test_constants.R
In opm: Analysing Phenotype Microarray and Growth Curve Data

library(testthat)
context("Testing the constants of the OPM package for consistency")


if (!exists("TEST.DIR"))
  attach(objects_for_testing())


expect_length <- function(actual, expected) {
  expect_equal(length(actual), expected)
}


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## NOT_YET
## UNTESTED

## BUG_MSG
## UNTESTED


################################################################################


## SEALED
## UNTESTED


################################################################################


## CSV_NAMES
test_that("the internally used CSV names are OK", {
  expect_is(CSV_NAMES, "character")
  expect_false(is.null(names(CSV_NAMES)))
})


## SPECIAL_PLATES
test_that("the so-called special plates are known plates", {
  expect_true(all(SPECIAL_PLATES %in% names(PLATE_MAP)))
  expect_false(is.null(names(SPECIAL_PLATES)))
})


## SP_PATTERN
## UNTESTED (see plate_type())


## THEOR_RANGE
test_that("the theoretical range is OK", {
  expect_length(THEOR_RANGE, 2L)
  expect_false(is.unsorted(THEOR_RANGE))
})


## HOUR
## UNTESTED


## CURVE_PARAMS
test_that("the internally used parameter names are OK", {
  # this strange test is intended to ensure that one thinks twice before
  # changing the constant
  expect_equal(CURVE_PARAMS, c("mu", "lambda", "A", "AUC"))
})


## DISC_PARAM
test_that("the parameter name for discretized values is OK", {
  expect_false(DISC_PARAM %in% CURVE_PARAMS)
})


## RESERVED_NAMES
test_that("the internally used reserved metadata names are OK", {
  # this strange test is intended to ensure that one thinks twice before
  # changing the constant
  wanted <- c("plate", "well", "time", "value", "parameter")
  expect_equal(names(RESERVED_NAMES), wanted)
})


## MEASUREMENT_COLUMN_MAP
test_that("measurement column map is consitent with reserved metadata names", {
  expect_true(all(names(MEASUREMENT_COLUMN_MAP) %in% RESERVED_NAMES))
})


## SOFTWARE
## UNTESTED


## VERSION
## UNTESTED


## UNKNOWN_VERSION
## UNTESTED


## PROGRAM
## UNTESTED


## METHOD
## UNTESTED


## OPTIONS
## UNTESTED


## COLORS
## UNTESTED


## KNOWN_METHODS
test_that("the known method names are OK", {
  expect_is(KNOWN_METHODS, "list")
  expect_true(all(vapply(KNOWN_METHODS, is.character, logical(1L))))
  expect_true("aggregation" %in% names(KNOWN_METHODS))
  expect_true("discretization" %in% names(KNOWN_METHODS))
})


## INSTRUMENT
test_that("instrument key fits to CSV names", {
  expect_false(INSTRUMENT %in% CSV_NAMES)
})


## HTML_DOCTYPE
## UNTESTED


## STR_NOTE
## UNTESTED


################################################################################


## MEMOIZED
## UNTESTED


## OPM_OPTIONS
## UNTESTED


################################################################################


## CHARACTER_STATES
test_that("character-state symbols are correctly defined", {
  expect_is(CHARACTER_STATES, "character")
  expect_length(CHARACTER_STATES, 32L)
  expect_true(all(nchar(CHARACTER_STATES) == 1L))
})


## MISSING_CHAR
test_that("the missing character symbol is correctly defined", {
  expect_is(MISSING_CHAR, "character")
  expect_length(MISSING_CHAR, 1L)
  expect_equal(nchar(MISSING_CHAR), 1L)
  expect_false(MISSING_CHAR %in% CHARACTER_STATES)
})


## PHYLO_FORMATS
test_that("phylogeny formats are defined", {
  expect_is(PHYLO_FORMATS, "character")
  expect_true(length(PHYLO_FORMATS) > 0L)
})


## `_GROUPING`
## UNTESTED


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## GREEK_LETTERS
## UNTESTED


## COMPOUND_NAME_HTML_MAP
## UNTESTED


## SUBSTRATE_PATTERN
test_that("SUBSTRATE_PATTERN matches what it should match", {
  m <- function(s, p) grepl(p, s, FALSE, TRUE)
  e <- function(x) as.logical(unlist(strsplit(x, "", TRUE), FALSE, FALSE))
  x <- c("B07\t\n(Substrate(s))", "A02 \r[My [other] substrate]", "F11", "foo")
  got <- m(x, SUBSTRATE_PATTERN["paren"])
  expect_equal(got, e("TFFF"))
  got <- m(x, SUBSTRATE_PATTERN["bracket"])
  expect_equal(got, e("FTFF"))
  got <- m(x, SUBSTRATE_PATTERN["either"])
  expect_equal(got, e("TTFF"))
  got <- m(x, SUBSTRATE_PATTERN["any"])
  expect_equal(got, e("TTTF"))
  got <- m(x, SUBSTRATE_PATTERN["plain"])
  expect_equal(got, e("FFTF"))
})


## AMINO_ACIDS
test_that("amino-acid spelling is consistent", {
  aa <- names(AMINO_ACIDS)[1:20] # proteinogenic ones must come first
  gly <- "Glycine"
  expect_true(gly %in% aa)
  expect_true(gly %in% WELL_MAP)
  expect_true(all(paste0("L-", setdiff(aa, gly)) %in% WELL_MAP))
})


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