Bio::T...s::soap(3pm)

💖 Bio::T...s::soap — the tea 💖

okay so this page is straight out of the User Contributed Perl Documentation, and it's all about Bio::T...s::soap — the SOAP-flavoured doorway into your analysis tools. come sit with me bestie, we're gonna get you fluent 🫶

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✨ NAME ✨

Bio::Tools::Run::Analysis::soap — a SOAP-based access to the analysis tools 🌈

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🦋 SYNOPSIS 🦋

okay so do NOT use this object directly, bestie, i'm begging. the vibe is: you go through the Bio::Tools::Run::Analysis module and let it handle things. like:

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

that's it. that's the whole move 💅

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🌸 DESCRIPTION 🌸

this object lets you execute and control a remote analysis tool (think: an application, a program) using the SOAP middleware. it's giving remote-control-but-for-bioinformatics.

all of its public methods are documented over in the interface module Bio::AnalysisI, and explained in the tutorial that lives in the analysis.pl script. iykyk 📖✨

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💌 FEEDBACK 💌

Mailing Lists 📮

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated, fr fr 🥹

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. like, there are so many experienced and responsive experts who will be able to 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 — the more detail the better, no cap 🌟

Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

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👑 AUTHOR 👑

Martin Senger (martin.senger@gmail.com)

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📜 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. slay 💜

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💀 DISCLAIMER 💀

this software is provided "as is" without warranty of any kind. that's it. that's the disclaimer. be aware 😭

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🌈 SEE ALSO 🌈

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

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🙈 BUGS AND LIMITATIONS 🙈

none known at the time of writing this. iconic behaviour, honestly ✨

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🎀 APPENDIX 🎀

here's the rest of the object methods. internal methods are preceded with an underscore _ — that's your little signal that they're the backstage crew, not the main characters.

_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 the calling object with the given arguments, and then — for some attributes, and only if they are not yet populated — it assigns some default values. lowkey a little makeover montage ✨

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. okay? okay. periodt 💅

-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). so like... don't forget it bestie 😭

-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).

⚠️ okay real talk: flip that '0' and you'd better have that job id saved somewhere, or that connection is GONE forever. no take-backs. 😭

-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. forever-girl summer, if you set it to zero 🏖️

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;

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and that's the whole page, bestie!! 🎀 this little gem is from perl v5.36.0, dated 2023-01-22, living its best life under the Bio::T...s::soap(3pm) name in the User Contributed Perl Documentation. mwah 💋 go run some analyses, you got this 💖✨🦋