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Man Pages
Bio::Phylo::PhyloWS::Service(3) User Contributed Perl Documentation Bio::Phylo::PhyloWS::Service(3)
 

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:
Record lookup
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 $format is a serialization format such as 'nexml'.
In order to provide this functionality, subclasses of this class must implement a method called "get_record" which is passed at least a named "-guid" argument that provides the local identifier. The "get_record" method must return a Bio::Phylo::Project object, which is subsequently serialized in the requested format by the "handle_request" method provided here.
Record search
Services that implement record searches are services that know how to process URL requests of the form "/phylows/$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.

handle_request()
 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
    

get_result()
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:
    
get_record()
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
    
get_query_result()
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
    
get_supported_formats()
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
    
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)
    
get_description()
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>
2017-10-30 perl v5.28.1

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