Bio::Phylo::PhyloWS::Service - Base class for phylogenetic web services
# inside a CGI script:
use CGI;
use Bio::Phylo::PhyloWS::Service::${child};
my $service = Bio::Phylo::PhyloWS::Service::${child}->new( '-url' => $url );
$service->handle_request(CGI->new);
This is the base class for services that implement the PhyloWS (http://evoinfo.nescent.org/PhyloWS) recommendations. Such services should subclass this class and implement any relevant abstract methods. Examples of this are Bio::Phylo::PhyloWS::Service::Tolweb and Bio::Phylo::PhyloWS::Service::Ubio.
PhyloWS services are web services for phylogenetics that provide two types of functionality:
Services that implement record lookups are services that know how to process URL requests of the form /phylows/$object_type/$authority:$identifier?format=$format, where $object_type is a string representing the type of object that is returned, e.g. 'tree', 'matrix', 'taxon', etc., $authority is a naming authority such as TB2 for TreeBASE2, $identifier is a local identifier for the object, for example an accession number, and $format is a serialization format such as 'nexml'.
In order to provide this functionality, subclasses of this class must implement a method called get_record which is passed at least a named -guid argument that provides the local identifier. The get_record method must return a Bio::Phylo::Project object, which is subsequently serialized in the requested format by the handle_request method provided here.
Services that implement record searches are services that know how to process URL requests of the form /phylows/$object_type/find?query=$query&format=$format, where $object_type is a string representing the type of object to search for, $query is a CQL query (http://www.loc.gov/standards/sru/specs/cql.html), and $format is the serialization format in which the returned results are represented.
In order to provide this functionality, subclasses of this class must implement a method called get_query_result, which is passed the $query parameter and which must return a Bio::Phylo::Project object that combines the search results (e.g. in a single taxa block for taxon searches).
CQL has different levels of support, services may only implement certain levels of support. The example services Bio::Phylo::PhyloWS::Service::Tolweb and Bio::Phylo::PhyloWS::Service::Ubio only proved Level 0, term-only support, meaning that $query is simply a term such as Homo+sapiens.
Child classes that implement some or all of the functionality described above can subsequently be made operational on a web server by calling them from a simple CGI script as shown in the SYNOPSIS section, where $child must be substituted by the actual class name of the child class (e.g. Tolweb). The $url parameter that is passed to the constructor is usually simply the URI of the CGI script, i.e. the environment variable $ENV{'SCRIPT_URI'} under most standard HTTP servers.
Type : Request handler Title : handle_request Usage : $service->handle_request($cgi); Function: Handles a service request Returns : prints out response and exits Args : Required: a CGI.pm object
Gets a phylows result, either a record lookup or a query result, depending on the internal state of the service object
Type : Accessor Title : get_result Usage : my $proj = $obj->get_result; Function: Gets a phylows result Returns : Bio::Phylo::Project Args : None Comments:
Gets a phylows record by its id
Type : Abstract Accessor
Title : get_record
Usage : my $record = $obj->get_record( -guid => $guid );
Function: Gets a phylows record by its id
Returns : Bio::Phylo::Project
Args : Required: -guid => $guid,
Optional: -format => $format
Comments: This is an ABSTRACT method that needs to be implemented
by a child class
Gets a phylows cql query result
Type : Abstract Accessor
Title : get_query_result
Usage : my $result = $obj->get_query_result( $query );
Function: Gets a query result
Returns : Bio::Phylo::Project
Args : Required: $query
Comments: This is an ABSTRACT method that needs to be implemented
by a child class
Gets an array ref of supported formats
Type : Abstract Accessor
Title : get_supported_formats
Usage : my @formats = @{ $obj->get_supported_formats };
Function: Gets an array ref of supported formats
Returns : ARRAY
Args : NONE
Comments: This is an ABSTRACT method that needs to be implemented
by a child class
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)
Gets an RSS1.0/XML representation of a phylows record
Type : Accessor
Title : get_description
Usage : my $desc = $obj->get_description;
Function: Gets an RSS1.0/XML representation of a phylows record
Returns : String
Args : None
Comments: This method creates a representation of a single record
(i.e. the service's base url + the record's guid)
that can be serialized in whichever formats are
supported
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
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
