Nothing
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)
}
################################################################################
## 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
################################################################################
## 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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