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