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last unit tests fix?

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-04 21:33:04 +02:00
parent 37f6db5ccd
commit aa06aad4ea
22 changed files with 275 additions and 256 deletions
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11
inst/tinytest/test-data.R
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@@ -68,10 +68,10 @@ df <- AMR:::MO_lookup
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
expect_true(all(c(
"mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "lpsn", "gbif", "status", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species"
"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies", "rank", "ref", "source",
"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
) %in% colnames(df)))
expect_inherits(AMR:::MO_CONS, "mo")
@@ -87,7 +87,8 @@ expect_true(NROW(uncategorised) == 0,
"All staphylococcal species categorised as CoNS/CoPS.",
paste0(
"Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")"
uncategorised$species, " (", uncategorised$mo, ")",
collapse = "\n"
)
)
)

2
inst/tinytest/test-eucast_rules.R
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@@ -41,7 +41,7 @@ expect_equal(
)
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned, keep_synonyms = TRUE, language = NULL)))
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))

12
inst/tinytest/test-mo_property.R
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@@ -59,7 +59,7 @@ expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
expect_equal(names(mo_info("Escherichia coli")), c(
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref",
"status", "synonyms", "gramstain", "url", "ref",
"snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
@@ -73,7 +73,7 @@ expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
MOs <- microorganisms
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en", keep_synonyms = TRUE))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
@@ -81,13 +81,13 @@ expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
gr <- mo_gramstain("Escherichia coli", language = NULL)
for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in langauge", l))
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
}
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase")], language = "nl") # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL),
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase")]) # gigantic test - will run ALL names
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE) # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL, keep_synonyms = TRUE),
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))