tests/testthat/test_flags.R

In dankelley/oceanglider: Analysis of Oceanographic Glider Data

# vim:textwidth=80:expandtab:shiftwidth=4:softtabstop=4
library(oceglider)
# library(testthat)

test_that("read.glider.seaexplorer.realtime flag names", {
    directory <- system.file("extdata/sea_explorer/realtime_raw", package = "oceglider")
    expect_silent(g <- read.glider.seaexplorer.raw(directory = directory, pattern = "pld1.sub", progressBar = FALSE))
    expect_equal(
        g@metadata$flagScheme,
        list(
            name = "IOOS",
            mapping = list(good = 1, not_evaluated = 2, questionable = 3, bad = 4, missing = 9),
            default = c(3, 4, 9)
        )
    )
})

test_that("read.glider.seaexplorer.raw flag names", {
    directory <- system.file("extdata/sea_explorer/delayed_raw", package = "oceglider")
    expect_silent(g <- read.glider.seaexplorer.raw(
        directory = directory,
        pattern = "pld1.raw",
        progressBar = FALSE
    ))
    expect_equal(
        g@metadata$flagScheme,
        list(
            name = "IOOS",
            mapping = list(good = 1, not_evaluated = 2, questionable = 3, bad = 4, missing = 9),
            default = c(3, 4, 9)
        )
    )
})

test_that("read.glider.seaexplorer.raw flag setting and handling", {
    # This is based on the example given by ?"handleFlags,glider-method"
    directory <- system.file("extdata/sea_explorer/realtime_raw", package = "oceglider")
    expect_silent(g <- read.glider.seaexplorer.raw(directory, "pld1.sub", progressBar = FALSE))
    # NOTE: this test was more hard-wired before issue40, e.g. it
    # demanded that the number of data read be 2784, but that number
    # became 3435 when read.glider.seaexplorer.raw() was changed to
    # address issue40.
    n <- length(g[["salinity"]])
    expect_equal(n, sum(g[["salinityFlag"]] == 2))
    S <- g[["salinity"]]
    badS <- is.na(S) | S < 31
    g2 <- setGliderFlags(g, "salinity", badS, 3)
    expect_true(all(g2[["salinityFlag"]][badS] == 3))
    g3 <- handleGliderFlags(g2) # , c(3, 4, 9)) # use default action, which is "NA"
    expect_true(all(g3[["salinityFlag"]][badS] == 3))
    expect_true(all(is.na(g3[["salinity"]][badS])))
})

test_that("read.glider.seaexplorer.raw flag setting and handling", {
    # This is based on the example given by ?"handleFlags,glider-method"
    directory <- system.file("extdata/sea_explorer/delayed_raw", package = "oceglider")
    expect_silent(g <- read.glider.seaexplorer.raw(directory, "pld1.raw",
        progressBar = FALSE
    ))
    # NOTE: this test was more hard-wired before issue40, e.g. it
    # demanded that the number of data read be 2784, but that number
    # became 3435 when read.glider.seaexplorer.raw() was changed to
    # address issue40.
    n <- length(g[["salinity"]])
    expect_equal(n, sum(g[["salinityFlag"]] == 2))
    S <- g[["salinity"]]
    badS <- is.na(S) | S < 31
    g2 <- setGliderFlags(g, "salinity", badS, 3)
    expect_true(all(g2[["salinityFlag"]][badS] == 3))
    g3 <- handleGliderFlags(g2, c(3, 4, 9)) # use default action, which is "NA"
    expect_true(all(g3[["salinityFlag"]][badS] == 3))
    expect_true(all(is.na(g3[["salinity"]][badS])))
})