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update Dev log
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‎source/content/.obsidian/workspace.json‎

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}
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],
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"direction": "horizontal",
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"width": 300
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"width": 300,
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"collapsed": true
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},
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"left-ribbon": {
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"hiddenItems": {

‎source/content/BSGOU-System/RNA-seq Tool Kits/DeVlog/20250729-fenA-processx_convert-theme.md‎

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# 1. Add code blocks for [loc](https://github.com/LabOnoM/ShinyAppsManager)
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## Basic functions
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1. Handle crash
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2. Email notification
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3. Communications with [loc](https://github.com/LabOnoM/ShinyAppsManager) based on [jwt](https://en.wikipedia.org/wiki/JSON_Web_Token)
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1. Handle crash (inside **header** of navbarPage)
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2. Handle shiny theme selection
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3. Handle live console
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4. Email notification (inside **header** of navbarPage)
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5. Live Console (inside **footer** of navbarPage)
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6. Communications with [loc](https://github.com/LabOnoM/ShinyAppsManager) based on [jwt](https://en.wikipedia.org/wiki/JSON_Web_Token)(inside **header** of navbarPage)
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Example codes:
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Helper functions (global.R)
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```R
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# Get Info ----
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print_to_console <- function(msg) {
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js_line <- gsub("\\\\", "\\\\\\\\", msg)
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js_line <- gsub("\"", "\\\\\"", js_line)
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shinyjs::runjs(sprintf(
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"if (document.getElementById('console')) {
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let el = document.getElementById('console');
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let lines = el.innerText.split('\\n');
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if (lines.length > 2000) {
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lines = lines.slice(lines.length - 1999); // keep last 1999 lines
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}
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lines.push(\"%s\");
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el.innerText = lines.join('\\n');
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el.scrollTop = el.scrollHeight;
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} else {
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console.warn('#console element not found!');
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}",
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js_line
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))
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return(js_line)
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}
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# 获取当前登录用户邮箱
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get_user_email <- function(token){
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headers <- add_headers(`Token` = token, `Content-Type` = "application/json")
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res <- try(GET('http://10.2.26.152:7156/sqx_fast/app/user/info', headers), silent = TRUE)
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if(!inherits(res, "try-error") && status_code(res) == 200){
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res_data <- fromJSON(content(res, "text", encoding = "UTF-8"))
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return(res_data$data$email)
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}
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return(NA)
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}
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if(!is.na(Sys.getenv("SHINY_SERVER_VERSION", unset = NA))){
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smtp_creds <- creds_envvar(
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user = Sys.getenv("EMAIL_USER"),
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pass_envvar = "EMAIL_PASS",
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host = "smtp.gmail.com",
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port = 587,
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use_ssl = TRUE
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)
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email <- "Email_Template.html" %>% file.path("..", "GlobalEnvironment", .) %>% readLines(., , warn = FALSE) %>%
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paste(., collapse = "\n") %>% HTML() %>% compose_email(body = .)
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email_fail <- "Email_Template_fail.html" %>% file.path("..", "GlobalEnvironment", .) %>% readLines(., , warn = FALSE) %>%
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paste(., collapse = "\n") %>% HTML() %>% compose_email(body = .)
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# get user home
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UsrHome <- file.path("/mnt","Public")
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}else{
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UsrHome <- path_home() %>% as.character()
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}
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options(shiny.fullstacktrace = TRUE)
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```
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Example codes: Error Trigger (server.R):
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```R
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tryCatch(
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., error = function(e) {
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isolate(values$error_state <- paste0("Error:\n", e$message))
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showNotification(e$message, type = "error")
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return(NULL)
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})
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```
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Example codes (server.R):
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```R
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# Initiation ----
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px <- reactiveVal(NULL)
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# Make reactive values ----
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values<-reactiveValues(
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is_on_shiny_server = !is.na(Sys.getenv("SHINY_SERVER_VERSION", unset = NA))
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)
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para<-reactiveValues()
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# Fetch information if running on BSGOU loc (local allocation controller) system.
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observe({
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req(values$is_on_shiny_server)
@@ -96,7 +170,120 @@ Example codes:
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observeEvent(input$Crash_modal_ok, {
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shiny::removeModal()
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})
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# Handle shiny theme selection ----
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observe({
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req(is.null(para$UI_Init))
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updateSelectInput(
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session = session, inputId = "shinytheme-selector",
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selected = "yeti"
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)
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isolate(para$UI_Init <- "Done")
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})
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# Handle live console----
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# Clean console history
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observeEvent(input$clear_console, {
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runjs("
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var consoleEl = document.getElementById('console');
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if (consoleEl) {
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consoleEl.innerText = '';
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} else {
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console.warn('#console element not found!');
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}
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")
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isolate({values$console_log <- NULL})
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})
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# Download console monitor log
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output$download_console <- downloadHandler(
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filename = function() {
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paste0("console_log_", Sys.Date(), ".log")
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},
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content = function(file) {
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writeLines(values$console_log, file)
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}
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)
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# Session End Function ----
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# Shutdown everything if connection closed
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session$onSessionEnded(function() {
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if(!is.na(Sys.getenv("SHINY_SERVER_VERSION"))){
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headers <- add_headers(`Token`=session$userData$token, `Content-Type`="application/json")
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connect_req_end = list(`appName`=session$userData$appName, `action`="disconnect", `id`=session$userData$id)
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connect_end_data <- try(
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url_execute(
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2, 'http://10.2.26.152/sqx_fast/app/workstation/shiny-connect-action',
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toJSON(connect_req_end, pretty = FALSE, auto_unbox = TRUE), headers
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), silent = TRUE
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)
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}
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stopApp()
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})
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```
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Example codes (ui.R):
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```R
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## For BSGOU ----
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header = tagList(
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### For lac system----
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uiOutput("conditional_head"), ## start-1嵌入代码开始，作用：异常跳转到预约系统首页
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## Costume CSS----
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tags$style(HTML(
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'.navbar-nav > li > a, .navbar-brand {
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padding-top: 3px !important;
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padding-bottom: 0px !important;
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margin-top: 2px;
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margin-bottom: 0px;
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height: 25px;
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}
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.navbar {
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min-height:26px !important;
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z-index:99999 !important;
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margin-top: 1px;
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margin-bottom: 1px;
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}'
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)),
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tags$head(
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## Google Analytics----
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# Embed Google Analytics
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tags$script(async = NA, src = "https://www.googletagmanager.com/gtag/js?id=G-RWF876HNKW"),
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tags$script(HTML("
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window.dataLayer = window.dataLayer || [];
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function gtag(){dataLayer.push(arguments);}
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gtag('js', new Date());
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gtag('config', 'G-RWF876HNKW');
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")),
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## Favicons----
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tags$link(rel = "icon", type = "image/png", sizes = "32x32", href = "GREP1_Logo_32x32.png"),
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tags$link(rel = "icon", type = "image/png", sizes = "16x16", href = "GREP1_Logo_32x32.png")
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),
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h5(HTML(
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"<strong>B</strong>ulk <strong>R</strong>NA-seq <strong>A</strong>uto-<strong>P</strong>ipeline"
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))
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),
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## Live Console----
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footer = absolutePanel(
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id = "ConsoleRealTime", class = "panel panel-default",
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bottom = 50, left = 25, width = "75%", fixed = FALSE,
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draggable = TRUE, height = "100px",
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style = "opacity: 0.95; z-index: 20;", ## z-index modification
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uiOutput("EmailNotif_ui"),
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# Horizontal bar
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tags$div(
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style = "display: flex; align-items: center; gap: 10px; padding-left: 5px;",
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HTML('<button data-toggle="collapse" data-target="#GlobalSettingMainPanel">Collapse</button>'),
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tags$a("Console Monitor"),
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downloadButton("download_console", "💾 Download Console Log"),
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actionButton("clear_console", "🧹 Clear Console", icon = icon("eraser"), class = "btn-danger")
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),
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tags$div(
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id = "GlobalSettingMainPanel",
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style = "max-height: 300px; overflow-y: auto; padding: 5px;",
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tags$div(
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id = "console",
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style = "white-space: pre-wrap; font-family: monospace; background-color: #111; color: #0f0; height: 280px; overflow-y: scroll; padding: 10px; border: 1px solid #333;"
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)
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)
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),
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```
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# 2. Convert Main loop with [processx](https://github.com/r-lib/processx)
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