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:
https://redmine.open-bio.org/projects/bioperl/
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;