Merge branch 'develop' into dk

R/accessors.R

@@ -64,9 +64,15 @@ oceDeleteData <- function(object, name)
 #' three possible forms (see \dQuote{Details}).
 #' @param originalName Optional character string giving an 'original' name (e.g.
 #' as stored in the header of a data file).
-#' @param note A note to be stored in the processing log. If an empty string
-#' (the default) then an entry will be constructed from the function call. If
-#' \code{NULL}, then no entry will be added to the processing log.
+#' @param note Either empty (the default), a character string, or \code{NULL},
+#' to control additions made to the processing log of the return value. If
+#' \code{note=""} then the an entry is created based on deparsing the function call.
+#' If \code{note} is a non-empty string, then that string gets added added
+#' to the processing log. Finally, if \code{note=NULL}, then nothing is
+#' added to the processing log. This last form is useful in cases where
+#' \code{oceSetData} is to be called many times in succession, resulting
+#' in an overly verbose processing log; in such cases, it might help
+#' to add a note by e.g. \code{processingLog(a) <- "QC (memo dek-2018-01/31)"}
 #'
 #' @examples
 #' data(ctd)
@@ -81,13 +87,9 @@ oceSetData <- function(object, name, value, unit, originalName, note="")
     if (!inherits(object, "oce"))
         stop("oceSetData() only works for oce objects")
     object@data[[name]] <- value
-    if (nchar(note) > 0)
-        object@processingLog <- processingLogAppend(object@processingLog, note)
-    else if (!is.null(note))
-        object@processingLog <- processingLogAppend(object@processingLog, paste(deparse(match.call()), sep="", collapse=""))
     if (!missing(unit)) {
-       if  (!("units" %in% names(object@metadata))) # some objects might not have units yet
-           object@metadata$units <- list()
+        if  (!("units" %in% names(object@metadata))) # some objects might not have units yet
+            object@metadata$units <- list()
         if (is.list(unit)) {
             ## message("case 1")
             if (is.null(names(unit)))
@@ -134,6 +136,14 @@ oceSetData <- function(object, name, value, unit, originalName, note="")
             object@metadata$dataNamesOriginal[[name]] <- originalName
         }
     }
+    if (!is.null(note)) {
+        if (nchar(note) > 0)
+            object@processingLog <- processingLogAppend(object@processingLog, note)
+        else
+            object@processingLog <- processingLogAppend(object@processingLog,
+                                                        paste(deparse(match.call()),
+                                                              sep="", collapse=""))
+    }
     object
 }
 
@@ -177,14 +187,28 @@ oceDeleteMetadata <- function(object, name)
 #' @param object an \code{oce} object
 #' @param name String indicating the name of the item to be set.
 #' @param value Value for the item.
-#' @param note A note to be stored in the processing log.
+#' @param note Either empty (the default), a character string, or \code{NULL},
+#' to control additions made to the processing log of the return value. If
+#' \code{note=""} then the an entry is created based on deparsing the function call.
+#' If \code{note} is a non-empty string, then that string gets added added
+#' to the processing log. Finally, if \code{note=NULL}, then nothing is
+#' added to the processing log.  This last form is useful in cases where
+#' \code{oceSetData} is to be called many times in succession, resulting
+#' in an overly verbose processing log; in such cases, it might help
+#' to add a note by e.g. \code{processingLog(a) <- "QC (memo dek-2018-01/31)"}
+#'
 oceSetMetadata <- function(object, name, value, note="")
 {
     if (!inherits(object, "oce"))
         stop("oceSetData() only works for oce objects")
     object@metadata[[name]] <- value
-    object@processingLog <- processingLogAppend(object@processingLog, paste(deparse(match.call()), sep="", collapse=""))
-    if (nchar(note) > 0)
-        object@processingLog <- processingLogAppend(object@processingLog, note)
+    if (!is.null(note)) {
+        if (nchar(note) > 0)
+            object@processingLog <- processingLogAppend(object@processingLog, note)
+        else
+            object@processingLog <- processingLogAppend(object@processingLog,
+                                                        paste(deparse(match.call()),
+                                                              sep="", collapse=""))
+    }
     object
 }

R/processingLog.R

@@ -7,6 +7,7 @@
 #' processingLogShow(ctd)
 #' processingLog(ctd) <- "test"
 #' processingLogShow(ctd)
+#' @family things related to processing logs
 "processingLog<-" <- function(x, value)
 {
     if (inherits(x, "oce")) {
@@ -31,6 +32,7 @@
 #' @param h either the \code{processingLog} slot of an object, or
 #' an \code{oce} object from which the processingLog will be extracted
 #' @param value A string indicating the text of the log entry.
+#' @family things related to processing logs
 processingLogAppend <- function(h, value="")
 {
     if (inherits(h, "oce"))
@@ -56,13 +58,15 @@ processingLogAppend <- function(h, value="")
 #' @return A \code{\link{list}} containing \code{time}, which is
 #' the \code{\link{Sys.time}} at the moment the function is called and
 #' \code{value}, a string that is set to the argument of the same name.
+#' @family things related to processing logs
 processingLogItem <- function(value="")
 {
     list(time=c(Sys.time()), value=value)
 }
 
 #' Show the processing log of an \code{oce} object
 #' @param x An \code{oce} object.
+#' @family things related to processing logs
 processingLogShow <- function(x)
 {
     cat("* Processing Log\n")