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


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');


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.


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Martin Senger (martin.senger@gmail.com)


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.


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


  • 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.


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 _.


 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.

               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

              -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
             -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;


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