Add show running workflow on reload if still running

Debug on reload function (add reload off select step tools)

main.R

@@ -647,6 +647,7 @@ generate_pages_server <- function() {
   res <- res + '\tif (!file.exists(paste0(input$results_dir,"/logs/runlog.txt"))){\n'
   res <- res + '\t\tfile.create(paste0(input$results_dir,"/logs/runlog.txt"))\n'
   res <- res + '\t}\n'
+  res <- res + '\t\tsystem(paste0("touch ",input$results_dir,"/logs/workflow.running"),wait = T)\n'
   res <- res + '\t\tsystem2("python3",paste("-u -m snakemake", "-s", "/workflow/Snakefile" ,\t"--configfile", paste0(input$results_dir,"/params.yml") ,\t"-d", input$results_dir ,\t"--cores", input$cores , sep = " " ),wait = FALSE, stdout = paste0(input$results_dir,"/logs/runlog.txt"), stderr = paste0(input$results_dir,"/logs/runlog.txt"))\n'
 
 
@@ -898,7 +899,6 @@ generate_app <- function() {
   res <- res + '\tif (file.exists(paste0(dossierAnalyse,"/params.yml"))){\n'
   res <- res + '\t\tparams = read_yaml(paste0(dossierAnalyse,"/params.yml"))\n'
   res <- res + '\t\tfor (param in names(params$params_types)){\n'
-  res <- res + '\t\t\tprint(params[param])\n'
   res <- res + '\t\t\tif (params$params_types[[param]] == "text"){\n'
   res <- res + '\t\t\t\tupdateTextInput(session, param, value = params[[param]])\n'
   res <- res + '\t\t\t}\n'
@@ -912,6 +912,9 @@ generate_app <- function() {
   res <- res + '\t\t\t\tupdateSelectInput(session, param, selected = params[[param]])\n'
   res <- res + '\t\t\t}\n'
   res <- res + '\t\t}\n'
+  res <- res + '\t\tfor (step in params$steps){\n'
+  res <- res + '\t\t\tupdateSelectInput(session, paste0("select",step$name), selected = params[[step$name]])\n'
+  res <- res + '\t\t}\n'
   res <- res + '\t}\n'
   res <- res + '\t# if rulegraph show it\n'
   res <- res + '\trulegraph = list.files(path=dossierAnalyse,pattern="rulegraph[[:digit:]]+.svg")\n'
@@ -929,6 +932,7 @@ generate_app <- function() {
   res <- res + '\n\n'
   
   res <- res + 'server <- function( input, output, session) {\n\n'
+  res <- res + '\trv <- reactiveValues(textstream = c(""), running = FALSE, timer = reactiveTimer(1000))\n\n'
 
   # Observe query to find user and directory
   res <- res + 'observeEvent(parseQueryString(session$clientData$url_search),{\n'
@@ -949,6 +953,9 @@ generate_app <- function() {
   res <- res + '\t\t\treload(dossierAnalyse,session,output)\n'
   res <- res + '\t\t\tupdateTextInput(session, "results_dir", value = dossierAnalyse)\n'
   res <- res + '\t\t\tshinyjs::disable("results_dir")\n'
+  res <- res + '\t\t\tif (file.exists(paste0(dossierAnalyse,"/logs/workflow.running"))){\n'
+  res <- res + '\t\t\t\trv$running = TRUE\n'
+  res <- res + '\t\t\t}\n'
   res <- res + '\t\t}\n'
   res <- res + '\t\telse{\n'
   res <- res + '\t\t\t# create new dir\n'
@@ -960,8 +967,6 @@ generate_app <- function() {
   res <- res + '\t})\n'
 
   # Observe if the workflow is running
-  res <- res + '\trv <- reactiveValues(textstream = c(""), running = FALSE, timer = reactiveTimer(1000))\n'
-  res <- res + '\n'
   res <- res + '\tobserve({\n'
   res <- res + '\t\trv$timer()\n'
   res <- res + '\t\tif (isolate(rv$running)){\n'
@@ -980,13 +985,13 @@ generate_app <- function() {
   res <- res + '\t\t\t\taddResourcePath("results", input$results_dir)\n'
   res <- res + '\t\t\t\toutUI = tags$iframe(src=paste0("/results/report.html"),width="100%", height="900px")\n'
   res <- res + '\t\t\t\toutput$report_html = renderUI(outUI)\n'
-  res <- res + '\t\t\t\tfile.remove(paste0(paste0(input$results_dir,"/logs/workflow_end.ok")))\n'
+  res <- res + '\t\t\t\tfile.remove(paste0(input$results_dir,"/logs/workflow_end.ok"))\n'
   res <- res + '\t\t\t}\n'
   res <- res + '\t\t\telse if (file.exists(paste0(isolate(input$results_dir),"/logs/workflow_end.error"))){\n'
   res <- res + '\t\t\t\trv$running = F\n'
   res <- res + '\t\t\t\ttoggle_inputs(reactiveValuesToList(input),T,F)\n'
   res <- res + '\t\t\t\toutput$report_html = renderUI(HTML(paste(readLines(paste0(input$results_dir,"/logs/workflow_end.error"),warn=F), collapse = "<br/>")))\n'
-  res <- res + '\t\t\t\tfile.remove(paste0(paste0(input$results_dir,"/logs/workflow_end.error")))\n'
+  res <- res + '\t\t\t\tfile.remove(paste0(input$results_dir,"/logs/workflow_end.error"))\n'
   res <- res + '\t\t\t}\n'
   res <- res + '\t\t\tshinyjs::runjs(\n'
   res <- res + '\t\t\t\t"var objDiv = document.getElementById(\'run_out\'); objDiv.scrollTop = objDiv.scrollHeight;"\n'