oracular (3) Bio::Tools::Run::Analysis::soap.3pm.gz

NAME

       Bio::Tools::Run::Analysis::soap - A SOAP-based access to the analysis tools

SYNOPSIS

       Do not use this object directly, it is recommended to access it and use it through the
       "Bio::Tools::Run::Analysis" module:

         use Bio::Tools::Run::Analysis;
         my $tool = Bio::Tools::Run::Analysis->new(-access => 'soap',
                                                   -name   => 'seqret');

DESCRIPTION

       This object allows to execute and to control a remote analysis tool (an application, a program) using the
       SOAP middleware,

       All its public methods are documented in the interface module "Bio::AnalysisI" and explained in tutorial
       available in the "analysis.pl" script.

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

AUTHOR

       Martin Senger (martin.senger@gmail.com)

COPYRIGHT

       Copyright (c) 2003, Martin Senger and EMBL-EBI.  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.

SEE ALSO

       •   http://www.ebi.ac.uk/soaplab/Perl_Client.html

BUGS AND LIMITATIONS

       None known at the time of writing this.

APPENDIX

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

   _initialize
        Usage   : my $tool = Bio::Tools::Run::Analysis->new(-access => 'soap',
                                                            -name => 'seqret',
                                                            ...);
                  (_initialize is internally called from the 'new()' method)
        Returns : nothing interesting
        Args    : This module recognises and uses following arguments:
                    -location
                    -name
                    -httpproxy
                    -timeout
                  Additionally, the main module Bio::Tools::Run::Analysis
                  recognises also:
                    -access

       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::Tools::Run::Analysis::new
       method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Analysis
       new method, not this one.

       -location
           A URL (also called an endpoint) defining where is located a Web Service representing this analysis
           tool.

           Default is "http://www.ebi.ac.uk/soaplab/services" (services running at European Bioinformatics
           Institute on top of most of EMBOSS analyses, and few others).

           For example, if you run your own Web Service using Java(TM) Apache Axis toolkit, the location might
           be something like "http://localhost:8080/axis/services".

       -name
           A name of a Web Service (also called a urn or a namespace).  There is no default value (which usually
           means that this parameter is mandatory unless your -location parameter includes also a Web Service
           name).

       -destroy_on_exit => '0'
           Default value is '1' which means that all Bio::Tools::Run::Analysis::Job objects - when being
           finalised - will send a request to the remote Web Service to forget the results of these jobs.

           If you change it to '0' make sure that you know the job identification - otherwise you will not be
           able to re-established connection with it (later, when you use your script again). This can be done
           by calling method "id" on the job object (such object is returned by any of these methods:
           "create_job", "run", "wait_for").

       -httpproxy
           In addition to the location parameter, you may need to specify also a location/URL of an HTTP proxy
           server (if your site requires one). The expected format is "http://server:port".  There is no default
           value.

       -timeout
           For long(er) running jobs the HTTP connection may be time-outed. In order to avoid it (or, vice-
           versa, to call timeout sooner) you may specify "timeout" with the number of seconds the connection
           will be kept alive. Zero means to keep it alive forever. The default value is two minutes.

   is_binary
         Usage   : if ($service->is_binary ('graph_result')) { ... }
         Returns : 1 or 0
         Args    : $name is a result name we are interested in

   VERSION and Revision
        Usage   : print $Bio::Tools::Run::Analysis::soap::VERSION;
                  print $Bio::Tools::Run::Analysis::soap::Revision;

   Defaults
        Usage   : print $Bio::Tools::Run::Analysis::soap::DEFAULT_LOCATION;