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ds.seq.R
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ds.seq.R
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#' @title Generates a sequence in the server-side
#' @description This function generates a sequence for given parameters
#' on the server-side.
#' @details This function is similar to a native R function \code{seq()}.
#' It creates a flexible range of sequence vectors that can then be used to help
#' manage and analyse data.
#'
#' \strong{Note}: the combinations of arguments that are not allowed
#' for the function \code{seq} in native R are also prohibited in \code{ds.seq}.
#'
#' To be specific, \code{FROM.value.char} argument
#' defines the start of the sequence and \code{BY.value.char} defines how
#' the sequence is incremented (or decremented) at each step. But where the
#' sequence stops can be defined in three different ways:\cr
#' (1) \code{TO.value.char} indicates the terminal value of the sequence.
#' For example, \code{ds.seq(FROM.value.char = "3", BY.value.char = "2",
#' TO.value.char = "7")} creates the sequence \code{3,5,7} on the server-side.\cr
#' (2) \code{LENGTH.OUT.value.char} indicates the length of the sequence.
#' For example, \code{ds.seq(FROM.value.char = "3", BY.value.char = "2",
#' LENGTH.OUT.value.char = "7")}
#' creates the sequence \code{3,5,7,9,11,13,15} on the server-side.\cr
#' (3) \code{ALONG.WITH.name} specifies the name of a variable on the server-side,
#' such that the sequence in each study will be equal in length to that variable.
#' For example, \code{ds.seq(FROM.value.char = "3", BY.value.char = "2",
#' ALONG.WITH.name = "var.x")}
#' creates a sequence such that if \code{var.x} is of length 100 in study 1 the
#' sequence written to study 1 will be \code{3,5,7,...,197,199,201} and if \code{var.x} is
#' of length 4 in study 2, the sequence written to study 2 will be \code{3,5,7,9}.\cr
#' Only one of the three arguments: \code{TO.value.char},
#' \code{LENGTH.OUT.value.char} and \code{ALONG.WITH.name} can be non-null in any one call.
#'
#' In \code{LENGTH.OUT.value.char} argument if you specify a number with a decimal point but
#' in character form this result in a sequence \code{length(integer) + 1}.
#' For example, \code{LENGTH.OUT.value.char = "1000.0001"}
#' generates a sequence of length 1001.
#'
#' Server function called: \code{seqDS}
#' @param FROM.value.char an integer or a number in character from specifying
#' the starting value for the sequence.
#' Default \code{"1"}.
#' @param TO.value.char an integer or a number in character from specifying
#' the terminal value for the sequence.
#' Default NULL.
#' For more information see \strong{Details}.
#' @param BY.value.char an integer or a number in character from specifying
#' the value to increment each step in the sequence.
#' Default \code{"1"}.
#' @param LENGTH.OUT.value.char an integer or a number in character from specifying
#' the length of the sequence at which point
#' its extension should be stopped.
#' Default NULL.
#' For more information see \strong{Details}.
#' @param ALONG.WITH.name a character string specifying the name of a standard vector
#' to generate a vector of the same length.
#' For more information see \strong{Details}.
#' @param newobj a character string that provides the name for the output variable
#' that is stored on the data servers. Default \code{seq.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.seq} returns to the server-side the generated sequence.
#' 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()
#'
#' # Log onto the remote Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' #Create 3 different sequences
#'
#' ds.seq(FROM.value.char = "1",
#' BY.value.char = "2",
#' TO.value.char = "7",
#' newobj = "new.seq1",
#' datasources = connections)
#'
#'
#' ds.seq(FROM.value.char = "4",
#' BY.value.char = "3",
#' LENGTH.OUT.value.char = "10",
#' newobj = "new.seq2",
#' datasources = connections)
#'
#' ds.seq(FROM.value.char = "2",
#' BY.value.char = "5",
#' ALONG.WITH.name = "D$GENDER",
#' newobj = "new.seq3",
#' datasources = connections)
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
#' }
#' @export
ds.seq<-function(FROM.value.char = "1", BY.value.char = "1", TO.value.char=NULL, LENGTH.OUT.value.char = NULL, ALONG.WITH.name=NULL,
newobj="newObj", datasources=NULL) {
###datasources
# 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)
}
###FROM.value.char
# check FROM.value.char is valid
FROM.valid<-1
if(!(is.null(FROM.value.char))) {
if(!is.character(FROM.value.char))FROM.valid<-0
if(!is.numeric(eval(parse(text=FROM.value.char))))FROM.valid<-0
}
if(!FROM.valid){
return("Error: If FROM.value.char is non.NULL, it must be a real number in inverted commas eg '-3.7' or '0'")
}
###TO.value.char
# check TO.value.char is valid
TO.valid<-1
if(!(is.null(TO.value.char))) {
if(!is.character(TO.value.char))TO.valid<-0
if(!is.numeric(eval(parse(text=TO.value.char))))TO.valid<-0
}
if(!TO.valid){
return("Error: If TO.value.char is non.NULL, it must be a real number in inverted commas eg '-3.7' or '0'")
}
###BY.value.char
# check BY.value.char is valid
BY.valid<-1
if(!(is.null(BY.value.char))) {
if(!is.character(BY.value.char))BY.valid<-0
if(!is.numeric(eval(parse(text=BY.value.char))))BY.valid<-0
}
if(!BY.valid){
return("Error: If FROM.value.char is non.NULL, it must be a real number in inverted commas eg '5' or '-98.7321'")
}
###LENGTH.OUT.value.char
# check LENGTH.OUT.value.char is valid
LENGTH.OUT.valid<-1
if(!(is.null(LENGTH.OUT.value.char))) {
if(!is.character(LENGTH.OUT.value.char))LENGTH.OUT.valid<-0
if(!is.numeric(eval(parse(text=LENGTH.OUT.value.char))))LENGTH.OUT.valid<-0
}
if(!LENGTH.OUT.valid){
return("Error: If LENGTH.OUT.value.char is non.NULL, it must be an integer in inverted commas eg '87187'")
}
###ALONG.WITH.name
# check if user has correctly provided the name of a column to hold ALONG.WITH.name
if(!(is.null(ALONG.WITH.name) || is.character(ALONG.WITH.name))){
return("Error: If ALONG.WITH.name is non.NULL, it must specify the name of a serverside vector in inverted commas")
}
###Either LENGTH.OUT.value.char or ALONG.WITH.name must be non-NULL
if(is.null(TO.value.char)&&is.null(LENGTH.OUT.value.char)&&is.null(ALONG.WITH.name)){
return("Error: Either TO.value.char or LENGTH.OUT.value.char or ALONG.WITH.name must be non-NULL, they cannot both be NULL")
}
# CALL THE PRIMARY SERVER SIDE FUNCTION
calltext <- call("seqDS", FROM.value.char,TO.value.char,BY.value.char,LENGTH.OUT.value.char,ALONG.WITH.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.seq