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Bio::Phylo::PhyloWS::SUsercContributedPPerl:DPhyloWS::Service::UbioNameBank(3)

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>

perl v5.24.1			 Bio::Phylo::PhyloWS::Service::UbioNameBank(3)

NAME | SYNOPSIS | DESCRIPTION | UBIO KEY CODES | METHODS | SEE ALSO | CITATION

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