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# testing Bio::DB::Query::HIVQuery
# $Id: HIVQuery.t 232 2008-12-11 14:51:51Z maj $
use strict;
use warnings;
BEGIN {
use Bio::Root::Test;
test_begin(
-tests => 41,
-requires_modules => [qw( XML::Simple )]
);
use_ok('Bio::DB::Query::HIVQuery');
use_ok('Bio::DB::HIV');
use_ok( 'Bio::Annotation::Collection' );
use_ok( 'Bio::Annotation::Comment' );
use_ok( 'Bio::Annotation::Reference' );
use_ok( 'Bio::DB::HIV::HIVQueryHelper' );
}
my $tobj= new Bio::DB::Query::HIVQuery(-RUN_OPTION=>0);
#object tests
isa_ok($tobj, 'Bio::DB::Query::HIVQuery');
#compliance tests
isa_ok($tobj, 'Bio::Root::Root');
can_ok($tobj, qw( count ids query ));
#methods
can_ok($tobj, qw(
get_annotations_by_ids
get_annotations_by_id
add_annotations_for_id
remove_annotations_for_ids
remove_annotations_for_id
remove_annotations
get_accessions
get_accessions_by_ids
get_accessions_by_id
)
);
#internals
can_ok($tobj, qw(
_do_query
_reset
_session_id
_run_option
add_id
lanl_base
map_db
make_search_if
search_
_map_db_uri
_make_search_if_uri
_search_uri
_schema_file
_schema
_lanl_query
_lanl_response
_create_lanl_query
_do_lanl_request
_parse_lanl_response
_parse_query_string
_sorry
)
);
#defaults tests
ok($tobj->_map_db_uri, "_map_db_uri set in default object");
ok($tobj->_make_search_if_uri, "_make_search_if_uri set in default object");
ok($tobj->_search_uri, "_search_uri set in default object");
ok($tobj->_schema_file, "_schema_file set in default object");
ok(defined $tobj->_run_option, "_run_option set in default object");
ok($tobj->{_annotations}, "annotations container available");
# query syntax (no run)
$tobj->_reset;
$tobj->query(['coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any']);
is($tobj->_do_query(0), 0, 'query syntax check 1');
$tobj->_reset;
$tobj->query({'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any'});
is($tobj->_do_query(0), 0, 'query syntax check 2');
$tobj->_reset;
$tobj->query({'query'=>{'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F']}, 'annot'=> ['country']});
is($tobj->_do_query(0),0, 'query syntax check 3');
$tobj->_reset;
$tobj->query("('CCR5 CXCR4', 'CXCR4')[coreceptor] (D F)[subtype] {[country]}");
is($tobj->_do_query(0),0, 'query parser check');
#multiquery parse
$tobj->_reset;
$tobj->query( "(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]");
is($tobj->_do_query(0),0, 'multiquery parse check');
SKIP: {
test_skip(-requires_module => 'HTML::Parser', -tests => 3);
no warnings; # HTML::Parser has an uninited value issue
use_ok('HTML::Parser');
use warnings;
# help test; just tests that file can be written and that tags are in matching
# pairs, with reasonable placement of <html> and </html>
my $hlpf = test_output_file();
my $a = 0;
my $html = 0;
my $h = HTML::Parser->new( empty_element_tags=>1, start_h => [sub {$a++; (shift eq 'html') && ($a==1) && $html++}, "tagname"], end_h => [sub {$a--; (shift eq 'html') && ($a==0) && $html++;}, "tagname"] );
ok($tobj->help($hlpf), "help html to file");
{
local $/;
undef $/;
open HP, $hlpf;
$h->parse(<HP>);
is_deeply([$a, $html], [0, 2], "help html parsed");
1;
}
}
#exceptions tests
#pre-run query exceptions
$tobj->verbose(2);
$tobj->_reset;
$tobj->query( "narb[scroob]" );
throws_ok {$tobj->_do_query} qr/BadParameter/, "bad field exception check";
$tobj->_reset;
$tobj->query( "narb[phenotype]" );
throws_ok {$tobj->_do_query} qr/BadParameter/, "bad match data exception check";
$tobj->_reset;
$tobj->query( [ 'cd4_count' => "" ] );
throws_ok {$tobj->_do_query} qr/BadParameter/, "empty field not ok exception check";
$tobj->_reset;
$tobj->{_schema} = undef;
throws_ok {$tobj->_do_query} qr/SchemaNotInit/, "uninitialized schema exception check";
throws_ok {$tobj->count} qr/Query not yet run/, "query not run (level 1) warning check";
throws_ok {$tobj->get_annotations_by_id($tobj->ids)} qr/Requires query run/, "query not run (level 2) warning check";
# network tests
SKIP : {
test_skip(-tests => 10,
-requires_networking => 1);
eval {$tobj = Bio::DB::Query::HIVQuery->new(-QUERY=>"(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]",-RUN_OPTION=>2)};
if ($@) {
diag($@);
skip("Network problems, skipping all", 10);
}
ok($tobj,"live query");
cmp_ok( $tobj->count, ">=", 12, "enough sequences returned");
# test query object handling of Bio::DB::HIV
my ($tdb, $seqio, $seq);
ok( $tdb = new Bio::DB::HIV, "create Bio::DB::HIV object");
eval {$seqio = $tdb->get_Stream_by_query($tobj)};
if ($@) {
diag($@);
skip("Network problems, skipping all", 7);
}
ok($seqio, "get SeqIO stream from query");
# test HIVAnnotProcessor indirectly
ok($seq = $seqio->next_seq, "access sequence stream");
ok($seq->annotation->get_value('Virus'), "'Virus' annotation present");
like ($seq->annotation->get_value('Virus','phenotype'), qr/SI/, "'Virus' phenotype annotation present");
like ($seq->annotation->get_value('Virus', 'subtype'), qr/[CD]/, "'Virus' subtype annotation present");
ok($seq->accession_number, "GenBank accession available");
# exception checks
$tobj->_reset;
$tobj->verbose(2);
$tobj->query( "2BR02B[accession]" );
throws_ok {$tobj->_do_query(2)} qr/no sequences/i, "no sequences warning check";
}
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