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Refactor/perf batch 10 #707

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3781574
chore: bootstrap batch-10 from batch-9
timcadman Apr 16, 2026
f0c10ee
refactor: batch-10 client-side splines, tables, misc functions
timcadman Apr 16, 2026
fa3051c
refactor: update ds.make tests for MODULE 5 removal
timcadman Apr 16, 2026
6123900
chore: update dsBase tar for CI
timcadman Apr 16, 2026
9defd02
docs: updated authorship
timcadman Apr 16, 2026
55c2fcb
docs: redocumented
timcadman Apr 16, 2026
e045b5e
test: add performance tests for batch 10 functions
timcadman Apr 16, 2026
32454bb
fix: align perf test calls with smoke test patterns
timcadman Apr 16, 2026
7c3e292
docs: add perf test alignment requirement to guide
timcadman Apr 16, 2026
0d6197f
fix: align perf test datasets with smoke tests
timcadman Apr 19, 2026
8ce6eef
docs: strengthen perf test requirements in guide
timcadman Apr 19, 2026
286212a
tidied up refactor
timcadman Sep 15, 2026
7cf224e
updated tests following refactor
timcadman Sep 16, 2026
4df6bf0
merged in updates
timcadman Sep 18, 2026
beb7830
New performance profile
StuartWheater Sep 18, 2026
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14 changes: 2 additions & 12 deletions R/ds.assign.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
#' @return \code{ds.assign} returns the R object assigned to a name
#' that is written to the server-side.
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#' @examples
#' \dontrun{
Expand Down Expand Up @@ -56,15 +57,7 @@
#'
ds.assign <- function(toAssign=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)
}
datasources <- .set_datasources(datasources)

if(is.null(toAssign)){
stop("Please give the name of object to assign or an expression to evaluate and assign.!\n", call.=FALSE)
Expand All @@ -78,7 +71,4 @@ ds.assign <- function(toAssign=NULL, newobj=NULL, datasources=NULL){
# now do the business
DSI::datashield.assign(datasources, newobj, as.symbol(toAssign))

# check that the new object has been created and display a message accordingly
finalcheck <- isAssigned(datasources, newobj)

}
14 changes: 2 additions & 12 deletions R/ds.elspline.R
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Expand Up @@ -23,27 +23,17 @@
#' @return an object of class "lspline" and "matrix", which its name is specified by the
#' \code{newobj} argument (or its default name "elspline.newobj"), is assigned on the serverside.
#' @author Demetris Avraam for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
ds.elspline <- function(x, n, marginal = FALSE, names = 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)
}
datasources <- .set_datasources(datasources)

if(is.null(x)){
stop("Please provide the name of the input variable x!", call.=FALSE)
}

# check if the input object is defined in all the studies
defined <- isDefined(datasources, x)

if(is.null(n)){
stop("Argument 'n' is missing, with no default!", call.=FALSE)
}
Expand Down
93 changes: 3 additions & 90 deletions R/ds.getWGSR.R
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Expand Up @@ -58,6 +58,7 @@
#' @return \code{ds.getWGSR} assigns a vector for each study that includes the z-scores for the
#' specified index. The created vectors are stored in the servers.
#' @author Demetris Avraam for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#' @examples
#' \dontrun{
Expand Down Expand Up @@ -102,15 +103,7 @@
#'
ds.getWGSR <- function(sex=NULL, firstPart=NULL, secondPart=NULL, index=NULL, standing=NA, thirdPart=NA, 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)
}
datasources <- .set_datasources(datasources)

if(is.null(sex)){
stop("Please provide the column name of the 'sex' variable!", call.=FALSE)
Expand All @@ -124,21 +117,6 @@ ds.getWGSR <- function(sex=NULL, firstPart=NULL, secondPart=NULL, index=NULL, st
stop("Please provide the column name of the 'secondPart' variable!", call.=FALSE)
}

# check if the input objects are defined in all the studies
isDefined(datasources, sex)
isDefined(datasources, firstPart)
isDefined(datasources, secondPart)

# if 'firstPart' or 'secondPart' are not numeric return an error message
typ.firstPart <- checkClass(datasources, firstPart)
typ.secondPart <- checkClass(datasources, secondPart)
if(!('numeric' %in% typ.firstPart)){
stop("The 'firstPart' variable must be a 'numeric' variable!", call.=FALSE)
}
if(!('numeric' %in% typ.secondPart)){
stop("The 'secondPart' variable must be a 'numeric' variable!", call.=FALSE)
}

if(!any(index %in% c("bfa", "hca", "hfa", "lfa", "mfa", "ssa", "tsa", "wfa", "wfh", "wfl"))){
stop("Please provide a correct abbreviation for the index!", call.=FALSE)
}
Expand All @@ -148,14 +126,6 @@ ds.getWGSR <- function(sex=NULL, firstPart=NULL, secondPart=NULL, index=NULL, st
stop("'thirdPart' variable should not be missing for index 'bfa'", call.=FALSE)
}

# If 'thirdPart' (age) is not numeric for BMI-for-age return an error message
if(index == "bfa"){
typ.thirdPart <- checkClass(datasources, thirdPart)
if(!('numeric' %in% typ.firstPart)){
stop("The 'thirdPart' variable must be a 'numeric' variable!", call.=FALSE)
}
}

# If 'standing' is not a value either 1, 2, 3, or NA return an error message
if(!any(standing %in% c(NA, 1, 2, 3))) {
stop("The 'standing' variable must be a numeric value either 1, 2, or 3!", call.=FALSE)
Expand All @@ -168,63 +138,6 @@ ds.getWGSR <- function(sex=NULL, firstPart=NULL, secondPart=NULL, index=NULL, st

cally <- call("getWGSRDS", sex, firstPart, secondPart, index, standing, thirdPart)
DSI::datashield.assign(datasources, newobj, cally)

#############################################################################################################
# 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
#######################################################################################################


}
14 changes: 2 additions & 12 deletions R/ds.hetcor.R
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Expand Up @@ -27,27 +27,17 @@
#' the method by which any missing data were handled: "complete.obs" or "pairwise.complete.obs"; TRUE
#' for ML estimates, FALSE for two-step estimates.
#' @author Demetris Avraam for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
ds.hetcor <- function(data=NULL, ML=TRUE, std.err=TRUE, bins=4, pd=TRUE, use="complete.obs", 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)
}
datasources <- .set_datasources(datasources)

if(is.null(data)){
stop("Please provide the name of the input object!", call.=FALSE)
}

# check if the input object is defined in all the studies
defined <- isDefined(datasources, data)

calltext <- call('hetcorDS', data, ML, std.err, bins, pd, use)
output <- DSI::datashield.aggregate(datasources, calltext)

Expand Down
11 changes: 2 additions & 9 deletions R/ds.lexis.R
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Expand Up @@ -134,6 +134,7 @@
#' the expanded version of the input table.
#'
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @seealso \code{\link{ds.glm}} for generalized linear models.
#' @export
#' @examples
Expand Down Expand Up @@ -202,15 +203,7 @@
#'
ds.lexis<-function(data=NULL, intervalWidth=NULL, idCol=NULL, entryCol=NULL, exitCol=NULL, statusCol=NULL, variables=NULL, expandDF=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)
}
datasources <- .set_datasources(datasources)

# check if user have provided the name of the column that holds the subject ids
if(is.null(idCol)){
Expand Down
14 changes: 2 additions & 12 deletions R/ds.lspline.R
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Expand Up @@ -20,27 +20,17 @@
#' @return an object of class "lspline" and "matrix", which its name is specified by the
#' \code{newobj} argument (or its default name "lspline.newobj"), is assigned on the serverside.
#' @author Demetris Avraam for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
ds.lspline <- function(x, knots = NULL, marginal = FALSE, names = 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)
}
datasources <- .set_datasources(datasources)

if(is.null(x)){
stop("Please provide the name of the input variable x!", call.=FALSE)
}

# check if the input object is defined in all the studies
defined <- isDefined(datasources, x)

if(is.null(knots)){
stop("Please provide a vector of knots!", call.=FALSE)
}
Expand Down
95 changes: 4 additions & 91 deletions R/ds.make.R
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Expand Up @@ -67,10 +67,10 @@
#' @param datasources a list of \code{\link[DSI]{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[DSI]{datashield.connections_default}}.
#' @return \code{ds.make} returns the new object which is written to the
#' server-side. Also a validity message is returned to the client-side indicating whether the new object has been correctly
#' created at each source.
#' @return \code{ds.make} writes the new object to the server-side; nothing is
#' returned to the client-side.
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#' @examples
#' \dontrun{
Expand Down Expand Up @@ -135,14 +135,7 @@
ds.make<-function(toAssign=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)
}
datasources <- .set_datasources(datasources)

if(is.null(toAssign)){
stop("Please give the name of object to assign or an expression to evaluate and assign.!\n", call.=FALSE)
Expand All @@ -156,86 +149,6 @@ ds.make<-function(toAssign=NULL, newobj=NULL, datasources=NULL){
# now do the business
DSI::datashield.assign(datasources, newobj, as.symbol(toAssign))

#############################################################################################################
#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.make
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