Merge pull request #44 from finddx/sample-classification

fix folders function
finddx · Jun 27, 2024 · 1f0726b · 1f0726b
2 parents 1182ac5 + cb94c41
commit 1f0726b
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Showing 9 changed files with 199 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,6 +22,7 @@ Imports:
     readxl (>= 1.3.1),
     rlang (>= 0.4.11),
     scales (>= 1.1.1),
+    stats,
     stringr (>= 1.4.0),
     tidyr (>= 1.2.0),
     tools (>= 4.1.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,6 +12,7 @@ export(as_label)
 export(as_name)
 export(auth_os)
 export(convert_os_df_to_wide)
+export(create_folders)
 export(create_save_workbook)
 export(data_table)
 export(enquo)
@@ -105,6 +106,7 @@ importFrom(rlang,as_name)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,sym)
+importFrom(stats,setNames)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_split)

diff --git a/R/create_folders.R b/R/create_folders.R
@@ -0,0 +1,47 @@
+# WARNING - Generated by {fusen} from dev/sample_selections.Rmd: do not edit by hand
+
+#' Create Project Folders
+#'
+#' This function creates a set of folders for a project, including a main folder and specified subfolders.
+#' It optionally assigns global variable names for each folder path, using a provided suffix.
+#'
+#' @param main_folder A string specifying the path of the main project folder.
+#' @param subfolders A character vector of subfolders to be created within the main folder.
+#'                   Default is c("data", "results", "doc").
+#' @param suffix A string to append to each subfolder name when creating global variables.
+#'               Default is "_folder".
+#' @importFrom stats  setNames
+#' @export
+#' @examples
+#' path_name <- tempfile(pattern = "main_folder") %>%
+#'     normalizePath(winslash = "/")
+#'
+#' create_folders(path_name)
+#'
+#' # Specify different subfolders and a custom suffix
+#' create_folders(path_name, c("archive", "temp", "shared"), "_dir")
+#'
+create_folders <- function(main_folder, subfolders = c("data", "results", "doc"), suffix = "_folder") {
+  # Create a list of folder paths by appending each subfolder name to the main folder path
+  folders_to_create <- setNames(
+    lapply(subfolders, function(subfolder) paste0(main_folder, "/", subfolder)),
+    paste0(subfolders, suffix)
+  )
+
+  # Add the main folder path to the list, without the suffix
+  folders_to_create$main_folder <- main_folder
+
+  # Create each folder if it does not exist
+  for (folder_name in names(folders_to_create)) {
+    folder_path <- folders_to_create[[folder_name]]
+    if (!dir.exists(folder_path)) {
+      dir.create(folder_path, recursive = TRUE)
+      cat(sprintf("Created folder: %s\n", folder_path))
+    } else {
+      cat(sprintf("Folder already exists: %s\n", folder_path))
+    }
+    # Optionally, assign folder path to global environment
+    assign(folder_name, folder_path, envir = .GlobalEnv)
+  }
+}
+
diff --git a/R/gen_clinical_data.R b/R/gen_clinical_data.R
@@ -120,7 +120,7 @@ gen_clinical_data <- function(clinical_data,
       stop("ppid_col is not present in the additional data set")
     }
     clinical_data <- merge(additional_data,
-                           clinical_data, by = ppid_col, all.x = TRUE) 
+                           clinical_data, by = ppid_col, all.y = TRUE) 
 
 
   }else{

diff --git a/dev/config_fusen.yaml b/dev/config_fusen.yaml
@@ -99,6 +99,7 @@ sample_selections.Rmd:
   R:
   - R/append_check_col.R
   - R/convert_os_df_to_wide.R
+  - R/create_folders.R
   - R/create_save_workbook.R
   - R/gen_clinical_data.R
   - R/make_clean_os_names.R
@@ -126,6 +127,7 @@ sample_selections.Rmd:
   - tests/testthat/test-gen_clinical_data.R
   - tests/testthat/test-samples_distributed_summary.R
   - tests/testthat/test-mark_all_duplicates.R
+  - tests/testthat/test-create_folders.R
   vignettes: vignettes/sample-selections-vignette.Rmd
   inflate:
     flat_file: dev/sample_selections.Rmd

diff --git a/dev/sample_selections.Rmd b/dev/sample_selections.Rmd
@@ -1256,7 +1256,7 @@ gen_clinical_data <- function(clinical_data,
       stop("ppid_col is not present in the additional data set")
     }
     clinical_data <- merge(additional_data,
-                           clinical_data, by = ppid_col, all.x = TRUE) 
+                           clinical_data, by = ppid_col, all.y = TRUE) 
     
     
   }else{
@@ -1536,6 +1536,77 @@ test_that("mark_all_duplicates works", {
 })
 ```
 
+# create_folders
+
+```{r function-create_folders}
+#' Create Project Folders
+#'
+#' This function creates a set of folders for a project, including a main folder and specified subfolders.
+#' It optionally assigns global variable names for each folder path, using a provided suffix.
+#'
+#' @param main_folder A string specifying the path of the main project folder.
+#' @param subfolders A character vector of subfolders to be created within the main folder.
+#'                   Default is c("data", "results", "doc").
+#' @param suffix A string to append to each subfolder name when creating global variables.
+#'               Default is "_folder".
+#' @importFrom stats  setNames
+#' @export
+create_folders <- function(main_folder, subfolders = c("data", "results", "doc"), suffix = "_folder") {
+  # Create a list of folder paths by appending each subfolder name to the main folder path
+  folders_to_create <- setNames(
+    lapply(subfolders, function(subfolder) paste0(main_folder, "/", subfolder)),
+    paste0(subfolders, suffix)
+  )
+  
+  # Add the main folder path to the list, without the suffix
+  folders_to_create$main_folder <- main_folder
+  
+  # Create each folder if it does not exist
+  for (folder_name in names(folders_to_create)) {
+    folder_path <- folders_to_create[[folder_name]]
+    if (!dir.exists(folder_path)) {
+      dir.create(folder_path, recursive = TRUE)
+      cat(sprintf("Created folder: %s\n", folder_path))
+    } else {
+      cat(sprintf("Folder already exists: %s\n", folder_path))
+    }
+    # Optionally, assign folder path to global environment
+    assign(folder_name, folder_path, envir = .GlobalEnv)
+  }
+}
+
+```
+
+```{r example-create_folders}
+path_name <- tempfile(pattern = "main_folder") %>%
+    normalizePath(winslash = "/")
+
+create_folders(path_name)
+
+# Specify different subfolders and a custom suffix
+create_folders(path_name, c("archive", "temp", "shared"), "_dir")
+
+```
+
+```{r tests-create_folders}
+# Test the function with custom subfolders and a custom suffix
+test_that("create_folders with custom subfolders and suffix", {
+  # Test setup: create a temporary path for testing
+  path_name <- tempfile(pattern = "main_folder") %>%
+    normalizePath(winslash = "/")
+
+  create_folders(path_name, c("archive", "temp", "shared"), "_dir")
+  expect_true(dir.exists(file.path(path_name, "archive")))
+  expect_true(dir.exists(file.path(path_name, "temp")))
+  expect_true(dir.exists(file.path(path_name, "shared")))
+  # Check if global variables are correctly assigned
+  expect_identical(get("archive_dir", envir = .GlobalEnv), file.path(path_name, "archive"))
+  expect_identical(get("temp_dir", envir = .GlobalEnv), file.path(path_name, "temp"))
+  expect_identical(get("shared_dir", envir = .GlobalEnv), file.path(path_name, "shared"))
+})
+
+```
+
 
 ```{r development-load}
 # Load already included functions if relevant

diff --git a/man/create_folders.Rd b/man/create_folders.Rd
diff --git a/tests/testthat/test-create_folders.R b/tests/testthat/test-create_folders.R
@@ -0,0 +1,18 @@
+# WARNING - Generated by {fusen} from dev/sample_selections.Rmd: do not edit by hand
+
+# Test the function with custom subfolders and a custom suffix
+test_that("create_folders with custom subfolders and suffix", {
+  # Test setup: create a temporary path for testing
+  path_name <- tempfile(pattern = "main_folder") %>%
+    normalizePath(winslash = "/")
+
+  create_folders(path_name, c("archive", "temp", "shared"), "_dir")
+  expect_true(dir.exists(file.path(path_name, "archive")))
+  expect_true(dir.exists(file.path(path_name, "temp")))
+  expect_true(dir.exists(file.path(path_name, "shared")))
+  # Check if global variables are correctly assigned
+  expect_identical(get("archive_dir", envir = .GlobalEnv), file.path(path_name, "archive"))
+  expect_identical(get("temp_dir", envir = .GlobalEnv), file.path(path_name, "temp"))
+  expect_identical(get("shared_dir", envir = .GlobalEnv), file.path(path_name, "shared"))
+})
+
diff --git a/vignettes/sample-selections-vignette.Rmd b/vignettes/sample-selections-vignette.Rmd
@@ -477,4 +477,25 @@ mark_all_duplicates(vec)
 
 
 
+# create_folders
+
+
+
+
+
+```{r example-create_folders}
+path_name <- tempfile(pattern = "main_folder") %>%
+    normalizePath(winslash = "/")
+
+create_folders(path_name)
+
+# Specify different subfolders and a custom suffix
+create_folders(path_name, c("archive", "temp", "shared"), "_dir")
+
+```
+
+
+
+
+