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.IX Title "Bio::Tools::Run::Analysis::soap 3pm"
.TH Bio::Tools::Run::Analysis::soap 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Analysis::soap \- A SOAP\-based access to the analysis tools
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this object directly, it is recommended to access it and use
it through the \f(CW\*(C`Bio::Tools::Run::Analysis\*(C'\fR module:
.PP
.Vb 3
\&  use Bio::Tools::Run::Analysis;
\&  my $tool = Bio::Tools::Run::Analysis\->new(\-access => \*(Aqsoap\*(Aq,
\&                                            \-name   => \*(Aqseqret\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object allows to execute and to control a remote analysis tool
(an application, a program) using the \s-1SOAP\s0 middleware,
.PP
All its public methods are documented in the interface module
\&\f(CW\*(C`Bio::AnalysisI\*(C'\fR and explained in tutorial available in the
\&\f(CW\*(C`analysis.pl\*(C'\fR script.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Martin Senger (martin.senger@gmail.com)
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (c) 2003, Martin Senger and EMBL-EBI.
All Rights Reserved.
.PP
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
.SH "DISCLAIMER"
.IX Header "DISCLAIMER"
This software is provided \*(L"as is\*(R" without warranty of any kind.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
.IP "\(bu" 4
http://www.ebi.ac.uk/soaplab/Perl_Client.html
.SH "BUGS AND LIMITATIONS"
.IX Header "BUGS AND LIMITATIONS"
None known at the time of writing this.
.SH "APPENDIX"
.IX Header "APPENDIX"
Here is the rest of the object methods.  Internal methods are preceded
with an underscore _.
.SS "_initialize"
.IX Subsection "_initialize"
.Vb 10
\& Usage   : my $tool = Bio::Tools::Run::Analysis\->new(\-access => \*(Aqsoap\*(Aq,
\&                                                     \-name => \*(Aqseqret\*(Aq,
\&                                                     ...);
\&           (_initialize is internally called from the \*(Aqnew()\*(Aq 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
.Ve
.PP
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.
.PP
This is an actual \fBnew()\fR method (except for the real object creation
and its blessing which is done in the parent class Bio::Root::Root in
method _create_object).
.PP
Note that this method is called always as an \fIobject\fR method (never
as a \fIclass\fR 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 \fInew\fR method, not this one.
.IP "\-location" 4
.IX Item "-location"
A \s-1URL\s0 (also called an \fIendpoint\fR) defining where is located a Web Service
representing this analysis tool.
.Sp
Default is \f(CW\*(C`http://www.ebi.ac.uk/soaplab/services\*(C'\fR (services running
at European Bioinformatics Institute on top of most of \s-1EMBOSS\s0
analyses, and few others).
.Sp
For example, if you run your own Web Service using Java(\s-1TM\s0) Apache Axis
toolkit, the location might be something like
\&\f(CW\*(C`http://localhost:8080/axis/services\*(C'\fR.
.IP "\-name" 4
.IX Item "-name"
A name of a Web Service (also called a \fIurn\fR or a \fInamespace\fR).
There is no default value (which usually means that this parameter is
mandatory unless your \fI\-location\fR parameter includes also a Web
Service name).
.IP "\-destroy_on_exit => '0'" 4
.IX Item "-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.
.Sp
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 \f(CW\*(C`id\*(C'\fR on the job object (such object is returned by any of
these methods: \f(CW\*(C`create_job\*(C'\fR, \f(CW\*(C`run\*(C'\fR, \f(CW\*(C`wait_for\*(C'\fR).
.IP "\-httpproxy" 4
.IX Item "-httpproxy"
In addition to the \fIlocation\fR parameter, you may need
to specify also a location/URL of an \s-1HTTP\s0 proxy server
(if your site requires one). The expected format is \f(CW\*(C`http://server:port\*(C'\fR.
There is no default value.
.IP "\-timeout" 4
.IX Item "-timeout"
For long(er) running jobs the \s-1HTTP\s0 connection may be time-outed. In
order to avoid it (or, vice-versa, to call timeout sooner) you may
specify \f(CW\*(C`timeout\*(C'\fR with the number of seconds the connection will be
kept alive. Zero means to keep it alive forever. The default value is
two minutes.
.SS "is_binary"
.IX Subsection "is_binary"
.Vb 3
\&  Usage   : if ($service\->is_binary (\*(Aqgraph_result\*(Aq)) { ... }
\&  Returns : 1 or 0
\&  Args    : $name is a result name we are interested in
.Ve
.SS "\s-1VERSION\s0 and Revision"
.IX Subsection "VERSION and Revision"
.Vb 2
\& Usage   : print $Bio::Tools::Run::Analysis::soap::VERSION;
\&           print $Bio::Tools::Run::Analysis::soap::Revision;
.Ve
.SS "Defaults"
.IX Subsection "Defaults"
.Vb 1
\& Usage   : print $Bio::Tools::Run::Analysis::soap::DEFAULT_LOCATION;
.Ve