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.\" ========================================================================
.\"
.IX Title "Bio::DB::GenericWebAgent 3pm"
.TH Bio::DB::GenericWebAgent 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::DB::GenericWebAgent \- helper base class for parameter\-based remote server
access and response retrieval.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # DO NOT USE DIRECTLY
\&
\&  See Bio::DB::EUtilities for an example implementation
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1WARNING:\s0 Please do \fB\s-1NOT\s0\fR spam the web servers with multiple requests.
.PP
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).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@lists.open\-bio.org               \- General discussion
\&  http://bioperl.org/Support.html  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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.
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Email cjfields at bioperl dot org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 7
\& 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.
.Ve
.SH "GenericWebAgent methods"
.IX Header "GenericWebAgent methods"
.SS "parameter_base"
.IX Subsection "parameter_base"
.Vb 5
\& Title   : parameter_base
\& Usage   : $dbi\->parameter_base($pobj);
\& Function: Get/Set Bio::ParameterBaseI.
\& Returns : Bio::ParameterBaseI object
\& Args    : Bio::ParameterBaseI object
.Ve
.SS "ua"
.IX Subsection "ua"
.Vb 5
\& Title   : ua
\& Usage   : $dbi\->ua;
\& Function: Get/Set LWP::UserAgent.
\& Returns : LWP::UserAgent
\& Args    : LWP::UserAgent
.Ve
.SS "get_Response"
.IX Subsection "get_Response"
.Vb 6
\& 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\*(Aqt 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
.Ve
.SS "get_Parser"
.IX Subsection "get_Parser"
.Vb 6
\& 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
.Ve
.SS "delay"
.IX Subsection "delay"
.Vb 5
\& 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
.Ve
.PP
\&\s-1NOTE:\s0 the default is to use the value specified by \fBdelay_policy()\fR.
This can be overridden by calling this method.
.SS "delay_policy"
.IX Subsection "delay_policy"
.Vb 5
\& 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
.Ve
.PP
\&\s-1NOTE:\s0 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.
.SS "_sleep"
.IX Subsection "_sleep"
.Vb 5
\& Title   : _sleep
\& Usage   : $self\->_sleep
\& Function: sleep for a number of seconds indicated by the delay policy
\& Returns : none
\& Args    : none
.Ve
.PP
\&\s-1NOTE:\s0 This method keeps track of the last time it was called and only
imposes a sleep if it was called more recently than the \fBdelay_policy()\fR
allows.
.SH "LWP::UserAgent related methods"
.IX Header "LWP::UserAgent related methods"
.SS "proxy"
.IX Subsection "proxy"
.Vb 9
\& Title   : proxy
\& Usage   : $httpproxy = $db\->proxy(\*(Aqhttp\*(Aq)  or
\&           $db\->proxy([\*(Aqhttp\*(Aq,\*(Aqftp\*(Aq], \*(Aqhttp://myproxy\*(Aq )
\& 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)
.Ve
.SS "authentication"
.IX Subsection "authentication"
.Vb 5
\& Title   : authentication
\& Usage   : $db\->authentication($user,$pass)
\& Function: Get/Set authentication credentials
\& Returns : Array of user/pass
\& Args    : Array or user/pass
.Ve