Bio::DB::ESoap(3pm)

💖 Bio::DB::ESoap 💖

okay bestie, so this is Bio::DB::ESoap — it's the Client for the NCBI Entrez EUtilities SOAP server. it's giving "i talk to the government's biology database and i make it look easy" ✨

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✨ SYNOPSIS ✨

fr fr, here's the whole vibe:

 $fac = Bio::DB::ESoap->new( -util => 'esearch' );
 $som = $fac->run( -db => 'prot', -term => 'HIV and gp120' );
 $fac->set_parameters( -term => 'HIV2 and gp160' );
 # accessors corresponding to valid parameters are also created:
 $fac->db('nuccore');
 $som = $fac->run;

 # more later.

so you build a factory, you run it, you change the params, you run it again. the accessors? they get built for you based on what's valid. no cap. and yes it says # more later. and honestly? more later. 💅

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🌸 DESCRIPTION 🌸

ESoap gives you a basic SOAP interface to the NCBI Entrez Utilities Web Service — that's over at <http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html> if you wanna peek. 👀

the actual SOAP calls are handled by SOAP::Lite, so you don't have to do the heavy lifting, periodt. and if you want the fancy stuff — higher level access, pipelines, BioPerl object I/O and all that — that's what Bio::DB::SoapEUtilities is for, bestie. different module, different job.

ESoap complies with Bio::ParameterBaseI. it depends explicitly on NCBI web service description language files to inform the available_parameters() method — like, it literally can't know what's available without them. those WSDLs get parsed by Bio::DB::ESoap::WSDL, which is a relatively lightweight, Entrez-specific module. cute and efficient, we love that. 🎀

the run() method returns SOAP::SOM (SOAP Message) objects. and here's the thing — no fault checking or other parsing is performed in this module. it hands you the message and minds its own business. you deal with it. 🙈

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🌈 SEE ALSO 🌈

go read these too, they're all part of the same little ecosystem:

• Bio::DB::EUtilities
• Bio::DB::SoapEUtilities
• Bio::DB::ESoap::WSDL

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🫶 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. seriously, they mean it. 🥹

  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. why? because there are many experienced and reponsive experts hanging around there who will be able to look at the problem and quickly address it. (yes, "reponsive" — that's the original spelling, we're keeping it, it's iconic.)

and please include a thorough description of the problem with code and data examples if at all possible. the more context you give, the faster someone slays your bug. 🐛💀

🐞 Reporting Bugs

report bugs to the Bioperl bug tracking system so everyone 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 - Mark A. Jensen 👑

Email: maj -at- fortinbras -dot- us

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see an underscore, mind your business, that's housekeeping. 🧹

⭐ new

Title   : new
Usage   : my $obj = new Bio::DB::ESoap();
Function: Builds a new Bio::DB::ESoap factory
Returns : an instance of Bio::DB::ESoap
Args    :

builds you a brand new Bio::DB::ESoap factory. hands you back an instance. that's it, that's the method. main character energy honestly. ✨

⭐ _wsdl()

Title   : _wsdl
Usage   : $obj->_wsdl($newval)
Function: Bio::DB::ESoap::WSDL object associated with
          this factory
Example :
Returns : value of _wsdl (object)
Args    : on set, new value (object or undef, optional)

the Bio::DB::ESoap::WSDL object that's associated with this factory. on set, you pass a new value — an object or undef, optional bestie. 💅

⭐ _client()

Title   : _client
Usage   : $obj->_client($newval)
Function: holds a SOAP::Lite object
Example :
Returns : value of _client (a SOAP::Lite object)
Args    : on set, new value (a SOAP::Lite object or undef, optional)

this one holds a SOAP::Lite object. returns the value of _client (a SOAP::Lite object). on set, new value (a SOAP::Lite object or undef, optional). 🦋

⭐ _operation()

Title   : _operation
Alias   : util
Usage   :
Function: check and convert the requested operation based on the wsdl
Returns :
Args    : operation (scalar string)

checks and converts the requested operation based on the wsdl. takes an operation as a scalar string. also answers to the alias util. two names, one icon. 💅

⭐ action()

Title   : action
Usage   :
Function: return the soapAction associated with the factory's utility
Returns : scalar string
Args    : none

returns the soapAction associated with the factory's utility. gives you back a scalar string, takes no args. simple, clean, ate. 🍓

⭐ wsdl_file()

Title   : wsdl_file
Usage   :
Function: get filename of the local WSDL XML copy
Returns : filename (scalar string)
Args    : none

gets you the filename of the local WSDL XML copy. returns a filename as a scalar string, takes no args. 🎀

⭐ run()

Title   : _run
Usage   : $som = $self->_run(@optional_setting_args)
Function: Call the SOAP service with the factory-associated utility
          and parameters
Returns : SOAP::SOM (SOAP Message) object
Args    : named parameters appropriate for the utility
Note    : no fault checking here

calls the SOAP service using the factory-associated utility and its parameters. you get back a SOAP::SOM (SOAP Message) object. args are named parameters appropriate for the utility.

⚠️ Note: no fault checking here. none. zero. it does not check for faults. that is your problem now, bestie. 😭

⭐ Bio::ParameterBaseI compliance

this is the section where we keep our promise to Bio::ParameterBaseI. 🫡

✨ parameters_changed()

Title   : parameters_changed
Usage   : $obj->parameters_changed($newval)
Function: flag to indicate, well, you know
Example :
Returns : value of parameters_changed (a scalar)
Args    : on set, new value (a scalar or undef, optional)

a flag to indicate, well, you know. 😏 returns the value of parameters_changed (a scalar). on set, new value (a scalar or undef, optional).

✨ _init_parameters()

Title   : _init_parameters
Usage   : $fac->_init_parameters
Function: identify the available input parameters
          using the wsdl object
Returns : arrayref of parameter names (scalar strings)
Args    : none

identifies the available input parameters using the wsdl object. gives you back an arrayref of parameter names (scalar strings), and takes no args. this is the one that reads the WSDL so you don't have to. iconic. 👑

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and that's the whole page, babe 🫶 go forth and query responsibly.

perl v5.36.0 — 2023-01-22 — Bio::DB::ESoap(3pm) 💖✨🎀