Update default behavior of 'Conf' objects

In recent scenarios and in perspective of up-coming changes, the default
behavior of 'Conf' objects upon initialization and update:

1) The default values are *not* automatically checked against the
allowed values anymore. This is mainly disabled to avoid confusion of
users. The constructor of the class 'Conf' is adapted accordingly.
2) When updating a configuration value, the program execution is now
stopped (using 'stop') on failure. Previously, the respective update has
been ignored while issuing a warning. This change helps preventing
confusion and analysis errors early in an analysis script. Accordingly,
the parameter 'stop.on.error' to all update methods is removed.

Furthermore, the code is streamlined, such that the super-constructor is
called from both subclasses 'NetworkConf' and 'ProjectConf'. Some log
statements are added/adjusted, too.

Signed-off-by: Claus Hunsen <[email protected]>

util-conf.R

@@ -76,7 +76,7 @@ Conf = R6::R6Class("Conf",
                 return(self$get.value(att))
             })
             names(current.values) = names(private$attributes)
-            self$update.values(current.values, stop.on.error = TRUE)
+            self$update.values(current.values)
         },
 
         #' Check whether the given 'value' is the correct datatype
@@ -125,8 +125,8 @@ Conf = R6::R6Class("Conf",
 
         #' The constructor, automatically checking the default values.
         initialize = function() {
-            ## FIXME do we need this?
-            private$check.values()
+            # ## check the default values for validity
+            # private$check.values()
         },
 
         ## * * printing ----------------------------------------------------
@@ -166,8 +166,7 @@ Conf = R6::R6Class("Conf",
         #'
         #' @param entry the entry name for the value
         #' @param value the new value
-        #' @param error call stop() on an error? [default: FALSE]
-        update.value = function(entry, value, stop.on.error = FALSE) {
+        update.value = function(entry, value) {
             ## construct list for updating
             updating = list(value)
             names(updating) = entry
@@ -179,10 +178,9 @@ Conf = R6::R6Class("Conf",
         #' 'updated.values' list.
         #'
         #' @param updated.values the new values for the attributes to be updated
-        #' @param error call stop() on an error? [default: FALSE]
-        update.values = function(updated.values = list(), stop.on.error = FALSE) {
+        update.values = function(updated.values = list()) {
             ## determine the function executed on an error
-            error.function = ifelse(stop.on.error, stop, logging::logwarn)
+            error.function = stop
 
             ## check values to update
             names.to.update = c()
@@ -219,9 +217,7 @@ Conf = R6::R6Class("Conf",
 
                     } else {
                         message = paste0(
-                            "Updating network-configuration attribute '%s' failed.",
-                            if (!stop.on.error) " The failure is ignored!\n",
-                            # "Current value: %s\n",
+                            "Updating network-configuration attribute '%s' failed.\n",
                             "Allowed values (%s of type '%s'): %s\n",
                             "Given value (of type '%s'): %s"
                         )
@@ -476,6 +472,10 @@ ProjectConf = R6::R6Class("ProjectConf", inherit = Conf,
         #'                 and \code{featureexpression}) [default: "feature"]
         initialize = function(data, selection.process, casestudy, artifact = c("feature", "file",
                                                                                "function", "featureexpression")) {
+
+            logging::loginfo("Construct project configuration: starting.")
+
+            ## call super constructor
             super$initialize()
 
             ## verify arguments using match.arg
@@ -486,8 +486,6 @@ ProjectConf = R6::R6Class("ProjectConf", inherit = Conf,
             private$casestudy = verify.argument.for.parameter(casestudy, "character", class(self)[1])
             private$artifact = verify.argument.for.parameter(artifact, "character", class(self)[1])
 
-            logging::loginfo("Construct project configuration: starting.")
-
             ## convert artifact to tagging
             tagging = ARTIFACT.TO.TAGGING[[ artifact ]]
             if (is.null(tagging)) {
@@ -762,16 +760,20 @@ NetworkConf = R6::R6Class("NetworkConf", inherit = Conf,
 
         #' The constructor, automatically checking the default values.
         initialize = function() {
-            # private$check.values()
+            logging::loginfo("Construct network configuration: starting.")
+
+            ## call super constructor
+            super$initialize()
+
+            logging::loginfo("Construct network configuration: finished.")
         },
 
         #' Update the attributes of the class with the new values given in the
         #' 'updated.values' list.
         #'
         #' @param updated.values the new values for the attributes to be updated
-        #' @param error call stop() on an error? [default: FALSE]
-        update.values = function(updated.values = list(), stop.on.error = FALSE) {
-            super$update.values(updated.values = updated.values, stop.on.error = stop.on.error)
+        update.values = function(updated.values = list()) {
+            super$update.values(updated.values = updated.values)
 
             ## 1) "date" and "artifact.type" always as edge attribute
             name = "edge.attributes"