1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
use lib 't';
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
use Test;
use DBStagTest;
plan tests => 5;
}
use DBIx::DBStag;
use DBI;
use Data::Stag;
use FileHandle;
use strict;
unless ($ENV{DBSTAG_DEVELOPER_MODE}) {
print "test feature.t takes a loooooong time, so I'm skipping it.\n";
print "if you want to run this test, set env DBSTAG_DEVELOPER_MODE\n";
ok(1) foreach (1..5);
exit 0;
}
drop();
my $dbh = connect_to_cleandb();
foreach my $f (qw(chado-cvterm.sql
chado-pub.sql
chado-feature.sql
chado-fr.sql
)) {
open(F, "t/data/$f") || die;
my $ddl = join('',<F>);
close(F);
$dbh->do($ddl);
}
foreach my $f (qw(relationship.chado-xml
sofa.chado-xml
CG10833.with-macros.chado-xml)) {
print "parsing..\n";
my $chado = Data::Stag->parse("t/data/$f");
print "parsed; now storing..\n";
$dbh->storenode($_) foreach $chado->subnodes;
}
ok(1);
my $fset =
$dbh->selectall_stag(q[
SELECT *
FROM feature
LEFT OUTER JOIN dbxref ON (feature.dbxref_id = dbxref.dbxref_id)
LEFT OUTER JOIN db ON (dbxref.db_id = db.db_id)
INNER JOIN cvterm AS ftype ON (feature.type_id = ftype.cvterm_id)
USE NESTING (set(feature(ftype)(dbxref(db))))
]);
print $fset->xml;
my @features = $fset->get_feature;
ok(@features,10);
my ($gene) = $fset->where(feature=>sub {
shift->find('cvterm/name') eq 'gene'
});
ok($gene->sget_name eq 'Cyp28d1');
$fset =
$dbh->selectall_stag(q[
SELECT subf.*
FROM feature
INNER JOIN feature_relationship ON (feature.feature_id = feature_relationship.object_id)
INNER JOIN feature AS subf ON (subf.feature_id = feature_relationship.subject_id)
WHERE feature.name='Cyp28d1-RA'
]);
print $fset->xml;
@features = $fset->get_subf;
ok(@features,7);
$fset =
$dbh->selectall_stag(q[
SELECT feature.*
FROM feature
INNER JOIN featureloc ON (feature.feature_id = featureloc.feature_id)
INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id)
WHERE srcf.uniquename='2L'
]);
@features = $fset->get_feature;
ok(@features,9);
$dbh->disconnect;
|
