style issue and failed test

pharmaverse · Jul 19, 2024 · 7a5988e · 7a5988e
1 parent 0008b2e
commit 7a5988e
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Showing 8 changed files with 159 additions and 104 deletions.
diff --git a/tests/testthat/test-derive_seq.R b/tests/testthat/test-derive_seq.R
@@ -9,9 +9,9 @@ test_that("`derive_seq()` works as expected", {
   expected_vsseq <- tibble::tribble(
     ~STUDYID, ~DOMAIN,     ~USUBJID,                  ~VSSPID, ~VSTESTCD,             ~VSDTC, ~VSTPTNUM, ~VSSEQ,
     "ABC123",    "VS", "ABC123-375", "/F:VTLS1-D:9795532-R:2",   "DIABP", "2020-09-01T13:31",        NA,     1L,
-    "ABC123",    "VS", "ABC123-375", "/F:VTLS2-D:9795533-R:2",   "DIABP", "2020-09-28T11:00",        2L,     2L,
+    "ABC123",    "VS", "ABC123-375", "/F:VTLS2-D:9795533-R:2",   "DIABP", "2020-09-28T11:00",         2,     2L,
     "ABC123",    "VS", "ABC123-375", "/F:VTLS1-D:9795532-R:2",    "TEMP", "2020-09-01T13:31",        NA,     3L,
-    "ABC123",    "VS", "ABC123-375", "/F:VTLS2-D:9795533-R:2",    "TEMP", "2020-09-28T11:00",        2L,     4L,
+    "ABC123",    "VS", "ABC123-375", "/F:VTLS2-D:9795533-R:2",    "TEMP", "2020-09-28T11:00",         2,     4L,
     "ABC123",    "VS", "ABC123-376", "/F:VTLS1-D:9795591-R:1",   "DIABP",       "2020-09-20",        NA,     1L,
     "ABC123",    "VS", "ABC123-376", "/F:VTLS1-D:9795591-R:1",    "TEMP",       "2020-09-20",        NA,     2L
   )
@@ -48,5 +48,4 @@ test_that("`is_seq_name()`: basic usage", {
   expect_false(is_seq_name("AEseq"))
 
   expect_false(is_seq_name("AESEQUENCE"))
-
 })
diff --git a/tests/testthat/test-dtc_parse_dttm.R b/tests/testthat/test-dtc_parse_dttm.R
@@ -1,14 +1,15 @@
 test_that("`parse_dttm()` works as expected", {
-
   # Year
   expected_y <- tibble::tribble(
     ~year, ~mon, ~mday, ~hour, ~min, ~sec,
     "2020",  NA,    NA,    NA,   NA,   NA
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("2020", "y"),
-                   expected_y)
+  expect_identical(
+    parse_dttm("2020", "y"),
+    expected_y
+  )
 
   # Year, Month
   expected_ym <- tibble::tribble(
@@ -17,8 +18,10 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("2020-05", "y-m"),
-                   expected_ym)
+  expect_identical(
+    parse_dttm("2020-05", "y-m"),
+    expected_ym
+  )
 
   # Year, Month, Day
   expected_ymd <- tibble::tribble(
@@ -27,8 +30,10 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("2020-05-11", "y-m-d"),
-                   expected_ymd)
+  expect_identical(
+    parse_dttm("2020-05-11", "y-m-d"),
+    expected_ymd
+  )
 
   # Year, Month, Day in other formats
   parse_dttm("2020 05 11", "y m d") |> expect_identical(expected_ymd)
@@ -38,50 +43,58 @@ test_that("`parse_dttm()` works as expected", {
   # Year, Month, Day, Hour, Minute
   expected_ymdhm <- tibble::tribble(
     ~year, ~mon, ~mday, ~hour, ~min, ~sec,
-    "2020", "05",  "11", "11", "45",   NA
+    "2020", "05", "11", "11", "45", NA
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("2020-05-11 11:45", "y-m-d H:M"),
-                   expected_ymdhm)
+  expect_identical(
+    parse_dttm("2020-05-11 11:45", "y-m-d H:M"),
+    expected_ymdhm
+  )
 
   # Year, Month, Day, Hour, Minute, Second
   expected_ymdhms <- tibble::tribble(
-    ~year,  ~mon, ~mday, ~hour, ~min,  ~sec,
-    "2020", "05",  "11", "11", "45", "15.6"
+    ~year, ~mon, ~mday, ~hour, ~min, ~sec,
+    "2020", "05", "11", "11", "45", "15.6"
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("2020-05-11 11:45:15.6", "y-m-d H:M:S"),
-                   expected_ymdhms)
+  expect_identical(
+    parse_dttm("2020-05-11 11:45:15.6", "y-m-d H:M:S"),
+    expected_ymdhms
+  )
 
   # Multiple records
   expected_ymdhm_1 <- tibble::tribble(
-    ~year, ~mon, ~mday, ~hour, ~min,  ~sec,
-    "2002", "05",  "11", "11", "45",    NA,
-    NA,       NA,    NA,   NA,   NA,    NA
+    ~year, ~mon, ~mday, ~hour, ~min, ~sec,
+    "2002", "05", "11", "11", "45", NA,
+    NA, NA, NA, NA, NA, NA
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm(c("2002-05-11 11:45", "-05-11 11:45"), "y-m-d H:M"),
-                   expected_ymdhm_1)
+  expect_identical(
+    parse_dttm(c("2002-05-11 11:45", "-05-11 11:45"), "y-m-d H:M"),
+    expected_ymdhm_1
+  )
 
   expected_ymdhm_2 <- tibble::tribble(
     ~year, ~mon, ~mday, ~hour, ~min, ~sec,
-    NA,      NA,    NA,   NA,   NA,    NA,
-    NA,    "05",  "11", "11", "45",    NA
+    NA, NA, NA, NA, NA, NA,
+    NA, "05", "11", "11", "45", NA
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm(c("2002-05-11 11:45", "-05-11 11:45"), "-m-d H:M"),
-                   expected_ymdhm_2)
+  expect_identical(
+    parse_dttm(c("2002-05-11 11:45", "-05-11 11:45"), "-m-d H:M"),
+    expected_ymdhm_2
+  )
 
 
 
   expected_ymdhm_3 <- tibble::tribble(
-    ~year, ~mon, ~mday, ~hour, ~min,  ~sec,
-    "2002", "05",  "11", "11", "45",    NA,
-    NA,     "05",  "11", "11", "45",    NA
+    ~year, ~mon, ~mday, ~hour, ~min, ~sec,
+    "2002", "05", "11", "11", "45", NA,
+    NA, "05", "11", "11", "45", NA
   ) |>
     as.matrix()
 
@@ -97,11 +110,15 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm("05 feb 1985 12 55 02", "d m y H M S"),
-                   expected_ymdhm_4)
+  expect_identical(
+    parse_dttm("05 feb 1985 12 55 02", "d m y H M S"),
+    expected_ymdhm_4
+  )
 
-  expect_identical(parse_dttm("12 55 02 05 feb 1985", "H M S d m y"),
-                   expected_ymdhm_4)
+  expect_identical(
+    parse_dttm("12 55 02 05 feb 1985", "H M S d m y"),
+    expected_ymdhm_4
+  )
 
   # UNK included
   expected_unk <- tibble::tribble(
@@ -112,8 +129,10 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"), "y-m-d"),
-                   expected_unk)
+  expect_identical(
+    parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"), "y-m-d"),
+    expected_unk
+  )
   expected_unk_1 <- tibble::tribble(
     ~year,   ~mon, ~mday, ~hour, ~min,  ~sec,
     "2020",  "05",  "18",    NA,   NA,    NA,
@@ -122,10 +141,13 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"),
-                              "y-m-d",
-                              na = "UN"),
-                   expected_unk_1)
+  expect_identical(
+    parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"),
+      "y-m-d",
+      na = "UN"
+    ),
+    expected_unk_1
+  )
 
   expected_unk_2 <- tibble::tribble(
     ~year,   ~mon, ~mday, ~hour, ~min,  ~sec,
@@ -135,8 +157,11 @@ test_that("`parse_dttm()` works as expected", {
   ) |>
     as.matrix()
 
-  expect_identical(parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"),
-                              "y-m-d",
-                              na = c("UN", "UNK")),
-                   expected_unk_2)
+  expect_identical(
+    parse_dttm(c("2020-05-18", "2020-UN-18", "2020-UNK-UN"),
+      "y-m-d",
+      na = c("UN", "UNK")
+    ),
+    expected_unk_2
+  )
 })
diff --git a/tests/testthat/test-dtc_problems.R b/tests/testthat/test-dtc_problems.R
@@ -24,6 +24,8 @@ test_that("`any_problems()`: basic usage", {
   cap_matrix_time <- parse_dttm(time, "H:M:S")
 
   cap_matrices <- list(cap_matrix_date, cap_matrix_time)
-  expect_identical(any_problems(cap_matrices),
-                   c(TRUE, TRUE, FALSE, FALSE))
+  expect_identical(
+    any_problems(cap_matrices),
+    c(TRUE, TRUE, FALSE, FALSE)
+  )
 })
diff --git a/tests/testthat/test-dtc_utils.R b/tests/testthat/test-dtc_utils.R
@@ -1,25 +1,25 @@
 test_that("`assert_dtc_fmt()`: basic usage", {
-
   fmt <- c("ymd", "y m d", "dmy", "HM", "H:M:S", "y-m-d H:M:S")
-  expect_identical(assert_dtc_fmt(fmt),
-                   fmt)
+  expect_identical(
+    assert_dtc_fmt(fmt),
+    fmt
+  )
 
   expect_error(assert_dtc_fmt("y years m months d days"))
 })
 
 test_that("`assert_dtc_format()`: basic usage", {
-
   expect_identical(assert_dtc_format("ymd"), "ymd")
   expect_identical(assert_dtc_format(c("ymd", "y-m-d")), c("ymd", "y-m-d"))
-  expect_identical(assert_dtc_format(list(c("ymd", "y-m-d"), "H:M:S")),
-                   list(c("ymd", "y-m-d"), "H:M:S"))
+  expect_identical(
+    assert_dtc_format(list(c("ymd", "y-m-d"), "H:M:S")),
+    list(c("ymd", "y-m-d"), "H:M:S")
+  )
 
   expect_error(assert_dtc_format("year, month, day"))
-
 })
 
 test_that("`assert_capture_matrix()`: basic usage", {
-
   cols <- c("year", "mon", "mday", "hour", "min", "sec")
   m <- matrix(NA_character_, nrow = 1L, ncol = 6L, dimnames = list(NULL, cols))
   expect_identical(assert_capture_matrix(m), m)
@@ -30,7 +30,6 @@ test_that("`assert_capture_matrix()`: basic usage", {
 })
 
 test_that("`complete_capture_matrix()`: basic usage", {
-
   # Input with no cols and rows
   input <- matrix(data = NA_character_, nrow = 0L, ncol = 0L)
   expected_output <- matrix(
@@ -40,8 +39,10 @@ test_that("`complete_capture_matrix()`: basic usage", {
     dimnames = list(NULL, c("year", "mon", "mday", "hour", "min", "sec"))
   )
 
-  expect_identical(complete_capture_matrix(input),
-                   expected_output)
+  expect_identical(
+    complete_capture_matrix(input),
+    expected_output
+  )
 
   # Input with no cols and 1 row
   input <- matrix(data = NA_character_, nrow = 1L)
@@ -52,8 +53,10 @@ test_that("`complete_capture_matrix()`: basic usage", {
     dimnames = list(NULL, c("year", "mon", "mday", "hour", "min", "sec"))
   )
 
-  expect_identical(complete_capture_matrix(input),
-                   expected_output)
+  expect_identical(
+    complete_capture_matrix(input),
+    expected_output
+  )
 
   # Input with incomplete cols
   input <-
@@ -71,8 +74,10 @@ test_that("`complete_capture_matrix()`: basic usage", {
     dimnames = list(NULL, c("year", "mon", "mday", "hour", "min", "sec"))
   )
 
-  expect_identical(complete_capture_matrix(input),
-                   expected_output)
+  expect_identical(
+    complete_capture_matrix(input),
+    expected_output
+  )
 
   # Input with year and second specified
   input <-
@@ -91,8 +96,10 @@ test_that("`complete_capture_matrix()`: basic usage", {
       dimnames = list(NULL, c("year", "mon", "mday", "hour", "min", "sec"))
     )
 
-  expect_identical(complete_capture_matrix(input),
-                   expected_output)
+  expect_identical(
+    complete_capture_matrix(input),
+    expected_output
+  )
 
   # Any other existing columns are dropped.
   input <-
@@ -110,12 +117,13 @@ test_that("`complete_capture_matrix()`: basic usage", {
     dimnames = list(NULL, c("year", "mon", "mday", "hour", "min", "sec"))
   )
 
-  expect_identical(complete_capture_matrix(input),
-                   expected_output)
+  expect_identical(
+    complete_capture_matrix(input),
+    expected_output
+  )
 })
 
 test_that("`coalesce_capture_matrices()`: basic usage", {
-
   cols <- c("year", "mon", "mday", "hour", "min", "sec")
   dates <- c("2020", "01", "01", "20", NA, NA)
   times <- c(NA, NA, NA, "10", "00", "05")