# vim:textwidth=128:expandtab:shiftwidth=4:softtabstop=4

library(argoFloats)
context("quality-control flags")

## > ## DEK 2020-12-31:
## > ## I am commenting the next block out because it is not robust against changes to
## > ## data(index).
## > ## Perhaps this block can be uncommented and made robust later.
## >
## > test_that("applyQC with default 'flag' and 'action' arguments",
## >           {
## >               skip_if_not(hasArgoTestCache())
## >               data(index)
## >               i <- subset(index, 1:5) # first 5 profiles
## >               raw <- expect_output(expect_warning(readProfiles(getProfiles(i, argoDefaultDestdir())), "^Of 5 profiles read"), "|====")
## >               clean <- applyQC(raw)
## >               for (i in raw[["length"]]) {
## >                   for (field in c("temperature", "salinity", "pressure")) {
## >                       bad <- raw[["argos", i]][[paste0(field, "Flag")]] %in% c(0,3,4,6,7,9)
## >                       expect_true(all(is.na(clean[["argos", i]][[field]]) == bad))
## >                   }
## >               }
## >           }
## > )

## > ## DEK 2020-12-31:
## > ## I am commenting the next block out because it is not robust against changes to
## > ## data(index).
## > ## Perhaps this block can be uncommented and made robust later.
## >
## > test_that("showing QC tests", {
## >     skip_if_not(hasArgoTestCache())
## >     data('index')
## >     subset <- expect_message(subset(index, 1), "Kept 1 cycles")
## >     ## DK: this was not used
## >     ##indexq <- expect_message(subset(index, 1),
## >     ##                         "Kept 1 cycles \\(0.105%\\)")
## >     profiles <- getProfiles(subset)
## >     argos <- expect_output(expect_warning(readProfiles(profiles), "^Of 1 profiles read"), "|===")
## >     argos1 <- argos[[1]]
## >     ## this is only a consistency check with values as of 2020-07-17, not a real
## >     ## test of what to expect.
## >     expect_output(showQCTests(argos[[1]]), "^Tests performed: 2 3 4 5 6 13 14 15 16 17 19\\n    Failed test 14 \\(Density Inversion test\\)*$")
## > })