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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
|
# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Biblio.t,v 1.10 2002/03/08 20:48:47 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Biblio.t'
use strict;
use vars qw($NUMTESTS);
my $error;
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; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 24;
}
my $testnum;
my $verbose = 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my $serror = 0; my $serror2 = 0;
my $ferror = 0; my $ferror2 = 0;
my $xerror = 0;
my $format = ($ENV{'TEST_DETAILS'} ? '%-25s' : '');
unless (eval "require SOAP::Lite; 1;") {
print STDERR "SOAP::Lite not installed. Skipping some tests.\n";
$serror = 1;
}
unless (eval "require IO::String; 1;") {
print STDERR "IO::String not installed. Skipping some tests.\n";
$serror2 = 1;
}
unless (eval "require XML::Parser; 1;") {
print STDERR "XML::Parser not installed. Skipping some tests.\n";
$xerror = 1;
}
use Bio::Root::IO;
my $testfile = Bio::Root::IO->catfile ('t','data','stress_test_medline.xml');
unless (-e $testfile) {
print STDERR "Cannot find testing data '$testfile'. Skipping some tests.\n";
$ferror = 1;
}
my $testfile2 = Bio::Root::IO->catfile ('t','data','stress_test_pubmed.xml');
unless (-e $testfile2) {
print STDERR "Cannot find testing data '$testfile2'. Skipping some tests.\n";
$ferror2 = 1;
}
# check 'use ...'
eval { require Bio::Biblio };
print sprintf ($format, 'use Bio::Biblio'); ok (%Bio::Biblio::);
print $@ if $@;
# check 'new...'
my $biblio;
eval { $biblio = new Bio::Biblio (-location => 'http://localhost:4567'); };
print sprintf ($format, "new Bio::Biblio "); skip ($serror, defined $biblio);
#print $@ if $@;
# check 'use ...IO...'
eval { require Bio::Biblio::IO };
print sprintf ($format, "use Bio::Biblio::IO "); ok (%Bio::Biblio::IO::);
my $io;
# check MEDLINE XML parser
print sprintf ($format, "new Bio::Biblio::IO (1)");
skip ($ferror || $xerror,
defined (eval { $io = new Bio::Biblio::IO ('-format' => 'medlinexml',
'-file' => $testfile,
'-result' => 'raw') }));
print $@ if $@;
print "Reading and parsing MEDLINE XML file...\n";
print sprintf ($format, " citation 1 "); skip ($ferror || $xerror, eval { $io->next_bibref->{'medlineID'} }, 'Text1');
print sprintf ($format, " citation 2 "); skip ($ferror || $xerror, eval { $io->next_bibref->{'medlineID'} }, 'Text248');
print sprintf ($format, " citation 3 "); skip ($ferror || $xerror, eval { $io->next_bibref->{'medlineID'} }, 'Text495');
print "Getting citations using callback...\n";
my (@ids) = ('Text1', 'Text248', 'Text495');
my $callback_used = 'no';
if ($ferror || $xerror) {
foreach my $i (1..3) {
print sprintf ($format, " citation $i "); skip (1,1);
}
} else {
$io = new Bio::Biblio::IO ('-format' => 'medlinexml',
'-file' => $testfile,
# '-result' => 'medline2ref', # this is default
'-callback' => \&callback);
}
print sprintf ($format, " calling callback "); skip ($ferror || $xerror, $callback_used, 'yes');
sub callback {
my $citation = shift;
$callback_used = 'yes';
print sprintf ($format, ' citation ' . (@ids+0) . ' '); skip ($ferror, $citation->{'_identifier'}, shift @ids);
}
print "Reading and parsing XML string...\n";
if ($xerror) {
print sprintf ($format, " citation 1 "); skip (1, 1);
print sprintf ($format, " citation 2 "); skip (1, 1);
} else {
$io = new Bio::Biblio::IO ('-format' => 'medlinexml',
'-data' => <<XMLDATA,
<MedlineCitationSet>
<MedlineCitation>
<MedlineID>12345678</MedlineID>
<Article><Journal></Journal></Article>
</MedlineCitation>
<MedlineCitation>
<MedlineID>abcdefgh</MedlineID>
<Article><Journal></Journal></Article>
</MedlineCitation>
</MedlineCitationSet>
XMLDATA
'-result' => 'medline2ref',
);
print sprintf ($format, " citation 1 "); ok ($io->next_bibref->{'_identifier'}, '12345678');
print sprintf ($format, " citation 2 "); ok ($io->next_bibref->{'_identifier'}, 'abcdefgh');
}
print "Reading and parsing XML string handle...\n";
#use IO::String;
if ($xerror || $serror2) {
print sprintf ($format, " citation 1 "); skip (1,1);
print sprintf ($format, " citation 2 "); skip (1,1);
} else {
my $data = <<XMLDATA;
<MedlineCitationSet>
<MedlineCitation>
<MedlineID>87654321</MedlineID>
<Article><Journal></Journal></Article>
</MedlineCitation>
<MedlineCitation>
<MedlineID>hgfedcba</MedlineID>
<Article><Journal></Journal></Article>
</MedlineCitation>
</MedlineCitationSet>
XMLDATA
$io = new Bio::Biblio::IO ('-format' => 'medlinexml',
'-fh' => IO::String->new ($data),
);
print sprintf ($format, " citation 1 "); ok (eval { $io->next_bibref->identifier }, '87654321');
print sprintf ($format, " citation 2 "); ok (eval { $io->next_bibref->identifier }, 'hgfedcba');
}
# check PUBMED XML parser
print sprintf ($format, "new Bio::Biblio::IO (2)");
skip ($ferror2 || $xerror,
defined (eval { $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
'-file' => $testfile2,
'-result' => 'pubmed2ref') }));
print "Reading and parsing PUBMED XML file...\n";
if ($xerror) {
foreach my $i (1..4) {
print sprintf ($format, " citation $i "); skip (1,"Can't read citation from PUBMED XML");
}
} else {
print sprintf ($format, " citation 1 "); skip ($ferror2, eval { $io->next_bibref->identifier }, '11223344');
print sprintf ($format, " citation 2 "); skip ($ferror2, eval { $io->next_bibref->identifier }, '21583752');
print sprintf ($format, " citation 3 "); skip ($ferror2, eval { $io->next_bibref->identifier }, '21465135');
print sprintf ($format, " citation 4 "); skip ($ferror2, eval { $io->next_bibref->identifier }, '21138228');
}
# test for FH
my $fh;
my @expvals = qw(11223344 21583752 21465135 21138228);
print "Testing FH\n";
eval {
$fh = Bio::Biblio::IO->newFh('-format' => 'pubmedxml',
'-file' => $testfile2,
'-result' => 'pubmed2ref');
while(<$fh>) {
ok($_->identifier,shift @expvals);
}
};
if( $@) {
foreach ( 1..4 ) { skip(1,"unable to use pubmedxml"); }
}
__END__
|
