Bio::Tools::Run::AnalyUser:Contributed Perl Bio::Tools::Run::Analysis::soap(3)NAMEBio::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://bugzilla.open-bio.org/
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
ยท 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;
perl v5.14.12011-07-21Bio::Tools::Run::Analysis::soap(3)
