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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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30
tests/testthat/test-mo_property.R
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@ -78,8 +78,10 @@ current_grampos_classes <- c(
"Thermoleophilia",
"Thermolithobacteria"
)
expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
current_grampos_classes)
expect_identical(
sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
current_grampos_classes
)
expect_equal(mo_species("Escherichia coli"), "coli")
expect_equal(mo_subspecies("Escherichia coli"), "")
@ -103,11 +105,15 @@ expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_true(length(mo_group_members("B_HACEK")) > 1)
expect_inherits(mo_group_members(c("Candida albicans", "Escherichia coli")), "list")
expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
c("facultative anaerobe", "anaerobe"))
expect_identical(
mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
c("facultative anaerobe", "anaerobe")
)
expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
c("1911", "72", "1", "16"))
expect_equal(
as.character(table(mo_pathogenicity(example_isolates$mo))),
c("1911", "72", "1", "16")
)
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
@ -118,8 +124,10 @@ expect_true(mo_url("Candida albicans") %like% "mycobank.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity of getting back full names
expect_identical(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE)))
expect_identical(
microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE))
)
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
@ -169,8 +177,10 @@ expect_identical(
expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))
expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
c("Shimwellia blattae", "Escherichia coli"))
expect_identical(
mo_current(c("Escherichia blattae", "Escherichia coli")),
c("Shimwellia blattae", "Escherichia coli")
)
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")