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Refactor/perf batch 5 #691

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95d36e9
chore: bootstrap batch-5 from batch-4
timcadman Apr 15, 2026
d1cf587
refactor: batch-5 matrix client functions
timcadman Apr 15, 2026
1f23991
chore: update dsBase tar with batch-5
timcadman Apr 15, 2026
196a343
test: add performance tests for batch 5 functions
timcadman Apr 16, 2026
5dff8ad
fix: remove third-party copyright from new tests
timcadman Apr 16, 2026
6a632e5
fix: correct perf test setup for batch 5 matrix functions
timcadman Apr 16, 2026
df8ab68
docs: sync REFACTOR_GUIDE.md from batch-9
timcadman Apr 16, 2026
f0d64f6
docs: sync REFACTOR_GUIDE.md from batch-10
timcadman Apr 16, 2026
1b42aa0
docs: sync REFACTOR_GUIDE.md
timcadman Apr 19, 2026
8fea89e
merged in 7.0 dev
timcadman Jul 23, 2026
36cf744
Update to roxygen2 8.1.0
StuartWheater Aug 18, 2026
7a06aa4
Updated perf profile
StuartWheater Aug 20, 2026
a3d2c4a
try: update dsBase tar
timcadman Aug 25, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -88,6 +88,6 @@ Suggests:
DSOpal,
DSMolgenisArmadillo,
DSLite
RoxygenNote: 8.0.0
Encoding: UTF-8
Language: en-GB
Config/roxygen2/version: 8.1.0
10 changes: 6 additions & 4 deletions NAMESPACE
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Expand Up @@ -121,7 +121,9 @@ import(DSI)
import(data.table)
importFrom(DSI,datashield.connections_find)
importFrom(cli,cli_abort)
importFrom(stats,as.formula)
importFrom(stats,na.omit)
importFrom(stats,ts)
importFrom(stats,weighted.mean)
importFrom(stats,
as.formula,
na.omit,
ts,
weighted.mean
)
96 changes: 3 additions & 93 deletions R/ds.matrix.R
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Expand Up @@ -48,11 +48,9 @@
#' @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.matrix} returns the created matrix which is written on the server-side.
#' In addition, two validity messages are returned
#' indicating whether the new matrix has been created in each data source and if so whether
#' it is in a valid form.
#' @return \code{ds.matrix} returns the created matrix which is written on the server-side.
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @examples
#' \dontrun{
#'
Expand Down Expand Up @@ -147,15 +145,7 @@
ds.matrix <- function(mdata = NA, from="clientside.scalar", nrows.scalar=NULL, ncols.scalar=NULL, byrow = FALSE,
dimnames = 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)

# check if a value has been provided for mdata
if(is.null(mdata)){
Expand Down Expand Up @@ -208,85 +198,5 @@ ds.matrix <- function(mdata = NA, from="clientside.scalar", nrows.scalar=NULL, n



#############################################################################################################
#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.matrix
101 changes: 4 additions & 97 deletions R/ds.matrixDet.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,10 @@
#' @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.matrixDet} returns the determinant of an existing matrix on the server-side.
#' The created new object is stored on the server-side.
#' Also, two validity messages are returned
#' indicating whether the matrix has been created in each data source and if so whether
#' it is in a valid form.
#' @return \code{ds.matrixDet} returns the determinant of an existing matrix on the server-side.
#' The created new object is stored on the server-side.
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @examples
#' \dontrun{
#'
Expand Down Expand Up @@ -83,23 +81,12 @@
#'
ds.matrixDet<-function(M1=NULL, newobj=NULL, logarithm=FALSE, 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 has provided the name of matrix representing M1
if(is.null(M1)){
return("Error: Please provide the name of the matrix representing M1")
}

# check if the input object is defined in all the studies
isDefined(datasources, M1)

# if no value or invalid value specified for logarithm, then specify a default
if(is.null(logarithm)){
Expand All @@ -119,85 +106,5 @@ ds.matrixDet<-function(M1=NULL, newobj=NULL, logarithm=FALSE, datasources=NULL){
calltext <- call("matrixDetDS2", M1, logarithm)
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 CORRECTLY MODULE #
#############################################################################################################

}
#ds.matrixDet
11 changes: 2 additions & 9 deletions R/ds.matrixDet.report.R
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Expand Up @@ -18,6 +18,7 @@
#' @return \code{ds.matrixDet.report} returns to the client-side
#' the determinant of a matrix that is stored on the server-side.
#' @author DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @examples
#' \dontrun{
#'
Expand Down Expand Up @@ -76,15 +77,7 @@
#'
ds.matrixDet.report<-function(M1=NULL, logarithm=FALSE, 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 has provided the name of matrix representing M1
if(is.null(M1)){
Expand Down
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