timcadman · Oct 30, 2026 · Nov 2, 2026
diff --git a/NAMESPACE b/NAMESPACE
@@ -121,6 +121,9 @@ import(DSI)
 import(data.table)
 importFrom(DSI,datashield.connections_find)
 importFrom(cli,cli_abort)
+importFrom(cli,cli_inform)
+importFrom(cli,cli_verbatim)
+importFrom(cli,cli_warn)
 importFrom(stats,
   as.formula,
   na.omit,

diff --git a/R/ds.Boole.R b/R/ds.Boole.R
@@ -104,32 +104,24 @@
 #'
 ds.Boole<-function(V1=NULL, V2=NULL, Boolean.operator=NULL, numeric.output=TRUE, na.assign="NA",newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # check if user has provided the name of the column or scalar that holds V1
-  if(is.null(V1)){
-    stop("Please provide the name of the column or scalar that holds V1!", call.=FALSE)
-  }
+  .checkArgProvided(V1, "the name of the column or scalar that holds V1")
 
   # check if user has provided the name of a column or scalar holding V2 or has declared a scalar value: eg '3'
-  if(is.null(V2)){
-    stop("Please provide the name of a column or scalar holding V2 or declare a scalar in character format: eg '3'", call.=FALSE)
-  }
+  .checkArgProvided(V2, "the name of a column or scalar that holds V2")
 
   # check if user has provided a Boolean operator in character format: eg '==' or '>=' or '<' or '!='
-  if(is.null(Boolean.operator)){
-    stop("Please provide a Boolean operator in character format: eg '==' or '>=' or '<' or '!='", call.=FALSE)
-  }
+  .checkArgProvided(Boolean.operator, "a Boolean operator in character format, such as '==' or '>='")
 
   #check if na.assign has legal value
   if(!(na.assign=="NA"||na.assign=="0"||na.assign=="1")){
-    stop("Error: na.assign must be a character string taking value 'NA', '0' or '1'- if <na.action> not specified default is 'NA'", call.=FALSE)
+    .abortInvalidChoice("na.assign", c("NA", "0", "1"))
   }
 
   # create a name by default if user did not provide a name for the new variable
-  if(is.null(newobj)){
-    newobj <- "boole.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "boole.newobj")
 
   #convert Boolean operator to numeric
 
@@ -163,9 +155,7 @@ ds.Boole<-function(V1=NULL, V2=NULL, Boolean.operator=NULL, numeric.output=TRUE,
   }
 
   # if no value spcified for output object, then specify a default
-  if(is.null(newobj)){
-    newobj <- paste0(V1,"_Boole")
-  }
+  newobj <- .resolveNewobjName(newobj, paste0(V1,"_Boole"))
 
   # CALL THE MAIN SERVER SIDE FUNCTION
   calltext <- call("BooleDS", V1, V2, BO.n, na.assign, numeric.output)

diff --git a/R/ds.abs.R b/R/ds.abs.R
@@ -73,17 +73,13 @@
 #'
 ds.abs <- function(x=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x)){
-    stop("Please provide the name of the input object!", call.=FALSE)
-  }
+  .checkArgProvided(x, "the name of the input object")
 
-  if(is.null(newobj)){
-    newobj <- "abs.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "abs.newobj")
 
   cally <- call("absDS", x)
   DSI::datashield.assign(datasources, newobj, cally)

 }
diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R
@@ -56,17 +56,13 @@
 #' 
 ds.asCharacter <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "ascharacter.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "ascharacter.newobj")
 
 	calltext <- call("asCharacterDS", x.name)
 	DSI::datashield.assign(datasources, newobj, calltext)

 }
diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R
@@ -55,17 +55,13 @@
 #' 
 ds.asDataMatrix <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "asdatamatrix.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "asdatamatrix.newobj")
 
 	calltext <- call("asDataMatrixDS", x.name)
 	DSI::datashield.assign(datasources, newobj, calltext)

 }
diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R
@@ -188,12 +188,10 @@
 ds.asFactor <- function(input.var.name=NULL, newobj.name=NULL, forced.factor.levels=NULL, fixed.dummy.vars=FALSE,
                         baseline.level=1, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # check if user has provided the name of the column that holds the input variable
-  if(is.null(input.var.name)){
-    stop("Please provide the name of the variable that is to be converted to a factor e.g. 'varname'", call.=FALSE)
-  }
+  .checkArgProvided(input.var.name, "the name of the variable to convert to a factor")
 
   # check if user has provided the name of the input variable in a correct character format
   if(!is.character(input.var.name)){
@@ -208,7 +206,7 @@
  #CALL THE FIRST SERVER SIDE FUNCTION (AN AGGREGATE FUNCTION)
  #TO DETERMINE ALL OF THE LEVELS REQUIRED
  calltext1 <- call("asFactorDS1", input.var.name)
  all.levels <- DSI::datashield.aggregate(datasources, calltext1)

  failed.levels <- FALSE
  for (levels in all.levels) {
@@ -237,7 +235,7 @@
  all.unique.levels.transmit <- paste0(all.unique.levels, collapse=",")

  calltext2 <- call("asFactorDS2", input.var.name, all.unique.levels.transmit, fixed.dummy.vars, baseline.level)
  DSI::datashield.assign(datasources, newobj.name, calltext2)

  return(list(all.unique.levels=all.unique.levels))


diff --git a/R/ds.asFactorSimple.R b/R/ds.asFactorSimple.R
@@ -24,12 +24,10 @@
 #'
 ds.asFactorSimple <- function(input.var.name=NULL, newobj.name=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # check if user has provided the name of the column that holds the input variable
-  if(is.null(input.var.name)){
-    stop("Please provide the name of the variable that is to be converted to a factor e.g. 'varname'", call.=FALSE)
-  }
+  .checkArgProvided(input.var.name, "the name of the variable to convert to a factor")
 
   # check if user has provided the name of the input variable in a correct character format
   if(!is.character(input.var.name)){
@@ -44,7 +42,7 @@

 #Call the only serverside function required for this simple version of asFactor
  calltext0 <- call("asFactorSimpleDS", input.var.name)
  DSI::datashield.assign(datasources, newobj.name, calltext0)

 }
 #ds.asFactorSimple
diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R
@@ -69,17 +69,13 @@
 #' @export
 ds.asInteger <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "asinteger.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "asinteger.newobj")
 
   calltext <- call("asIntegerDS", x.name)
   DSI::datashield.assign(datasources, newobj, calltext)

 }
diff --git a/R/ds.asList.R b/R/ds.asList.R
@@ -57,15 +57,11 @@
 #' 
 ds.asList <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "aslist.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "aslist.newobj")
 
   datashield.assign(datasources, newobj, call("asListDS", x.name))
 

diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R
@@ -56,17 +56,13 @@
 #' 
 ds.asLogical <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "aslogical.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "aslogical.newobj")
 
 	calltext <- call("asLogicalDS", x.name)
 	DSI::datashield.assign(datasources, newobj, calltext)

 }
diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R
@@ -58,17 +58,13 @@
 #' 
 ds.asMatrix <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "asmatrix.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "asmatrix.newobj")
 
 	calltext <- call("asMatrixDS", x.name)
 	DSI::datashield.assign(datasources, newobj, calltext)

 }
diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R
@@ -70,15 +70,11 @@
 #' 
 ds.asNumeric <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(x.name)){
-    stop("Please provide the name of the input vector!", call.=FALSE)
-  }
+  .checkArgProvided(x.name, "the name of the input vector")
 
-  if(is.null(newobj)){
-    newobj <- "asnumeric.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "asnumeric.newobj")
 
   calltext <- call("asNumericDS", x.name)
   DSI::datashield.assign(datasources, newobj, calltext)

diff --git a/R/ds.assign.R b/R/ds.assign.R
@@ -57,16 +57,12 @@
 #'
 ds.assign <- function(toAssign=NULL, newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
-  if(is.null(toAssign)){
-    stop("Please give the name of object to assign or an expression to evaluate and assign.!\n", call.=FALSE)
-  }
+  .checkArgProvided(toAssign, "the name of the object to assign or an expression to evaluate")
 
   # create a name by default if user did not provide a name for the new variable
-  if(is.null(newobj)){
-    newobj <- "assign.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "assign.newobj")
 
   # now do the business
   DSI::datashield.assign(datasources, newobj, as.symbol(toAssign))

diff --git a/R/ds.auc.R b/R/ds.auc.R
@@ -16,17 +16,13 @@
 #'
 ds.auc <- function(pred=NULL, y=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # verify that 'pred' was set
-  if(is.null(pred)){
-    stop("Please provide the name of the vector with predicted values", call.=FALSE)
-  }
+  .checkArgProvided(pred, "the name of the vector of predicted values")
 
   # verify that 'y' was set
-  if(is.null(y)){
-    stop("Please provide the name of the outcome variable", call.=FALSE)
-  }
+  .checkArgProvided(y, "the name of the outcome variable")
 
   cally <- call('aucDS', pred, y)
   output <- DSI::datashield.aggregate(datasources, cally)

diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R
@@ -87,16 +87,16 @@
 ds.boxPlot <- function(x, variables = NULL, group = NULL, group2 = NULL, xlabel = "x axis", 
                        ylabel = "y axis", type = "pooled", datasources = NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # Ensure type is 'pooled' or 'split'
   if((length(type) == 1) && (! any(type %in% c("pooled", "split")))){
-    stop("[type] can only be set to 'pooled' or 'split'")
+    .abortInvalidChoice("type", c("pooled", "split"))
   }
 
   # Determine class of x for dispatch
   cls <- datashield.aggregate(datasources, call("classDS", x))
-  .checkClassConsistency(lapply(cls, function(study.class) list(class = study.class)), object_name = x)
+  .checkClassConsistency(lapply(cls, function(study.class) list(class = study.class)), objectName = x)
   cls <- unique(unlist(cls))
 
   if(!any(c("numeric", "data.frame") %in% cls)){

diff --git a/R/ds.boxPlotGG.R b/R/ds.boxPlotGG.R
@@ -24,7 +24,7 @@
 
 ds.boxPlotGG <- function(x, group = NULL, group2 = NULL, xlabel = "x axis", ylabel = "y axis", type = "pooled", datasources = NULL){
   x_var <- lower <- upper <- ymin <- ymax <- middle <- fill <- NULL
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   plot_data <- datashield.aggregate(datasources, call("boxPlotGGDS", data_table.name=x, group=group, group2=group2))
 
@@ -132,7 +132,7 @@ ds.boxPlotGG <- function(x, group = NULL, group2 = NULL, xlabel = "x axis", ylab
     plt <- do.call(gridExtra::grid.arrange, plt)
 
   }
-  else{stop("Invalid type")}
+  else{.abortInvalidChoice("type", c("pooled", "split"))}
 
   return(plt)
 

diff --git a/R/ds.boxPlotGG_data_Treatment.R b/R/ds.boxPlotGG_data_Treatment.R
@@ -20,7 +20,7 @@
 
 ds.boxPlotGG_data_Treatment <- function(table, variables, group = NULL, group2 = NULL, datasources = NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   datashield.assign.expr(datasources, "boxPlotRawData", call("boxPlotGG_data_TreatmentDS", table.name = table, variables = variables, group = group, group2 = group2))
 

diff --git a/R/ds.boxPlotGG_data_Treatment_numeric.R b/R/ds.boxPlotGG_data_Treatment_numeric.R
@@ -15,7 +15,7 @@
 
 ds.boxPlotGG_data_Treatment_numeric <- function(vector, datasources = NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   datashield.assign.expr(datasources, "boxPlotRawDataNumeric", call("boxPlotGG_data_Treatment_numericDS", vector.name = vector))
 

diff --git a/R/ds.boxPlotGG_numeric.R b/R/ds.boxPlotGG_numeric.R
@@ -12,7 +12,7 @@
 
 ds.boxPlotGG_numeric <- function(x, xlabel = "x axis", ylabel = "y axis", type = "pooled", datasources = NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   ds.boxPlotGG_data_Treatment_numeric(x, datasources)
 

diff --git a/R/ds.boxPlotGG_table.R b/R/ds.boxPlotGG_table.R
@@ -18,7 +18,7 @@
 ds.boxPlotGG_table <- function(x, variables, group = NULL, group2 = NULL, xlabel = "x axis", 
                                ylabel = "y axis", type = "pooled", datasources = NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   ds.boxPlotGG_data_Treatment(x, variables, group, group2, datasources)
 

diff --git a/R/ds.bp_standards.R b/R/ds.bp_standards.R
@@ -32,32 +32,22 @@
 ds.bp_standards <- function(sex=NULL, age=NULL, height=NULL, bp=NULL, systolic=TRUE, 
                             newobj=NULL, datasources=NULL){
 
-  datasources <- .set_datasources(datasources)
+  datasources <- .resolveDatasources(datasources)
 
   # verify that 'sex' was set
-  if(is.null(sex)){
-    stop("Please provide the name of the sex variable", call.=FALSE)
-  }
+  .checkArgProvided(sex, "the name of the sex variable")
 
   # verify that 'age' was set
-  if(is.null(age)){
-    stop("Please provide the name of the age in months variable", call.=FALSE)
-  }
+  .checkArgProvided(age, "the name of the age in months variable")
 
   # verify that 'height' was set
-  if(is.null(height)){
-    stop("Please provide the name of the height in cm variable", call.=FALSE)
-  }
+  .checkArgProvided(height, "the name of the height in cm variable")
 
   # verify that 'bp' was set
-  if(is.null(bp)){
-    stop("Please provide the name of the blood pressure variable", call.=FALSE)
-  }
+  .checkArgProvided(bp, "the name of the blood pressure variable")
 
   # if no output object specified then provide a default name
-  if(is.null(newobj)){
-    newobj <- "bp.newobj"
-  }
+  newobj <- .resolveNewobjName(newobj, "bp.newobj")
 
   # call the server-side assign function
   cally <- call('bp_standardsDS', sex, age, height, bp, systolic)