From 4fd4ec3ba5aaae3bfcd5be68f944b07c3b2ae792 Mon Sep 17 00:00:00 2001
From: Stuart Watt <stuart@morungos.com>
Date: Fri, 3 Nov 2023 15:30:39 -0300
Subject: [PATCH] Add uncertainty validation for external

Resolves #352

## Testing Notes

Should now throw an error when any external file has an `uncertainty` value without a valid, present `unit_uncertainty`

## Technical Notes

Adds uncertainty unit validation and checks
---
 R/import_functions.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/R/import_functions.R b/R/import_functions.R
index 7aa1a67..254b29d 100644
--- a/R/import_functions.R
+++ b/R/import_functions.R
@@ -836,6 +836,18 @@ read_contaminants <- function(file, data_dir = ".", info) {
       colClasses = var_id[ok]
     )
     
+    # additional validations
+
+    # every valid `uncertainty` must have a valid `unit_uncertainty`
+    uncertainty_present <- which(complete.cases(data$uncertainty))
+    uncertainty_present_valid_units <- 
+      data$unit_uncertainty[uncertainty_present] %in% c("%", "U2", "SD")
+    if (! all(uncertainty_present_valid_units)) {
+      stop(
+        "Missing or invalid uncertainty units for specified uncertainty values. ",
+        "Please check that all uncertainty values have a valid unit: %, U2, or SD"
+      )
+    }
   }