R/ds.asNumeric.R

In datashield/dsBaseClient: DataSHIELD Client Functions

#' 
#' @title Converts a server-side R object into a numeric class 
#' @description Coerces an R object into a numeric class. 
#' This function is based on the native R function \code{as.numeric}.
#' @details This function is based on the native R function \code{as.numeric}.
#' However, it behaves differently with some specific classes of variables. For example, if the input 
#' object is of class factor, it first converts its values into characters and then convert those to
#' numerics. This behavior is important for the case where the input object is of class factor having
#' numbers as levels. In that case, the native R 
#' \code{as.numeric} function returns the underlying level codes and not the values as numbers. 
#' For example \code{as.numeric} in R converts the factor vector: \cr
#' 0 1 1 2 1 0 1 0 2 2 2 1 \cr
#' Levels: 0 1 2 \cr
#' to the following numeric vector:
#' 1 2 2 3 2 1 2 1 3 3 3 2 \cr
#' In contrast DataSHIELD converts an input factor with numeric 
#' levels to its original numeric values.
#' 
#' Server function called: \code{asNumericDS}
#' 
#' @param x.name a character string providing the name of the input object to be coerced to 
#' a numeric. 
#' @param newobj a character string that provides the name for the output object
#'  that is stored on the data servers. Default \code{asnumeric.newobj}. 
#' @param datasources a list of \code{\link{DSConnection-class}} 
#' objects obtained after login. If the \code{datasources} argument is not specified
#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
#' @return \code{ds.asNumeric} returns the R object converted into a numeric class
#' that is written to the server-side. Also, two validity messages are returned 
#' to the client-side indicating the name of the \code{newobj} which 
#' has been created in each data source and if 
#' it is in a valid form.
#' @examples 
#' \dontrun{
#'   ## Version 6, for version 5 see the Wiki
#'   
#'   # connecting to the Opal servers
#' 
#'   require('DSI')
#'   require('DSOpal')
#'   require('dsBaseClient')
#'
#'   builder <- DSI::newDSLoginBuilder()
#'   builder$append(server = "study1", 
#'                  url = "http://192.168.56.100:8080/", 
#'                  user = "administrator", password = "datashield_test&", 
#'                  table = "CNSIM.CNSIM1", driver = "OpalDriver")
#'   builder$append(server = "study2", 
#'                  url = "http://192.168.56.100:8080/", 
#'                  user = "administrator", password = "datashield_test&", 
#'                  table = "CNSIM.CNSIM2", driver = "OpalDriver")
#'   builder$append(server = "study3",
#'                  url = "http://192.168.56.100:8080/", 
#'                  user = "administrator", password = "datashield_test&", 
#'                  table = "CNSIM.CNSIM3", driver = "OpalDriver")
#'   logindata <- builder$build()
#'   
#'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
#'   
#'   # Converting the R object into a numeric class
#'   ds.asNumeric(x.name = "D$LAB_TSC",
#'                   newobj = "num.obj",
#'                   datasources = connections[1]) #only the first Opal server is used ("study1")
#'   ds.class(x = "num.obj", datasources = connections[1]) 
#'                 
#'   # Clear the Datashield R sessions and logout                 
#'   datashield.logout(connections) 
#'   
#' }   
#' @author DataSHIELD Development Team
#' @export
#' 
ds.asNumeric <- function(x.name=NULL, newobj=NULL, datasources=NULL){

  # look for DS connections
  if(is.null(datasources)){
    datasources <- datashield.connections_find()
  }

  # ensure datasources is a list of DSConnection-class
  if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){
    stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE)
  }

  if(is.null(x.name)){
    stop("Please provide the name of the input vector!", call.=FALSE)
  }
  
  # check if the input object is defined in all the studies
  isDefined(datasources, x.name)

  # create a name by default if user did not provide a name for the new variable
  if(is.null(newobj)){
    newobj <- "asnumeric.newobj"
  }

  # call the server side function that does the job
  calltext <- call("asNumericDS", x.name)
  DSI::datashield.assign(datasources, newobj, calltext)


#############################################################################################################
#DataSHIELD CLIENTSIDE MODULE: CHECK KEY DATA OBJECTS SUCCESSFULLY CREATED                                  #
																											#
#SET APPROPRIATE PARAMETERS FOR THIS PARTICULAR FUNCTION                                                 	#
test.obj.name<-newobj																					 	#
																											#																											#
																											#
# CALL SEVERSIDE FUNCTION                                                                                	#
calltext <- call("testObjExistsDS", test.obj.name)													 	#
																											#
object.info<-DSI::datashield.aggregate(datasources, calltext)												 	#
																											#
# CHECK IN EACH SOURCE WHETHER OBJECT NAME EXISTS														 	#
# AND WHETHER OBJECT PHYSICALLY EXISTS WITH A NON-NULL CLASS											 	#
num.datasources<-length(object.info)																	 	#
																											#
																											#
obj.name.exists.in.all.sources<-TRUE																	 	#
obj.non.null.in.all.sources<-TRUE																		 	#
																											#
for(j in 1:num.datasources){																			 	#
	if(!object.info[[j]]$test.obj.exists){																 	#
		obj.name.exists.in.all.sources<-FALSE															 	#
		}																								 	#
	if(is.null(object.info[[j]]$test.obj.class) || ("ABSENT" %in% object.info[[j]]$test.obj.class)){														 	#
		obj.non.null.in.all.sources<-FALSE																 	#
		}																								 	#
	}																									 	#
																											#
if(obj.name.exists.in.all.sources && obj.non.null.in.all.sources){										 	#
																											#
	return.message<-																					 	#
    paste0("A data object <", test.obj.name, "> has been created in all specified data sources")		 	#
																											#
																											#
	}else{																								 	#
																											#
    return.message.1<-																					 	#
	paste0("Error: A valid data object <", test.obj.name, "> does NOT exist in ALL specified data sources")	#
																											#
	return.message.2<-																					 	#
	paste0("It is either ABSENT and/or has no valid content/class,see return.info above")				 	#
																											#
	return.message.3<-																					 	#
	paste0("Please use ds.ls() to identify where missing")												 	#
																											#
																											#
	return.message<-list(return.message.1,return.message.2,return.message.3)							 	#
																											#
	}																										#
																											#
	calltext <- call("messageDS", test.obj.name)															#
    studyside.message<-DSI::datashield.aggregate(datasources, calltext)											#
																											#
	no.errors<-TRUE																							#
	for(nd in 1:num.datasources){																			#
		if(studyside.message[[nd]]!="ALL OK: there are no studysideMessage(s) on this datasource"){			#
		no.errors<-FALSE																					#
		}																									#
	}																										#
																											#
																											#
	if(no.errors){																							#
	validity.check<-paste0("<",test.obj.name, "> appears valid in all sources")							    #
	return(list(is.object.created=return.message,validity.check=validity.check))						    #
	}																										#
																											#
if(!no.errors){																								#
	validity.check<-paste0("<",test.obj.name,"> invalid in at least one source. See studyside.messages:")   #
	return(list(is.object.created=return.message,validity.check=validity.check,					    		#
	            studyside.messages=studyside.message))			                                            #
	}																										#
																											#
#END OF CHECK OBJECT CREATED CORECTLY MODULE															 	#
#############################################################################################################

}
# ds.asNumeric