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fix unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-04 14:41:02 +02:00
parent 082e52a0dd
commit 37f6db5ccd
19 changed files with 297 additions and 234 deletions
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38
inst/tinytest/test-mo.R
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@@ -40,7 +40,7 @@ expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
@@ -53,9 +53,8 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
@@ -90,14 +89,13 @@ expect_identical(
"staaur",
"S. aureus",
"S aureus",
"Sthafilokkockus aureeuzz",
"Sthafilokkockus aureus",
"Staphylococcus aureus",
"MRSA",
"VISA",
"meth.-resis. S. aureus (MRSA)"
))
"VISA"
), minimum_matching_score = 0)
)),
rep("B_STPHY_AURS", 10)
rep("B_STPHY_AURS", 9)
)
expect_identical(
as.character(
@@ -148,8 +146,8 @@ expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
@@ -213,19 +211,17 @@ expect_equal(
# check empty values
expect_equal(
as.character(suppressWarnings(as.mo(""))),
as.character(as.mo("")),
NA_character_
)
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
@@ -250,7 +246,7 @@ expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))
# combination of existing mo and other code
expect_identical(
as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
c("B_ESCHR_COLI", "B_ESCHR_COLI")
)
@@ -274,7 +270,7 @@ expect_equal(
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
)
expect_stdout(print(mo_uncertainties()))
x <- as.mo("S. aur")
x <- as.mo("Sta. aur")
# many hits
expect_stdout(print(mo_uncertainties()))