From 71db246d5cddd7e03cfc913b05fed0c07f41e4ea Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sun, 28 Aug 2022 19:17:12 +0200
Subject: [PATCH] unit test fix

---
 .github/workflows/check-pr.yaml     |   3 ++
 .github/workflows/check.yaml        |   1 +
 .github/workflows/codecovr.yaml     |  42 ++++++----------------------
 .github/workflows/lintr.yaml        |  29 ++++++-------------
 DESCRIPTION                         |   4 +--
 NEWS.md                             |   2 +-
 R/first_isolate.R                   |   2 +-
 R/mo.R                              |  12 +++++---
 data-raw/_install_deps.R            |   1 -
 data-raw/_pre_commit_hook.R         |   5 ++++
 data-raw/microorganisms.old.dta     | Bin 2125139 -> 2125139 bytes
 data-raw/microorganisms.old.feather | Bin 580522 -> 579858 bytes
 data-raw/microorganisms.old.md5     |   2 +-
 data-raw/microorganisms.old.parquet | Bin 469907 -> 469183 bytes
 data-raw/microorganisms.old.rds     | Bin 212828 -> 212840 bytes
 data-raw/microorganisms.old.sas     | Bin 2191360 -> 2191360 bytes
 data-raw/microorganisms.old.sav     | Bin 1348687 -> 1348687 bytes
 data-raw/microorganisms.old.xlsx    | Bin 503125 -> 503125 bytes
 data/microorganisms.codes.rda       | Bin 25888 -> 23456 bytes
 data/microorganisms.old.rda         | Bin 212716 -> 212732 bytes
 inst/tinytest/test-_misc.R          |   2 +-
 inst/tinytest/test-ab_property.R    |   6 ++--
 inst/tinytest/test-count.R          |   2 +-
 inst/tinytest/test-data.R           |   1 -
 inst/tinytest/test-first_isolate.R  |   4 +--
 inst/tinytest/test-proportion.R     |   2 +-
 tests/tinytest.R                    |   5 ++--
 27 files changed, 51 insertions(+), 74 deletions(-)

diff --git a/.github/workflows/check-pr.yaml b/.github/workflows/check-pr.yaml
index 0a51be69..f91b8bca 100644
--- a/.github/workflows/check-pr.yaml
+++ b/.github/workflows/check-pr.yaml
@@ -32,6 +32,9 @@ name: R-code-check-PR
 
 jobs:
   R-code-check-PR:
+    # do not run if we are the authors - the other checks will already run
+    if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
+    
     runs-on: ${{ matrix.config.os }}
 
     continue-on-error: ${{ matrix.config.allowfail }}
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 56f463fc..bec95ebd 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -131,6 +131,7 @@ jobs:
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
           # during 'R CMD check', R_LIBS_USER will be overwritten, so:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          # this is a required value to run the unit tests:
           R_RUN_TINYTEST: true
         run: |
           cd ..
diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml
index cf935069..b0bafc5a 100644
--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@@ -33,54 +33,30 @@ name: code-coverage
 
 jobs:
   code-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
     steps:
       - uses: actions/checkout@v3
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: release
-      
-      - uses: r-lib/actions/setup-pandoc@v2
-        # with:
-        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
+          # use RStudio Package Manager to quickly install packages
+          use-public-rspm: true
 
-      - name: Query dependencies
-        # this will change once a week, so it will cache dependency updates
-        run: |
-          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
-        shell: Rscript {0}
-        
-      - name: Restore cached R packages
-        # this step will add the step 'Post Restore cached R packages' on a succesful run
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
-
-      - name: Unpack AMR and install R dependencies
-        run: |
-          tar -xf data-raw/AMR_latest.tar.gz
-          Rscript -e "source('data-raw/_install_deps.R')"
-        shell: bash
-        
-      - name: Show session info
-        run: |
-          options(width = 100)
-          utils::sessionInfo()
-          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
-        shell: Rscript {0}
+          extra-packages: any::covr
 
       - name: Test coverage
         env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          install.packages("covr", repos = "https://cran.rstudio.com/")
-          library(AMR)
-          library(tinytest)
           x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
           print(x)
         shell: Rscript {0}
diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml
index 8f302eed..fecc0d56 100644
--- a/.github/workflows/lintr.yaml
+++ b/.github/workflows/lintr.yaml
@@ -33,34 +33,23 @@ name: lintr
 
 jobs:
   lintr:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          r-version: release
+          # use RStudio Package Manager to quickly install packages
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr
 
       - name: Lint
         run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
diff --git a/DESCRIPTION b/DESCRIPTION
index dc3381d1..527ce06f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9034
+Version: 1.8.1.9039
 Date: 2022-08-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -42,7 +42,7 @@ Suggests:
   rvest,
   tinytest,
   xml2
-VignetteBuilder: knitr
+VignetteBuilder: knitr,rmarkdown
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
diff --git a/NEWS.md b/NEWS.md
index 9050d52d..55ee8c17 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.1.9034
+# AMR 1.8.1.9039
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
diff --git a/R/first_isolate.R b/R/first_isolate.R
index 869e9fb9..e0eb7615 100755
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -529,7 +529,7 @@ first_isolate <- function(x = NULL,
   }
   if (!is.null(col_icu)) {
     if (icu_exclude == TRUE) {
-      message_("Excluding ", format(sum(!col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
+      message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
         add_fn = font_black,
         as_note = FALSE
       )
diff --git a/R/mo.R b/R/mo.R
index 952d0dd0..968a8f23 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -204,12 +204,12 @@ as.mo <- function(x,
     ))
   }
 
+  reference_df <- repair_reference_df(reference_df)
   if (!is.null(reference_df) &&
     check_validity_mo_source(reference_df) &&
     isFALSE(Becker) &&
     isFALSE(Lancefield) &&
-    all(x %in% unlist(reference_df), na.rm = TRUE)) {
-    reference_df <- repair_reference_df(reference_df)
+    all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
     suppressWarnings(
       y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
         pm_left_join(reference_df, by = "x") %pm>%
@@ -221,6 +221,7 @@ as.mo <- function(x,
     y <- x
   } else {
     # will be checked for mo class in validation and uses exec_as.mo internally if necessary
+
     y <- mo_validate(
       x = x, property = "mo",
       Becker = Becker, Lancefield = Lancefield,
@@ -420,7 +421,7 @@ exec_as.mo <- function(x,
   }
 
   # all empty
-  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
+  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0, na.rm = TRUE)) {
     if (property == "mo") {
       return(set_clean_class(rep(NA_character_, length(x_input)),
         new_class = c("mo", "character")
@@ -428,7 +429,7 @@ exec_as.mo <- function(x,
     } else {
       return(rep(NA_character_, length(x_input)))
     }
-  } else if (all(x %in% reference_df[, 1, drop = TRUE][[1]])) {
+  } else if (all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
     # all in reference df
     colnames(reference_df)[1] <- "x"
     suppressWarnings(
@@ -2357,6 +2358,9 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
 }
 
 repair_reference_df <- function(reference_df) {
+  if (is.null(reference_df)) {
+    return(NULL)
+  }
   # has valid own reference_df
   reference_df <- reference_df %pm>%
     pm_filter(!is.na(mo))
diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R
index f22b7aea..d0529fd9 100644
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@@ -26,7 +26,6 @@
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
 install.packages(getwd(), repos = NULL, type = "source")
-# install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
 
 pkg_suggests <- gsub(
   "[^a-zA-Z0-9]+", "",
diff --git a/data-raw/_pre_commit_hook.R b/data-raw/_pre_commit_hook.R
index e744e285..0eea76f5 100644
--- a/data-raw/_pre_commit_hook.R
+++ b/data-raw/_pre_commit_hook.R
@@ -475,6 +475,11 @@ rm(current_globalenv)
 devtools::load_all(quiet = TRUE)
 
 
+# Update URLs -------------------------------------------------------------
+usethis::ui_info("Checking URLs for redirects")
+invisible(capture.output(urlchecker::url_update()))
+
+
 # Document pkg ------------------------------------------------------------
 usethis::ui_info("Documenting package")
 suppressMessages(devtools::document(quiet = TRUE))
diff --git a/data-raw/microorganisms.old.dta b/data-raw/microorganisms.old.dta
index 4e7a735855bb046707d3096ee5b45f7e54ee3a8d..552c99a23461c98009f843122ed75e0e8ac96974 100644
GIT binary patch
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diff --git a/data-raw/microorganisms.old.feather b/data-raw/microorganisms.old.feather
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diff --git a/data-raw/microorganisms.old.md5 b/data-raw/microorganisms.old.md5
index ce38bc35..ad0f168b 100644
--- a/data-raw/microorganisms.old.md5
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diff --git a/data-raw/microorganisms.old.rds b/data-raw/microorganisms.old.rds
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diff --git a/data-raw/microorganisms.old.sas b/data-raw/microorganisms.old.sas
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diff --git a/data-raw/microorganisms.old.sav b/data-raw/microorganisms.old.sav
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diff --git a/data-raw/microorganisms.old.xlsx b/data-raw/microorganisms.old.xlsx
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delta 586
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diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda
index a970048f6e035a906e0936577a9d781de030e051..c93820187e7b9822420f7e64e40d5a1a337df78c 100644
GIT binary patch
delta 123
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b!oc`z8{?%DT&0S0Z0!tqyO}@|jFC|QS3xq$

delta 2574
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diff --git a/data/microorganisms.old.rda b/data/microorganisms.old.rda
index d3a1c6c86b5865387b6422370c5156b1d60fb5ec..a42d6023f9ddcad8d0bd344ebe5b820f4d6de38a 100644
GIT binary patch
delta 162
zcmV;T0A2s={S5s541k0Iv;r&81F&wbw=U2EMQ(qcuDNh$nlA7c8AbDxOtQ|{m^2!5
z%HT>Ix|;4)kau!B3bz)RAO;Dm!|qsyAboTx3!>1ZLbn_s(Zi3%FVley67?RtXQ`*^
zaC|8@l&^mcp@UXAURBPWu~(<bT--m07VdIl!d87?00000knPIs00Gtg4E@$m4y?)d
QJ}?Rmivj=u00045T9$@MQvd(}

delta 145
zcmV;C0B-;M{S55=41k0Iv;r&81D9@}w=U2EMQ(YYHbq?}J_7CRsYtIjP5>+Th4oLK
z>fzL*uzD22B&9v!R3=ggVi3S{IUq$R0abjhsX!!{p&~ai*s~;aw_5=^gx)NKeM)fR
zr>hy|n7cABy-s9{_Y4g?rvLx|2pe)u00GDS4CK~NVV5APJ}?c70ssI200CKAQ&Bq@

diff --git a/inst/tinytest/test-_misc.R b/inst/tinytest/test-_misc.R
index 6871292c..ff511589 100755
--- a/inst/tinytest/test-_misc.R
+++ b/inst/tinytest/test-_misc.R
@@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
 }
 
-# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
+# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
 }
diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R
index b80e4db2..4ce82eeb 100644
--- a/inst/tinytest/test-ab_property.R
+++ b/inst/tinytest/test-ab_property.R
@@ -68,15 +68,15 @@ expect_true(ab_url("AMX") %like% "whocc.no")
 expect_warning(ab_url("ASP"))
 
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25])),
+  colnames(set_ab_names(example_isolates[, 17:22])),
   c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
+  colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
   c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
+  colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
   c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
 )
 
diff --git a/inst/tinytest/test-count.R b/inst/tinytest/test-count.R
index 262018bf..ac64d773 100644
--- a/inst/tinytest/test-count.R
+++ b/inst/tinytest/test-count.R
@@ -79,7 +79,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination = count_susceptible(CIP, GEN)
       ) %>%
       pull(combination),
-    c(253, 465, 192, 558)
+    c(946, 428, 94)
   )
 
   # count_df
diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R
index 4086f6d2..22e2b003 100644
--- a/inst/tinytest/test-data.R
+++ b/inst/tinytest/test-data.R
@@ -57,7 +57,6 @@ expect_identical(as.ab(antibiotics$name), antibiotics$ab)
 datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
 for (i in seq_len(length(datasets))) {
   dataset <- get(datasets[i], envir = asNamespace("AMR"))
-  expect_identical(class(dataset), "data.frame")
   expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
 }
 
diff --git a/inst/tinytest/test-first_isolate.R b/inst/tinytest/test-first_isolate.R
index 2ec4fe53..ceb0d86a 100755
--- a/inst/tinytest/test-first_isolate.R
+++ b/inst/tinytest/test-first_isolate.R
@@ -75,7 +75,7 @@ expect_equal(
     ),
     na.rm = TRUE
   ),
-  941
+  942
 )
 
 # set 1500 random observations to be of specimen type 'Urine'
@@ -160,7 +160,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
 
   # support for WHONET
   expect_message(example_isolates %>%
-    select(-patient_id) %>%
+    select(-patient) %>%
     mutate(
       `First name` = "test",
       `Last name` = "test",
diff --git a/inst/tinytest/test-proportion.R b/inst/tinytest/test-proportion.R
index bfaab47a..79e6683f 100755
--- a/inst/tinytest/test-proportion.R
+++ b/inst/tinytest/test-proportion.R
@@ -84,7 +84,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination_n = n_rsi(CIP, GEN)
       ) %>%
       pull(combination_n),
-    c(305, 617, 241, 711)
+    c(1181, 577, 116)
   )
 
   # proportion_df
diff --git a/tests/tinytest.R b/tests/tinytest.R
index 2753f082..b54662b4 100644
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@@ -27,8 +27,9 @@
 if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
   # env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
   .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
-  if (AMR:::pkg_is_available("tinytest")) {
+  if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
     library(AMR)
+    set_AMR_locale("English")
     out <- test_package("AMR",
       testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
         "inst/tinytest",
@@ -37,7 +38,7 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
       verbose = 99,
       color = FALSE
     )
-    cat("SUMMARY:\n")
+    cat("\n\nSUMMARY:\n")
     print(summary(out))
   }
 }