Update with current v7.0-dev

DESCRIPTION

@@ -64,7 +64,7 @@ Authors@R: c(person(given = "Paul",
                                 affiliation = "Genomics Coordination Centre, UMCG, Netherlands")))
 License: GPL-3
 Depends:
-    R (>= 4.0.0),
+    R (>= 4.1.0),
     DSI (>= 1.7.1)
 Imports:
     cli,
@@ -88,6 +88,6 @@ Suggests:
     DSOpal,
     DSMolgenisArmadillo,
     DSLite
-RoxygenNote: 8.0.0
 Encoding: UTF-8
 Language: en-GB
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -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
+)

R/ds.matrix.R

@@ -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{
 #' 
@@ -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)){
@@ -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

R/ds.matrixDet.R

@@ -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{
 #' 
@@ -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)){
@@ -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

R/ds.matrixDet.report.R

@@ -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{
 #' 
@@ -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)){