rename args fail_on_ to stop_on_; add stop_on_fail; add tests; closes #8

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataverifyr
 Type: Package
 Title: A Lightweight, Flexible, and Fast Data Validation Package that Can Handle All Sizes of Data
-Version: 0.1.6.9002
+Version: 0.1.6.9003
 Authors@R: c(
       person(given = "David",
              family = "Zimmermann-Kollenda",

NEWS.md

@@ -1,3 +1,11 @@
+
+# dataverifyr 0.1.7
+
+* rename args `fail_on_X` to `stop_on_X`
+* adds `stop_on_fail` to [`check_data()`], so that the examples using `read_custom()` make sense (eg in the Readme); thanks [FedericoComoglio](https://github.com/FedericoComoglio) for pointing it out!
+* fix bug when dplyr backend is used + add tests; thanks [FedericoComoglio](https://github.com/FedericoComoglio) for reporting the bug!
+* expose [`detect_backend()`] to allow user the check which backend is used
+
 # dataverifyr 0.1.6
 
 * allow multiline rules in yaml file

R/check_data.R

@@ -4,8 +4,9 @@
 #' [`arrow::arrow_table`], [`arrow::open_dataset`], or [`dplyr::tbl`] (SQL connection)
 #' @param rules a list of [`rule`]s
 #' @param xname optional, a name for the x variable (only used for errors)
-#' @param fail_on_warn if the function should throw an error on a warning
-#' @param fail_on_error if the function should throw an error on a failed rule
+#' @param stop_on_fail when any of the rules fail, throw an error with stop
+#' @param stop_on_warn when a warning is found in the code execution, throw an error with stop
+#' @param stop_on_error when an error is found in the code execution, throw an error with stop
 #'
 #' @return a data.frame-like object with one row for each rule and its results
 #' @export
@@ -22,7 +23,8 @@
 #'
 #' check_data(mtcars, rs)
 check_data <- function(x, rules, xname = deparse(substitute(x)),
-                       fail_on_warn = FALSE, fail_on_error = FALSE) {
+                       stop_on_fail = FALSE, stop_on_warn = FALSE,
+                       stop_on_error = FALSE) {
 
   # if rules is a yaml file, read it in
   if (length(rules) == 1 && is.character(rules)) rules <- read_rules(rules)
@@ -42,19 +44,19 @@ check_data <- function(x, rules, xname = deparse(substitute(x)),
 
   res <- check_(x, rules, backend = backend)
 
-  # fails on warning and/or error
-  if (fail_on_warn && any(res$warn != "") ||
-      fail_on_error && any(res$error != "")) {
-    warn <- fail_on_warn && any(res$warn != "")
-    err <- fail_on_error && any(res$error != "")
+  # stops on fail, warning and/or error
+  fail <- stop_on_fail && any(res$fail != 0)
+  warn <- stop_on_warn && any(res$warn != "")
+  err <- stop_on_error && any(res$error != "")
 
-    txt <- sprintf("In dataset '%s' found %s%s%s",
-                   xname,
-                   if (warn) sprintf("%s warnings", sum(res$warn != "")),
-                   if (warn && err) " and ",
-                   if (err) sprintf("%s errors", sum(res$error != "")))
-    stop(txt)
+  if (fail || warn || err) {
+    tt <- paste(c(
+      if (fail) sprintf("%s rule fails", sum(res$fail != 0)),
+      if (warn) sprintf("%s warnings", sum(res$warn != "")),
+      if (err) sprintf("%s errors", sum(res$error != ""))
+    ), collapse = ", ")
 
+    stop(sprintf("In dataset '%s' found %s", xname, tt))
   }
 
   res

R/rule.R

@@ -7,7 +7,12 @@
 #' [arrow documentation](https://arrow.apache.org/docs/r/reference/acero.html#function-mappings)).
 #' The expression can be given as a string as well.
 #' @param name an optional name for the rule for reference
-#' @param allow_na does the rule allow for NA values? default value is FALSE
+#' @param allow_na does the rule allow for NA values in the data? default value is FALSE.
+#' Note that when NAs are introduced in the expression, `allow_na` has no effect.
+#' Eg when the rule `as.numeric(vs) %in% c(0, 1)` finds the values of `vs` as
+#' `c("1", "A")`, the rule will throw a fail regardless of the value of `allow_na`
+#' as the NA is introduced in the expression and is not found in the original data.
+#' However, when the values of `vs` are `c("1", NA)`, `allow_na` will have an effect.
 #' @param negate is the rule negated, only applies to the expression not allow_na,
 #' that is, if `expr = mpg > 10`, `allow_na = TRUE`, and `negate = TRUE`, it would
 #' match all `mpg <= 10` as well as NAs.

README.Rmd

@@ -110,7 +110,7 @@ read_custom <- function(file, rules) {
   data <- read.csv(file) # or however you read in your data
   # if the check_data detects a fail: the read_custom function will stop
   check_data(data, rules, xname = file,
-             fail_on_error = TRUE, fail_on_warn = TRUE)
+             stop_on_fail = TRUE, stop_on_warn = TRUE, stop_on_error = TRUE)
   # ...
   data
 }
@@ -119,8 +119,8 @@ data <- read_custom("correct_data.csv", rules)
 
 # an error is thrown when warnings or errors are found
 data <- read_custom("wrong_data.csv", rules)
-#> Error in check_data(data, rules, fail_on_error = TRUE, fail_on_warn = TRUE) : 
-#>   In dataset 'wrong_data.csv' found 1 warnings and 1 errors
+#> Error in check_data(data, rules, stop_on_fail = TRUE, stop_on_error = TRUE, stop_on_warn = TRUE) : 
+#>   In dataset 'wrong_data.csv' found 2 rule fails, 1 warnings, 1 errors
 ```
 
 

README.md

@@ -162,7 +162,7 @@ read_custom <- function(file, rules) {
   data <- read.csv(file) # or however you read in your data
   # if the check_data detects a fail: the read_custom function will stop
   check_data(data, rules, xname = file,
-             fail_on_error = TRUE, fail_on_warn = TRUE)
+             stop_on_fail = TRUE, stop_on_warn = TRUE, stop_on_error = TRUE)
   # ...
   data
 }
@@ -171,8 +171,8 @@ data <- read_custom("correct_data.csv", rules)
 
 # an error is thrown when warnings or errors are found
 data <- read_custom("wrong_data.csv", rules)
-#> Error in check_data(data, rules, fail_on_error = TRUE, fail_on_warn = TRUE) : 
-#>   In dataset 'wrong_data.csv' found 1 warnings and 1 errors
+#> Error in check_data(data, rules, stop_on_fail = TRUE, stop_on_error = TRUE, stop_on_warn = TRUE) : 
+#>   In dataset 'wrong_data.csv' found 2 rule fails, 1 warnings, 1 errors
 ```
 
 ## Backends

tests/testthat/test-check_data.R

@@ -9,7 +9,7 @@ rules <- ruleset(
   rule(cyl %in% c(4, 6, 8), "r1"),
   rule(mpg < 10 & mpg > 34, "r2", negate = TRUE),
   rule(disp > 100, "r3", allow_na = TRUE), # data validation "fails"
-  rule(as.numeric(hp) > 0 & as.numeric(hp) < 400, "r4"), # creates warning + 1 NA
+  rule(as.numeric(hp) > 0 & as.numeric(hp) < 400, "r4"), # creates warning + 1 NA -> result in fail
   rule(does_not_exist %in% c("a", "b", "c"), "r5") # creates a stop
 )
 
@@ -210,7 +210,86 @@ test_that("Test extra functionality", {
   expect_equal(res[, !"time"], res2[, !"time"])
   unlink(rule_file)
 
-  # fails on warn and fail on error work =====
-  expect_error(check_data(data, rules, fail_on_warn = TRUE))
-  expect_error(check_data(data, rules, fail_on_error = TRUE))
+  # stop on warn and fail on error work =====
+  expect_error(check_data(data, rules, stop_on_fail = TRUE))
+  expect_error(check_data(data, rules, stop_on_warn = TRUE))
+  expect_error(check_data(data, rules, stop_on_error = TRUE))
+})
+
+test_that("Special case where a warning with allowed missing values returned a fail", {
+  rules <- ruleset(
+    rule(as.numeric(vs) %in% c(0, 1), allow_na = TRUE)
+    # conversion will introduce warning but allow_na should pass it
+  )
+  data <- mtcars
+  data$vs <- as.character(data$vs)
+  data$vs[1] <- "asd"
+
+  res <- check_data(data, rules)
+  expect_equal(res$fail, 1)
+  expect_equal(res$warn, "NAs introduced by coercion")
+})
+
+
+test_that("Extra tests for stop_on_fail with custom reader", {
+  rules <- ruleset(
+    rule(mpg > 10 & mpg < 30), # mpg goes up to 34
+    rule(cyl %in% c(4, 8)), # missing 6 cyl
+    rule(as.numeric(vs) %in% c(0, 1), allow_na = TRUE) # conversion can introduce warning
+  )
+
+  read_custom <- function(file, rules) {
+    data <- read.csv(file)
+    # expected: if the check_data detects a fail: the read_custom function will stop
+    check_data(data, rules, xname = file,
+               stop_on_fail = TRUE, stop_on_warn = TRUE, stop_on_error = TRUE)
+    data
+  }
+
+  d <- mtcars
+  d$name <- rownames(d)
+  rownames(d) <- NULL
+
+  # normal use case, no fails, warnings, errors
+  data_ok <- d[d$mpg <= 30 & d$cyl != 6, ]
+  rownames(data_ok) <- NULL
+
+  file_ok <- tempfile(fileext = ".csv")
+  write.csv(data_ok, file_ok, row.names = FALSE)
+
+  data_ok_got <- read_custom(file_ok, rules)
+  expect_equal(data_ok_got, data_ok)
+
+  # fail use case, no warnings, errors
+  data_fail <- d
+  file_fail <- tempfile(fileext = ".csv")
+  write.csv(data_fail, file_fail, row.names = FALSE)
+
+  expect_error(
+    read_custom(file_fail, rules),
+    "In dataset '.*' found 2 rule fails"
+  )
+
+  # warn use case, no fails, no errors
+  data_warn <- data_ok
+  data_warn$vs <- as.character(data_warn$vs)
+  data_warn$vs[3] <- "asd" # will throw warning
+
+  file_warn <- tempfile(fileext = ".csv")
+  write.csv(data_warn, file_warn, row.names = FALSE)
+
+  # see `allow_na` in `?rule` for an explanation why this fails
+  expect_error(
+    read_custom(file_warn, rules),
+    "In dataset '.*' found 1 rule fails, 1 warnings"
+  )
+
+  # error use case results in rule fails as well, no warnings
+  rules_error <- ruleset(
+    rule(stop("Not going to work..."))
+  )
+  expect_error(
+    read_custom(file_ok, rules_error),
+    "In dataset '.*' found 1 rule fails, 1 errors"
+  )
 })