Merge pull request #79 from habitus-eu/jhmigueles-issue42_tsvGGIR

R/GGIRshiny.R

@@ -13,7 +13,6 @@ GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c(),
                      do.Counts = FALSE) {
   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"))
@@ -24,26 +23,53 @@ GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c(),
                "}",
                "if (length(args) == 5) {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
-               " overwrite = FALSE, do.neishabouricounts = args[3],",
+               " do.neishabouricounts = as.logical(args[3]),",
                "configfile = args[4], loglocation = args[5],",
                "do.parallel = TRUE)",
                "} else {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
-               " overwrite = FALSE, do.neishabouricounts = as.logical(args[3]),",
+               " do.neishabouricounts = as.logical(args[3]),",
                "configfile = args[4], do.parallel = TRUE)",
                "}",
-               "HabitusGUI::Counts2csv(outputdir = paste0(args[2], \"/output_\", basename(args[1])), configfile = args[4])"),
+               "if (as.logical(args[3]) ==  TRUE) {",
+               "HabitusGUI::Counts2csv(outputdir = paste0(args[2], \"/output_\", basename(args[1])), configfile = args[4])",
+               "}"),
              fileConn)
   close(fileConn)
-
-   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)
-
+  if (.Platform$OS.type == "windows") {
+    logFile = paste0(outputdir, "/GGIR.log")
+    fileConn = file(logFile)
+    writeLines(c("Hello, this Shiny app is primarily designed for Linux.",
+                 "In Windows OS live progress of the analysis can be followed in the RStudio console.",
+                 "In Unix-like systems the progress would be shown here inside this window in the Shiny app."), fileConn)
+    close(fileConn)
+
+    basecommand = paste0(outputdir, "/ggir_cmdline.R ",
+                         rawaccdir, " ",
+                         outputdir, " ",
+                         do.Counts, " ",
+                         configfile, " ",
+                         sleepdiary)
+    system2(command = "Rscript", args = basecommand,
+            stdout = "",
+            stderr = "", wait = TRUE)
+    write.table(x = paste0(""),
+                file = paste0(outputdir, "/GGIR.log"))
+
+    fileConn = file(logFile)
+    writeLines(c(""), fileConn)
+    close(fileConn)
+
+  } else {
+    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

@@ -12,7 +12,6 @@
 # HabitusGUI::myApp(homedir="~/projects")
 # pkgload::load_all("."); myApp(homedir="~/projects/fontys")
 # roxygen2::roxygenise()
-#/Member Files: LineMatthiesen#8897
 
 
 # create temp log file
@@ -610,8 +609,17 @@ overflow-y:scroll; max-height: 300px; background: ghostwhite;}")),
             id_ggir = showNotification("GGIR and Counts 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
+            config = read.csv(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 Counts 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
+            }
           }
           if (file.exists(paste0(global$data_out, "/sleepdiary.csv"))) { # because this is not a global variable
             sleepdiaryfile_local = paste0(global$data_out, "/sleepdiary.csv")
@@ -625,7 +633,7 @@ overflow-y:scroll; max-height: 300px; background: ghostwhite;}")),
           output$mylog_GGIR <- renderText({
             paste(mylog_GGIR(), collapse = '\n')
           })
-
+          print
           # Start GGIR
           x_ggir <- r_bg(func = function(GGIRshiny, rawaccdir, outputdir, 
                                          sleepdiary, configfile, do.Counts){

R/update_params.R

@@ -47,6 +47,26 @@ update_params = function(new_params = c(), file = c(), format="json_palmspy") {
       ind = which(rownames(params) %in% rownames(new_params)[j] == TRUE)
       params$value[ind] = new_params$value[j]
     }
+    # match acc.metric with do.metric arguments
+    do_metrics = c("do.zcx", "do.zcy", "do.zcz", 
+                   "do.en", "do.enmo", "do.enmoa",
+                   "do.lfen", "do.lfenmo",
+                   "do.bfen", "do.hfen", "do.hfenplus",
+                   "do.mad", "do.brondcounts", "do.neishabouricounts",
+                   "do.roll_med_acc_x", "do.roll_med_acc_y", "do.roll_med_acc_z", 
+                   "do.dev_roll_med_acc_x", "do.dev_roll_med_acc_y", "do.dev_roll_med_acc_z",
+                   "do.lfx", "do.lfy", "do.lfz", "do.hfx", "do.hfy", "do.hfz",
+                   "do.bfx", "do.bfy", "do.bfz")
+    acc.metric = params["acc.metric", "value"]
+    # if neishabouri counts, remove reference to axis
+    if (grepl("Neishabouri", acc.metric)) acc.metric = gsub("_x|_y|_z|_vm", "", acc.metric)
+    do_argument = grep(acc.metric, rownames(params), value = TRUE, ignore.case = TRUE)
+    # to avoid detecting also enmoa and lfenmo when selecting enmo 
+    # (this does not occur with any other metric):
+    if (acc.metric == "ENMO") do_argument = "do.enmo"
+    # set metric of interest to TRUE and rest to FALSE
+    params[do_argument, "value"] = TRUE
+    params[do_metrics[-which(do_metrics == do_argument)], "value"] = FALSE 
     write.csv(x = params, file = file, row.names = FALSE)
   } else if (format == "csv_palmsplusr") {
     params = read.csv(file = file, sep = ",")

inst/NEWS.Rd

@@ -2,6 +2,13 @@
 \title{News for Package \pkg{HabitusGUI}}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
+\section{Changes in version 0.1.6 (GitHub-only-release date: ?-?-2023)}{
+  \itemize{
+    \item Revised tsv file for GGIR configuration
+    \item Now able to handle acc.metric in GGIR
+    \item tsv GGIR file revised and testfile for config GGIR is updated
+  }
+}
 \section{Changes in version 0.1.6 (GitHub-only-release date: 15-03-2023)}{
   \itemize{
     \item GGIR config file is now checked when it is loaded