Merge pull request #231 from pharmaverse/230_debian

Closes #230 - debian issues

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: datacutr
 Type: Package
 Title: SDTM Datacut
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: c(
     person("Tim", "Barnett", email = "timothy.barnett@roche.com", role = c("cph","aut", "cre")), 
     person("Nathan", "Rees", email = "nathan.rees@roche.com", role = c("aut")), 

NEWS.md

@@ -1,3 +1,11 @@
+# datacutr 0.2.2
+
+## Updates of Existing Functions
+None
+
+## Various
+Tests using temporary directories cleaned up
+
 # datacutr 0.2.1
 
 ## Updates of Existing Functions

tests/testthat/test-process_cut.R

@@ -63,9 +63,6 @@ expected <- list(
   ae = ae_cut, lb = lb_cut, ts = ts_cut
 )
 
-# Create temporary directory for testing output file
-temp_dir <- tempdir()
-
 # Test that every type of datacut gives the expected result, when special_dm=TRUE -----------
 
 test_that("Test that every type of datacut gives the expected result, when special_dm=TRUE", {
@@ -177,6 +174,9 @@ test_that("Test that process_cut() errors when special_dm = TRUE and dm is also
 # Test Read-out file -------------
 # Test that read-out file is ran successfully when special_dm = TRUE
 test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
+  # Run test
   process_cut(
     source_sdtm_data = source_data,
     patient_cut_v = c("sc", "ds"),
@@ -189,10 +189,10 @@ test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE"
     cut_var = DCUTDTM,
     special_dm = TRUE,
     read_out = TRUE,
-    out_path = paste0(temp_dir, "/dummyfile")
+    out_path = paste0(temp_dir)
   )
-  expect_true(dir.exists(temp_dir) & (length(list.files(paste0(temp_dir, "/dummyfile")))) > 0)
-  unlink(paste0(temp_dir, "/dummyfile"), recursive = TRUE)
+  expect_true(dir.exists(temp_dir) & (length(list.files(temp_dir))) > 0)
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that every type of datacut gives the expected result, when special_dm=FALSE -----------
@@ -221,6 +221,9 @@ test_that("Test that every type of datacut gives the expected result, when speci
 
 # Test that Read-out file is ran successfully when special_dm = FALSE
 test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
+  # Run test
   process_cut(
     source_sdtm_data = source_data,
     patient_cut_v = c("sc", "ds"),
@@ -233,8 +236,8 @@ test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE"
     cut_var = DCUTDTM,
     special_dm = FALSE,
     read_out = TRUE,
-    out_path = paste0(temp_dir, "/dummyfile")
+    out_path = temp_dir
   )
-  expect_true(dir.exists(temp_dir) & (length(list.files(paste0(temp_dir, "/dummyfile"))) > 0))
-  unlink(paste0(temp_dir, "/dummyfile"), recursive = TRUE)
+  expect_true(dir.exists(temp_dir) & (length(list.files(temp_dir)) > 0))
+  unlink(temp_dir, recursive = TRUE)
 })

tests/testthat/test-read_out.R

@@ -75,189 +75,226 @@ dm_cut <- tibble::tribble(
 # Test that .Rmd gives the expected result when all fields are set to default or contain valid data -----------
 # Correct .Rmd file is run successfully when fields contain correct data inputs
 test_that("Correct .Rmd file is run successfully when fields contain correct data inputs", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   # Call read_out() to generate the .Rmd file
   result <- read_out(
     dcut = dcut,
     patient_cut_data = pt_cut_data,
     date_cut_data = dt_cut_data,
     dm_cut = dm_cut,
     no_cut_list = no_cut_ls,
-    out_path = tempdir()
+    out_path = temp_dir
   )
   # Assert that the output file is generated successfully
-  expect_true(file.exists(result))
-  unlink(result, recursive = TRUE)
+  expect_true(dir.exists(temp_dir) & (length(list.files(temp_dir))) > 0)
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that Correct .Rmd file is ran successfully when fields are empty
 test_that("Correct .Rmd file is ran successfully when fields are empty", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   # Call read_out() to generate the .Rmd file
-  result <- read_out(out_path = tempdir())
+  result <- read_out(out_path = temp_dir)
   # Assert that the output file is generated successfully
-  expect_true(file.exists(result))
-  unlink(result, recursive = TRUE)
+  expect_true(dir.exists(temp_dir) & (length(list.files(temp_dir))) > 0)
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test read_out() errors when data cut fields are incorrect input types -----------
 ## DCUT ----
 # Test that read_out() errors dcut data frame does not contain the var DCUTDTC
 test_that("Test that read_out() errors dcut data frame does not contain the var DCUTDTC", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(read_out(
     dcut = sc,
     patient_cut_data = pt_cut_data,
     date_cut_data = dt_cut_data,
     dm_cut = dm_cut,
     no_cut_list = no_cut_ls,
-    out_path = tempdir()
+    out_path = temp_dir
   ))
+  unlink(temp_dir, recursive = TRUE)
 })
 
 ## Patient_cut_data ----
 # Test that read_out() errors when patient_cut_data input is not a list
 test_that("Test that read_out() errors when patient_cut_data input is not a list", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = sc,
       date_cut_data = dt_cut_data,
       dm_cut = dm_cut,
       no_cut_list = no_cut_ls,
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "patient_cut_data must be a list. \n
 Note: If you have not used or do not with to view patient cut on any SDTMv domains, then
 please leave patient_cut_data empty, in which case a default value of NULL will be used."
   )
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when elements in the patient_cut_data list are not data frames
 test_that("Test that read_out() errors when elements in the patient_cut_data list are not data frames", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(read_out(
     dcut = dcut,
     patient_cut_data = list("sc", "ds"),
     date_cut_data = dt_cut_data,
     dm_cut = dm_cut,
     no_cut_list = no_cut_ls,
-    out_path = tempdir()
+    out_path = temp_dir
   ))
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when data frames in patient_cut_data are unnamed
 test_that("Test that read_out() errors when data frames in patient_cut_data are unnamed", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = list(sc, ds),
       date_cut_data = dt_cut_data,
       dm_cut = dm_cut,
       no_cut_list = no_cut_ls,
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "All elements patient_cut_data must be named with corresponding domain"
   )
+  unlink(temp_dir, recursive = TRUE)
 })
 
 ## Date_cut_data ----
 # Test that read_out() errors when date_cut_data input is not a list
 test_that("Test that read_out() errors when date_cut_data input is not a list", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = pt_cut_data,
       date_cut_data = ae,
       dm_cut = dm_cut,
       no_cut_list = no_cut_ls,
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "date_cut_data must be a list. \n
 Note: If you have not used or do not with to view date cut on any SDTMv domains, then please
 leave date_cut_data empty, in which case a default value of NULL will be used."
   )
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when elements in the date_cut_data list are not data frames
 test_that("Test that read_out() errors when elements in the date_cut_data list are not data frames", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(read_out(
     dcut = dcut,
     patient_cut_data = pt_cut_data,
     date_cut_data = list("ae", "lb"),
     dm_cut = dm_cut,
     no_cut_list = no_cut_ls,
-    out_path = tempdir()
+    out_path = temp_dir
   ))
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when data frames in date_cut_data are unnamed
 test_that("Test that read_out() errors when data frames in date_cut_data are unnamed", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = pt_cut_data,
       date_cut_data = list(ae, lb),
       dm_cut = dm_cut,
       no_cut_list = no_cut_ls,
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "All elements in date_cut_data must be named with corresponding domain"
   )
+  unlink(temp_dir, recursive = TRUE)
 })
 
 ## dm_cut ----
 # Test that read_out() errors when dm_cut data frame does not contain the vars DCUT_TEMP_REMOVE & DCUT_TEMP_DTHCHANG
 test_that("Test that read_out() errors when dm_cut data frame does not contain the vars DCUT_TEMP_REMOVE & DCUT_TEMP_DTHCHANGE", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(read_out(
     dcut = dcut,
     patient_cut_data = pt_cut_data,
     date_cut_data = dt_cut_data,
     dm_cut = sc,
     no_cut_list = no_cut_ls,
-    out_path = tempdir()
+    out_path = temp_dir
   ))
+  unlink(temp_dir, recursive = TRUE)
 })
 
 
 ## no_cut_list ----
 # Test that read_out() errors when no_cut_list is not a list
 test_that("Test that read_out() errors when no_cut_list is not a list", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = pt_cut_data,
       date_cut_data = dt_cut_data,
       dm_cut = dm_cut,
       no_cut_list = ds,
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "no_cut_list must be a list. \n
 Note: If you have not used or do not with to view the SDTMv domains where no cut has been
 applied, then please leave no_cut_list empty, in which case a default value of NULL will be
 used."
   )
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when elements in the no_cut_list list are not data frames
 test_that("Test that read_out() errors when elements in the no_cut_list list are not data frames", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(read_out(
     dcut = dcut,
     patient_cut_data = pt_cut_data,
     date_cut_data = dt_cut_data,
     dm_cut = dm_cut,
     no_cut_list = ls("ts"),
-    out_path = tempdir()
+    out_path = temp_dir
   ))
+  unlink(temp_dir, recursive = TRUE)
 })
 
 # Test that read_out() errors when elements in the no_cut_list list are not named with the corresponding domain
 test_that("Test that read_out() errors when elements in the no_cut_list list are not named with the corresponding domain", {
+  # Create temporary directory for testing output file
+  temp_dir <- tempdir()
   expect_error(
     read_out(
       dcut = dcut,
       patient_cut_data = pt_cut_data,
       date_cut_data = dt_cut_data,
       dm_cut = dm_cut,
       no_cut_list = list(ts, ae),
-      out_path = tempdir()
+      out_path = temp_dir
     ),
     regexp = "All elements in no_cut_list must be named with corresponding domain"
   )
+  unlink(temp_dir, recursive = TRUE)
 })