Summary

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

Package variables

Included modules

Inherit

Bio::DB::QueryI Bio::Root::Root

Synopsis

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

Description

Do not use this class directly. See Bio::DB::QueryI and one of the
implementor classes (such as Bio::DB::GenBankQuery) for information.
Those writing subclasses must define _get_params() and
_parse_response(), and possibly override _request_method().

Methods

Methods description

 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

 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

 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

 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

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

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

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

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

 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

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

 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

Methods code

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);
  $query ||= join ',',ref($ids) ? @$ids : $ids;
  $query && $self->query($query);
  $verbose && $self->verbose($verbose);

  my $ua = new LWP::UserAgent;
  $ua->agent(ref($self) ."/$VERSION");
  $self->ua($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)     if $self->verbose;
  my $response = $self->ua->request($request);
  return unless $response->is_success;
  $self->debug("response is ".$response->content) if $self->verbose;
  $self->_parse_response($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;

}

General documentation

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
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Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via email or the
web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email lstein@cshl.org

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