libbio-perl-perl 1.7.2-2 / usr / share / perl5 / Bio / DB / GenericWebAgent.pm

#
# BioPerl module for Bio::DB::GenericWebAgent
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Interfaces with new GenericWebAgent interface

=head1 NAME

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

=head1 SYNOPSIS

  # DO NOT USE DIRECTLY

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

=head1 DESCRIPTION

WARNING: Please do B<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).

=head1 FEEDBACK

=head2 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://bioperl.org/Support.html  - About the mailing lists

=head2 Support

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

I<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.

=head2 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://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Email cjfields at bioperl dot org

=head1 APPENDIX

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

=cut

# Let the code begin...

package Bio::DB::GenericWebAgent;
use strict;
use warnings;
use base qw(Bio::Root::Root);
use LWP::UserAgent;

my $LAST_INVOCATION_TIME = 0;

my $TIME_HIRES = 0;

BEGIN {
    eval {
        use Time::HiRes;
    };
    unless ($@) {
        $TIME_HIRES = 1;
    }
}

=head2 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.

=cut

sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    $self->ua(LWP::UserAgent->new(env_proxy => 1,
            agent => ref($self)));
    $self->delay($self->delay_policy);
    return $self;
}

=head1 GenericWebAgent methods

=head2 parameter_base

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

=cut

# this will likely be overridden in subclasses

sub parameter_base {
    my ($self, $pobj) = @_;
    if ($pobj) {
        $self->throw('Not a Bio::ParameterBaseI')
            if !$pobj->isa('Bio::ParameterBaseI');
        $self->{'_parameter_base'} = $pobj;
    }
    return $self->{'_parameter_base'};
}

=head2 ua

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

=cut

sub ua {
	my ($self, $ua) = @_;
	if( defined $ua && $ua->isa("LWP::UserAgent") ) {
		$self->{'_ua'} = $ua;
	}
	return $self->{'_ua'};
}

=head2 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

=cut

# TODO deal with small state-related bug with file

sub get_Response {
    my ($self, @args) = @_;
    my ($cache, $file, $cb, $size) = $self->_rearrange([qw(CACHE_RESPONSE FILE CB READ_SIZE_HINT)],@args);
    $self->throw("Can't have both callback and file") if $file && $cb;
    # make -file accept more perl-like write-append type data.
    $file =~ s{^>}{} if $file;
    my @opts = grep {defined $_} ($file || $cb, $size);
    $cache = (defined $cache && $cache == 0) ? 0 : 1;
    my $pobj = $self->parameter_base;
    if ($pobj->parameters_changed ||
        !$cache  ||
        !$self->{_response_cache} ||
        !$self->{_response_cache}->content) {
        my $ua = $self->ua;
        $self->_sleep; # institute delay policy
        $self->throw('No parameter object set; cannot form a suitable remote request') unless $pobj;
        my $request = $pobj->to_request;
        if ($self->authentication) {
            $request->proxy_authorization_basic($self->authentication)
        }
        $self->debug("Request is: \n",$request->as_string);
        # I'm relying on the useragent to throw the proper errors here
        my $response = $ua->request($request, @opts);
        if ($response->is_error) {
            $self->throw("Response Error\n".$response->message);
        }
        return $self->{_response_cache} = $response;
    } else {
        $self->debug("Returning cached HTTP::Response object\n");
        if ($file) {
            $self->_dump_request_content($file);
            # size isn't passed here, as the content is completely retrieved above
        } elsif ($cb) {
            $cb && ref($cb) eq 'CODE' && $cb->($self->{_response_cache}->content);
        }
        return $self->{_response_cache};
    }
}

=head2 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

=cut

sub get_Parser {
    shift->throw_not_implemented;
}

=head2 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.

=cut

sub delay {
   my $self = shift;
   return $self->{'_delay'} = shift if @_;
   return $self->{'_delay'};
}

=head2 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.

=cut

sub delay_policy {
   my $self = shift;
   return 3;
}

=head2 _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.

=cut

sub _sleep {
    my $self = shift;
    my $last_invocation = $LAST_INVOCATION_TIME;
    if (time - $LAST_INVOCATION_TIME < $self->delay) {
        my $delay = $self->delay - (time - $LAST_INVOCATION_TIME);
        $self->debug("sleeping for $delay seconds\n");
        if ($TIME_HIRES) {
            # allows precise sleep timeout (builtin only allows integer seconds)
            Time::HiRes::sleep($delay);
        } else {
            # allows precise sleep timeout (builtin only allows integer seconds)

            # I hate this hack , but needed if we support 5.6.1 and
            # don't want additional Time::HiRes prereq
            select undef, undef, undef, $delay;
        }
    }
    $LAST_INVOCATION_TIME = time;
}

=head1 LWP::UserAgent related methods

=head2 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)

=cut

sub proxy {
    my ($self,$protocol,$proxy,$username,$password) = @_;
    return if ( !defined $protocol || !defined $proxy );
    $self->authentication($username, $password)
    if ($username && $password);
    return $self->ua->proxy($protocol,$proxy);
}

=head2 authentication

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

=cut

sub authentication{
   my ($self,$u,$p) = @_;
   if( defined $u && defined $p ) {
       $self->{'_authentication'} = [ $u,$p];
   }
   $self->{'_authentication'} && return @{$self->{'_authentication'}};
}

# private method to dump any cached request data content into a passed filename

sub _dump_request_content {
    my ($self, $file) = @_;
    return unless defined $self->{_response_cache};
    $self->throw("Must pass file name") unless $file;
    require Bio::Root::IO;
    my $out = Bio::Root::IO->new(-file => ">$file");
    $out->_print($self->{_response_cache}->content);
    $out->flush();
    $out->close;
}

1;