Update Metadata_methods.R

Add adduct file format validity checks to avoid downstream errors

R/Metadata_methods.R

@@ -147,12 +147,14 @@ function(struct, db = "hmdb", adcharge = 1, admult = 1, DBfile = "",
  stop("Please input a valid DB name")
  )
  struct@metadata@ExpParam@DB <- dbdata
+
  #Set corresponding adduct table
  if(adductfile != ""){
- struct@metadata@ExpParam@adlist <- tryCatch(
- read.csv(adductfile),
- error = function(cond){stop("Invalid csv address")
- })
+ ad <- tryCatch(read.csv(adductfile), 
+ error = function(cond){stop("Invalid csv address")})
+ check_adduct_validity(ad)
+ struct@metadata@ExpParam@adlist <- ad
+
  } else {
  ad <- adductTables(adcharge, admult)
  ion <- struct@metadata@ExpParam@ion
@@ -178,6 +180,29 @@ function(struct, db = "hmdb", adcharge = 1, admult = 1, DBfile = "",
  return(struct)
 })
 
+check_adduct_validity <- function(adduct_df){
+ adduct_fields <- c("adduct", "Charge", "Mult", "massdiff", "Ion_mode",
+ "Formula_add", "Formula_ded")
+ missing <- !colnames(adduct_df) %in% adduct_fields
+ if(any(missing)){
+ stop("The following adduct fields are missing:",
+ colnames(adduct_df)[missing])
+ }
+ if(ncol(adduct_df) != 7){
+ warning("The number of adduct fields does not match with expectations")
+ }
+ if(colnames(adduct_df) != adduct_fields){
+ stop("The adduct fields aren't ordered correctly\n",
+ "Expected order: ", paste(adduct_fields, collapse ="/"))
+ }
+ if(nrow(adduct_df) == 0){
+ stop("No adduct rows in the dataframe")
+ }
+}
+
+
+
+
 #' @title addAd
 #' @description Adds new custom adducts to the RHermesExp adduct
 #' list