NAME

Bio::Phylo::PhyloWS::Service::Tolweb - PhyloWS service wrapper for Tree of Life

SYNOPSIS

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

 my $cgi = CGI->new;
 my $service = Bio::Phylo::PhyloWS::Service::Tolweb->new( '-url' => $url );
 $service->handle_request($cgi);

DESCRIPTION

This is an example implementation of a PhyloWS service. The service wraps around the Tree of Life XML services described at http://tolweb.org/tree/home.pages/downloadtree.html.

When doing a record lookup this service returns project objects that include the focal node (identified by its PhyloWS ID) and the nearest child and parent nodes that have web pages.

When querying, this service returns a project object with one taxa block containing zero or more taxon objects that matched the query.

When URLs to this service specify format=html in the query string, this service returns redirect URLs to web pages on the Tree of Life web project site at http://tolweb.org. The redirect URLs either point to search result listings or to node pages, depending on whether the redirect is for a record query or a record lookup, respectively.

METHODS

ACCESSORS

get_record()

Gets a tolweb record by its id

 Type    : Accessor
 Title   : get_record
 Usage   : my $record = $obj->get_record( -guid => $guid );
 Function: Gets a tolweb 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 the node
           identifier in the Tree of Life

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://tolweb.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 group search
 Comments: The $query is a simple CQL level 0 term-only query

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 newick html json phyloxml rss1) ]
 Args    : NONE

get_authority()

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

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

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