BioPerl

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Bio/Root/HTTPget.pm  view on Meta::CPAN

 Args    :

=cut

sub _http_connect {
  my ($host,$port,$timeout) = @_;
  my $sock = IO::Socket::INET->new(Proto     => 'tcp',
                                   Type      => SOCK_STREAM,
				   PeerHost  => $host,
				   PeerPort  => $port,
				   Timeout   => $timeout,
				  );
  $sock;
}


=head2 _encode_base64

 Title   :
 Usage   : 
 Function:

Bio/Root/Utilities.pm  view on Meta::CPAN

    }
    $SIG{ALRM} = sub { die "Timed out!"; };
    my $result;
    eval {
        $alarm_available && alarm( $TIMEOUT_SECS );
        $result = read($FH, $buffer, $BUFSIZ); # read the $BUFSIZ characters of file
        $alarm_available && alarm(0);
    };
    if($@ =~ /Timed out!/) {
        $self->throw( "Timed out while waiting for input.",
                      "Timeout period = $TIMEOUT_SECS seconds.\n"
                     ."For longer time before timing out, edit \$TIMEOUT_SECS in Bio::Root::Utilities.pm.");

    } elsif(not $result) {
        my $err = $@;
        $self->throw("read taste failed to read from FileHandle.", $err);

    } elsif($@ =~ /\S/) {
        my $err = $@;
        $self->throw("Unexpected error during read: $err");
    }

t/Tools/Run/RemoteBlast.t  view on Meta::CPAN

                    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);
    }
}

t/Tools/Run/RemoteBlast.t  view on Meta::CPAN

                    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);
    }
}

t/Tools/Run/RemoteBlast.t  view on Meta::CPAN

            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);
    }
}

t/Tools/Run/RemoteBlast_rpsblast.t  view on Meta::CPAN

                    print "score is ", $hsp->bits, "\n";
                }
            }
        }
        cmp_ok($count, '>=', 45, 'HSPs returned');
    }
    elsif ($attempt > 10) {
        # have a test fail here (there should not be repeated failed attempts to
        # get reports)
        ok(0,'Exceeded maximum attempts on server to retrieve report');
        diag("Timeout, did not return report after ".($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);
    }
}