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lib/Bio/Tools/Run/AnalysisFactory/soap.pm  view on Meta::CPAN

	my $soap = shift;
	my $res = shift;
	my $msg =
	    ref $res ?
		"--- SOAP FAULT ---\n" .
		'faultcode:   ' . $res->faultcode . "\n" .
		'faultstring: ' . Bio::Tools::Run::AnalysisFactory::soap::_clean_msg ($res->faultstring)
	      : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
        Bio::Tools::Run::AnalysisFactory::soap->throw ($msg);
    }
;

@ISA = qw(Bio::Tools::Run::AnalysisFactory);

BEGIN {
    $Revision = q[$Id$];

    # where to go...
    $DEFAULT_LOCATION = 'http://www.ebi.ac.uk/soaplab/services';

    # ...and what to find there
    # (this is a list of service names available from the given location;
    #  those that do not exist are ignored; if none exists then only
    #  location - without any service name appended - is used)
    @DEFAULT_DIR_SERVICE = ('AnalysisFactory', 'GowlabFactory');
}

# -----------------------------------------------------------------------------

=head2 _initialize

 Usage   : my $factory = Bio::Tools::Run::AnalysisFactory->new(@args);
           (_initialize is internally called from the 'new()' method)
 Returns : nothing interesting
 Args    : This module recognises and uses following arguments:
             -location
             -httpproxy
             -soap
	   Additionally, the main module Bio::Tools::Run::AnalysisFactory
           recognises also:
             -access

It populates calling object with the given arguments, and then - for
some attributes and only if they are not yet populated - it assigns
some default values.

This is an actual new() method (except for the real object creation
and its blessing which is done in the parent class Bio::Root::Root in
method _create_object).

Note that this method is called always as an I<object> method (never as
a I<class> method) - and that the object who calls this method may
already be partly initiated (from Bio::Tools::Run::AnalysisFactory::new method);
so if you need to do some tricks with the 'class invocation' you need to
change Bio::Tools::Run::AnalysisFactory I<new> method, not this one.

=over

=item -location

A URL (also called an I<endpoint>) defining where is located a Web Service
functioning for this object.

Default is C<http://www.ebi.ac.uk/soaplab/services> (a service running
at European Bioinformatics Institute on top of most of the EMBOSS
analyses, and on top of few others).

For example, if you run your own Web Service using Java(TM) Apache Axis
toolkit, the location might be something like
C<http://localhost:8080/axis/services>.

=item -httpproxy

In addition to the I<location> parameter, you may need
to specify also a location/URL of an HTTP proxy server
(if your site requires one). The expected format is C<http://server:port>.
There is no default value.

=item -soap

Defines your own SOAP::Lite object. Useful if you need finer-grained
access to many features and attributes of the wonderful Paul Kulchenko's
module.

=back

=cut

# '

sub _initialize {
    my ($self, @args) = @_;
    
    # make a hashtable from @args
    my %param = @args;
    @param { map { lc $_ } keys %param } = values %param; # lowercase keys

    # copy all @args into this object (overwriting what may already be
    # there) - changing '-key' into '_key'
    my $new_key;
    foreach my $key (keys %param) {
	($new_key = $key) =~ s/^-/_/;
	$self->{ $new_key } = $param { $key };
    }

    # finally add default values for those keys who have default value
    # and who are not yet in the object
    $self->{'_location'} = $DEFAULT_LOCATION unless $self->{'_location'};

    # create a SOAP object which will do the main job
    # ('uri' (representing a service name) will be added before each call) 
    unless ($self->{'_soap'}) {
	if (defined $self->{'_httpproxy'}) {
	    $self->{'_soap'} = SOAP::Lite
		-> proxy ($self->{'_location'},
			  proxy => ['http' => $self->{'_httpproxy'}]);
	} else {
	    $self->{'_soap'} = SOAP::Lite
		-> proxy ($self->{'_location'});
	}
    }

lib/Bio/Tools/Run/AnalysisFactory/soap.pm  view on Meta::CPAN

sub available_categories {
    my ($self) = @_;
    my $soap = $self->{'_soap'};

    my @result = ();
    my $okay = 0;
    foreach my $service_name (@DEFAULT_DIR_SERVICE) {
	$soap-> uri ($service_name);
	eval {
	    push (@result, @{ $soap->getAvailableCategories->result });
	};
	$okay = 1 unless $@;
    }
    return $soap->getAvailableCategories->result unless $okay;
    \@result;
}

# String[] getAvailableAnalyses()
# String[] getAvailableAnalysesInCategory (String categoryName)
sub available_analyses {
    my ($self, $category) = @_;
    my $soap = $self->{'_soap'};

    my @result = ();
    my $okay = 0;

    if (defined $category) {
	foreach my $service_name (@DEFAULT_DIR_SERVICE) {
	    $soap-> uri ($service_name);
	    eval {
		push (@result, @{ $soap->getAvailableAnalysesInCategory (SOAP::Data->type (string => $category))->result });
	    };
	    $okay = 1 unless $@;
	}
	return
	    $soap->getAvailableAnalysesInCategory (SOAP::Data->type (string => $category))
	    ->result unless $okay;
	\@result;

    } else {
	foreach my $service_name (@DEFAULT_DIR_SERVICE) {
	    $soap-> uri ($service_name);
	    eval {
		push (@result, @{ $soap->getAvailableAnalyses->result });
	    };
	    $okay = 1 unless $@;
	}
	return
	    $soap->getAvailableAnalyses->result unless $okay;
	\@result;
    }
}

# String getServiceLocation (String analysisName)
sub create_analysis {
    my ($self, $name) = @_;

    # service name
    my @name  = ('-name', $name) if $name;

    # ask for an endpoint
    my $soap = $self->{'_soap'};
    my $location;
    foreach my $service_name (@DEFAULT_DIR_SERVICE) {
	$soap-> uri ($service_name);
	eval {
	    $location = $soap->getServiceLocation (SOAP::Data->type (string => $name))->result;
	};
	last if defined $location;
    }
    unless (defined $location) {
	$location = $soap->getServiceLocation (SOAP::Data->type (string => $name)) ->result;
    }
    my @location  = ('-location', $location) if $location;

    # share some of my properties with the new Bio::Analysis object
    my @access  = ('-access', $self->{'_access'}) if $self->{'_access'};
    my @httpproxy = ('-httpproxy', $self->{'_httpproxy'}) if $self->{'_httpproxy'};

    Bio::Tools::Run::Analysis->new(@name, @location, @httpproxy, @access);
}



=head2 VERSION and Revision

 Usage   : print $Bio::Tools::Run::AnalysisFactory::soap::VERSION;
           print $Bio::Tools::Run::AnalysisFactory::soap::Revision;

=cut


1;
__END__