Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies

SYNOPSIS

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  # Do not use this class directly.  See Bio::DB::QueryI and one of
  # the implementor classes (such as Bio::DB::GenBankQuery) for
  # information.

See Bio::DB::QueryI, Bio::DB::GenBankQuery

DESCRIPTION

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Do not use this class directly. See Bio::DB::QueryI and one of the implementor classes (such as Bio::DB::Query::GenBank) for information.

Those writing subclasses must define _get_params() and _parse_response(), and possibly override _request_method().

FEEDBACK

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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@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

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.

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/

AUTHOR - Lincoln Stein

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Email lstein@cshl.org

APPENDIX

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

new

 Title   : new
 Usage   : $db = Bio::DB::WebQuery->new(@args)
 Function: create new query object
 Returns : new query object
 Args    : -db       database (e.g. 'protein')
           -ids      array ref of ids (overrides query)
           -verbose  turn on verbose debugging

This method creates a new query object. Typically you will specify a -db and a -query argument. The value of -query is a database-specific string.

If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to the database.

ua

 Title   : ua
 Usage   : my $ua = $self->ua or 
           $self->ua($ua)
 Function: Get/Set a LWP::UserAgent for use
 Returns : reference to LWP::UserAgent Object
 Args    : $ua - must be a LWP::UserAgent

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

ids

 Title   : ids
 Usage   : @ids = $db->ids([@ids])
 Function: get/set matching ids
 Returns : array of sequence ids
 Args    : (optional) array ref with new set of ids

query

 Title   : query
 Usage   : $query = $db->query([$query])
 Function: get/set query string
 Returns : string
 Args    : (optional) new query string

_fetch_ids

 Title   : _fetch_ids
 Usage   : @ids = $db->_fetch_ids
 Function: run query, get ids
 Returns : array of sequence ids
 Args    : none

_run_query

 Title   : _run_query
 Usage   : $success = $db->_run_query
 Function: run query, parse results
 Returns : true if successful
 Args    : none

_truncated

 Title   : _truncated
 Usage   : $flag = $db->_truncated([$newflag])
 Function: get/set truncation flag
 Returns : boolean
 Args    : new flag

Some databases will truncate output unless explicitly asked not to. This flag allows a "two probe" attempt.

_get_request

 Title   : _get_request
 Usage   : $http_request = $db->_get_request(@params)
 Function: create an HTTP::Request with indicated parameters
 Returns : HTTP::Request object
 Args    : CGI parameter list

_parse_response

 Title   : _parse_response
 Usage   : $db->_parse_response($content)
 Function: parse out response
 Returns : empty
 Args    : none
 Throws  : 'unparseable output exception'

NOTE: This method must be implemented by subclass.

_request_parameters

 Title   : _request_parameters
 Usage   : ($method,$base,@params = $db->_request_parameters
 Function: return information needed to construct the request
 Returns : list of method, url base and key=>value pairs
 Args    : none

NOTE: This method must be implemented by subclass.

_generate_id_string

 Title   : _generate_id_string
 Usage   : $string = $db->_generate_id_string
 Function: joins IDs together in string (implementation-dependent)
 Returns : string of concatenated IDs
 Args    : array ref of ids (normally passed into the constructor)

NOTE: This method must be implemented by subclass.

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::DB::WebQuery.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Lincoln Stein <lstein@cshl.org>
#
# Copyright Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#


# Let the code begin...

package Bio::DB::Query::WebQuery;
use strict;
use URI;
use LWP::UserAgent;
use HTTP::Request::Common;

use base qw(Bio::Root::Root Bio::DB::QueryI);


# Borrowed shamelessly from WebDBSeqI.  Some of this code should be
# refactored.
sub new {
  my $class = shift;
  my $self  = $class->SUPER::new(@_);

  my ($query,$ids,$verbose) = $self->_rearrange(['QUERY','IDS','VERBOSE'],@_);
  $self->throw('must provide one of the the -query or -ids arguments')
    unless defined($query) || defined($ids);
  if ($ids) {
    $query = $self->_generate_id_string($ids);
  }
  $self->query($query);
  $verbose && $self->verbose($verbose);

  my $ua = new LWP::UserAgent(env_proxy => 1);
  $ua->agent(ref($self) ."/".($Bio::DB::Query::WebQuery::VERSION || '0.1'));
  $self->ua($ua);
  $self->{'_authentication'} = [];
  $self;
}


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


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


sub authentication{
   my ($self,$u,$p) = @_;

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


sub ids     {
  my $self = shift;
  if (@_) {
    my $d = $self->{'_ids'};
    my $arg = shift;
    $self->{'_ids'} = ref $arg ? $arg : [$arg];
    return $d ? @$d : ();
  } else {
    $self->_fetch_ids;
    return @{$self->{'_ids'} || []};
  }
}


sub query   {
  my $self = shift;
  my $d    = $self->{'_query'};
  $self->{'_query'} = shift if @_;
  $d;
}


sub _fetch_ids     {
  my $self = shift;
  $self->_run_query;
  $self->_run_query(1) if $self->_truncated;
  $self->throw('Id list has been truncated even after maxids requested')
    if $self->_truncated;
  return @{$self->{'_ids'}} if $self->{'_ids'};
}


sub _run_query {
  my $self   = shift;
  my $force  = shift;

  # allow the query to be run one extra time if truncated
  return $self->{'_ran_query'} if $self->{'_ran_query'}++ && !$force;

  my $request = $self->_get_request;
  $self->debug("request is ".$request->url."\n");
  my $response = $self->ua->request($request);
  return unless $response->is_success;
  $self->debug("response is ".$response->content."\n");
  $self->_parse_response($response->content);
  1;
}


sub _truncated {
  my $self = shift;
  my $d = $self->{'_truncated'};
  $self->{'_truncated'} = shift if @_;
  $d;
}


sub _get_request {
  my $self   = shift;
  my ($method,$base,@params) = $self->_request_parameters;
  my $uri = URI->new($base);
  my $request;
  if ($method eq 'get') {
    $uri->query_form(@params);
    $request = GET $uri;
  } else {
    $request = POST $uri,\@params;
  }

  $request->proxy_authorization_basic($self->authentication)
	if $self->authentication;
  $request;
}


sub _parse_response {
  my $self    = shift;
  my $content = shift;
  $self->throw_not_implemented;
}


sub _request_parameters {
  my $self = shift;
  $self->throw_not_implemented;
}


sub _generate_id_string {
  my $self = shift;
  $self->throw_not_implemented;
}

1;