@@ -366,7 +366,7 @@ import_association_file <- function(path,

     import_stats_rep <- NULL

     missing_stats_rep <- NULL

     if (import_iss) {

-        dots <- rlang::dots_list(.named = TRUE)

+        dots <- rlang::dots_list(..., .named = TRUE)

         dots <- dots[!names(dots) %in% c(

             "association_file",

             "report_path",

@@ -274,7 +274,7 @@

             function(x) {

                 el <- getElement(t_readr, x)

                 el <- if (is.null(el)) {

-                  "guess"

+                    "guess"

                 } else if (el == "c") {

                     "text"

                 } else if (el %in% c("i", "d")) {

@@ -357,11 +357,6 @@

 # @param df The imported association file (data.frame or tibble)

 # @param root_folder Path to the root folder

 # @keywords internal

-#' @importFrom dplyr select distinct mutate

-#' @importFrom fs dir_ls path dir_exists

-#' @importFrom purrr pmap_dfr is_empty

-#' @importFrom stringr str_replace_all

-#' @importFrom tibble tibble

 #' @importFrom rlang .data `:=`

 #

 # @return A data frame containing, for each ProjectID and

@@ -379,70 +374,90 @@

         ) %>%

         dplyr::distinct()

     path_cols <- .path_cols_names()

-    results_df <- purrr::pmap_dfr(

-        temp_df,

-        function(...) {

-            cur <- tibble::tibble(...)

-            if (is.na(cur$PathToFolderProjectID)) {

-                return(cur %>%

-                    dplyr::mutate(

-                        !!path_cols$project := NA_character_,

-                        !!path_cols$quant := NA_character_,

-                        !!path_cols$iss := NA_character_

-                    ))

-            }

-            project_folder <- fs::path(

-                fs::path(root_folder),

-                cur$PathToFolderProjectID

-            )

-            quant_folder <- paste0(fs::path(

+    proj_folders_exist <- temp_df %>%

+        dplyr::select(.data$PathToFolderProjectID) %>%

+        dplyr::distinct() %>%

+        dplyr::mutate(Found := !is.na(

+            .data$PathToFolderProjectID

+        ) &

+            unname(fs::dir_exists(

+                fs::path(

+                    fs::path(root_folder),

+                    .data$PathToFolderProjectID

+                )

+            )))

+    partial_check <- temp_df %>%

+        dplyr::left_join(proj_folders_exist, by = "PathToFolderProjectID")

+    temp_df <- partial_check %>%

+        dplyr::filter(Found == TRUE)

+    partial_check <- partial_check %>%

+        dplyr::filter(Found == FALSE) %>%

+        dplyr::mutate(

+            !!path_cols$project := NA_character_,

+            !!path_cols$quant := NA_character_,

+            !!path_cols$iss := NA_character_

+        )

+    FUN <- function(...) {

+        cur <- tibble::tibble(...)

+        project_folder <- fs::path(

+            fs::path(root_folder),

+            cur$PathToFolderProjectID

+        )

+        quant_folder <- if (!is.na(cur$concatenatePoolIDSeqRun)) {

+            paste0(fs::path(

                 "quantification",

                 fs::path(cur$concatenatePoolIDSeqRun)

             ), "$")

-            iss_folder <- paste0(fs::path(

+        } else {

+            if (getOption("ISAnalytics.verbose") == TRUE) {

+                rlang::inform(c(paste(

+                    "Warning: found NA",

+                    "concatenatePoolIDSeqRun field"

+                ),

+                i = "Check association file for possible issues"

+                ))

+            }

+            NA_character_

+        }

+        iss_folder <- if (!is.na(cur$concatenatePoolIDSeqRun)) {

+            paste0(fs::path(

                 "iss",

                 fs::path(cur$concatenatePoolIDSeqRun)

             ), "$")

-            dirExists <- fs::dir_exists(project_folder)

-            if (!dirExists) {

-                return(cur %>%

-                    dplyr::mutate(

-                        !!path_cols$project := NA_character_,

-                        !!path_cols$quant := NA_character_,

-                        !!path_cols$iss := NA_character_

-                    ))

-            }

-            quant_found <- fs::dir_ls(

-                path = project_folder, recurse = TRUE,

-                type = "directory", fail = FALSE,

-                regexp = quant_folder

-            )

-            if (length(quant_found) == 0) {

-                quant_found <- NA_character_

-            }

-            iss_found <- fs::dir_ls(

-                path = project_folder, recurse = TRUE,

-                type = "directory", fail = FALSE,

-                regexp = iss_folder

-            )

-            if (length(iss_found) == 0) {

-                iss_found <- NA_character_

-            }

-            return(

-                cur %>%

-                    dplyr::mutate(

-                        !!path_cols$project := project_folder,

-                        !!path_cols$quant := quant_found,

-                        !!path_cols$iss := iss_found

-                    )

-            )

+        } else {

+            NA_character_

+        }

+        quant_found <- unique(fs::dir_ls(

+            path = project_folder, recurse = TRUE,

+            type = "directory", fail = FALSE,

+            regexp = quant_folder

+        ))

+        if (length(quant_found) == 0 || all(is.na(quant_found))) {

+            quant_found <- NA_character_

+        }

+        iss_found <- unique(fs::dir_ls(

+            path = project_folder, recurse = TRUE,

+            type = "directory", fail = FALSE,

+            regexp = iss_folder

+        ))

+        if (length(iss_found) == 0 || all(is.na(iss_found))) {

+            iss_found <- NA_character_

         }

+        return(

+            cur %>%

+                dplyr::mutate(

+                    !!path_cols$project := project_folder,

+                    !!path_cols$quant := quant_found,

+                    !!path_cols$iss := iss_found

+                )

+        )

+    }

+    results_df <- purrr::pmap_dfr(

+        temp_df,

+        FUN

     )

     checker_df <- results_df %>%

-        dplyr::mutate(

-            Found = ifelse(!is.na(.data[[path_cols$project]]), TRUE, FALSE),

-            .before = .data[[path_cols$project]]

-        )

+        dplyr::bind_rows(partial_check)

     checker_df

 }

@@ -2313,19 +2328,20 @@

     exceeding <- nrow(nested) %% max_workers

     ampl <- trunc(nrow(nested) / max_workers)

     chunks <- unlist(lapply(seq_len(max_workers),

-                            FUN = rep_len,

-                            length.out = ampl))

+        FUN = rep_len,

+        length.out = ampl

+    ))

     if (exceeding > 0) {

-      chunks <- c(chunks, rep_len(

-        x = tail(max_workers, n = 1),

-        length.out = exceeding

-      ))

+        chunks <- c(chunks, rep_len(

+            x = tail(max_workers, n = 1),

+            length.out = exceeding

+        ))

     }

     chunks <- tibble::as_tibble_col(chunks, column_name = "chunk")

     nested <- nested %>% tibble::add_column(chunks)

     split_data <- nested %>%

-      dplyr::group_by(.data$chunk) %>%

-      dplyr::group_split(.keep = FALSE)

+        dplyr::group_by(.data$chunk) %>%

+        dplyr::group_split(.keep = FALSE)

     # Register backend according to platform

     if (.Platform$OS.type == "windows") {

@@ -97,6 +97,27 @@ test_that(paste(func_name[2], "finds missing projects for incorrect fs"), {

     )

 })

+test_that(paste(func_name[2], "no error for NA concat"), {

+    withr::with_dir(tempdir(), {

+        fake_pj <- fs::path("Project")

+        fs::dir_create(fake_pj)

+        fs::dir_create(fs::path(fake_pj, "fold_1_NA"))

+        fs::dir_create(fs::path(fake_pj, "fold_2_NA"))

+        fs::dir_create(fs::path(fake_pj, "fold_3_NA"))

+        test_df <- tibble::tribble(

+            ~ProjectID, ~PoolID, ~concatenatePoolIDSeqRun, ~PathToFolderProjectID,

+            "Project", "POOL1", NA_character_, "/Project",

+            "Project", "POOL2", NA_character_, "/Project",

+            "Project", "POOL3", NA_character_, "/Project",

+        )

+        expect_error(

+            {

+                checks <- .check_file_system_alignment(test_df, ".")

+            },

+            regexp = NA

+        )

+    })

+})

 #------------------------------------------------------------------------------#

 # Tests .update_af_after_alignment