/ 
BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::GenericWebAgent

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.

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

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.

LWP::UserAgent related methods

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