Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
Bio::DB::GenericWebAgeUser)Contributed Perl DocumenBio::DB::GenericWebAgent(3)

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


	 See Bio::DB::EUtilities for an	example	implementation

       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

   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.		    - General discussion  - About the mailing lists

       Please direct usage questions or	support	issues to the mailing list:

       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

       Email cjfields at bioperl dot org

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

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

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

	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

	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

	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.

	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.

	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()

LWP::UserAgent related methods
	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)

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

perl v5.32.0			  2019-12-07	   Bio::DB::GenericWebAgent(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX | GenericWebAgent methods | LWP::UserAgent related methods

Want to link to this manual page? Use this URL:

home | help