Merge pull request #101 from habitus-eu/issue16_tidyup_countcalculation

Tidy up code now count calculation is removed

DESCRIPTION

@@ -10,8 +10,7 @@ Authors@R:
            email = "[email protected]"))
 License: Apache License version 2.0 | file LICENSE
 Imports: shiny, shinyFiles, GGIR, bslib, methods, jsonlite, DT, 
-    magrittr, shinyjs, callr, hbGPS, hbGIS,  actilifecounts, ActCR, 
-    GGIRread, read.gt3x, readxl
+    magrittr, shinyjs, callr, hbGPS, hbGIS
 Remotes: habitus-eu/hbGPS, habitus-eu/hbGIS
 LazyData: true
 Suggests: testthat, covr, rmarkdown

R/GGIRshiny.R

@@ -4,36 +4,31 @@
 #' @param outputdir Path to output directory
 #' @param sleepdiary Path to sleep diary
 #' @param configfile Configfile path
-#' @param do.Counts Boolean to indicate whether BrondCounts should be derived
 #' @return no object is returned, only a new file is created in the output directory
 #' @import GGIR
 #' @importFrom utils write.table
 #' @export
+#' 
 
-GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c(),
-                     do.Counts = FALSE) {
+GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c()) {
   if (length(sleepdiary) == 0) sleepdiary = c()
   if (length(configfile) == 0) configfile = c()
+
   # create R script with the code to run the data analysis via a command line call
   # in this way turning off or restarting the app will not kill the data analysis
   fileConn <- file(paste0(outputdir, "/ggir_cmdline.R"))
   writeLines(c("#!/usr/bin/env Rscript",
                "args = commandArgs(trailingOnly = TRUE)",
-               "if (length(args) < 4) {",
-               "stop(\"At least four arguments are expected\", call. = FALSE)",
+               "if (length(args) < 3) {",
+               "stop(\"At least three arguments are expected\", call. = FALSE)",
                "}",
-               "if (length(args) == 5) {",
+               "if (length(args) == 4) {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
-               " do.neishabouricounts = as.logical(args[3]),",
-               "configfile = args[4], loglocation = args[5],",
+               "configfile = args[3], loglocation = args[4],",
                "do.parallel = TRUE)",
                "} else {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
-               " do.neishabouricounts = as.logical(args[3]),",
-               "configfile = args[4], do.parallel = TRUE)",
-               "}",
-               "if (as.logical(args[3]) ==  TRUE) {",
-               "HabitusGUI::Counts2csv(outputdir = paste0(args[2], \"/output_\", basename(args[1])), configfile = args[4])",
+               "configfile = args[3], do.parallel = TRUE)",
                "}"),
              fileConn)
   close(fileConn)
@@ -49,7 +44,6 @@ GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c(),
     basecommand = paste0(outputdir, "/ggir_cmdline.R ",
                          rawaccdir, " ",
                          outputdir, " ",
-                         do.Counts, " ",
                          configfile, " ",
                          sleepdiary)
     system2(command = "Rscript", args = basecommand,
@@ -66,11 +60,9 @@ GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c(),
     basecommand = paste0("cd ", outputdir, " ; nohup Rscript ggir_cmdline.R ",
                          rawaccdir, " ",
                          outputdir, " ",
-                         do.Counts, " ",
                          configfile, " ",
                          sleepdiary, " > ", outputdir, "/GGIR.log 2>&1 &")
     system2(command = "cd", args = gsub(pattern = "cd ", replacement = "", x = basecommand),
             stdout = "", stderr = "", wait = TRUE)
   }
-
 }

R/myApp.R

@@ -13,7 +13,8 @@
 # pkgload::load_all("."); HabitusGUI::myApp(homedir="~/projects/fontys") 
 # HabitusGUI::myApp(homedir="~/projects")
 # pkgload::load_all("."); myApp(homedir="D:/Dropbox/Work/sharedfolder/DATA/Habitus")
-# myApp(homedir="D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/NBBB2010")
+# myApp(homedir="D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing")
+
 
 # roxygen2::roxygenise()
 
@@ -799,38 +800,29 @@ myApp <- function(homedir=getwd(), ...) {
     # Apply GGIR after button is pressed
     #========================================================================
     runGGIR <- eventReactive(input$start_ggir, {
-      GGIRCounts_message = ""
+      GGIR_message = ""
 
       if ("GGIR" %in% input$tools) {
-        GGIRCounts_message = ""
+        GGIR_message = ""
         # Basic check before running function:
-        ready_to_run_ggirCounts = FALSE
+        ready_to_run_ggir = FALSE
         if (dir.exists(global$raw_acc_in)) {
           acc_files_available = length(dir(path = global$raw_acc_in, pattern = "csv|bin|gt3x|bin|cwa|wav", recursive = FALSE, full.names = FALSE)) > 0
           if (acc_files_available == TRUE) {
-            ready_to_run_ggirCounts = TRUE
+            ready_to_run_ggir = TRUE
           } else {
-            GGIRCounts_message = paste0("No count files found in ", global$raw_acc_in)
+            GGIR_message = paste0("No files found in ", global$raw_acc_in)
           }
         } else {
-          GGIRCounts_message = paste0("Folder that is supposed to hold acceleration files does not exist: ", global$raw_acc_in)
+          GGIR_message = paste0("Folder that is supposed to hold acceleration files does not exist: ", global$raw_acc_in)
         }
         # Only run function when checks are met:
-        if (ready_to_run_ggirCounts == TRUE) {
+        if (ready_to_run_ggir == TRUE) {
           shinyjs::hide(id = "start_ggir")
-            # this line makes that if user is trying to use a config defined in a previous
-            # run, the data path is correctly defined
-            config = read.csv(as.character(configfileGGIR()))
-            config.Counts = config$value[which(config$argument == "do.neishabouricounts")]
-            if (as.logical(config.Counts) == TRUE) {
-              # if counts was not selected as a tool, but acc.metric was defined as 
-              # NeishabouriCount, then turn do.Counts to TRUE
-              id_ggir = showNotification("GGIR and CountConverter in progress ...", type = "message", duration = NULL, closeButton = FALSE)
-              do.Counts = TRUE
-            } else {
-              id_ggir = showNotification("GGIR in progress ...", type = "message", duration = NULL, closeButton = FALSE)
-              do.Counts = FALSE
-            }
+          # this line makes that if user is trying to use a config defined in a previous
+          # run, the data path is correctly defined
+          config = read.csv(as.character(configfileGGIR()))
+          id_ggir = showNotification("GGIR in progress ...", type = "message", duration = NULL, closeButton = FALSE)
 
           if (file.exists(paste0(global$data_out, "/sleepdiary.csv"))) { # because this is not a global variable
             sleepdiaryfile_local = paste0(global$data_out, "/sleepdiary.csv")
@@ -848,16 +840,15 @@ myApp <- function(homedir=getwd(), ...) {
           })
           # Start GGIR
           x_ggir <- r_bg(func = function(GGIRshiny, rawaccdir, outputdir, 
-                                         sleepdiary, configfile, do.Counts){
+                                         sleepdiary, configfile){
             GGIRshiny(rawaccdir, outputdir, 
-                      sleepdiary, configfile, do.Counts)
+                      sleepdiary, configfile)
           },
           args = list(GGIRshiny = GGIRshiny,
                       rawaccdir = isolate(global$raw_acc_in),
                       outputdir = global$data_out, 
                       sleepdiary = sleepdiaryfile_local,
-                      configfile = cleanPath(paste0(global$data_out, "/config.csv")),
-                      do.Counts = do.Counts),
+                      configfile = cleanPath(paste0(global$data_out, "/config.csv"))),
           stdout = "",
           stderr = "")
 
@@ -867,11 +858,15 @@ myApp <- function(homedir=getwd(), ...) {
           observe({
             if (x_ggir$poll_io(0)[["process"]] != "ready") {
               # Copy local log file to server to update progress log
-              if (file.exists(logfile)) file.copy(from = logfile, to = stdout_GGIR_tmp, overwrite = TRUE)
+              if (file.exists(logfile)) {
+                file.copy(from = logfile, to = stdout_GGIR_tmp, overwrite = TRUE)
+              }
               invalidateLater(2000)
             } else {
               # Copy local log file to server to update progress log
-              if (file.exists(logfile)) file.copy(from = logfile, to = stdout_GGIR_tmp, overwrite = TRUE)
+              if (file.exists(logfile)) {
+                file.copy(from = logfile, to = stdout_GGIR_tmp, overwrite = TRUE)
+              }
               on.exit(removeNotification(id_ggir), add = TRUE)
 
               # Delete Rscript that is created by GGIRshiny because user does not need this
@@ -884,14 +879,14 @@ myApp <- function(homedir=getwd(), ...) {
               expected_outputdir_ggir = paste0(global$data_out, "/output_", basename(global$raw_acc_in))
               expected_ggiroutput_file = paste0(global$data_out, "/output_", basename(global$raw_acc_in), "/results/part2_daysummary.csv")
               if (file.exists(expected_ggiroutput_file) == TRUE) { # checks whether ggir output was created
-                GGIRCounts_message = paste0(#"GGIR successfully completed at ", Sys.time(), 
+                GGIR_message = paste0(#"GGIR successfully completed at ", Sys.time(), 
                   "Output is stored in: ",  #<br/>
                   expected_outputdir_ggir,
                   "<br/>The table below shows the content of part2_daysummary.csv:")
                 GGIRpart2 = read.csv(expected_ggiroutput_file, nrow = 100)
                 output$GGIRpart2 <- DT::renderDataTable(GGIRpart2, options = list(scrollX = TRUE))
                 output$ggir_end_message <- renderUI({
-                  HTML(paste0(GGIRCounts_message))
+                  HTML(paste0(GGIR_message))
                 })
               }
             }
@@ -976,6 +971,7 @@ myApp <- function(homedir=getwd(), ...) {
                       configfile =  paste0(global$data_out, "/config_hbGPS.csv")),
           stdout = stdout_hbGPS_tmp,
           stderr = "2>&1")
+
           observe({
             if (x_hbGPS$poll_io(0)[["process"]] != "ready") {
               invalidateLater(5000)

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true