Bio-CIPRES

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lib/Bio/CIPRES.pm  view on Meta::CPAN

    $self->{agent} = LWP::UserAgent->new(
        agent    => __PACKAGE__ . "/$VERSION",
        ssl_opts => {verify_hostname => 0},
        timeout  => $self->{cfg}->{timeout},
    );
   
    # create URI object for easier protocol/port parsing
    $self->{uri} = URI->new( $self->{cfg}->{url} );

    my $netloc = join ':', $self->{uri}->host, $self->{uri}->port;
    $self->{agent}->credentials(
        $netloc,
        $DOMAIN,
        $self->{cfg}->{user},
        $self->{cfg}->{pass}
    );

    my %headers = ( 'cipres-appkey' => $self->{cfg}->{app_id} );

    $self->{account} = uri_escape( $self->{cfg}->{user} );

lib/Bio/CIPRES.pm  view on Meta::CPAN

Takes a single argument (string containing the job handle/ID) and returns a
L<Bio::CIPRES::Job> object representing the appropriate job, or undef if not
found.

=back

=head1 TESTING

The distribution can be installed and tested in the usual ways. Note however,
that running the full test suite requires CIPRES REST credentials (not shipped
with package for obvious reasons). If a credentials file is found at
"$ENV{HOME}/.cipres", the full test suite will be run -- otherwise only
rudimentary tests will be run and most will be skipped.

=head1 CAVEATS AND BUGS

This is code is in alpha testing stage and the API is not guaranteed to be
stable.

Currently the use of UMBRELLA authentication is not implemented.

t/90-cipres.t  view on Meta::CPAN

use Test::More;
use Net::Ping;
use List::Util qw/first/;
use LWP::Simple;

use Bio::CIPRES;
use Bio::CIPRES::Error qw/:constants/;

# The first SKIP block contains limited tests which can be run without valid
# credentials. Mostly this checks that the server connection can be initiated
# and that the expected Error objects are returned on failure;

SKIP: {
   
    my $p = Net::Ping->new();

    # Check for necessary network connections and skip otherwise
    skip "CIPRES server not reachable", 7 if (! $p->ping($Bio::CIPRES::SERVER));
    skip "CIPRES httpd not reachable", 7
        if (! is_success(getprint("https://$Bio::CIPRES::SERVER")));

    # direct config with bogus credentials
    my $ua = Bio::CIPRES->new(
        user   => 'foo',
        pass   => 'bar',
        app_id => 'baz',
    );

    isa_ok( $ua, 'Bio::CIPRES' );
    ok( $ua->{cfg}->{user} eq 'foo' );

    # config from file with bogus credentials
    $ua = Bio::CIPRES->new(
        conf => 't/test_data/cipres.conf',
    );

    isa_ok( $ua, 'Bio::CIPRES' );
    ok( $ua->{cfg}->{user} eq 'bar' );

    # job submission should fail with authentication error
    eval { $ua->submit_job() };
    ok( $@, "submit_job threw expected exception" );

t/90-cipres.t  view on Meta::CPAN

    cmp_ok( $@,  '==', ERR_AUTHENTICATION, "exception == ERR_AUTHENTICATION");

}

# The second SKIP block contains more substantial tests that will run in a
# real config file is found. These will usually only be run on the developer's
# system.

SKIP: {

    # Skip the rest if no user credentials found
    skip "No valid credentials available", 21
        if ( ! -r "$ENV{HOME}/.cipres"
        && (! defined $ENV{CIPRES_USER} || ! defined $ENV{CIPRES_PASS}) );

    # additional tests for Bio::CIPRES::Error
    eval { Bio::CIPRES::Error->new() };
    ok($@ =~ /Undefined XML string in constructor/, "new Error missing XML" );
    eval { Bio::CIPRES::Error->new('foo') };
    ok($@ =~ /Start tag expected/, "new Error invalid XML" );

    # Good (testing) credentials
    my $ua = -r "$ENV{HOME}/.cipres"
      ? Bio::CIPRES->new(
            conf => "$ENV{HOME}/.cipres",
        )
      : Bio::CIPRES->new(
            user => $ENV{CIPRES_USER},
            pass => $ENV{CIPRES_PASS},
        );
    isa_ok( $ua, 'Bio::CIPRES' );