Bio::DB::Query WebQuery
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Summary
Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies
Package variables
No package variables defined.
Included modules
HTTP::Request::Common
LWP::UserAgent
URI
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.
See Bio::DB::QueryI, Bio::DB::GenBankQuery
Description
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().
Methods
newDescriptionCode
uaDescriptionCode
proxyDescriptionCode
authenticationDescriptionCode
idsDescriptionCode
queryDescriptionCode
_fetch_idsDescriptionCode
_run_queryDescriptionCode
_truncatedDescriptionCode
_get_requestDescriptionCode
_parse_responseDescriptionCode
_request_parametersDescriptionCode
_generate_id_stringDescriptionCode
Methods description
newcode    nextTop
 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.
uacodeprevnextTop
 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
proxycodeprevnextTop
 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)
authenticationcodeprevnextTop
 Title   : authentication
Usage : $db->authentication($user,$pass)
Function: Get/Set authentication credentials
Returns : Array of user/pass
Args : Array or user/pass
idscodeprevnextTop
 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
querycodeprevnextTop
 Title   : query
Usage : $query = $db->query([$query])
Function: get/set query string
Returns : string
Args : (optional) new query string
_fetch_idscodeprevnextTop
 Title   : _fetch_ids
Usage : @ids = $db->_fetch_ids
Function: run query, get ids
Returns : array of sequence ids
Args : none
_run_querycodeprevnextTop
 Title   : _run_query
Usage : $success = $db->_run_query
Function: run query, parse results
Returns : true if successful
Args : none
_truncatedcodeprevnextTop
 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_requestcodeprevnextTop
 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_responsecodeprevnextTop
 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_parameterscodeprevnextTop
 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_stringcodeprevnextTop
 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.
Methods code
newdescriptionprevnextTop
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'} = [];
  $self;
}
uadescriptionprevnextTop
sub ua {
   my ($self, $ua) = @_;
   my $d = $self->{'_ua'};
   if( defined $ua && $ua->isa("LWP::UserAgent") ) {
      $self->{'_ua'} = $ua;
   }
   $d;
}
proxydescriptionprevnextTop
sub proxy {
    my ($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,$proxy);
}
authenticationdescriptionprevnextTop
sub authentication {
   my ($self,$u,$p) = @_;

   if( defined $u && defined $p ) {
       $self->{'_authentication'} = [ $u,$p];
   }
   return @{$self->{'_authentication'}};
}
idsdescriptionprevnextTop
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'} || []};
  }
}
querydescriptionprevnextTop
sub query {
  my $self = shift;
  my $d    = $self->{'_query'};
  $self->{'_query'} = shift if @_;
  $d;
}
_fetch_idsdescriptionprevnextTop
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'};
}
_run_querydescriptionprevnextTop
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;
}
_truncateddescriptionprevnextTop
sub _truncated {
  my $self = shift;
  my $d = $self->{'_truncated'};
  $self->{'_truncated'} = shift if @_;
  $d;
}
_get_requestdescriptionprevnextTop
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;
}
_parse_responsedescriptionprevnextTop
sub _parse_response {
  my $self    = shift;
  my $content = shift;
  $self->throw_not_implemented;
}
_request_parametersdescriptionprevnextTop
sub _request_parameters {
  my $self = shift;
  $self->throw_not_implemented;
}
_generate_id_stringdescriptionprevnextTop
sub _generate_id_string {
  my $self = shift;
  $self->throw_not_implemented;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 SteinTop
Email lstein@cshl.org
APPENDIXTop
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _