Summary

Bio::DB::GDB - Database object interface to GDB HTTP query

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    use Bio::DB::GDB;

    $gdb = new Bio::DB::GDB;

    $info = $gdb->get_info(-type => 'marker',
			                  -id => 'D1S243'); # Marker name

   print "genbank id is ", $info->{'gdbid'},
    "\nprimers are (fwd, rev) ", join(",", @{$info->{'primers'}}), 
    "\nproduct length is ", $info->{'length'}, "\n";

Description

This class allows connections to the Genome Database (GDB) and queries
to retrieve any database objects. See http://www.gdb.org/ or any
mirror for details.

Methods

Methods description

 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   : get_params
 Usage   : my %params = $self->get_params($mode)
 Function: Returns key,value pairs to be passed to query
            for mode ('marker', 'gene')
 Returns : a key,value pair hash
 Args    : 'marker' or 'gene' mode for retrieval

 Title   : get_info
 Usage   : my $info = $self->get_info(-type => 'marker',
				      -id   => 'D1S234'); 
 Function: Returns key,value pairs specific
 Returns : a key,value pair hash
 Args    : -type => 'marker' or 'gene' mode for retrieval
           -id   => unique id to query for

 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: HTTP::Request
 Returns : 
 Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

Methods code

sub new {

    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my $ua = new LWP::UserAgent(env_proxy => 1);
    $ua->agent(ref($self) ."/$MODVERSION");
    $self->ua($ua);    

    return $self;

}

sub ua {

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

}

sub get_params {

    my ($self, $mode) = @_;
    return %{$PARAMSTRING{$mode}};

}

sub get_info {

    my ($self, @args) = @_;
    my ( $type, $id) = $self->_rearrange([qw(TYPE ID)], @args);
    if( !defined $type ) {
	$self->throw("Must specify a type you are querying for");
    } elsif( !defined $id ) {
	$self->throw("Must specify a id to query for");
    }
    my %params = $self->get_params($type);

    $params{'displayName'} = $id;

    if( $type eq 'marker' ) {
	# do more specific stuff?
    } elsif( $type eq 'gene' ) {
	# do more specific stuff?
    }
    my $url = $self->get_request(%params);    
    
    my ($resp) = $self->_request($url);
    if( ! defined $resp || ! ref($resp) ) {
	$self->warn("Did not get any data for url ". $url->uri);
	return;
    }
    my $content = $resp->content;	
    if( $content =~ /ERROR/ || length($resp->content) == 0 ) {
	$self->warn("Error getting for url " . $url->uri . "!\n");
	return;
    }
    my (@primers, $length, $markerurl, $realname);
    my $state = 0;
    my $title = 0;
    my $p;
    $p = new HTML::Parser( api_version => 3,
			   start_h => [ sub { 
			       return if( $title == 2 || $state == 3);
			       my($tag,$attr,$text) = @_;
			       return if( !defined $tag);
			       if( $tag eq 'table' ) {
				   $state = 1;
			       } elsif( $tag eq 'title' ) {
				   $title = 1;
			       } elsif( $state == 2 && 
					$tag eq 'a' &&
					$attr->{'href'} ) {
				   $state = 3; 
				   if( $text =~ m(href="?(http://.+)"?\s*>) ) { 
				       $markerurl = $1;
				   }
			       } 
			   }, "tagname, attr, text" ],

}

sub get_request {

    my ($self, %params) = @_;
    if( ! %params ) {
	$self->throw("must provide parameters with which to query");
    }
    my $url = $BASEADDRESS;    
    my $querystr = '?' . join("&", map { "$_=$params{$_}" } keys %params);
    return GET $url . $querystr;

}

sub _request {

    my ($self, $url,$tmpfile) = @_;
    my ($resp);
    if( defined $tmpfile && $tmpfile ne '' ) { 
	$resp =  $self->ua->request($url, $tmpfile);
    } else { $resp =  $self->ua->request($url); } 

    if( $resp->is_error  ) {
	$self->throw($resp->as_string() . "\nError getting for url " .
		     $url->uri . "!\n");
	return;
    }
    return $resp;

}

sub _gdb_search_tag_start {

}

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

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:

  http://bugzilla.open-bio.org/

Email jason@bioperl.org

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