Background data check

R-pkg/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: diyabcGUI
 Type: Package
 Title: Graphical User Interface for DYIABC-RF software
-Version: 1.0.14
-Date: 2021-03-12
+Version: 1.1.0
+Date: 2021-04-26
 Authors@R: c(
     person(
         "Ghislain", "Durif", comment="diyabcGUI main developer",
@@ -55,15 +55,18 @@ VignetteBuilder: knitr
 Imports:
     dplyr,
     fs,
+    future,
     ggplot2,
     lubridate, 
     jsonlite, 
     magrittr, 
+    mime,
     parallel, pbapply, processx,
+    readr,
     rlang,
     shiny, 
     shinybusy (>= 0.2.2), 
-    shinydashboard, shinyFiles, 
+    shinydashboard, shinyFeedback, shinyFiles, 
     shinyhelper, shinyjs, shinyWidgets, 
     stringr, 
     tibble,

R-pkg/NAMESPACE

@@ -25,6 +25,9 @@ importFrom(fs,file_chmod)
 importFrom(fs,file_copy)
 importFrom(fs,file_delete)
 importFrom(fs,path_home)
+importFrom(future,future)
+importFrom(future,multisession)
+importFrom(future,plan)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotate)
@@ -53,12 +56,16 @@ importFrom(ggplot2,ylim)
 importFrom(jsonlite,fromJSON)
 importFrom(lubridate,now)
 importFrom(magrittr,"%>%")
+importFrom(mime,guess_type)
 importFrom(parallel,detectCores)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
 importFrom(pbapply,pblapply)
 importFrom(processx,process)
+importFrom(readr,read_file)
 importFrom(rlang,duplicate)
+importFrom(shinyFeedback,feedbackWarning)
+importFrom(shinyFeedback,useShinyFeedback)
 importFrom(shinyWidgets,actionBttn)
 importFrom(shinyWidgets,actionGroupButtons)
 importFrom(shinyWidgets,ask_confirmation)
@@ -74,7 +81,9 @@ importFrom(shinydashboard,dashboardHeader)
 importFrom(shinydashboard,dashboardPage)
 importFrom(shinydashboard,dashboardSidebar)
 importFrom(shinydashboard,menuItem)
+importFrom(shinydashboard,renderMenu)
 importFrom(shinydashboard,sidebarMenu)
+importFrom(shinydashboard,sidebarMenuOutput)
 importFrom(shinydashboard,tabItem)
 importFrom(shinydashboard,tabItems)
 importFrom(shinydashboard,updateTabItems)

R-pkg/R/01_directory.R

@@ -75,3 +75,44 @@ mk_proj_dir <- function(tag = "diyabc") {
     # output
     return(tmp_dir)
 }
+
+
+#' Clean project directory
+#' @keywords internal
+#' @description Remove all files and sub-folders in a given project directory.
+#' @author Ghislain Durif
+#' @param proj_dir character string, path to project directory.
+clean_proj_dir <- function(proj_dir) {
+    # check if project directory exists
+    if(length(proj_dir) != 1 && !dir.exists(proj_dir)) {
+        stop("Input argument should be a valid path to a project directory")
+    }
+    # sub-folders
+    subdir_list <- list.dirs(proj_dir, full.names = FALSE, recursive = FALSE)
+    subdir_list <- subdir_list[subdir_list != ""]
+    if(length(subdir_list) > 0) {
+        fs::dir_delete(file.path(proj_dir, subdir_list))
+    }
+    # files
+    file_list <- list.files(proj_dir)
+    if(length(file_list) > 0) {
+        fs::file_delete(file.path(proj_dir, file_list))
+    }
+}
+
+
+#' Clean binary directory
+#' @keywords internal
+#' @author Ghislain Durif
+clean_bin_dir <- function() {
+    # bin directory
+    path <- bin_dir()
+    # existing binary file
+    existing_bin_files <- list.files(path)
+    existing_bin_files <- existing_bin_files[str_detect(existing_bin_files, 
+                                                        "diyabc|abcranger|dll")]
+    # delete diyabc/abcranger files
+    if(length(existing_bin_files) > 0) {
+        fs::file_delete(file.path(path, existing_bin_files))
+    }
+}

R-pkg/R/02_regex.R

@@ -12,6 +12,13 @@ num_regex <- function() {
     return("[0-9]+\\.?[0-9]*")
 }
 
+#' return numerical (xxEyy notation) regex
+#' @keywords internal
+#' @author Ghislain Durif
+numexp_regex <- function() {
+    return("[0-9]+\\.?[0-9]*((E|e)\\-?[0-9]+)?")
+}
+
 #' return event numerical rate regex
 #' @keywords internal
 #' @author Ghislain Durif

R-pkg/R/03_utils.R

@@ -42,21 +42,6 @@ find_bin <- function(prog = "diyabc") {
     return(bin_file)
 }
 
-#' Clean binary directory
-#' @keywords internal
-#' @author Ghislain Durif
-clean_bin_dir <- function() {
-    # bin directory
-    path <- bin_dir()
-    # existing binary file
-    existing_bin_files <- list.files(path)
-    existing_bin_files <- existing_bin_files[str_detect(existing_bin_files, 
-                                                        "diyabc|abcranger|dll")]
-    # delete diyabc/abcranger files
-    if(length(existing_bin_files) > 0) {
-        fs::file_delete(file.path(path, existing_bin_files))
-    }
-}
 
 #' Find which OS is running
 #' @keywords internal