Provided by: libbio-perl-perl_1.6.923-1_all
Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.
# DO NOT USE DIRECTLY 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).
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. email@example.com - 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: firstname.lastname@example.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/
Email cjfields at bioperl dot org
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.
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