NAME

BiomobyUtils


DESCRIPTION

Utilities library


AUTHORS

 Sebastien.Carrere@toulouse.inra.fr 
 Sebastien.Letort@toulouse.inra.fr


METHODS

function GetRegisteredInputArticleNames

 Title        : GetRegisteredInputArticleNames

procedure Exit

 Title        : Exit
 Usage        : &Exit($message)
 Prerequisite : none
 Function     : print a message on STDERR and exit program
 Returns      : none 
 Args         : $message Message to print out
 Globals      : none

function SetMobyCentralENV

 Title        : SetMobyCentralENV
 Usage        : $mobycentral_name = &SetMobyCentralENV($rh_param,$central_conf)
 Prerequisite : none
 Function     : Parse config file to get MobyCentral(s) to connect to
                Update %ENV with correct MOBY_URI and MOBY_SERVER variables
 Returns      : $mobycentral_name: mobycentral name as defined in configuration file
 Args         : $rh_param: ParamParser structure
                $central_conf: central configuration file
 Globals      : none

function ReturnHashWhichCentralConf

 Title        : ReturnHashWhichCentralConf
 Usage        : $rh_which_central_conf = &ReturnHashWhichCentralConf($rh_param,\@a_central_conf)
 Prerequisite : none
 Function     : Parse central(s) config file to get configuration file associated to a mobycentral name 
 Returns      : $rh_which_central_conf: an hash ref
 Args         : $rh_param: ParamParser structure
                $ra_central_conf: reference to the list of configuration files
 Globals      : none

function AddToDispatcher

 Title        : AddToDispatcher
 Usage        : &AddToDispatcher($dispatcher_url,$service_name)
 Prerequisite : none
 Function     : Add service name to the file used by dispatcher CGI to 
                construct hash of services available
 Returns      : undef if OK
 Args         : $dispatcher_url: CGI used by service as dispatcher
                $service_name: service name
                $module_name: module containing your Service sub used in LIPMServices.pm BEGIN BLOCK
 Globals      : none

function RemoveFromDispatcher

 Title        : RemoveFromDispatcher
 Usage        : &RemoveFromDispatcher($dispatcher_url,$service_name)
 Prerequisite : none
 Function     : Remove service name from the file used by dispatcher CGI to 
                construct hash of services available
 Returns      : undef if OK
 Args         : $dispatcher_url: CGI used by service as dispatcher
                $service_name: service name
 Globals      : none

function GetDispatcherServicesFile

 Title        : GetDispatcherServicesFile
 Usage        : &GetDispatcherServicesFile($dispatcher_url)
 Prerequisite : none
 Function     : From a dispatcher URL, get the file name used by the
                dispatcher CGI to build hash of available services
 Returns      : $services_file: file containing services names
 Args         : $dispatcher_url: CGI used by service as dispatcher
 Globals      : none

function InitializeServiceParameters

 Title        : InitializeServiceParameters
 Usage        : &InitializeServiceParameters($rh_param)
 Prerequisite : none
 Function     : From service configuration file, build a service 
                parameters strucure initialized with default values
 Returns      : \%h_param_service: Hash ref for service parameters strucure (param1 => default, param2 => default, ...)
 Args         : $rh_param: ParamParser Structure
 Globals      : none

function IsTheCorrectObject

 Title        : IsTheCorrectObject
 Usage        : &IsTheCorrectObject($tested_nodename,$object_for_service)
 Prerequisite : none
 Function     : Test if a XML nodeName is the one requested
                Usefull for data extraction (is the node tested a FASTA node ?)
                This function gives priority to Canadian Ontology server, then Local.
 Returns      : boolean
 Args         : $tested_nodename: XML node tested
                $object_for_service: requested node
 Globals      : none

function _ISA_by_carrere

 Title        : _ISA_by_carrere
 Usage        : &_ISA_by_carrere($central_instance, $tested_nodename,$object_for_service)
 Prerequisite : none
 Function     : Test if an object ISA another (recursively).
                I use this home-made sub because ISA sub from PERL-API
                use only the Canadian OntologyServer.
                So if our object is not registered in Canadian Central, ISA 
                doesn't work ...
 Returns      : boolean
 Args         : $central_instance: MOBY::Client::Central->new object
                $tested_nodename: XML node tested
                $object_for_service: requested node
 Globals      : none

function GetNodeContent