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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
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
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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