Bio::Tools::Run::AnalysisFactory soap
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools
Package variables
Privates (from "my" definitions)
$res = shift
$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"
Included modules
Bio::Tools::Run::Analysis
Bio::Tools::Run::AnalysisFactory
SOAP::Lite on_fault => sub { my $soap = shift
Inherit
Bio::Tools::Run::AnalysisFactory
Synopsis
Do not use this object directly, it is recommended to access it and use
it through the Bio::Tools::Run::AnalysisFactory module:
  use Bio::Tools::Run::AnalysisFactory;
  my $list = Bio::Tools::Run::AnalysisFactory->new(-access => 'soap')
     ->available_analyses;
  print join ("\n", @$list) . "\n";
Description
All public methods are documented in the interface module
Bio::Factory::AnalysisI.
Methods
BEGIN Code
_initializeDescriptionCode
_clean_msg
No description
Code
available_categories
No description
Code
available_analyses
No description
Code
create_analysis
No description
Code
Methods description
_initializecode    nextTop
 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 object method (never as
a 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 new method, not this one.
    -location
    A URL (also called an endpoint) defining where is located a Web Service
functioning for this object.
    Default is 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
http://localhost:8080/axis/services.
    -httpproxy
    In addition to the 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 http://server:port.
There is no default value.
    -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.
Methods code
BEGINTop
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');
}
_initializedescriptionprevnextTop
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'});
	}
    }
}
_clean_msgdescriptionprevnextTop
sub _clean_msg {
    my ($msg) = @_;
    $msg =~ s/^org\.embl\.ebi\.SoaplabShare\.SoaplabException\:\s*//;
    $msg;
}

# String[] getAvailableCategories()
}
available_categoriesdescriptionprevnextTop
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)
}
available_analysesdescriptionprevnextTop
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)
}
create_analysisdescriptionprevnextTop
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);
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Martin Senger (martin.senger@gmail.com)
COPYRIGHTTop
Copyright (c) 2003, Martin Senger and EMBL-EBI.
All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
    *
http://www.ebi.ac.uk/soaplab/Perl_Client.html
BUGS AND LIMITATIONSTop
None known at the time of writing this.
APPENDIXTop
The main documentation details are in
Bio::Factory::AnalysisI.
VERSION and RevisionTop
 Usage   : print $Bio::Tools::Run::AnalysisFactory::soap::VERSION;
           print $Bio::Tools::Run::AnalysisFactory::soap::Revision;