better error and warning messages for tabMWRacc type as individual an…

…d invalid accchk entries #61
massbays-tech · Sep 28, 2023 · b94c95a · b94c95a
1 parent aa1b9a7
commit b94c95a
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Showing 2 changed files with 45 additions and 9 deletions.
diff --git a/R/tabMWRacc.R b/R/tabMWRacc.R
@@ -48,6 +48,8 @@ tabMWRacc <- function(res = NULL, acc = NULL, frecom = NULL, fset = NULL, runchk
 
   utilMWRinputcheck(mget(ls()))
 
+  accchkall <- c('Field Blanks', 'Lab Blanks', 'Field Duplicates', 'Lab Duplicates', 'Lab Spikes / Instrument Checks')
+
   type <- match.arg(type)
 
   # table theme
@@ -56,9 +58,8 @@ tabMWRacc <- function(res = NULL, acc = NULL, frecom = NULL, fset = NULL, runchk
     flextable::autofit(x)
   }
 
-  if(type %in% c('summary', 'percent')){
-    accchk <- c('Field Blanks', 'Lab Blanks', 'Field Duplicates', 'Lab Duplicates', 'Lab Spikes / Instrument Checks')
-  }
+  if(type %in% c('summary', 'percent'))
+    accchk <- accchkall
 
   # get accuracy summary
   accsum <- qcMWRacc(res = res, acc = acc, frecom = frecom, fset = fset, runchk = runchk, warn = warn, accchk = accchk, suffix = suffix)
@@ -68,13 +69,34 @@ tabMWRacc <- function(res = NULL, acc = NULL, frecom = NULL, fset = NULL, runchk
     if(length(accchk) != 1)
       stop('accchk must have only one entry for type = "individual"')
 
+    if(!accchk %in% accchkall)
+      stop('accchk must be one of ', paste(accchkall, collapse  = ', '))
+
     totab <- accsum[[1]]
 
     # warning if no data to use for table
     if(is.null(totab)){
-      if(warn)
-        warning(paste('No data to check for', accchk), call. = FALSE)
+
+      # identify valid entries for accchk
+      chk <- qcMWRacc(res = res, acc = acc, frecom = frecom, fset = fset, runchk = F, warn = F, 
+                      accchk = accchkall, suffix = suffix
+      ) %>% 
+        lapply(is.null) %>% 
+        unlist()
+
+      # check if accsum completely empty
+      if(all(chk))
+        stop('No QC records or reference values for parameters with defined DQOs. Cannot create QC tables.', call. = FALSE)
+
+      # warning for invalid accchk entry, indication of valid acchk entries
+      if(warn){
+        valent <- paste(names(chk)[!chk], collapse = ', ')
+        msg <- paste0('No data to check for ', accchk, ', valid accchk entries include ', valent)
+        warning(msg, call. = FALSE)
+      }
+
       return(NULL)
+
     }
 
     totab <- totab %>% 

diff --git a/tests/testthat/test-tabMWRacc.R b/tests/testthat/test-tabMWRacc.R
@@ -1,13 +1,20 @@
 test_that("Checking output format type error if individual and more than one table type", {
-  expect_error(tabMWRacc(resdat, accdat, frecomdat, runchk = F, warn = F, type = 'individual'))
+  expect_error(tabMWRacc(resdat, accdat, frecomdat, runchk = F, warn = F, type = 'individual'),
+               'accchk must have only one entry for type = "individual"')
+})
+
+test_that("Checking output format type error if individual and incorrect accchk", {
+  expect_error(tabMWRacc(resdat, accdat, frecomdat, runchk = F, warn = F, type = 'individual', accchk = 'asdf'),
+               'accchk must be one of Field Blanks, Lab Blanks, Field Duplicates, Lab Duplicates, Lab Spikes / Instrument Checks')
 })
 
 test_that("Checking output format type warning if individual and no table", {
   chk <- resdat %>% 
     filter(!`Activity Type` == 'Quality Control Sample-Field Blank')
   expect_warning(
     expect_null(
-      tabMWRacc(chk, accdat, frecomdat, runchk = F, warn = T, type = 'individual', accchk = 'Field Blanks')
+      tabMWRacc(chk, accdat, frecomdat, runchk = F, warn = T, type = 'individual', accchk = 'Field Blanks'),
+      'No data to check for Field Blanks, valid accchk entries include Lab Blanks, Field Duplicates, Lab Duplicates, Lab Spikes / Instrument Checks'
     )
   )
 })
@@ -33,9 +40,16 @@ test_that("Checking output warning if missing completeness data and format type
   expect_warning(tabMWRacc(respth, accpth, chk, runchk = F, warn = T, type = 'percent'))
 })
 
-test_that("Checking error if no QC records or reference values", {
+test_that("Checking error if no QC records or reference values and type as percent", {
+  chk <- readMWRacc(accpth, runchk = F, warn = F) %>% 
+    mutate_at(vars(matches('Duplicate|Blank|Accuracy')), function(x) NA)
+
+  expect_error(tabMWRacc(respth, chk, frecompth, runchk = F, warn = T, type = 'percent'), 'No QC records or reference values for parameters with defined DQOs. Cannot create QC tables.')
+})
+
+test_that("Checking error if no QC records or reference values and type as individual", {
   chk <- readMWRacc(accpth, runchk = F, warn = F) %>% 
     mutate_at(vars(matches('Duplicate|Blank|Accuracy')), function(x) NA)
 
-  expect_error(tabMWRacc(respth, chk, frecompth, runchk = F, warn = T, type = 'percent'))
+  expect_error(tabMWRacc(respth, chk, frecompth, runchk = F, warn = T, type = 'individual', accchk = 'Field Blanks'), 'No QC records or reference values for parameters with defined DQOs. Cannot create QC tables.')
 })