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ds.Boole.R
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ds.Boole.R
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#'
#' @title Converts a server-side R object into Boolean indicators
#' @description It compares R objects using the standard set of
#' Boolean operators (\code{==, !=, >, >=, <, <=}) to create a
#' vector with Boolean indicators that can be of class logical (\code{TRUE/FALSE})
#' or numeric (\code{1/0}).
#'
#' @details A combination of different Boolean operators using \code{AND} operator
#' can be obtained by multiplying two or more
#' binary/Boolean vectors together. In this way, observations taking the value 1 in every vector
#' will then take the value 1 in the final vector (after multiplication)
#' while all others will take the value 0. Instead the combination using \code{OR} operator
#' can be obtained by the sum of two or more vectors and applying
#' \code{ds.Boole} using the operator \code{>= 1}.
#'
#' In \code{na.assign} if \code{'NA'} is specified, the missing values
#' remain as \code{NA}s in the output vector. If \code{'1'} or \code{'0'} is specified the
#' missing values are converted to 1 or 0 respectively or \code{TRUE}
#' or \code{FALSE} depending on the argument \code{numeric.output}.
#'
#'
#'
#' Server function called: \code{BooleDS}
#'
#' @param V1 A character string specifying the name of the vector to which the Boolean operator
#' is to be applied.
#' @param V2 A character string specifying the name of the vector to compare with \code{V1}.
#' @param Boolean.operator A character string specifying one of six possible Boolean operators:
#' \code{'==', '!=', '>', '>=', '<'} and \code{'<='}.
#' @param numeric.output logical. If TRUE the output variable should be of class numeric (\code{1/0}).
#' If FALSE the output variable should be of class logical (\code{TRUE/FALSE}).
#' Default TRUE.
#' @param na.assign A character string taking values \code{'NA'},\code{'1'} or \code{'0'}.
#' Default \code{'NA'}. For more information see details.
#' @param newobj a character string that provides the name for the output
#' object that is stored on the data servers. Default \code{boole.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.Boole} returns the object specified by the \code{newobj} argument
#' which 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()
#'
#' # Log onto the remote Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Generating Boolean indicators
#' ds.Boole(V1 = "D$LAB_TSC",
#' V2 = "D$LAB_TRIG",
#' Boolean.operator = ">",
#' numeric.output = TRUE, #Output vector of 0 and 1
#' na.assign = "NA",
#' newobj = "Boole.vec",
#' datasources = connections[1]) #only the first server is used ("study1")
#'
#' ds.Boole(V1 = "D$LAB_TSC",
#' V2 = "D$LAB_TRIG",
#' Boolean.operator = "<",
#' numeric.output = FALSE, #Output vector of TRUE and FALSE
#' na.assign = "1", #NA values are converted to TRUE
#' newobj = "Boole.vec",
#' datasources = connections[2]) #only the second server is used ("study2")
#'
#' ds.Boole(V1 = "D$LAB_TSC",
#' V2 = "D$LAB_TRIG",
#' Boolean.operator = ">",
#' numeric.output = TRUE, #Output vector of 0 and 1
#' na.assign = "0", #NA values are converted to 0
#' newobj = "Boole.vec",
#' datasources = connections) #All servers are used
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
#' }
#'
#' @author DataSHIELD Development Team
#' @export
#'
ds.Boole<-function(V1=NULL, V2=NULL, Boolean.operator=NULL, numeric.output=TRUE, na.assign="NA",newobj=NULL, datasources=NULL){
# look for DS connections
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
# check if user has provided the name of the column or scalar that holds V1
if(is.null(V1)){
stop("Please provide the name of the column or scalar that holds V1!", call.=FALSE)
}
# check if user has provided the name of a column or scalar holding V2 or has declared a scalar value: eg '3'
if(is.null(V2)){
stop("Please provide the name of a column or scalar holding V2 or declare a scalar in character format: eg '3'", call.=FALSE)
}
# check if user has provided a Boolean operator in character format: eg '==' or '>=' or '<' or '!='
if(is.null(Boolean.operator)){
stop("Please provide a Boolean operator in character format: eg '==' or '>=' or '<' or '!='", call.=FALSE)
}
#check if na.assign has legal value
if(!(na.assign=="NA"||na.assign=="0"||na.assign=="1")){
stop("Error: na.assign must be a character string taking value 'NA', '0' or '1'- if <na.action> not specified default is 'NA'", call.=FALSE)
}
# create a name by default if user did not provide a name for the new variable
if(is.null(newobj)){
newobj <- "boole.newobj"
}
#convert Boolean operator to numeric
BO.n<-0
if(Boolean.operator == "=="){
BO.n<-1
}
if(Boolean.operator == "!="){
BO.n<-2
}
if(Boolean.operator == "<"){
BO.n<-3
}
if(Boolean.operator == "<="){
BO.n<-4
}
if(Boolean.operator == ">"){
BO.n<-5
}
if(Boolean.operator == ">="){
BO.n<-6
}
if(BO.n == 0){
stop(paste0("An unrecognized Boolean operator, ", Boolean.operator, ", has provide"), call.=FALSE)
}
# if no value spcified for output object, then specify a default
if(is.null(newobj)){
newobj <- paste0(V1,"_Boole")
}
# CALL THE MAIN SERVER SIDE FUNCTION
calltext <- call("BooleDS", V1, V2, BO.n, na.assign,numeric.output)
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) || 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<-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.Boole