#
# BioPerl module for Bio::Tools::EUtilities::Query
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Part of the EUtilities BioPerl package
=head1 NAME
Bio::Tools::EUtilities::Query - parse and collect esearch, epost, espell,
egquery information
=head1 SYNOPSIS
### should not create instance directly; Bio::Tools::EUtilities does this ###
# can also use '-response' (for HTTP::Response objects) or '-fh' (for
# filehandles)
my $info = Bio::Tools::EUtilities->new(-eutil => 'esearch',
-file => 'esearch.xml');
# esearch
# esearch with history
# egquery
# espell (just for completeness, really)
=head1 DESCRIPTION
Pluggable module for handling query-related data returned from eutils.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l@lists.open-bio.org - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via the web.
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Email cjfields at bioperl dot org
=head1 APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
=cut
# Let the code begin...
package Bio::Tools::EUtilities::Query;
use strict;
use warnings;
use Bio::Tools::EUtilities::Query::GlobalQuery;
use Bio::Tools::EUtilities::History;
use base qw(Bio::Tools::EUtilities);
=head1 Bio::Tools::EUtilities::Query methods
=cut
# private EUtilDataI method
{
my %TYPE = (
'espell' => 'spelling',
'esearch' => 'singledbquery',
'egquery' => 'multidbquery',
'epost' => 'history'
);
sub _add_data {
my ($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};
}
}
}
=head2 to_string
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
=cut
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;