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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Test::RequiresInternet;
use Test::Most tests => 18;
use_ok('Bio::DB::Query::GenBank');
use_ok('Bio::DB::GenBank');
}
my %expected_lengths = (
'MUSIGHBA1' => 408,
'AF303112' => 1611,
'AF041456' => 1156,
'AY080910' => 798,
'AY080909' => 1042,
'AF155220' => 1172,
'AF442768' => 2547,
);
my ($gb, $seq, $seqio, $seqin, $query);
my %params;
if (defined $ENV{BIOPERLEMAIL}) {
$params{'-email'} = $ENV{BIOPERLEMAIL};
$params{'-delay'} = 2;
}
$params{'-verbose'} = $ENV{BIOPERLDEBUG};
# test query facility
ok $query = Bio::DB::Query::GenBank->new('-db' => 'nucleotide',
'-query' => 'Onchocerca volvulus[Organism]',
'-mindate' => '2002/1/1',
'-maxdate' => '2002/12/31', %params), 'Bio::DB::Query::GenBank';
SKIP: {
cmp_ok $query->count, '>', 0;
my @ids = $query->ids;
cmp_ok @ids, '>', 0;
is @ids, $query->count;
ok $gb = Bio::DB::GenBank->new(%params);
eval {$seqio = $gb->get_Stream_by_query($query);};
skip "Couldn't connect to complete GenBank query tests. Skipping those tests", 5 if $@;
my $done = 0;
while (my $s = $seqio->next_seq) {
is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
undef $gb; # test the case where the db is gone,
# but the pipeline should remain until seqio goes away
$done++;
}
skip('No seqs returned', 5) if !$done;
is $done, 1;
}
$seq = $seqio = undef;
# test query facility (again)
ok $query = Bio::DB::Query::GenBank->new('-db' => 'nucleotide',
'-ids' => [qw(J00522 AF303112 2981014)],
%params);
SKIP: {
cmp_ok $query->count, '>', 0;
my @ids = $query->ids;
cmp_ok @ids, '>', 0;
is @ids, $query->count;
$gb = Bio::DB::GenBank->new(%params);
eval {$seqio = $gb->get_Stream_by_query($query);};
skip "Couldn't connect to complete GenBank query tests. Skipping those tests: $@", 4 if $@;
my $done = 0;
while (my $s = $seqio->next_seq) {
is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
$done++;
}
skip('No seqs returned', 4) if !$done;
is $done, 3;
$seqio->close(); # the key to preventing errors during make test, no idea why
}
$seq = $seqio = undef;
# and yet again, for bug 2133
$query = Bio::DB::Query::GenBank->new('-query' => 'AF303112',
'-ids' => [qw(J00522 AF303112 2981014)],
%params);
is $query->query, 'J00522[PACC]|AF303112[PACC]|2981014[UID]';
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