R/ds.matrixTranspose.R

In datashield/dsBaseClient: DataSHIELD Client Functions

#' @title Transposes a server-side matrix
#' @description Transposes a matrix and writes the output to the server-side
#' @details This operation converts matrix
#' \code{A} to matrix \code{C} where element \code{C[i,j]} of 
#' matrix \code{C} equals element \code{A[j,i]} of matrix
#' \code{A}. Matrix \code{A}, therefore, has the same number 
#' of rows as matrix \code{C} has columns and vice versa.
#' 
#' Server function called: \code{matrixTransposeDS}
#' 
#' @param M1 a character string specifying the name of the matrix.  
#' @param newobj a character string that provides the name for the output 
#' variable that is stored on the data servers. 
#' Default \code{matrixtranspose.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.matrixTranspose} returns to the server-side the transpose matrix. 
#' Also, two validity messages are returned to the client-side 
#' indicating whether the new object has been created in each data source and if so whether
#' it is in a valid form. 
#' @author DataSHIELD Development Team
#' @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") 
#'   
#'             
#'   #Example 1: Transpose the server-side matrix
#'   
#'   #Create the server-side vector 
#'   
#'   ds.rUnif(samp.size = 9,
#'            min = -10.5,
#'            max = 10.5,
#'            newobj = "ss.vector.9",
#'            seed.as.integer = 5575,
#'            force.output.to.k.decimal.places = 0,
#'            datasources = connections)
#'            
#'   #Create the server-side matrix
#'            
#'   ds.matrix(mdata = "ss.vector.9",
#'             from = "serverside.vector",
#'             nrows.scalar = 3,
#'             ncols.scalar = 4,
#'             byrow = TRUE,
#'             newobj = "matrix",
#'             datasources = connections)
#'    
#'   #Transpose the matrix
#'   
#'   ds.matrixTranspose(M1 = "matrix",
#'                      newobj = "matrix.transpose",
#'                      datasources = connections)
#'   
#'   # clear the Datashield R sessions and logout
#'   datashield.logout(connections)
#' }
#' @export
#'
ds.matrixTranspose<-function(M1=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)
  }

  # check if user has provided the name of matrix representing M1
  if(is.null(M1)){
    return("Error: Please provide the name of the matrix representing M1")
  }

  # if no value spcified for output object, then specify a default
  if(is.null(newobj)){
    newobj <- "matrixtranspose.newobj"
  }

# CALL THE MAIN SERVER SIDE FUNCTION
  calltext <- call("matrixTransposeDS", M1)
  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																					 	#
																											#
#TRACER																									 	#
#return(test.obj.name)																					 	#
#}                                                                                   					 	#
																											#
																											#
# 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.matrixTranspose