Bio::DB::GenericWebAgent.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.

SYNOPSIS

   # DO NOT USE DIRECTLY
   
   See Bio::DB::EUtilities for an example implementation
 
 

DESCRIPTION

WARNING: Please do NOT spam the web servers with multiple requests.

Bio::DB::GenericWebAgent is a generic wrapper around a web agent (LWP::UserAgent), an object which can retain, format, and build parameters for the user agent (Bio::ParameterBaseI), and a BioPerl class parser that processes response content received by the user agent. The Bio::ParameterBaseI object should be state-aware, e.g. know when changes occur to parameters, so that identical requests are not repeatedly sent to the server (this base class takes this into consideration).

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 one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@lists.open-bio.org               - General discussion
   http://www.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 the bugs and their resolution. Bug reports can be submitted via the web.
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Email cjfields at bioperl dot org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : Bio::DB::GenericWebAgent->new(@args);
  Function: Create new Bio::DB::GenericWebAgent instance.
  Returns : 
  Args    : None specific to this base class.  Inheriting classes will
            likely set specific parameters in their constructor;
            Bio::DB::GenericWebAgent is primarily a test bed.
 
 

GenericWebAgent methods

parameter_base

  Title   : parameter_base
  Usage   : $dbi->parameter_base($pobj);
  Function: Get/Set Bio::ParameterBaseI.
  Returns : Bio::ParameterBaseI object
  Args    : Bio::ParameterBaseI object
 
 

ua

  Title   : ua
  Usage   : $dbi->ua;
  Function: Get/Set LWP::UserAgent.
  Returns : LWP::UserAgent
  Args    : LWP::UserAgent
 
 

get_Response

  Title   : get_Response
  Usage   : $agent->get_Response;
  Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from
            Bio::ParameterBaseI implementation).
  Returns : HTTP::Response object or data if callback is used
  Args    : (optional)
 
            -cache_response - flag to cache HTTP::Response object; 
                              Default is 1 (TRUE, caching ON)
 
            These are passed on to LWP::UserAgent::request() if stipulated
 
            -cb     - use a LWP::UserAgent-compliant callback
            -file   - dumps the response to a file (handy for large responses)
                      Note: can't use file and callback at the same time
            -read_size_hint - bytes of content to read in at a time to pass to callback
  Note    : Caching and parameter checking are set
 
 

get_Parser

  Title   : get_Parser
  Usage   : $agent->get_Parser;
  Function: Return HTTP::Response content (file, fh, object) attached to defined parser
  Returns : None
  Args    : None
  Note    : Abstract method; defined by implementation
 
 

delay

  Title   : delay
  Usage   : $secs = $self->delay($secs)
  Function: get/set number of seconds to delay between fetches
  Returns : number of seconds to delay
  Args    : new value
 
 

NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method.

delay_policy

  Title   : delay_policy
  Usage   : $secs = $self->delay_policy
  Function: return number of seconds to delay between calls to remote db
  Returns : number of seconds to delay
  Args    : none
 
 

NOTE: The default delay policy is 3s. Override in subclasses to implement delays. The timer has only second resolution, so the delay will actually be +/- 1s.

_sleep

  Title   : _sleep
  Usage   : $self->_sleep
  Function: sleep for a number of seconds indicated by the delay policy
  Returns : none
  Args    : none
 
 

NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows.

proxy

  Title   : proxy
  Usage   : $httpproxy = $db->proxy('http')  or
            $db->proxy(['http','ftp'], 'http://myproxy' )
  Function: Get/Set a proxy for use of proxy
  Returns : a string indicating the proxy
  Args    : $protocol : an array ref of the protocol(s) to set/get
            $proxyurl : url of the proxy to use for the specified protocol
            $username : username (if proxy requires authentication)
            $password : password (if proxy requires authentication)
 
 

authentication

  Title   : authentication
  Usage   : $db->authentication($user,$pass)
  Function: Get/Set authentication credentials
  Returns : Array of user/pass
  Args    : Array or user/pass