Nothing
library(testthat)
context("Testing the substrate-information content of the OPM package")
if (!exists("TEST.DIR"))
attach(objects_for_testing())
################################################################################
## SUBSTRATE_INFO
test_that("CAS numbers and other IDs are OK", {
na_or_match <- function(x, pattern, what) {
expect_true(all(is.na(x) | grepl(pattern, x, FALSE, TRUE)),
sprintf("=> not all %s IDs matched expected pattern", what))
}
expect_true(setequal(colnames(SUBSTRATE_INFO),
c("METACYC", "CAS", "KEGG", "MESH", "DRUG", "CHEBI", "SEED")))
na_or_match(cas <- SUBSTRATE_INFO[, "CAS"], "^\\d", "CAS")
expect_true(all(is_cas(cas[!is.na(cas)]))) # more specific check
na_or_match(SUBSTRATE_INFO[, "KEGG"], "^C\\d{5}$", "KEGG-compound")
na_or_match(SUBSTRATE_INFO[, "DRUG"], "^D\\d{5}$", "KEGG-drug")
na_or_match(SUBSTRATE_INFO[, "CHEBI"], "^\\d+$", "ChEBI")
# the Metacyc IDs are less regular, let alone the MeSH names
na_or_match(SUBSTRATE_INFO[, "METACYC"], "^\\w+((\\+|--?)\\w+)*$", "Metacyc")
na_or_match(SUBSTRATE_INFO[, "MESH"], "^[^\\s].*[^\\s]$", "MeSH")
na_or_match(SUBSTRATE_INFO[, "SEED"], "^cpd\\d+$", "SEED")
})
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