NAME

Bio::Phylo::PhyloWS::Service::UbioNameBank - PhyloWS service wrapper for uBio NameBank records

SYNOPSIS

# inside a CGI script:
use CGI;
use Bio::Phylo::PhyloWS::Service::UbioNameBank;

# obtain a key code from http://www.ubio.org/index.php?pagename=form
# and define it as an environment variable:
$ENV{'UBIO_KEYCODE'} = '******';
my $cgi = CGI->new;
my $service = Bio::Phylo::PhyloWS::Service::UbioNameBank->new( '-base_uri' => $url );
$service->handle_request($cgi);

DESCRIPTION

This is an example implementation of a PhyloWS service. The service wraps around some of the uBio XML services described at http://www.ubio.org/index.php?pagename=xml_services.

Record lookups for this service return project objects that capture the RDF metadata for a single NameBank record as semantic annotations to a taxon object. An example of the sort of metadata that can be expected is shown here: http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:2481730

Queries on this service run namebank searches and return project objects that capture the NameBank search XML (an example is shown here: http://www.ubio.org/webservices/examples/namebank_search.xml) as semantic annotations to taxon objects.

URLs to this service that specify format=html in the query string redirect to web pages on the uBio site at http://www.ubio.org. The redirect URLs either point to search result listings or to NameBank record pages, depending on whether the redirect is for a record query or a record lookup, respectively.

UBIO KEY CODES

Some functionality of this service requires a key code to the uBio API. Such key codes can be obtained from http://www.ubio.org/index.php?pagename=form. When deploying this service on a web server (e.g. as shown in the SYNOPSIS) this code must be provided in an environment variable called UBIO_KEYCODE.

METHODS

ACCESSORS

get_record()

Gets a uBio namebank record by its id

Type    : Accessor
Title   : get_record
Usage   : my $record = $obj->get_record( -guid => $guid );
Function: Gets a uBio namebank record by its id
Returns : Bio::Phylo::Project
Args    : Required: -guid => $guid
Comments: For the $guid argument, this method only cares
          whether the last part of the argument is a series
          of integers, which are understood to be namebank
          identifiers

get_authority()

Gets the authority prefix (e.g. TB2) for the implementing service

Type    : Authority
Title   : get_authority
Usage   : my $auth = $obj->get_authority;
Function: Gets authority prefix
Returns : 'uBioNB'
Args    : None

get_supported_formats()

Gets an array ref of supported formats

Type    : Accessor
Title   : get_supported_formats
Usage   : my @formats = @{ $obj->get_supported_formats };
Function: Gets an array ref of supported formats
Returns : [ qw(nexml nexus html json) ]
Args    : NONE

get_redirect()

Gets a redirect URL if relevant

Type    : Accessor
Title   : get_redirect
Usage   : my $url = $obj->get_redirect;
Function: Gets a redirect URL if relevant
Returns : String
Args    : $cgi
Comments: This method is called by handle_request so that
          services can 303 redirect a record lookup to 
          another URL. By default, this method returns 
          undef (i.e. no redirect), but if this implementation
          is called to handle a request that specifies 
          'format=html' the request is forwarded to the
          appropriate page on the http://www.ubio.org website

get_query_result()

Gets a query result and returns it as a project object

Type    : Accessor
Title   : get_query_result
Usage   : my $proj = $obj->get_query_result($query);
Function: Gets a query result
Returns : Bio::Phylo::Project
Args    : A simple query string for a namebank search
Comments: The $query is a simple CQL level 0 term-only query

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63