File Coverage

blib/lib/Bio/Tools/EUtilities/Query.pm

Criterion	Covered	Total	%
statement	46	68	67.6
branch	9	18	50.0
condition	10	31	32.2
subroutine	7	8	87.5
pod	1	1	100.0
total	73	126	57.9

package Bio::Tools::EUtilities::Query;
$Bio::Tools::EUtilities::Query::VERSION = '1.77';
use utf8;
use strict;
use warnings;
use Bio::Tools::EUtilities::Query::GlobalQuery;
use Bio::Tools::EUtilities::History;
use base qw(Bio::Tools::EUtilities);

# ABSTRACT: Parse and collect esearch, epost, espell, egquery information.
# AUTHOR:   Chris Fields
# OWNER:    2006-2013 Chris Fields
# LICENSE:  Perl_5



# private EUtilDataI method

{
my %TYPE = (
    'espell'    => 'spelling',
    'esearch'   => 'singledbquery',
    'egquery'   => 'multidbquery',
    'epost'     => 'history'
    );

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;

__END__