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# -*-Perl-*- Test Harness script for Bioperl
# $Id: esearch.t 15112 2008-12-08 18:12:38Z sendu $
#
use strict;
use warnings;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 33,
-requires_module => 'XML::Simple');
use_ok('Bio::Tools::EUtilities');
use_ok('Bio::Tools::EUtilities::EUtilParameters');
}
my @ids = qw(6679096 31543332 134288853 483581 20805941 187951953 169158074
123228044 148676374 114326469 148707003 187952787 123233807 148694865 148694864
148694863 148694861 148694862 8705244 8568086);
# test any Query-related methods (term related)
# Normal esearch
my $eutil = Bio::Tools::EUtilities->new(
-eutil => 'esearch',
-file => test_input_file('eutils','esearch1.xml'));
# w/o a ParameterBase, only IDs, count, retstart/retmax, optionally History
is ($eutil->get_count, 534, 'get_count');
my $history = $eutil->next_History;
is($history, undef);
my @ids2 = $eutil->get_ids;
is_deeply(\@ids2, \@ids, 'get_ids');
is($eutil->get_retstart, 0,'get_retstart');
is($eutil->get_retmax, 20,'get_retmax');
is($eutil->get_translation_from, 'Mus musculus','get_translation_from');
is($eutil->get_translation_to, '("Mus musculus"[Organism:__txid10090] OR Mus musculus)','get_translation_to');
# the database isn't carried into the parsers unless a EUtilParameters is present
is($eutil->get_db, undef, 'get_db');
is($eutil->get_database, undef, 'get_database');
is($eutil->get_term, undef,'get_term');
# add Parameters
my $pb = Bio::Tools::EUtilities::EUtilParameters->new(-eutil => 'esearch',
-db => 'protein',
-term => 'Notch AND Mus musculus');
$eutil->parameter_base($pb);
# now will work...
is($eutil->get_db, 'protein', 'get_db');
is($eutil->get_database, 'protein', 'get_database');
is($eutil->get_term, 'Notch AND Mus musculus','get_term');
# espell only (should be undef)
is($eutil->get_corrected_query, undef ,'get_corrected_query');
is($eutil->get_replaced_terms, undef ,'get_replaced_terms');
# test esearch data with History
$eutil = Bio::Tools::EUtilities->new(
-eutil => 'esearch',
-file => test_input_file('eutils','esearch2.xml'));
is ($eutil->get_count, 534, 'get_count');
$history = $eutil->next_History;
isa_ok($history, 'Bio::Tools::EUtilities::HistoryI');
is($history->get_webenv,
'00m7eJh8lyG3wiC2SE2hd7Im_w5o3z3q4_JK9-Rn266ix_eRXkjNOYQxHp@03F17619941CFD71_0005SID',
'get_webenv');
is($history->get_query_key, 1, 'get_query_key');
is(join(',',$history->history),
'00m7eJh8lyG3wiC2SE2hd7Im_w5o3z3q4_JK9-Rn266ix_eRXkjNOYQxHp@03F17619941CFD71_0005SID,1', 'history');
@ids2 = $eutil->get_ids;
is_deeply(\@ids2, \@ids, 'get_ids');
is($eutil->get_retstart, 0,'get_retstart');
is($eutil->get_retmax, 20,'get_retmax');
is($eutil->get_translation_from, 'Mus musculus','get_translation_from');
is($eutil->get_translation_to, '("Mus musculus"[Organism:__txid10090] OR Mus musculus)','get_translation_to');
# the database isn't carried into the parsers
is($eutil->get_db, undef, 'get_db');
is($eutil->get_database, undef, 'get_database');
# the term isn't carried into the parsers
is($eutil->get_term, undef,'get_term');
# espell only (should be undef)
is($eutil->get_corrected_query, undef ,'get_corrected_query');
is($eutil->get_replaced_terms, undef ,'get_replaced_terms');
my @qs = $eutil->get_GlobalQueries;
is(scalar(@qs), 0, 'get_GlobalQueries')
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