diff BiodbLogger.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BiodbLogger.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,47 @@
+# vi: fdm=marker
+
+##########################
+# CLASS DECLARATION {{{1 #
+##########################
+
+BiodbLogger <- methods::setRefClass("BiodbLogger", contains = 'BiodbObserver', fields = list(.verbose.level = 'integer', .debug.level = 'integer', .file = 'ANY', .fail.on.error = 'logical', .signal.warnings = 'logical'))
+
+####################
+# CONSTRUCTOR {{{1 #
+####################
+
+BiodbLogger$methods( initialize = function(verbose.level = 1, debug.level = 1, file = NULL, ...) {
+
+	.verbose.level <<- if ( ! is.null(verbose.level) && ! is.na(verbose.level)) verbose.level else 1
+	.debug.level <<- if ( ! is.null(debug.level) && ! is.na(debug.level)) debug.level else 1
+	.file <<- if ( ! is.null(file) && ! is.na(file)) file else stderr()
+	.fail.on.error <<- TRUE
+	.signal.warnings <<- TRUE
+
+	callSuper(...)
+})
+
+################
+# MESSAGE {{{1 #
+################
+
+BiodbLogger$methods( message = function(type = MSG.INFO, msg, level = 1) {
+	type %in% biodb::MSG.TYPES || .self$message(biodb::MSG.ERROR, paste0("Unknown message type ", type, "."))
+
+	display = TRUE
+	if (type == biodb::MSG.INFO && .self$.verbose.level < level)
+		display = FALSE
+	if (type == biodb::MSG.DEBUG && .self$.debug.level < level)
+		display = FALSE
+
+	if (display)
+		cat(type, ': ', msg, "\n", sep = '', file = .self$.file)
+
+	# Raise error
+	if (type == biodb::MSG.ERROR && .self$.fail.on.error)
+		stop(msg)
+
+	# Raise warning
+	if (type == biodb::MSG.WARNING && .self$.signal.warnings)
+		warning(msg)
+})