parameters()

 Title   : request_parameters
 Usage   : @params = $wsdl->request_parameters($operation_name)
 Function: get array of request (input) fields required by 
           specified operation, according to the WSDL
 Returns : hash of arrays of hashes...
 Args    : scalar string (operation or action name)

result_parameters()

 Title   : result_parameters
 Usage   : $result_hash = $wsdl->result_parameters
 Function: retrieve a hash structure describing the 
           result of running the specified operation
           according to the WSDL
 Returns : hash of arrays of hashes...
 Args    : operation (scalar string)

operations()

 Title   : operations
 Usage   : @opns = $wsdl->operations;
 Function: get a hashref with elts ( $operation_name => $soapAction )
           for all operations defined by this WSDL 
 Returns : array of scalar strings
 Args    : none

service()

 Title   : service
 Usage   : $wsdl->service
 Function: gets the SOAP service url associated with this WSDL
 Returns : scalar string
 Args    : none

db()

 Title   : db
 Usage   : 
 Function: If this is an efetch WSDL, returns the db name
           associated with it
 Returns : scalar string or undef
 Args    : none

Internals

_operation_bookmarks()

 Title   : _operation_bookmarks
 Usage   : 
 Function: find useful WSDL elements associated with the specified
           operation; return a hashref of the form
           { $key => $XML_Twig_Elt_obj, }
 Returns : hashref with keys:
            portType namespace schema
            i_msg_type i_msg_elt
            o_msg_type o_msg_elt
 Args    : operation name (scalar string)
 Note    : will import schema if necessary

_parse()

 Title   : _parse
 Usage   : $wsdl->_parse
 Function: parse the wsdl at url and create accessors for 
           section twig elts
 Returns : self
 Args    :

root()

 Title   : root
 Usage   : $obj->root($newval)
 Function: holds the root Twig elt of the parsed WSDL
 Example : 
 Returns : value of root (an XML::Twig::Elt)
 Args    : on set, new value (an XML::Twig::Elt or undef, optional)

url()

 Title   : url
 Usage   : $obj->url($newval)
 Function: get/set the WSDL url
 Example : 
 Returns : value of url (a scalar string)
 Args    : on set, new value (a scalar or undef, optional)

wsdl()

 Title   : wsdl
 Usage   : $obj->wsdl($newval)
 Function: get/set wsdl XML filename
 Example : 
 Returns : value of wsdl (a scalar string)
 Args    : on set, new value (a scalar string or undef, optional)

_twig()

 Title   : _twig
 Usage   : $obj->_twig($newval)
 Function: XML::Twig object for handling the wsdl
 Example : 
 Returns : value of _twig (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

_sections()

 Title   : _sections
 Usage   : $obj->_sections($newval)
 Function: holds hashref of twigs corresponding to main wsdl 
           elements; filled by _parse()
 Example : 
 Returns : value of _sections (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

_cache()

 Title   : _cache
 Usage   : $wsdl->_cache($newval)
 Function: holds the wsdl info cache
 Example : 
 Returns : value of _cache (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

_parsed()

 Title   : _parsed
 Usage   : $obj->_parsed($newval)
 Function: flag to indicate wsdl already parsed
 Example : 
 Returns : value of _parsed (a scalar)
 Args    : on set, new value (a scalar or undef, optional)