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Perf batch 1 #656

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35eb732
refactor: batch 1 client functions remove redundant server calls
timcadman Mar 10, 2026
9ba8796
Update client tests: replace MODULE 5 checks with ds.class verification
timcadman Mar 12, 2026
92c58ff
revert whitespace changes
timcadman Mar 13, 2026
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -62,6 +62,7 @@ Depends:
R (>= 4.0.0),
DSI (>= 1.7.1)
Imports:
cli,
fields,
metafor,
meta,
Expand Down
2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -119,6 +119,8 @@ export(ds.var)
export(ds.vectorCalc)
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)
Expand Down
26 changes: 1 addition & 25 deletions R/ds.abs.R
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Expand Up @@ -72,41 +72,17 @@
#'
ds.abs <- function(x=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 object!", call.=FALSE)
}

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

# call the internal function that checks the input object is of the same class in all studies.
typ <- checkClass(datasources, x)

# call the internal function that checks the input object(s) is(are) of the same class in all studies.
if(!('numeric' %in% typ) && !('integer' %in% typ)){
stop("Only objects of type 'numeric' or 'integer' are allowed.", call.=FALSE)
}

# create a name by default if the user did not provide a name for the new variable
if(is.null(newobj)){
newobj <- "abs.newobj"
}

# call the server side function that does the operation
cally <- call("absDS", x)
DSI::datashield.assign(datasources, newobj, cally)

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

}
100 changes: 2 additions & 98 deletions R/ds.asCharacter.R
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Expand Up @@ -13,9 +13,7 @@
#' 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.asCharacter} returns the object converted into a class character
#' that 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.
#' that is written to the server-side.
#' @examples
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
Expand Down Expand Up @@ -57,111 +55,17 @@
#'
ds.asCharacter <- function(x.name=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.name)){
stop("Please provide the name of the input vector!", call.=FALSE)
}

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

# create a name by default if user did not provide a name for the new variable
if(is.null(newobj)){
newobj <- "ascharacter.newobj"
}

# call the server side function that does the job

calltext <- call("asCharacterDS", x.name)

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 #
# #
#
# 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.asCharacter
100 changes: 2 additions & 98 deletions R/ds.asDataMatrix.R
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Expand Up @@ -12,11 +12,7 @@
#' 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.asDataMatrix} returns the object converted into a matrix
#' that 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.
#' that is written to the server-side.
#' @examples
#' \dontrun{
#' ## Version 6, for version 5 see the Wiki
Expand Down Expand Up @@ -58,109 +54,17 @@
#'
ds.asDataMatrix <- function(x.name=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.name)){
stop("Please provide the name of the input vector!", call.=FALSE)
}

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

# create a name by default if user did not provide a name for the new variable
if(is.null(newobj)){
newobj <- "asdatamatrix.newobj"
}

# call the server side function that does the job
calltext <- call("asDataMatrixDS", x.name)
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 #
# #
#
# 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.asDataMatrix
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