load packages required for validation, recursively discover files for validation

R/validateMassBank.R

 #' Validate a record against a set of RUnit tests
 #' 
-#' Validates a plaintext-MassBankrecord. The Unit Tests to be used
+#' Validates a plaintext-MassBankrecord, or recursively all records
+#' below a directory. The Unit Tests to be used
 #' are installed in RMassBank/
 #' 
 #' @aliases validate
-#' @usage validate(File)
-#' @param File The filepath to the plaintext-records
+#' @usage validate(path)
+#' @param path The filepath to a single record, or a directory to search recursively
+#' @examples
+#' \dontrun{
+#' validate("/tmp/MassBank/OpenData/record/")
+#' }
 #' @export
-validate <- function(File){
+validate <- function(path) {
+
+        if (!require(ontoCAT)) {
+          error("Package ontoCAT missing. Validation requires package ontoCAT and RUnit")
+        }
+
+        if (!require(RUnit)) {
+          error("Package RUnit missing. Validation requires package ontoCAT and RUnit")
+        }
+
 	# Is the argument a directory?
 	# If yes, list the files
 	RMassBank.env$Instrument_List <- .getInstruments()
 	RMassBank.env$testnumber <- 1
-	if(file.info(File[1])$isdir){
-	    Files <- list.files(path = File, full.names = TRUE)
-	} else {Files <- File}
+	if(file.info(path[1])$isdir){
+	    Files <- list.files(path = path,
+                                recursive=TRUE, 
+                                full.names = TRUE)
+	} else {Files <- path}
 	# Parsing with the help the parseMassBank-function
 	RMassBank.env$mb <- lapply(Files,parseMassBank)
 	# Test RMassBank Objects with RUnit
@@ -124,4 +140,4 @@ smiles2mass <- function(SMILES){
 	do.isotopes(massfromformula)
 	mass <- get.exact.mass(massfromformula)
 	return(mass)
-}
\ No newline at end of file
+}

inst/unitTests/runit.MS2.test.R

@@ -45,7 +45,7 @@ test.PrecursorType <- function(){
 test.smilesvsexactmass <- function(){
 	Mass_Calculated_Through_Smiles <- smiles2mass(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$SMILES']])
 	Exact_Mass <- RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']]
-	checkEquals(Mass_Calculated_Through_Smiles, Exact_Mass, Exact_Mass/100)
+	checkEquals(Mass_Calculated_Through_Smiles, Exact_Mass, tolerance = Exact_Mass/100)
 }
 
 test.sumintensities <- function(){

man/validate.Rd

@@ -2,13 +2,20 @@
 \alias{validate}
 \title{Validate a record against a set of RUnit tests}
 \usage{
-  validate(File)
+  validate(path)
 }
 \arguments{
-  \item{File}{The filepath to the plaintext-records}
+  \item{path}{The filepath to a single record, or a
+  directory to search recursively}
 }
 \description{
-  Validates a plaintext-MassBankrecord. The Unit Tests to
-  be used are installed in RMassBank/
+  Validates a plaintext-MassBankrecord, or recursively all
+  records below a directory. The Unit Tests to be used are
+  installed in RMassBank/
+}
+\examples{
+\dontrun{
+validate("/tmp/MassBank/OpenData/record/")
+}
 }