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Bio::DB::Biblio::soap(User Contributed Perl DocumentatBio::DB::Biblio::soap(3)

NAME
       Bio::DB::Biblio::soap - A SOAP-based access to a bibliographic query
       service

SYNOPSIS
       Do not use this object directly, it is recommended to access it and use
       it through the Bio::Biblio module:

	 use Bio::Biblio;
	 my $biblio = Bio::Biblio->new (-access => 'soap');

DESCRIPTION
       This object contains the real implementation of a Bibliographic Query
       Service as defined in Bio::DB::BiblioI - using a SOAP protocol to
       access a WebService (a remote server) that represents a bibliographic
       repository.

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 lists

   Support
       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.

   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://bugzilla.open-bio.org/

AUTHOR
       Martin Senger (martin.senger@gmail.com)

COPYRIGHT
       Copyright (c) 2002 European Bioinformatics Institute. All Rights
       Reserved.

       This module is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.

DISCLAIMER
       This software is provided "as is" without warranty of any kind.

BUGS AND LIMITATIONS
       ·   Methods returning a boolean value (has_next, exists and contains)
	   can be used only with SOAP::Lite version 0.52 and newer (probably
	   due to a bug in the older SOAP::Lite).

       ·   It does not use WSDL.

       ·   More testing and debugging needed to ensure that returned citations
	   are properly transferred even if they contain foreign characters.

APPENDIX
       The main documentation details are to be found in Bio::DB::BiblioI.

       Here is the rest of the object methods.	Internal methods are preceded
       with an underscore _.

   _initialize
	Usage	: my $obj = Bio::Biblio->new(-access => 'soap' ...);
		  (_initialize is internally called from this constructor)
	Returns : nothing interesting
	Args	: This module recognises and uses following arguments:

		    -namespace => 'urn'
		      The namespace used by the WebService that is being
		      accessed. It is a string which guarantees its world-wide
		      uniqueness - therefore it often has a style of a URL -
		      but it does not mean that such pseudo-URL really exists.

		      ## TODO: This namespace is no longer valid (check for deprecation
		      ## or update)

		      Default is 'http://industry.ebi.ac.uk/openBQS'.

		    -destroy_on_exit => '0'
		       Default value is '1' which means that all Bio::Biblio
		       objects - when being finalised - will send a request
		       to the remote WebService to forget the query collections
		       they represent.

		       If you change it to '0' make sure that you know the
		       query collection identification - otherwise you will
		       not be able to re-established connection with it.
		       This can be done by calling method get_collection_id.

		     -collection_id => '...'
		       It defines what query collection will this object work
		       with. Use this argument when you know a collection ID
		       of an existing query collection and when you wish to
		       re-established connection with it.

		       By default, the collection IDs are set automatically
		       by the query methods - they return Bio::Biblio objects
		       already having a collection ID.

		       A missing or undefined collection ID means that the
		       object represents the whole bibliographic repository
		       (which again means that some methods, like get_all,
		       will be probably refused).

		     -soap => a SOAP::Lite object
		       Usually all Bio::Biblio objects share an instance of
		       the underlying SOAP::Lite module. But you are free
		       to have more - perhaps with different characteristics.

		       See the code for attributes of the default SOAP::Lite
		       object.

		     -httpproxy => 'http://server:port'
			In addition to the 'location' parameter, you may need
			to specify also a location/URL of a HTTP proxy server
			(if your site requires one).

		  Additionally, the main module Bio::Biblio recognises
		  also:
		    -access => '...'
		    -location => '...'

       It populates calling object with the given arguments, and then - for
       some attributes and only if they are not yet populated - it assigns
       some default values.

       This is an actual new() method (except for the real object creation and
       its blessing which is done in the parent class Bio::Root::Root in
       method _create_object).

       Note that this method is called always as an object method (never as a
       class method) - and that the object who calls this method may already
       be partly initiated (from Bio::Biblio::new method); so if you need to
       do some tricks with the 'class invocation' you need to change
       Bio::Biblio::new method, not this one.

   VERSION and Revision
	Usage	: print $Bio::DB::Biblio::soap::VERSION;
		  print $Bio::DB::Biblio::soap::Revision;

   Defaults
	Usage	: print $Bio::DB::Biblio::soap::DEFAULT_SERVICE;
		  print $Bio::DB::Biblio::soap::DEFAULT_NAMESPACE;

perl v5.14.1			  2011-07-22	      Bio::DB::Biblio::soap(3)
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