# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 21,
-requires_modules => [qw(IO::String
LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::Tools::Run::RemoteBlast');
}
my $prog = 'blastp';
my $db = 'swissprot';
my $e_val = '1e-10';
my $v = test_debug();
SKIP: {
my $remote_blast
= Bio::Tools::Run::RemoteBlast->new(-verbose => $v,
-prog => $prog,
-data => $db,
-expect => $e_val,
);
$remote_blast->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');
my $inputfilename = test_input_file('ecolitst.fa');
ok( -e $inputfilename);
ok(1, 'Text BLAST');
my $attempt = 1;
my $status;
eval{
$status = $remote_blast->submit_blast($inputfilename);
};
ok($status,'BLAST text output submitted');
skip("Error accessing remote BLAST interface: $@", 5) if $@;
cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
diag("Time remaining: ".$remote_blast->get_rtoe) if $v;
my @rids = $remote_blast->each_rid;
is(@rids, 1, 'should only be one RID');
skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
diag("Retrieving $rids[0]...\n") if $v;
my $max_attempts = 20;
my $rc;
while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
if ( !ref($rc) ) {
if ( $rc < 0 ) {
skip("need a better solution for when 'Server failed to return any data'",3);
}
sleep 30;
diag("Retrieval attempt: $attempt\n") if $v;
$attempt++ < $max_attempts ? next : last;
}
else {
last;
}
}
if ($rc) {
ok(1,'retrieve_blast succeeded');
$remote_blast->remove_rid($rids[0]);
my $count = 0;
isa_ok($rc, 'Bio::SearchIO');
while (my $result = $rc->next_result) {
while ( my $hit = $result->next_hit ) {
$count++;
next unless ( $v > 0);
print "sbjct name is ", $hit->name, "\n";
while ( my $hsp = $hit->next_hsp ) {
print "score is ", $hsp->bits, "\n";
}
}
}
is($count, 3, 'HSPs returned');
}
elsif ($attempt > $max_attempts) {
# have a test fail here (there should not be repeated failed attempts to
# get reports)
ok(0,'Exceeded maximum attempts on server to retrieve report');
diag("Timeout, did not return report after ".($attempt - 1)." attempts");
skip('Remote server timeout problems', 2);
}
else {
# have a test fail here (whatever is returned should be eval as true and
# be a SearchIO)
ok(0,"Other problem on remote server, no report returned: $rc");
skip('Possible remote server problems', 2);
}
}
SKIP: {
# test blasttable
my $remote_blast
= Bio::Tools::Run::RemoteBlast->new(-verbose => $v,
-prog => $prog,
-data => $db,
-readmethod => 'blasttable',
-expect => $e_val,
);
$remote_blast->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');
$remote_blast->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');
my $inputfilename = test_input_file('ecolitst.fa');
my $attempt = 1;
my $status;
eval{
$status = $remote_blast->submit_blast($inputfilename);
};
ok($status,'Tabular BLAST submitted');
skip("Error accessing remote BLAST interface: $@", 5) if $@;
cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
diag("Time remaining: ".$remote_blast->get_rtoe) if $v;
my @rids = $remote_blast->each_rid;
is(@rids, 1, 'should only be one RID');
skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
diag("waiting [$rids[0]]...") if $v;
my $max_attempts = 20;
my $rc;
while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
if ( !ref($rc) ) {
if ( $rc < 0 ) {
skip("need a better solution for when 'Server failed to return any data'",3);
}
sleep 30;
diag("Retrieval attempt: $attempt") if $v;
$attempt++ < $max_attempts ? next : last;
}
else {
last;
}
}
if ($rc) {
ok(1,'retrieve_blast succeeded');
$remote_blast->remove_rid($rids[0]);
my $count = 0;
isa_ok($rc, 'Bio::SearchIO');
while (my $result = $rc->next_result) {
while ( my $hit = $result->next_hit ) {
$count++;
next unless ( $v > 0);
print "sbjct name is ", $hit->name, "\n";
while ( my $hsp = $hit->next_hsp ) {
print "score is ", $hsp->bits, "\n";
}
}
}
is($count, 3, 'HSPs returned');
}
elsif ($attempt > $max_attempts) {
# have a test fail here (there should not be repeated failed attempts to
# get reports)
ok(0,'Exceeded maximum attempts on server to retrieve report');
diag("Timeout, did not return report after ".($attempt - 1)." attempts");
skip('Remote server timeout problems', 2);
}
else {
# have a test fail here (whatever is returned should be eval as true and
# be a SearchIO)
ok(0,"Other problem on remote server, no report returned: $rc");
skip('Possible remote server problems', 2);
}
}
SKIP: {
test_skip(-tests => 6,
-requires_module => 'Bio::SearchIO::blastxml');
my $remote_blast
= Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
-data => $db,
-readmethod => 'xml',
-expect => $e_val,
);
$remote_blast->submit_parameter('ENTREZ_QUERY',
'Escherichia coli[ORGN]');
$remote_blast->retrieve_parameter('FORMAT_TYPE', 'XML');
my $inputfilename = test_input_file('ecolitst.fa');
my $attempt = 1;
my $status;
eval{
$status = $remote_blast->submit_blast($inputfilename);
};
ok($status,'XML BLAST submitted');
skip("Error accessing remote BLAST interface: $@", 5) if $@;
cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
diag("Time remaining: ".$remote_blast->get_rtoe) if $v;
my @rids = $remote_blast->each_rid;
is(@rids, 1, 'should only be one RID');
skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;
diag("waiting [$rids[0]]...") if $v;
# This blast usually takes 2x time compared to the other two
my $max_attempts = 30;
my $rc;
while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
if ( !ref($rc) ) {
if ( $rc < 0 ) {
skip("need a better solution for when 'Server failed to return any data'",3);
}
sleep 30;
diag("Retrieval attempt: $attempt") if $v;
$attempt++ < $max_attempts ? next : last;
}
else {
last;
}
}
if ($rc) {
ok(1,'retrieve_blast succeeded');
$remote_blast->remove_rid($rids[0]);
my $count = 0;
isa_ok($rc, 'Bio::SearchIO');
while (my $result = $rc->next_result) {
while ( my $hit = $result->next_hit ) {
$count++;
}
}
is($count, 3, 'HSPs returned');
}
elsif ($attempt > $max_attempts) {
# have a test fail here (there should not be repeated failed attempts to
# get reports)
ok(0,'Exceeded maximum attempts on server to retrieve report');
diag("Timeout, did not return report after ".($attempt - 1)." attempts");
skip('Remote server timeout problems', 2);
}
else {
# have a test fail here (whatever is returned should be eval as true and
# be a SearchIO)
ok(0,"Other problem on remote server, no report returned: $rc");
skip('Possible remote server problems', 2);
}
}