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refactor: batch-5 matrix server functions #497

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07b817e
refactor: batch-5 matrix server functions
timcadman Apr 15, 2026
8aa7033
tidied up PR
timcadman Jul 17, 2026
598e7c6
added stuart as author
timcadman Jul 17, 2026
12d90f6
Merge branch 'v7.0-dev' of github.com:datashield/dsBase into refactor…
timcadman Jul 17, 2026
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3 changes: 2 additions & 1 deletion R/matrixDS.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
#' @return Output is the matrix A written
#' to the serverside. For more details see help for ds.matrix
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
matrixDS <- function(mdata.transmit, from, nrows.transmit, ncols.transmit, byrow, dimnames){
Expand Down Expand Up @@ -92,7 +93,7 @@ if(!is.null(dimnames))

if(from=="serverside.vector"||from=="serverside.scalar")
{
mdata<-eval(parse(text=mdata.transmit), envir = parent.frame())
mdata <- .loadServersideObject(mdata.transmit)
}


Expand Down
35 changes: 3 additions & 32 deletions R/matrixDetDS1.R
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Expand Up @@ -11,42 +11,13 @@
#' @return Output is the determinant of the matrix identified by argument <M1>
#' which is returned to the clientside. For more details see help for ds.matrixDet
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export

matrixDetDS1 <- function(M1.name=NULL,logarithm){

#########################################################################
# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS #
thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.tab<-as.numeric(thr$nfilter.tab) #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
#nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
error.message<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(error.message, call. = FALSE)
}

#EVAL M1

M1<-eval(parse(text=M1.name), envir = parent.frame())

if(!is.matrix(M1)&&!is.data.frame(M1))
{
error.message<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(error.message, call. = FALSE)
}
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#coerce to matrix if a data.frame
if(is.data.frame(M1))
Expand Down
35 changes: 3 additions & 32 deletions R/matrixDetDS2.R
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Expand Up @@ -11,42 +11,13 @@
#' @return Output is the determinant of the matrix identified by argument <M1>
#' which is written to the serverside. For more details see help for ds.matrixDet
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export

matrixDetDS2 <- function(M1.name=NULL,logarithm){

#########################################################################
# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS #
thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.tab<-as.numeric(thr$nfilter.tab) #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
#nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}

#EVAL M1

M1<-eval(parse(text=M1.name), envir = parent.frame())

if(!is.matrix(M1)&&!is.data.frame(M1))
{
studysideMessage<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#coerce to matrix if a data.frame
if(is.data.frame(M1))
Expand Down
3 changes: 2 additions & 1 deletion R/matrixDiagDS.R
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Expand Up @@ -17,6 +17,7 @@
#' (or default name diag_<x1>) which is written to the serverside.
#' For more details see help for \code{ds.matrixDiag}.
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
matrixDiagDS <- function(x1.transmit,aim,nrows.transmit){
#########################################################################
Expand Down Expand Up @@ -65,7 +66,7 @@ if(aim=="serverside.vector.2.matrix"||aim=="serverside.scalar.2.matrix"||aim=="s
{
#x1 is name of the serverside vector, scalar or matrix

x1<-eval(parse(text=x1.transmit), envir = parent.frame())
x1 <- .loadServersideObject(x1.transmit)

#coerce to matrix if x1 is a data.frame
if(is.data.frame(x1))
Expand Down
26 changes: 4 additions & 22 deletions R/matrixDimnamesDS.R
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Expand Up @@ -18,6 +18,7 @@
#' (or default name diag_<x1>) with specified dimnames (row and column
#' names) which is written to the serverside.
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
matrixDimnamesDS <- function(M1.name=NULL,dimnames){

Expand All @@ -28,23 +29,11 @@ thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}


#Check length of dimnames string not so long as to provide a risk of hidden code
#This could legitimately be quite long so allow 2*nfilter.string

Expand All @@ -61,15 +50,8 @@ if(!is.null(dimnames))
}
}

#EVAL M1

M1<-eval(parse(text=M1.name), envir = parent.frame())

if(!is.matrix(M1)&&!is.data.frame(M1))
{
studysideMessage<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#coerce to matrix if a data.frame
if(is.data.frame(M1))
Expand Down
36 changes: 3 additions & 33 deletions R/matrixInvertDS.R
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Expand Up @@ -8,43 +8,13 @@
#' @return Output is the matrix representing the inverse of A which is written
#' to the serverside. For more details see help for ds.matrixInvert
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
matrixInvertDS <- function(M1.name=NULL){

#########################################################################
# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS #
thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.tab<-as.numeric(thr$nfilter.tab) #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
#nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}

#EVAL M1


M1<-eval(parse(text=M1.name), envir = parent.frame())

if(!is.matrix(M1)&&!is.data.frame(M1))
{
studysideMessage<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#coerce to matrix if a data.frame
if(is.data.frame(M1))
Expand Down
55 changes: 5 additions & 50 deletions R/matrixMultDS.R
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Expand Up @@ -13,61 +13,16 @@
#' @return Output is the matrix representing the product of M1 and M2 which is written
#' to the serverside. For more details see help for ds.matrixMult
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
matrixMultDS <- function(M1.name=NULL, M2.name=NULL){

#########################################################################
# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS #
thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.tab<-as.numeric(thr$nfilter.tab) #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
#nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################
#EVAL M1 and M2
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}

#Check length of M2.name not so long as to provide a risk of hidden code
length.M2.name<-length(unlist(strsplit(M2.name,'')))

if(length.M2.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M2.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}

M1<-eval(parse(text=M1.name), envir = parent.frame())
M2<-eval(parse(text=M2.name), envir = parent.frame())



if(!is.matrix(M1)&&!is.data.frame(M1))
{
studysideMessage<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}

if(!is.matrix(M2)&&!is.data.frame(M2))
{
studysideMessage<-"FAILED: M2 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}
M2 <- .loadServersideObject(M2.name)
.checkClass(obj = M2, obj_name = M2.name, permitted_classes = c("matrix", "data.frame"))

if(is.data.frame(M1))
{
Expand Down
35 changes: 3 additions & 32 deletions R/matrixTransposeDS.R
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Expand Up @@ -9,42 +9,13 @@
#' @return Output is the matrix representing the transpose of A which is written
#' to the serverside. For more details see help for ds.matrixTranspose
#' @author Paul Burton for DataSHIELD Development Team
#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
#' @export
#'
matrixTransposeDS <- function(M1.name=NULL){
#########################################################################
# DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS #
thr<-dsBase::listDisclosureSettingsDS() #
#nfilter.tab<-as.numeric(thr$nfilter.tab) #
#nfilter.glm<-as.numeric(thr$nfilter.glm) #
#nfilter.subset<-as.numeric(thr$nfilter.subset) #
#nfilter.string<-as.numeric(thr$nfilter.string) #
nfilter.stringShort<-as.numeric(thr$nfilter.stringShort) #
#nfilter.kNN<-as.numeric(thr$nfilter.kNN) #
#datashield.privacyLevel<-as.numeric(thr$datashield.privacyLevel) #
#########################################################################

#Check length of M1.name not so long as to provide a risk of hidden code
length.M1.name<-length(unlist(strsplit(M1.name,'')))

if(length.M1.name>nfilter.stringShort)
{
studysideMessage<-
paste0("FAILED: M1.name is too long it could hide concealed code, please shorten to <= nfilter.stringShort = ",
nfilter.stringShort," characters")
stop(studysideMessage, call. = FALSE)
}


#EVAL M1

M1<-eval(parse(text=M1.name), envir = parent.frame())

if(!is.matrix(M1)&&!is.data.frame(M1))
{
studysideMessage<-"FAILED: M1 must be of class matrix or data.frame, please respecify"
stop(studysideMessage, call. = FALSE)
}
M1 <- .loadServersideObject(M1.name)
.checkClass(obj = M1, obj_name = M1.name, permitted_classes = c("matrix", "data.frame"))

#coerce to matrix if a data.frame
if(is.data.frame(M1))
Expand Down
2 changes: 2 additions & 0 deletions man/matrixDS.Rd
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2 changes: 2 additions & 0 deletions man/matrixDetDS1.Rd
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2 changes: 2 additions & 0 deletions man/matrixDetDS2.Rd
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2 changes: 2 additions & 0 deletions man/matrixDiagDS.Rd
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2 changes: 2 additions & 0 deletions man/matrixMultDS.Rd
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2 changes: 2 additions & 0 deletions man/matrixTransposeDS.Rd
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