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;