++ed by:

5 PAUSE user(s)
6 non-PAUSE user(s).

Christopher Fields


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 consideration).


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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() allows.

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

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