P281424/AMR
1
0 Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-11-16 00:10:57 +01:00
Code Releases Activity
Files
4be73528430a662322e6536c507a6b952532c9c0
AMR/tests/testthat/test-session_cache.R
T

163 lines
9.8 KiB
R
Raw Blame History

# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-session_cache.R", {
skip_on_cran()
# as.ab() ----
ab_reset_session()
# a `fast_mode` result must never be reused by a regular coercion
expect_true(is.na(suppressWarnings(as.ab("amxcilin", fast_mode = TRUE, info = FALSE))))
expect_identical(as.character(suppressWarnings(as.ab("amxcilin", info = FALSE))), "AMX")
expect_true(all(c("amxcilin") %in% AMR:::AMR_env$ab_previously_coerced$input))
expect_identical(colnames(AMR:::AMR_env$ab_previously_coerced), c("key", "input", "value"))
# second run comes from the cache and gives the same result
expect_identical(as.character(as.ab("amxcilin", info = FALSE)), "AMX")
# separate calls accumulate in the cache, and repeated input adds no rows
suppressWarnings(as.ab("ciproflxacin", info = FALSE))
expect_true(all(c("amxcilin", "ciproflxacin") %in% AMR:::AMR_env$ab_previously_coerced$input))
n_cached <- NROW(AMR:::AMR_env$ab_previously_coerced)
as.ab(c("amxcilin", "ciproflxacin"), info = FALSE)
expect_identical(NROW(AMR:::AMR_env$ab_previously_coerced), n_cached)
# a cached value is really used, not recomputed
amr_env <- AMR:::AMR_env
cache_bak <- amr_env$ab_previously_coerced
amr_env$ab_previously_coerced$value[amr_env$ab_previously_coerced$input == "amxcilin"] <- "GEN"
expect_identical(as.character(as.ab("amxcilin", info = FALSE)), "GEN")
amr_env$ab_previously_coerced <- cache_bak
# ATC codes and synonyms are looked up in the session index
expect_identical(as.character(as.ab(c("J01CA04", "J01MA02", "amoxil", "cipro"), info = FALSE)), c("AMX", "CIP", "AMX", "CIP"))
# resetting does not touch microorganism uncertainties
suppressWarnings(as.mo("Klebsiela pneumonia", info = FALSE))
n_uncertain <- NROW(mo_uncertainties())
expect_message(ab_reset_session())
expect_identical(NROW(mo_uncertainties()), n_uncertain)
expect_identical(NROW(AMR:::AMR_env$ab_previously_coerced), 0L)
# as.mo() ----
mo_reset_session()
x <- c("Klebsiela pneumonia", "Stafylococcus aureus")
expect_identical(as.character(suppressWarnings(as.mo(x, info = FALSE))), c("B_KLBSL_PNMN", "B_STPHY_AURS"))
expect_true(all(x %in% AMR:::AMR_env$mo_previously_coerced$input))
expect_identical(NROW(mo_uncertainties()), 2L)
# second run comes from the cache, and the uncertainties are still complete
expect_identical(as.character(suppressWarnings(as.mo(rev(x), info = FALSE))), c("B_STPHY_AURS", "B_KLBSL_PNMN"))
expect_identical(sort(mo_uncertainties()$original_input), sort(x))
# separate calls accumulate in the cache, also in interactive sessions without an mo_source file, where the default `reference_df = get_mo_source()` once emptied the cache on every call
mo_reset_session()
suppressWarnings(as.mo(x[1], info = FALSE))
suppressWarnings(as.mo(x[2], info = FALSE))
expect_true(all(x %in% AMR:::AMR_env$mo_previously_coerced$input))
n_cached <- NROW(AMR:::AMR_env$mo_previously_coerced)
invisible(get_mo_source(destination = tempfile(fileext = ".rds")))
expect_identical(NROW(AMR:::AMR_env$mo_previously_coerced), n_cached)
# repeated input adds no rows
suppressWarnings(as.mo(x, info = FALSE))
expect_identical(NROW(AMR:::AMR_env$mo_previously_coerced), n_cached)
# a cached value is really used, not recomputed
amr_env <- AMR:::AMR_env
cache_bak <- amr_env$mo_previously_coerced
amr_env$mo_previously_coerced$value[amr_env$mo_previously_coerced$input == x[1]] <- "B_ESCHR_COLI"
expect_identical(as.character(suppressWarnings(as.mo(x[1], info = FALSE))), "B_ESCHR_COLI")
amr_env$mo_previously_coerced <- cache_bak
# another minimum_matching_score is another cache key
n_cached <- NROW(AMR:::AMR_env$mo_previously_coerced)
suppressWarnings(as.mo(x, minimum_matching_score = 0.1, info = FALSE))
expect_identical(NROW(AMR:::AMR_env$mo_previously_coerced), n_cached + 2L)
# cached results are keyed on the original input, also when it is cleaned before fuzzy matching
mo_reset_session()
suppressWarnings(as.mo("Klebsiela pneumonia group", info = FALSE))
expect_true("Klebsiela pneumonia group" %in% AMR:::AMR_env$mo_previously_coerced$input)
# input that could not be coerced is also remembered
expect_identical(as.character(suppressWarnings(as.mo("xq", info = FALSE))), "UNKNOWN")
expect_warning(as.mo("xq", info = FALSE))
expect_identical(mo_failures(), "xq")
# valid codes of outdated names are replaced, also on the fast path
syn <- AMR:::AMR_env$MO_lookup$mo[AMR:::AMR_env$MO_lookup$status == "synonym"][1:5]
expect_false(any(as.mo(syn, keep_synonyms = FALSE, info = FALSE) %in% syn, na.rm = TRUE))
expect_identical(as.character(as.mo(syn, keep_synonyms = TRUE, info = FALSE)), as.character(syn))
# SNOMED codes
expect_identical(as.character(as.mo(c(112283007, 3092008), info = FALSE)), c("B_ESCHR_COLI", "B_STPHY_AURS"))
# synonym_mo_to_accepted_mo() ----
all_mo <- as.character(AMR:::AMR_env$MO_lookup$mo)
for (fill in c(TRUE, FALSE)) {
AMR:::reset_mo_cache()
expect_identical(
AMR:::synonym_mo_to_accepted_mo(c(all_mo, NA, "invalid"), fill_in_accepted = fill),
AMR:::synonym_mo_to_accepted_mo_uncached(c(all_mo, NA, "invalid"), fill_in_accepted = fill, dataset = AMR:::AMR_env$MO_lookup)
)
# now from the memoised mapping
expect_identical(
AMR:::synonym_mo_to_accepted_mo(rev(all_mo), fill_in_accepted = fill),
AMR:::synonym_mo_to_accepted_mo_uncached(rev(all_mo), fill_in_accepted = fill, dataset = AMR:::AMR_env$MO_lookup)
)
}
# mo_*() functions ----
x <- as.mo(c("B_ESCHR_COLI", "B_STPHY_AURS", NA, "B_ESCHR_COLI", "UNKNOWN"))
expect_identical(mo_name(x, language = NULL), c("Escherichia coli", "Staphylococcus aureus", NA, "Escherichia coli", "(unknown name)"))
expect_identical(mo_genus(rep(x, 3), language = NULL), rep(mo_genus(x, language = NULL), 3))
expect_identical(mo_snomed(x[c(1, 1, 3)]), list(mo_snomed(x[1])[[1]], mo_snomed(x[1])[[1]], NULL))
expect_identical(mo_property(x, "prevalence"), as.double(AMR:::AMR_env$MO_lookup$prevalence[match(x, AMR:::AMR_env$MO_lookup$mo)]))
# input that already contains the property is returned as is
expect_identical(mo_genus(c("Escherichia", "Escherichia", NA)), c("Escherichia", "Escherichia", NA))
# character input with duplicates
expect_identical(mo_name(c("E. coli", "S. aureus", "E. coli"), language = NULL), c("Escherichia coli", "Staphylococcus aureus", "Escherichia coli"))
# factors
expect_identical(mo_gramstain(factor(c("E. coli", "S. aureus", "E. coli")), language = NULL), c("Gram-negative", "Gram-positive", "Gram-negative"))
# synonyms are replaced unless keep_synonyms = TRUE
expect_false(any(mo_name(syn, keep_synonyms = FALSE, language = NULL) == mo_name(syn, keep_synonyms = TRUE, language = NULL)))
# invalidation ----
mo_reset_session()
suppressWarnings(as.mo("Klebsiela pneumonia", info = FALSE))
invisible(AMR:::get_mo_index())
invisible(AMR:::synonym_mo_to_accepted_mo("B_ESCHR_COLI"))
suppressMessages(add_custom_microorganisms(data.frame(genus = "Testbacterium", species = "cachei")))
expect_identical(NROW(AMR:::AMR_env$mo_previously_coerced), 0L)
expect_null(AMR:::AMR_env$MO_index)
expect_null(AMR:::AMR_env$mo_accepted)
expect_identical(mo_name("Testbacterium cachei", language = NULL), "Testbacterium cachei")
suppressMessages(clear_custom_microorganisms())
expect_identical(NROW(AMR:::AMR_env$mo_previously_coerced), 0L)
ab_reset_session()
expect_true(is.na(suppressWarnings(as.ab("Qwxzqwxz", info = FALSE))))
invisible(AMR:::get_ab_index())
suppressMessages(add_custom_antimicrobials(data.frame(ab = "TESTCD", name = "Qwxzqwxz", group = "Test group")))
expect_identical(NROW(AMR:::AMR_env$ab_previously_coerced), 0L)
expect_null(AMR:::AMR_env$AB_index)
expect_identical(as.character(as.ab("Qwxzqwxz", info = FALSE)), "TESTCD")
suppressMessages(clear_custom_antimicrobials())
expect_true(is.na(suppressWarnings(as.ab("Qwxzqwxz", info = FALSE))))
})
View Git Blame Copy Permalink