Summary

Bio::DB::DBFetch - Database object for retrieving using the dbfetch script

Package variables

Included modules

Inherit

Bio::DB::WebDBSeqI

Synopsis

  #do not use this module directly

Description

Allows the dynamic retrieval of entries from databases using the
dbfetch script at EBI:
http:EEwww.ebi.ac.ukEcgi-binEdbfetch.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
This is a superclass which is called by instantiable subclasses with
correct parameters.

Methods

Methods description

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

 Title   : postprocess_data
 Usage   : $self->postprocess_data ( 'type' => 'string',
				     'location' => \$datastr);
 Function: process downloaded data before loading into a Bio::SeqIO
 Returns : void
 Args    : hash with two keys - 'type' can be 'string' or 'file'
                              - 'location' either file location or string
                                           reference containing data

 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none

  Title   : get_Stream_by_id
  Usage   : $seq = $db->get_Stream_by_id($ref);
  Function: Retrieves Seq objects from the server 'en masse', rather than one
            at a time.  For large numbers of sequences, this is far superior
            than get_Stream_by_[id/acc]().
  Example :
  Returns : a Bio::SeqIO stream object
  Args    : $ref : either an array reference, a filename, or a filehandle
            from which to get the list of unique ids/accession numbers.

 Title   : get_Seq_by_version
 Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 Function: Gets a Bio::Seq object by accession number
 Returns : A Bio::Seq object
 Args    : version number (as a string)
 Throws  : "version does not exist" exception

 Title   : request_format
 Usage   : my ($req_format, $ioformat) = $self->request_format;
           $self->request_format("genbank");
           $self->request_format("fasta");
 Function: Get/Set sequence format retrieval. The get-form will normally not
           be used outside of this and derived modules.
 Returns : Array of two strings, the first representing the format for
           retrieval, and the second specifying the corresponding SeqIO format.
 Args    : $format = sequence format

 Title   : servertype
 Usage   : my $servertype = $self->servertype
	    $self->servertype($servertype);
 Function: Get/Set server type
 Returns : string
 Args    : server type string [optional]

 Title   : hostlocation
 Usage   : my $location = $self->hostlocation()
          $self->hostlocation($location)
 Function: Set/Get Hostlocation
 Returns : string representing hostlocation
 Args    : string specifying hostlocation [optional]

 Title   : location
 Usage   : my $url = $self->location_url()
 Function: Get host url
 Returns : string representing url
 Args    : none

 Title   : hosts
 Usage   : 
 Function: get/set for host hash 
 Returns : 
 Args    : optional hash

 Title   : formatmap
 Usage   : 
 Function: get/set for format hash
 Returns : 
 Args    : optional hash

Methods code

BEGIN {

 	    # global vars
    $DEFAULTSERVERTYPE = 'dbfetch';
    $DEFAULTLOCATION = 'ebi';

}

sub get_request {

    my ($self, @qualifiers) = @_;
    my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
					    @qualifiers);

    $self->throw("Must specify a value for UIDs to fetch")
	unless defined $uids;
    my $tmp;
    my $format_string = '';
    $format ||= $self->default_format;
    ($format, $tmp) = $self->request_format($format);
    $format_string = "&format=$format" if $format ne $self->default_format;
    my $url = $self->location_url();
    my $uid;
    if( ref($uids) =~ /ARRAY/i ) {
	$uid = join (',', @$uids);
	$self->warn ('The server will accept maximum of 50 entries in a request. The rest are ignored.')
	    if scalar @$uids >50;
    } else {
	$uid = $uids;
    }

    return GET $url. $format_string. '&id='. $uid;

}

sub postprocess_data {

  my ($self, %args) = @_;
  if ($args{type} eq 'string') {
    ${$args{location}} =~ s/^\s+//;  # get rid of leading whitespace
  }
  elsif ($args{type} eq 'file') {
    open F,$args{location} or $self->throw("Cannot open $args{location}: $!");
    my @data = <F>;
    for (@data) {
      last unless /^\s+$/;
      shift @data;
    }
    open F,">$args{location}" or $self->throw("Cannot write to $args{location}: $!");
    print F @data;
    close F;
  }

}

sub default_format {

    my ($self) = @_;
    return $self->{'_default_format'};

}

sub get_Stream_by_id {

    my ($self, $ids) = @_;
    return $self->get_seq_stream('-uids' => $ids, '-mode' => 'batch');

}

sub get_Seq_by_version {

   my ($self,$seqid) = @_;
   my $seqio = $self->get_Stream_by_acc([$seqid]);
   $self->throw("version does not exist") if( !defined $seqio );
   return $seqio->next_seq();

}

sub request_format {

    my ($self, $value) = @_;
    if( defined $value ) {
	$value = lc $value;
	$self->{'_format'} = $value;
	return ($value, $value);
    }
    $value = $self->{'_format'};
    if( $value and defined $self->formatmap->{$value} ) {
	return ($value, $self->formatmap->{$value});
    } else {
	# Try to fall back to a default.
	return ($self->default_format, $self->default_format );
    }

}

sub servertype {

    my ($self, $servertype) = @_;
    if( defined $servertype && $servertype ne '') {		
	 $self->throw("You gave an invalid server type ($servertype)".
			  " - available types are ".
			  keys %{$self->hosts}) unless( $self->hosts->{$servertype} );
	 $self->{'_servertype'} = $servertype;
    }
    $self->{'_servertype'} = $DEFAULTSERVERTYPE unless $self->{'_servertype'};
    return $self->{'_servertype'};

}

sub hostlocation {

    my ($self, $location ) = @_;
    $location = lc $location;
    my $servertype = $self->servertype;
    $self->throw("Must have a valid servertype defined not $servertype")
	unless defined $servertype; 
    my %hosts = %{$self->hosts->{$servertype}->{'hosts'}};
    if( defined $location && $location ne '' ) {
	if( ! $hosts{$location} ) {
	    $self->throw("Must specify a known host, not $location,".
			 " possible values (".
			 join(",", sort keys %hosts ). ")");
	}
	$self->{'_hostlocation'} = $location;
    }
    $self->{'_hostlocation'} = $DEFAULTLOCATION unless $self->{'_hostlocation'};
    return $self->{'_hostlocation'};

}

sub location_url {

    my ($self) = @_;
    my $servertype = $self->servertype();
    my $location = $self->hostlocation();
    if( ! defined $location || !defined $servertype )  {	
	$self->throw("must have a valid hostlocation and servertype set before calling location_url");
    }
    return sprintf($self->hosts->{$servertype}->{'baseurl'},
		   $self->hosts->{$servertype}->{'hosts'}->{$location});

}

sub hosts {

    my ($self, $value) = @_;
    if (defined $value) {
	$self->{'_hosts'} = $value;
    }
    unless (exists $self->{'_hosts'}) {
	return ('');
    } else {
	return $self->{'_hosts'};
    }

}

sub formatmap {

    my ($self, $value) = @_;
    if (defined $value) {
	$self->{'_formatmap'} = $value;
    }
    unless (exists $self->{'_formatmap'}) {
	return ('');
    } else {
	return $self->{'_formatmap'};
    }

}

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://bio.perl.org/MailList.html             - 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 email
or the web:

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

Email Heikki Lehvaslaiho <Heikki@ebi.ac.uk>

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

These methods allow subclasses to pass parameters.