Author: David Granjon

# Auditing Shiny apps

#### David Granjon

# Audit Shiny apps with {shinytest2}

Have you ever dreamed of profiling, load testing your Shiny app at each commit, without having to manually run any script?

In this vignette, we’ll see how one can design and automate Shiny apps audit pipelines with `{shinytest2}`.

## Introduction

This case study consists of analyzing a particularly non-optimized app, whose code is defined below. This app simulates a stiff oscillator, also known as Van der Pol model. Under the hood, this system (composed of 2 differential equations) is integrated with the `{deSolve}` package. Stiff systems need a much smaller time step than classic systems, thereby requiring more time to solve:

    van_der_pol <- function(t, y, mu) {
      d_x <- y[2]
      d_y <- mu * (1 - y[1]^2) * y[2] - y[1]
      list(c(X = d_x, Y = d_y))
    }

    server <- function(input, output) {
      output$brussels <- renderPlot({
        y0 <- c(X = input$X, Y = input$Y)
        times <- seq(0, 1000, .01)
        out <- deSolve::ode(y0, times, van_der_pol, input$mu)
        par(mfrow = c(1, 1))
        plot(out[, 2:3], type = "l", xlab = "X", ylab = "Y", main = "state diagram")
      })
    }

    ui <- fluidPage(
      headerPanel("Van der Pol oscillator"),
      sidebarLayout(
        sidebarPanel(
          h3("Init values"),
          numericInput("X", label = "X", min = 0.0, max = 5,  value = 1, step = 0.2),
          numericInput("Y", label = "Y", min = 0.0, max = 5,  value = 1, step = 0.2),

          h3("Parameters"),
          numericInput("mu", label = "mu", min = 0.0, max = 5,  value = 1, step = 0.1)
        ),
        mainPanel(
          h3("Simulation results"),
          plotOutput("brussels")
        )
      )
    )

    shinyApp(ui = ui, server = server)

As a first test, you can run the app by calling `runApp(system.file("vig-apps/non-optimized-app/", package = "shinytest2"))` locally and notice how slow it is to perform one computation. The next question is, how does this app scale? The answer is likely “No it doesn’t!”, but we would like to know exactly how bad it is. This is where load testing comes to play.

## Load testing with {shinytest2}

Shiny app load testing aims at running multiple identical user sessions in parallel and measure the resulting app response. It answers many questions, such as:

- What is the time necessary to get to the homepage?
- How much time does it take to perform the first computation?
- Will all session end at the same time?

A load test is composed a three phases:

- Similarly to `{shinytest2}`, `{shinyloadtest}` records a user session with `shinyloadtest::record_session()`.
- This session is subsequently replayed by a Java-based tool, `shinycannon`, able to simulate multiple sessions during a chosen amount of time.
- Sessions are analyzed by `shinyloadtest::load_runs()` and an HTML report generated with `shinyloadtest::shinyloadtest_report()`.

In general, the first step is done manually, that is, you play with the app as if you were a real business user and stop the session when satisfied. However, because of `{shinytest2}` headless capabilities, we could manipulate the app with `{shinytest2}` helpers such as `set_inputs` or raw JavaScript code to achieve the same goal.

There is, however, a tiny technical obstacle to overcome. By default, `{shinytest2}` starts the app on a given port and the headless browser, namely Chrome, is then connected to the same port. This would be an issue with `{shinyloadtest}` since the recorder does not listen to the same port, which is `8600`. In practice, we’ll have to:

- Start the Shiny app as a background process on a given port.
- Fire the load test recorder on port `8600`.
- Connect Chrome to the recorder on port `8600`.

### Launch the background app

You may have already noticed that when launching a Shiny app, you can’t run anything else in the R console while the app is live. The explanation is pretty simple: R performs tasks sequentially and can only perform one calculation at a time.

How do we start the app without blocking the main R process? We leverage the `{callr}` package, which exposes a convenient API to start R processes in the background, that is, without blocking the main R process. The code below shows how to start a Shiny app located at `path` on a specific port and run the load test recorder on the same port:

    # Main shiny app
    shiny_bg <- function(path, port) {
      options(shiny.port = port)
      shiny::runApp(path)
    }

    # Start recorder
    recorder_bg <- function(port) {
      shinyloadtest::record_session(
        target_app_url = sprintf("http://127.0.0.1:%s", port),
        host = "127.0.0.1",
        port = 8600,
        output_file = "recording.log",
        open_browser = FALSE
      )
    }

We can pass this to the `start_r_bg()` function:

    start_r_bg <- function(fun, path = NULL, port = 3515) {

      # remove NULL elements
      args <- Filter(Negate(is.null), list(path = path, port = port))

      process <- callr::r_bg(
        func = fun,
        args = args,
        stderr= "",
        stdout = ""
      )

      while (any(is.na(pingr::ping_port("127.0.0.1", 3515)))) {
        message("Waiting for Shiny app to start...")
        Sys.sleep(0.1)
      }

      attempt::stop_if_not(
        process$is_alive(),
        msg = "Unable to launch the subprocess"
      )

      process
    }

where `r_bg()` starts a background R process, passing the corresponding function and parameters. Besides, we provide some log elements and safety guard in case the app can’t start. To launch the app and recorder we can call:

    target <- start_r_bg(shiny_bg, path = system.file("vig-apps/non-optimized-app/", package = "shinytest2"))
    # Listening on 127.0.0.1:3515
    recorder <- start_r_bg(recorder_bg)
    # Listening on 127.0.0.1:8600

### Connect Chrome

The previous part was the most technical step. Now, we only have to start a Chrome headless browser on port `8600`, where the load test recorder runs. You’ll notice that `{shinytest2}` also supports remote urls. We should increase the value of `load_timout` to 15 seconds to help us avoid producing this annoying `{shinytest2}` warning:

    {shinytest2} R  info 15:25:37.36 Error while initializing AppDriver:
    Shiny app did not become stable in 10000ms.

    # Start AppDriver with recorder url
    chrome <- shinytest2::AppDriver$new("http://127.0.0.1:8600", load_timeout = 15 * 1000)

If your running under Linux OS, below shows the list of R processes running so far in the background:

    $ netstat -lntp

    Proto Recv-Q Send-Q Local Address           Foreign Address         State       PID/Program name
    tcp        0      0 127.0.0.1:8600          0.0.0.0:*               LISTEN      361115/R
    tcp        0      0 127.0.0.1:3515          0.0.0.0:*               LISTEN      361101/R
    tcp        0      0 127.0.0.1:44179         0.0.0.0:*               LISTEN      359555/google-chrom

If everything is successful, you should see a Client connected message in the R console. We then change the `mu` parameter input without forgetting the timeout:

    app$set_inputs(mu = 4, timeout_ = 15 * 1000)

We can inspect the logs with the help of `chrome$get_log()`, to check whether everything run smoothly:

    app$get_logs()
    #> {shinytest2} R  info 14:27:00.80 Start AppDriver initialization
    #> {shinytest2} R  info 14:27:00.82 Creating new ChromoteSession
    #> {shinytest2} R  info 14:27:02.20 Navigating to Shiny app
    #> {shinytest2} R  info 14:27:02.57 Injecting shiny-tracer.js
    #> {chromote}   JS info 14:27:02.61 shinytest2; jQuery not found
    #> {chromote}   JS info 14:27:02.63 shinytest2; Loaded
    #> {shinytest2} R  info 14:27:02.64 Waiting for Shiny to become ready
    #> {chromote}   JS info 14:27:02.72 shinytest2; jQuery found
    #> {chromote}   JS info 14:27:02.73 shinytest2; Waiting for shiny session to connect
    #> {chromote}   JS info 14:27:03.12 shinytest2; Connected
    #> {shinytest2} R  info 14:27:03.17 Waiting for Shiny to become idle for 200ms within 10000ms
    #> {chromote}   JS info 14:27:03.18 shinytest2; Waiting for Shiny to be stable
    #> {chromote}   JS info 14:27:03.27 shinytest2; shiny:busy
    #> {chromote}   JS info 14:27:06.28 shinytest2; shiny:idle
    #> {chromote}   JS info 14:27:06.30 shinytest2; shiny:value brussels
    #> {chromote}   JS info 14:27:06.48 shinytest2; Shiny has been idle for 200ms
    #> {shinytest2} R  info 14:27:06.48 Shiny app started
    #> {shinytest2} R  info 14:30:17.79 Setting inputs: 'mu'', ''X'', ''Y'
    #> {chromote}   JS info 14:30:17.81 shinytest2; inputQueue: adding mu
    #> {chromote}   JS info 14:30:17.81 shinytest2; inputQueue: adding X
    #> {chromote}   JS info 14:30:17.81 shinytest2; inputQueue: adding Y
    #> {chromote}   JS info 14:30:17.82 shinytest2; inputQueue: flushing mu
    #> {chromote}   JS info 14:30:17.83 shinytest2; inputQueue: flushing X
    #> {chromote}   JS info 14:30:17.83 shinytest2; inputQueue: flushing Y
    #> {chromote}   JS info 14:30:17.87 shinytest2; shiny:busy
    #> {chromote}   JS info 14:30:20.42 shinytest2; shiny:idle
    #> {chromote}   JS info 14:30:20.46 shinytest2; shiny:value brussels
    #> {shinytest2} R  info 14:30:20.47 Finished setting inputs. Timedout: FALSE

Once satisfied, we may close the headless connection to stop the recorder:

    # clean
    app$stop()
    # needed to avoid
    # java.lang.IllegalStateException: last event in log not a
    # WS_CLOSE (did you close the tab after recording?)
    Sys.sleep(2)

### Replay with shinycannon

If you remember, the final step consists of replaying the main session in parallel. We start `shinycannon` with 5 workers and wait:

    target_url <- "http://127.0.0.1:3515"
    workers <- 5
    system(
      sprintf(
        "shinycannon recording.log %s --workers %s --loaded-duration-minutes 2 --output-dir run1",
        target_url, workers
      )
    )

    # shinycannon replay
    #2022-05-09 14:37:18.549 INFO [thread00] - Detected target application type: R/Shiny
    #2022-05-09 14:37:18.560 INFO [thread00] - Waiting for warmup to complete
    #2022-05-09 14:37:18.554 INFO [thread01] - Warming up
    #2022-05-09 14:37:18.562 INFO [progress] - Running: 0, Failed: 0, Done: 0
    #2022-05-09 14:37:23.563 INFO [progress] - Running: 1, Failed: 0, Done: 0

Some error message in the `shinycannon` logs can be explained by failures during the `{shinytest2}` driver initialization. If this error persist, best practice is to restart R, cleanup everything and start again.

### Report generation

The report generation is quite straightforward:

    # Close the running app
    target$kill()

    # Treat data and generate report
    df <- shinyloadtest::load_runs("run1")
    shinyloadtest::shinyloadtest_report(
      df,
      "public/index.html",
      self_contained = TRUE,
      open_browser = FALSE
    )

We don’t forget to clean the target app so as to kill the underlying process. Note that if you want to deploy the report on GitHub Pages, you have to name it `index.html`.

### Automating with GitHub Actions

Now, it is time to integrate the current pipeline in a CI/CD workflow. For convenience, we wrap all the previous steps in a single function:

    ## File: R/audit-app.R
    record_loadtest <- function(path, timeout = 15, workers = 5) {
      message("\n---- BEGIN LOAD-TEST ---- \n")
      # start app + recorder
      target <- start_r_bg(shiny_bg, path = path)
      recorder <- start_r_bg(recorder_bg)

      # start headless chrome (points to recorder!).
      # AppDriver also support remote urls.
      app <- shinytest2::AppDriver$new(
        "http://127.0.0.1:8600",
        load_timeout = timeout * 1000
      )

      app$set_inputs(mu = 4, timeout_ = timeout * 1000)

      # clean
      app$stop()
      # needed to avoid
      # java.lang.IllegalStateException: last event in log not a
      # WS_CLOSE (did you close the tab after recording?)
      Sys.sleep(2)

      # shinycannon (maybe expose other params later ...)
      target_url <- "http://127.0.0.1:3515"
      system(
        sprintf(
          "shinycannon recording.log %s --workers %s --loaded-duration-minutes 2 --output-dir run1",
          target_url, workers
        )
      )

      target$kill()

      # Treat data and generate report
      df <- shinyloadtest::load_runs("run1")
      shinyloadtest::shinyloadtest_report(
        df,
        "public/index.html",
        self_contained = TRUE,
        open_browser = FALSE
      )
    }

Below is the necessary GitHub Actions yaml file. Overall, this will:

- Run each time code is pushed to GitHub.
- Run in parallel on 3 different Ubuntu flavors.
- Install R, some system dependencies, and R packages. Install shinycannon tools for load-testing.
- Deploy the load test report to GitHub Pages.

    on:
      push:
        branches: [main, master]
      pull_request:
        branches: [main, master]

    name: shiny-loadtest-ci

    jobs:
      shiny-loadtest-ci:
        runs-on: ${{ matrix.config.os }}
        permissions:
          contents: write

        name: ${{ matrix.config.os }} (${{ matrix.config.r }})

        strategy:
          fail-fast: false
          matrix:
            config:
              - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
              - {os: ubuntu-latest,   r: 'release'}
              - {os: ubuntu-latest,   r: 'oldrel-1'}

        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
          R_KEEP_PKG_SOURCE: yes

        steps:
          - uses: actions/checkout@v2
          - uses: r-lib/actions/setup-r@v2
          - uses: r-lib/actions/setup-r-dependencies@v2
            with:
              cache-version: 2
              extra-packages: |
                any::shinyloadtest
                any::lubridate
                any::DT
                any::callr
                any::shinytest2
                any::deSolve
                any::attempt

          - name: Install shinycannon 💥
            run: |
              sudo bash -c 'apt-get update; apt-get install -y default-jre-headless; apt-get clean; rm -rf /var/lib/apt/lists/*'
              wget https://github.com/rstudio/shinycannon/releases/download/v1.1.3/shinycannon_1.1.3-dd43f6b_amd64.deb
              sudo dpkg -i ./*.deb

          - name: Run load test 🏥
            shell: Rscript {0}
            run: |
                source("R/audit-app.R")
                record_loadtest(path = "app.R");

          - name: Deploy to GitHub pages 🚀
            if: github.event_name != 'pull_request'
            uses: JamesIves/github-pages-deploy-action@4.1.4
            with:
              clean: false
              branch: gh-pages
              folder: public

If you want to test it on your end, below are lines of code to setup a RStudio project and link it to GitHub:

    # Inside the project
    # Use audit GitHub Actions workflow
    usethis::use_github_action(url = "https://raw.githubusercontent.com/rstudio/shinytest2/main/inst/gha/app-audit.yaml")
    # Copy audit script
    dir.create("R", showWarnings = FALSE)
    file.copy(system.file("gha/audit-app.R", package = "shinytest2"), "R/audit-app.R")
    # Create your app.R file
    file.create("app.R")

    message("TODO: User - Copy in your app code to `app.R`!")

    # To test it locally
    source("R/audit-app.R")
    record_loadtest("app.R")

    # Test the audit with GitHub Actions
    usethis::use_description()
    usethis::use_git()
    usethis::use_github()
    usethis::use_github_pages()

If you test it locally within a package, you may want to ignore `public`, `recording.log` by adding them in the `.Rbuildignore` file, which will avoid unnecessary warnings during any future `devtools::check()`:

    usethis::use_build_ignore(c("public", "recording.log"))

An example is available here.

As shown in the above report, especially in the session duration tab, the app is clearly not able to handle 5 simultaneous user due to the very large computations being performed by the Shiny server:

- The red area is over represented for most sessions, which means many users have to wait significant amount of time before seeing the app. This is a critical issue, most users will leave the app at this moment.
- The blue area is also large, showing that most time is spent for computations. Given the single-threaded nature of R, there are high chances other users might be blocked by already ongoing computations. This is also frustrating, as people may think the app has crashed.

Even though out of this vignette scope, one quick and significant optimization would be to set a caching system with `shiny::bind_cache()`. As shown in the following figure, adding cache is so fast that `shinycannon` was able to start more than 1000 sessions in 2 minutes.