Fix build tests (#63)

* Update variables to pass tests * Update indiv number of variables * Change exists tests to read * Set an environment var to make testthat use multiple CPUs --------- Co-authored-by: James McMahon <[email protected]>
Public-Health-Scotland · Dec 12, 2023 · a69a61c · a69a61c
1 parent e29241e
commit a69a61c
Show file tree

Hide file tree

Showing 7 changed files with 38 additions and 35 deletions.
diff --git a/.Renviron b/.Renviron
@@ -0,0 +1 @@
+TESTTHAT_CPUS = 12
diff --git a/tests/testthat/test-files_exist.R b/tests/testthat/test-files_exist.R
diff --git a/tests/testthat/test-files_readable.R b/tests/testthat/test-files_readable.R
@@ -0,0 +1,28 @@
+skip_on_ci()
+
+
+test_that("Episode files are readable", {
+  # Episode files
+  expect_true(fs::file_access(gen_file_path("1415", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1516", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1617", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1718", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1819", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1920", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2021", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2122", "episode"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2223", "episode"), mode = "read"))
+})
+
+
+test_that("Individual files are readable", {
+  expect_true(fs::file_access(gen_file_path("1415", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1516", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1617", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1718", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1819", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("1920", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2021", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2122", "individual"), mode = "read"))
+  expect_true(fs::file_access(gen_file_path("2223", "individual"), mode = "read"))
+})
diff --git a/tests/testthat/test-multiple_selections.R b/tests/testthat/test-multiple_selections.R
@@ -5,27 +5,27 @@ test_that("select years and recid", {
   set.seed(50)
 
   acute_only <- read_slf_episode(c("1718", "1819"),
-    col_select = c("year", "anon_chi", "recid", "keydate1_dateformat"),
+    col_select = c("year", "anon_chi", "recid", "record_keydate1"),
     recids = "01B"
   ) %>%
     dplyr::slice_sample(n = 200000)
 
   expect_equal(
     names(acute_only),
-    c("year", "anon_chi", "recid", "keydate1_dateformat")
+    c("year", "anon_chi", "recid", "record_keydate1")
   )
   expect_equal(unique(acute_only$year), c("1718", "1819"))
   expect_equal(unique(acute_only$recid), "01B")
 
   hosp_only <- read_slf_episode(c("1718", "1819"),
-    col_select = c("year", "anon_chi", "recid", "keydate1_dateformat"),
+    col_select = c("year", "anon_chi", "recid", "record_keydate1"),
     recids = c("01B", "02B", "04B", "GLS")
   ) %>%
     dplyr::slice_sample(n = 200000)
 
   expect_equal(
     names(hosp_only),
-    c("year", "anon_chi", "recid", "keydate1_dateformat")
+    c("year", "anon_chi", "recid", "record_keydate1")
   )
   expect_equal(unique(hosp_only$year), c("1718", "1819"))
   expect_equal(sort(unique(hosp_only$recid)), c("01B", "02B", "04B", "GLS"))

diff --git a/tests/testthat/test-multiple_years.R b/tests/testthat/test-multiple_years.R
@@ -8,7 +8,7 @@ test_that("read multiple years works for individual file", {
   indiv <- read_slf_individual(c("1718", "1819"),
     col_select = c("year", "anon_chi")
   ) %>%
-    dplyr::slice_sample(n = 50)
+    dplyr::slice_sample(n = 100)
 
   # Test for anything odd
   expect_s3_class(indiv, "tbl_df")
@@ -34,7 +34,7 @@ test_that("read multiple years works for episode file", {
   ep <- read_slf_episode(c("1718", "1819"),
     col_select = c("year", "anon_chi")
   ) %>%
-    dplyr::slice_sample(n = 50)
+    dplyr::slice_sample(n = 100)
 
   # Test for anything odd
   expect_s3_class(ep, "tbl_df")

diff --git a/tests/testthat/test-partnership_selection.R b/tests/testthat/test-partnership_selection.R
@@ -45,15 +45,15 @@ test_that("Can still do filtering if variable is not selected", {
   # Don't choose to read the partnership variable
   indiv_1718_edinburgh <- read_slf_individual("1718",
     partnerships = "S37000012",
-    col_select = c("hri_scot")
+    col_select = c("anon_chi")
   ) %>%
     dplyr::slice_sample(n = 1000)
 
   # We shouldn't have the partnership variable
   expect_false("hscp2018" %in% names(indiv_1718_edinburgh))
 
   # Should still have the variables we picked
-  expect_true("hri_scot" %in% names(indiv_1718_edinburgh))
+  expect_true("anon_chi" %in% names(indiv_1718_edinburgh))
 
   # Should have at least 100 records (checks we're not getting an empty file)
   expect_gte(nrow(indiv_1718_edinburgh), 100)

diff --git a/tests/testthat/test-read_slf_individual.R b/tests/testthat/test-read_slf_individual.R
@@ -16,7 +16,7 @@ test_that("Reads individual file correctly", {
     expect_equal(nrow(indiv_file), 100)
 
     # Test for correct number of variables (will need updating)
-    expect_length(indiv_file, 184)
+    expect_length(indiv_file, 180)
   }
 })