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ds.dataFrameSort.R
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ds.dataFrameSort.R
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#'
#' @title Sorting data frames in the server-side
#' @description Sorts a data frame using a specified sort key.
#' @details It sorts a specified
#' data.frame on the serverside using a sort key also on the server-side. The
#' sort key can either sit in the data.frame or outside it.
#' The sort key can be forced to be interpreted as alphabetic or numeric.
#'
#' When a numeric vector is sorted alphabetically, the order can look confusing.
#' For example, if we have a numeric vector to sort:\cr
#' vector.2.sort = c(-192, 76, 841, NA, 1670, 163, 147, 101, -112, -231, -9, 119, 112, NA)\cr
#'
#' When sorting numbers in an ascending (default) manner,
#' the largest negative numbers get ordered first
#' leading up to the largest positive numbers
#' and finally (by default in R) NAs being positioned at the end of the vector:\cr
#' numeric.sort = c(-231, -192, -112, -9, 76, 101, 112, 119, 147, 163, 841, 1670, NA, NA)\cr
#'
#' Instead, if the same vector is sorted alphabetically the the resultant vector is:
#'
#' alphabetic.sort = (-112, -192, -231, -9, 101, 112, 119, 147, 163, 1670, 76, 841, NA, NA)\cr
#'
#' Server function called: \code{dataFrameSortDS}.
#'
#' @param df.name a character string providing the name of the data frame
#' to be sorted.
#' @param sort.key.name a character string providing the name for the sort key.
#' @param sort.descending logical, if TRUE the data frame will be sorted.
#' by the sort key in descending order. Default = FALSE (sort order ascending).
#' @param sort.method a character string that specifies the method to be used
#' to sort the data frame. This can be set as
#' \code{"alphabetic"},\code{"a"} or \code{"numeric"}, \code{"n"}.
#' @param newobj a character string that provides the name for the output data frame
#' that is stored on the data servers. Default \code{dataframesort.newobj}.
#' where \code{df.name} is the first argument of \code{ds.dataFrameSort()}.
#' @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.dataFrameSort} returns the sorted data frame 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")
#'
#' # Sorting the data frame
#' ds.dataFrameSort(df.name = "D",
#' sort.key.name = "D$LAB_TSC",
#' sort.descending = TRUE,
#' sort.method = "numeric",
#' newobj = "df.sort",
#' datasources = connections[1]) #only the first Opal server is used ("study1")
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
#'
#' }
#' @author DataSHIELD Development Team
#' @export
ds.dataFrameSort<-function(df.name=NULL, sort.key.name=NULL, sort.descending=FALSE,
sort.method="default", newobj=NULL, datasources=NULL){
# if no opal login details are provided look for 'opal' objects in the environment
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
if(is.null(sort.method))
{
sort.method<-"default"
}
if(sort.method!="numeric"&&sort.method!="n"&&sort.method!="alphabetic"&&sort.method!="a")
{
sort.method<-"default"
}
if(sort.method=="n")
{
sort.method<-"numeric"
}
if(sort.method=="a")
{
sort.method<-"alphabetic"
}
if(is.null(sort.descending))
{
sort.descending<-FALSE
}
if(is.null(newobj)){
newobj<-"dataframesort.newobj"
}
#Call to assign function
calltext <- call("dataFrameSortDS", df.name, sort.key.name, sort.descending, sort.method)
datashield.assign(datasources, newobj, calltext)
###########################################################################################################
#DataSHIELD CLIENTSIDE MODULE: CHECK KEY DATA OBJECTS SUCCESSFULLY CREATED #
# #
#SET APPROPRIATE PARAMETERS FOR THIS PARTICULAR FUNCTION #
test.obj.name<-newobj #
# #
# #
# CALL SEVERSIDE FUNCTION #
calltext <- call("testObjExistsDS", test.obj.name) #
# #
# object.info<-opal::datashield.aggregate(datasources, calltext) #
object.info<-datashield.aggregate(datasources, calltext) #
# #
# CHECK IN EACH SOURCE WHETHER OBJECT NAME EXISTS #
# AND WHETHER OBJECT PHYSICALLY EXISTS WITH A NON-NULL CLASS #
num.datasources<-length(object.info) #
# #
# #
obj.name.exists.in.all.sources<-TRUE #
obj.non.null.in.all.sources<-TRUE #
# #
for(j in 1:num.datasources){ #
if(!object.info[[j]]$test.obj.exists){ #
obj.name.exists.in.all.sources<-FALSE #
} #
if(is.null(object.info[[j]]$test.obj.class) || object.info[[j]]$test.obj.class=="ABSENT"){ # #
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<-opal::datashield.aggregate(datasources, calltext) #
studyside.message<-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, #
studyside.messages=studyside.message)) #
} #
#
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 CORRECTLY MODULE #
###########################################################################################################
}
#ds.dataFrameSort