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(v3.0.1.9135) Fix get_mo_source() removing the mo_source file at the default location, returning the wrong mo_source, and throwing an error after the original file was moved, and run the unit tests in CI also in a real interactive session and with a user setup, a Dutch locale, and CLSI as default guideline, with tests that no longer assume an English locale or EUCAST
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dr. M.S. (Matthijs) Berends committed
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# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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# Runs all unit tests from source, see run_tests.sh. Quits with status 1 on any failure or error, and with status 2 if the tests could not be run at all.
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# Every top-level error must end in quit(), since an interactive session would otherwise continue reading "1" from stdin.
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status <- tryCatch(
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{
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if (identical(Sys.getenv("AMR_TEST_INTERACTIVE"), "true") && !interactive()) {
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stop("AMR_TEST_INTERACTIVE is set, but this R session is not interactive")
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}
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cat("Interactive:", interactive(), "| LANG:", Sys.getenv("LANG"), "| AMR options:", paste(names(options())[grepl("^AMR_", names(options()))], collapse = ", "), "\n")
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# report all failures, not only the first 10
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options(warn = 1, testthat.summary.max_reports = Inf, testthat.progress.max_fails = Inf)
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res <- as.data.frame(testthat::test_local(Sys.getenv("AMR_TEST_PKG_DIR", "."), reporter = "summary", stop_on_failure = FALSE))
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cat("\nFiles:", length(unique(res$file)), "| failed:", sum(res$failed), "| errors:", sum(res$error), "| skipped:", sum(res$skipped), "| passed:", sum(res$passed), "\n")
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as.integer(sum(res$failed) > 0 || any(res$error))
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},
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error = function(e) {
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cat("Tests could not be run:", conditionMessage(e), "\n")
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2L
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}
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)
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quit(save = "no", status = status)
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Executable
+51
@@ -0,0 +1,51 @@
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#!/bin/bash
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# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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# Runs an R script, in a real interactive R session if AMR_TEST_INTERACTIVE is "true", and exits with its status.
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# Usage: run_tests.sh <script.R>
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# R CMD check and Rscript are never interactive, so code behind interactive() is otherwise never run in CI.
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# In an interactive session, R reads both its commands and the answers to prompts from stdin, and it ignores -f. Therefore stdin holds one source() line, followed by an endless stream of "1", which means 'proceed' in every utils::menu() prompt of this package.
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# A timeout prevents an unanswerable prompt from hanging the job.
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set +e +o pipefail
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script="$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
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if [ "$AMR_TEST_INTERACTIVE" = "true" ]; then
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{ echo "source('$script')"; yes 1; } | timeout 3600 R --interactive --no-save --quiet
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status=${PIPESTATUS[1]}
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else
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timeout 3600 Rscript "$script"
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status=$?
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fi
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if [ "$status" = "124" ]; then
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echo "Timed out, possibly on a prompt that could not be answered"
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fi
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exit $status
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@@ -0,0 +1,67 @@
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# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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# Sets up the user environment of a test scenario in the home directory, before run_tests.sh runs the tests. Run it through run_tests.sh with AMR_TEST_INTERACTIVE=true, since set_mo_source() only works in interactive sessions.
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# AMR_TEST_SCENARIO can contain one or more of these words, separated by a comma:
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# - "user": an existing ~/mo_source.rds, and the options AMR_custom_ab and AMR_custom_mo set to RDS files
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# - "clsi": the option AMR_guideline set to "CLSI"
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# The options are written to ~/.Rprofile, so that they are set at start-up as with users.
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status <- tryCatch(
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{
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stopifnot(interactive())
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scenarios <- trimws(strsplit(Sys.getenv("AMR_TEST_SCENARIO"), ",")[[1]])
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stopifnot(length(scenarios) > 0, all(scenarios %in% c("user", "clsi")))
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pkgload::load_all(Sys.getenv("AMR_TEST_PKG_DIR", "."), quiet = TRUE)
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opts <- character(0)
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if ("user" %in% scenarios) {
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dir.create("~/amr_fixtures", showWarnings = FALSE)
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write.csv(data.frame(lab_code = c("AMRTEST_ECOLI", "AMRTEST_SAUR"), mo = c("B_ESCHR_COLI", "B_STPHY_AURS")), "~/amr_fixtures/mo_source.csv", row.names = FALSE)
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set_mo_source("~/amr_fixtures/mo_source.csv")
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stopifnot(file.exists("~/mo_source.rds"))
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saveRDS(data.frame(ab = "AMRTST", name = "Amrtestacillin", group = "Test antimicrobials"), "~/amr_fixtures/custom_ab.rds")
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saveRDS(data.frame(genus = "Amrtestbacterium", species = "scenarii"), "~/amr_fixtures/custom_mo.rds")
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opts <- c(opts, paste0("AMR_custom_ab = '", path.expand("~/amr_fixtures/custom_ab.rds"), "'"), paste0("AMR_custom_mo = '", path.expand("~/amr_fixtures/custom_mo.rds"), "'"))
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}
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if ("clsi" %in% scenarios) {
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opts <- c(opts, "AMR_guideline = 'CLSI'")
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}
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if (length(opts) > 0) {
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write(paste0("options(", paste(opts, collapse = ", "), ")"), "~/.Rprofile", append = TRUE)
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}
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cat("Scenario set up:", paste(scenarios, collapse = ", "), "\n")
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if (file.exists("~/.Rprofile")) cat(readLines("~/.Rprofile"), sep = "\n")
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0L
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},
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error = function(e) {
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cat("Scenario could not be set up:", conditionMessage(e), "\n")
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2L
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}
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)
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quit(save = "no", status = status)
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