Summary

Bio::DB::EUtilities::esearch - Base interface class for handling web
queries and data retrieval from Entrez Utilities from NCBI.
You shouldn't use this class directly.

Package variables

Included modules

Inherit

Bio::DB::EUtilities

Synopsis

*** Give standard usage here

Description

*** Describe the object here

Methods

Methods description

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

 Title   : esearch_count
 Usage   : $count = $db->esearch_count;
 Function: return count of number of entries retrieved by query
 Returns : integer
 Args    : none

Methods code

sub _initialize {

    my ($self, @args ) = @_;
    $self->SUPER::_initialize(@args);
	my ($term, $field, $reldate, $mindate, $maxdate, $datetype, $rettype, $retstart, 
        $retmax, $sort, $usehistory) = 
	  $self->_rearrange([qw(TERM FIELD RELDATE MINDATE MAXDATE DATETYPE RETTYPE
        RETSTART RETMAX SORT USEHISTORY)],
		@args);    
    # set by default
    $self->_eutil($EUTIL);
    $datetype ||= 'mdat';
    $self->datetype($datetype) if $datetype;
	$term			&& $self->term($term);
	$field			&& $self->field($field);
	$reldate		&& $self->reldate($reldate);
	$mindate		&& $self->mindate($mindate);
	$maxdate		&& $self->maxdate($maxdate);
    $retstart       && $self->retstart($retstart);
    $retmax         && $self->retmax($retmax);
    $rettype        && $self->rettype($rettype);
    $sort           && $self->sort_results($sort);
	$usehistory		&& $self->usehistory($usehistory);

}

sub parse_response {

    my $self    = shift;
    my $response = shift if @_;
    if (!$response || !$response->isa("HTTP::Response")) {
        $self->throw("Need HTTP::Response object");
    }
    my $history = $self->usehistory;
    my $db = $self->db;
    my $xs = XML::Simple->new();
    my $simple = $xs->XMLin($response->content);
    #$self->debug("Response dumper:\n".Dumper($simple));
    # check for major and minor errors and warnings
    if ($simple->{ERROR}) {
        $self->throw("NCBI esearch nonrecoverable error: ".$simple->{ERROR});
    }
    if ($simple->{ErrorList} || $simple->{WarningList}) {
        my %errorlist = %{ $simple->{ErrorList} };
        my %warninglist = %{ $simple->{WarningList} };
        my ($err_warn);
        for my $key (sort keys %errorlist) {
            $err_warn .= "Error : $key = $errorlist{$key}\n";
        }    
        for my $key (sort keys %warninglist) {
            $err_warn .= "Warning : $key = $warninglist{$key}\n";
        }
        chomp($err_warn);
        $self->warn("NCBI esearch Errors/Warnings:\n".$err_warn)
    }
	my $count = $simple->{Count};
	$self->esearch_count($count);
    my $id_ref = $simple->{IdList}->{Id};
    $self->_add_db_ids($id_ref) if ($id_ref);
    if ($history && $history eq 'y') {
        my $webenv = $simple->{WebEnv};
        my $querykey = $simple->{QueryKey};
		my $cookie = Bio::DB::EUtilities::Cookie->new(
										 -term 		=> $self->term,
										 -webenv    => $webenv,
										 -querykey  => $querykey,
										 -eutil     => 'esearch',
                                         -database  => $db,
										 -total		=> $count
										);
        $self->add_cookie($cookie);
	}

}

sub esearch_count {

    my $self = shift;
    return $self->{'_esearch_count'} = shift if @_;
    return $self->{'_esearch_count'};

}

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.

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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 the web.

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

Email cjfields at uiuc dot edu

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