Toolbar

Summary

Bio::Tools::EUtilities::Query - parse and collect esearch, epost, espell,
egquery information

Package variables

Included modules

Inherit

Bio::Tools::EUtilities

Synopsis

  ### should not create instance directly; Bio::Tools::EUtilities does this ###

  # can also use '-response' (for HTTP::Response objects) or '-fh' (for
  # filehandles)
  
  my $info = Bio::Tools::EUtilities->new(-eutil => 'esearch',
                                         -file => 'esearch.xml');

  # esearch

  # esearch with history

  # egquery

  # espell (just for completeness, really)

Description

Pluggable module for handling query-related data returned from eutils.

Methods

Methods description

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting
 Note     : Used generally for debugging and for the print_* methods

Methods code

sub _add_data {

    my ($self, $qdata) = @_;
    my $eutil = $self->eutil;
    if (!$qdata || ref($qdata) !~ /HASH/i) {
        $self->throw("Bad $eutil data");
    }
    if (exists $qdata->{WebEnv}) {
        my $cookie = Bio::Tools::EUtilities::History->new(-eutil => $eutil,
                            -verbose => $self->verbose);
        $cookie->_add_data($qdata);
        push @{$self->{'_histories'}}, $cookie;
    }
    my $type = exists $TYPE{$eutil} ? $TYPE{$eutil} :
        $self->throw("Unrecognized eutil $eutil");
    $self->datatype($type); # reset type based on what's present
    for my $key (sort keys %$qdata) {
        if ($key eq 'eGQueryResult' && exists $qdata->{$key}->{ResultItem}) {
            for my $gquery (@{ $qdata->{eGQueryResult}->{ResultItem} }) {
                $self->{'_term'} = $gquery->{Term} = $qdata->{Term};
                my $qd = Bio::Tools::EUtilities::Query::GlobalQuery->new(-eutil => 'egquery',
                                                            -datatype => 'globalquery',
                                                            -verbose => $self->verbose);
                $qd->_add_data($gquery);
                push @{ $self->{'_globalqueries'} }, $qd;
            }
        }
        if ($key eq 'IdList' &&
            exists $qdata->{IdList}->{Id}) {
            $self->{'_id'} = $qdata->{IdList}->{Id};
            delete $qdata->{IdList};
        }
        if ($key eq 'TranslationSet' &&
            exists $qdata->{TranslationSet}->{Translation}) {
            $self->{'_translation'} = $qdata->{TranslationSet}->{Translation};
            delete $qdata->{TranslationSet};
        }
        next if (ref $qdata->{$key} eq 'HASH' && !keys %{$qdata->{$key}});
        $self->{'_'.lc $key} = $qdata->{$key};
    }
}

}

sub to_string {

    my $self = shift;
    my %data = (
        'DB'    => [1, join(', ',$self->get_databases) || ''],
        'Query' => [2, $self->get_term || ''],
        'IDs'   => [4, join(', ',$self->get_ids) || ''],
    );
    my $string = $self->SUPER::to_string;
    if ($self->eutil eq 'esearch') {
        $data{'Count'} = [3, $self->get_count ];
        $data{'Translation From'} = [5, $self->get_translation_from || ''];
        $data{'Translation To'} = [6, $self->get_translation_to || ''];
        $data{'RetStart'} = [7, $self->get_retstart];
        $data{'RetMax'} = [8, $self->get_retmax];
        $data{'Translation'} = [9, $self->get_query_translation || ''];
    }
    if ($self->eutil eq 'espell') {
        $data{'Corrected'} = [3, $self->get_corrected_query || ''];
        $data{'Replaced'} = [4, join(',',$self->get_replaced_terms) || ''];
    }
    for my $k (sort {$data{$a}->[0] <=> $data{$b}->[0]} keys %data) {
        $string .= sprintf("%-20s:%s\n",$k, $self->_text_wrap('',' 'x 20 .':', $data{$k}->[1]));
    }
    while (my $h = $self->next_History) {
        $string .= $h->to_string;
    }
    while (my $gq = $self->next_GlobalQuery) {
        $string .= $gq->to_string;
    }
    return $string;
}

1;

}

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@lists.open-bio.org               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

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.

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/

Email cjfields at bioperl dot org

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