Add two example apps to showcase DDL and Custom transformation

.github/workflows/deploy.yml

@@ -10,6 +10,8 @@ on:
     paths:
       - RNA-seq/**
       - basic-teal/**
+      - delayed-data/**
+      - custom-transform/**
       - efficacy/**
       - exploratory/**
       - longitudinal/**
@@ -45,6 +47,8 @@ jobs:
         directory:
           - RNA-seq
           - basic-teal
+          - delayed-data
+          - custom-transform
           - efficacy
           - exploratory
           - longitudinal
@@ -63,6 +67,15 @@ jobs:
             echo "BRANCH_NAME=main" >> $GITHUB_ENV
           fi
 
+      - name: Check if deployment should be skipped
+        id: skip_check
+        run: |
+          if [[ "${{ matrix.channel }}" == "dev" && ("${{ matrix.directory }}" == "delayed-data" || "${{ matrix.directory }}" == "custom-transform") ]]; then
+            echo "skip=true" >> $GITHUB_OUTPUT
+          else
+            echo "skip=false" >> $GITHUB_OUTPUT
+          fi
+
       - name: Setup job token 🔑
         id: github-token
         run: |
@@ -150,6 +163,7 @@ jobs:
 
       - name: Install R packages using renv and update the renv snapshot
         shell: Rscript {0}
+        if: steps.skip_check.outputs.skip == 'false'
         working-directory: ${{ matrix.directory }}
         run: |
           options(renv.config.cache.symlinks = FALSE)
@@ -164,7 +178,7 @@ jobs:
         run: cat renv.lock
 
       - name: Front end test to check if the app works fine
-        if: steps.find-cypress.outputs.has-cypress-tests == 'true'
+        if: steps.find-cypress.outputs.has-cypress-tests == 'true' && steps.skip_check.outputs.skip == 'false'
         uses: cypress-io/github-action@v6
         with:
           build: npm install cypress --save-dev
@@ -175,12 +189,14 @@ jobs:
 
       - name: Install deployment-related R package dependencies
         shell: Rscript {0}
+        if: steps.skip_check.outputs.skip == 'false'
         working-directory: ${{ matrix.directory }}
         run: |
           install.packages(c("BiocManager", "rsconnect"))
 
       - name: Deploy 🖨 ${{ matrix.directory }} 🎨
         shell: Rscript {0}
+        if: steps.skip_check.outputs.skip == 'false'
         working-directory: ${{ matrix.directory }}
         run: |
           rsconnect::setAccountInfo(
@@ -201,6 +217,7 @@ jobs:
           )
 
       - name: Commit and push changes 📌
+        if: steps.skip_check.outputs.skip == 'false'
         run: |
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions"

.gitignore

@@ -57,3 +57,9 @@ rsconnect/
 
 # Markdown generated files
 */README.html
+
+# Node modules
+*/tests/node_modules
+
+# Teal lock file
+*/teal_app.lock

README.md

@@ -13,19 +13,19 @@ A gallery of sample apps based on the [`teal`](https://github.com/insightsengine
 
 The Stable version of the apps use the latest released packages while the dev version of the apps use the development packages which are installed from the `main` branch of the respective package repository. The specific versions used can be seen in the `Session Info` of the deployed app.
 
-
-| Stable version                                    | Dev version                                     |
-|---------------------------------------------------|-------------------------------------------------|
-| [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_stable/)          | [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_dev/)         |
-| [exploratory](https://genentech.shinyapps.io/NEST_exploratory_stable/)        | [exploratory](https://genentech.shinyapps.io/NEST_exploratory_dev/)       |
-| [safety](https://genentech.shinyapps.io/NEST_safety_stable/)                  | [safety](https://genentech.shinyapps.io/NEST_safety_dev/)                 |
-| [efficacy](https://genentech.shinyapps.io/NEST_efficacy_stable/)              | [efficacy](https://genentech.shinyapps.io/NEST_efficacy_dev/)             |
-| [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_stable/) | [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_dev/)|
-| [early-dev](https://genentech.shinyapps.io/NEST_early-dev_stable/)             | [early-dev](https://genentech.shinyapps.io/NEST_early-dev_dev/)           |
-| [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_stable/)       | [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_dev/)     |
-| [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_stable/)                 | [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_dev/)               |
-| [python](https://genentech.shinyapps.io/NEST_python_stable/)                   | [python](https://genentech.shinyapps.io/NEST_python_dev/)                 |
-
+| Stable version                                                                   | Dev version                                                                   |
+| -------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- |
+| [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_stable/)             | [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_dev/)             |
+| delayed-data - NOT DEPLOYED         | [delayed-data](https://genentech.shinyapps.io/NEST_delayed-data_dev/)         |
+| custom-transform - NOT DEPLOYED | [custom-transform](https://genentech.shinyapps.io/NEST_custom-transform_dev/) |
+| [exploratory](https://genentech.shinyapps.io/NEST_exploratory_stable/)           | [exploratory](https://genentech.shinyapps.io/NEST_exploratory_dev/)           |
+| [safety](https://genentech.shinyapps.io/NEST_safety_stable/)                     | [safety](https://genentech.shinyapps.io/NEST_safety_dev/)                     |
+| [efficacy](https://genentech.shinyapps.io/NEST_efficacy_stable/)                 | [efficacy](https://genentech.shinyapps.io/NEST_efficacy_dev/)                 |
+| [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_stable/)   | [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_dev/)   |
+| [early-dev](https://genentech.shinyapps.io/NEST_early-dev_stable/)               | [early-dev](https://genentech.shinyapps.io/NEST_early-dev_dev/)               |
+| [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_stable/)         | [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_dev/)         |
+| [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_stable/)                   | [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_dev/)                   |
+| [python](https://genentech.shinyapps.io/NEST_python_stable/)                     | [python](https://genentech.shinyapps.io/NEST_python_dev/)                     |
 
 ## Running the apps
 
@@ -74,5 +74,5 @@ Adding a sample app involves the following steps:
 #### Optional/Soft requirements
 
 1. You can snapshot the teal app dependencies using `{renv}` but make sure to snapshot using GitHub references to the teal packages.
-2. Create a GIF recording ([KAP](https://getkap.co/) is a good tool for this). Make sure that the dimensions of the GIF is 970x555 px and the size is about 1 MB. (It can be done by recording using KAP in 1470x840 px and rendering 5fps and downsizing 33%). Place the GIF inside the `_internal/quarto/assets/img` directory. Also, make sure that the name of the GIF is `APP_NAME.gif`. Also, make sure to place a static image with the name dimention called `APP_NAME.png` that will be displayed in the demo page when the card is not hovered.
+2. Create a GIF recording ([LICEcap](https://www.cockos.com/licecap/) is a good tool for this). Make sure that the dimensions of the GIF is 970x555 px and the size is about 1 MB. Place the GIF inside the `_internal/quarto/assets/img` directory. Also, make sure that the name of the GIF is `APP_NAME.gif`. Also, make sure to place a static image with the name dimention called `APP_NAME.png` that will be displayed in the demo page when the card is not hovered.
 3. Add front-end tests with the help of cypress. Copy the contents of the `js` directory within some other app's directory inside your app directory to get the node dependencies. Place the cypress tests inside the `tests/cypress` inside your app's directory. Please refer to an existing app's tests so that the `.github/deploy.yaml` will automaticall run the cypress tests.

_internal/quarto/demo-apps.yml

@@ -2,6 +2,8 @@
   deployment_server: https://genentech.shinyapps.io/
   apps:
     - title: basic-teal
+    - title: delayed-data
+    - title: custom-transform
     - title: exploratory
     - title: safety
     - title: efficacy

custom-transform/.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

custom-transform/README.md

@@ -0,0 +1,20 @@
+
+<!-- Generated by app_readme_template.Rmd and generate_app_readme.R: do not edit by hand-->
+
+# custom-transform app
+
+### Run the app yourself
+
+    source("https://raw.github.com/insightsengineering/teal.gallery/main/_internal/utils/sourceme.R")
+
+    # Run the app
+    restore_and_run("custom-transform", package_repo = "https://insightsengineering.r-universe.dev")
+
+### View the deployed app
+
+Deployed app:
+<https://genentech.shinyapps.io/NEST_custom-transform_stable>
+
+### Preview the app
+
+![](../_internal/quarto/assets/img/custom-transform.gif)<!-- -->

custom-transform/app.R

@@ -0,0 +1,137 @@
+library(teal)
+
+my_transformers <- list(
+  teal_transform_module(
+    label = "Keep first 6 from IRIS",
+    ui = function(id) {
+      ns <- NS(id)
+      div(
+        checkboxInput(ns("check"), label = "Toggle `head(iris)`"),
+      )
+    },
+    server = function(id, data) {
+      moduleServer(id, function(input, output, session) {
+        eventReactive(input$check, {
+          req(data())
+          if (input$check) {
+            within(data(), iris <- head(iris, 6))
+          } else {
+            data()
+          }
+        })
+      })
+    }
+  ),
+  teal_transform_module(
+    label = "Merge datasets to get ANL",
+    ui = function(id) {
+      ns <- NS(id)
+      tagList(
+        div("Choose the two datasets to merge:"),
+        teal.widgets::optionalSelectInput(ns("merge_a"), "Merge A", choices = NULL),
+        teal.widgets::optionalSelectInput(ns("merge_b"), "Merge B", choices = NULL)
+      )
+    },
+    server = function(id, data) {
+      checkmate::assert_class(data, "reactive")
+      moduleServer(id, function(input, output, session) {
+        iv <- shinyvalidate::InputValidator$new()
+        iv$add_rule("merge_a", shinyvalidate::sv_required("Please select dataset A"))
+        iv$add_rule("merge_b", shinyvalidate::sv_required("Please select dataset B"))
+        iv$enable()
+
+        reactive_datanames <- reactive({
+          req(data())
+          teal.data::datanames(data())
+        })
+        observeEvent(reactive_datanames(), {
+          selected_a <- isolate(input$merge_a)
+          if (identical(selected_a, "")) selected_a <- restoreInput(session$ns("merge_a"), NULL)
+          teal.widgets::updateOptionalSelectInput(
+            session = session,
+            inputId = "merge_a",
+            choices = reactive_datanames(),
+            selected = restoreInput(session$ns("merge_a"), selected_a)
+          )
+
+          selected_b <- isolate(input$merge_b)
+          if (identical(selected_b, "")) selected <- restoreInput(session$ns("merge_b"), NULL)
+          teal.widgets::updateOptionalSelectInput(
+            session = session,
+            inputId = "merge_b",
+            choices = reactive_datanames(),
+            selected = restoreInput(session$ns("merge_b"), selected_b)
+          )
+        })
+
+        merge_a <- reactive(input$merge_a)
+        merge_b <- reactive(input$merge_b)
+
+        reactive({
+          new_data <- within(
+            data(),
+            ANL <- dplyr::left_join(merge_a, merge_b),
+            merge_a = tryCatch(as.name(merge_a()), error = function(e) as.name("DatasetA")),
+            merge_b = tryCatch(as.name(merge_b()), error = function(e) as.name("DatasetA"))
+          )
+          teal.data::datanames(new_data) <- c(teal.data::datanames(new_data), "ANL")
+          new_data
+        })
+      })
+    }
+  )
+)
+
+data <- teal_data() %>%
+  within(
+    {
+      ADSL <- teal.data::rADSL
+      ADTTE <- teal.data::rADTTE
+      iris <- iris
+
+      CO2 <- CO2
+      factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
+      CO2[factors] <- lapply(CO2[factors], as.character)
+    }
+  )
+join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
+teal.data::datanames(data) <- c("ADSL", "ADTTE", "iris", "CO2")
+
+nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png"
+app_source <- "https://github.com/insightsengineering/teal.gallery/tree/main/basic-teal"
+gh_issues_page <- "https://github.com/insightsengineering/teal.gallery/issues"
+
+header <- tags$span(
+  style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",
+  tags$span("Teal app with custom transform", style = "font-size: 30px;"),
+  tags$span(
+    style = "display: flex; align-items: center;",
+    tags$img(src = nest_logo, alt = "NEST logo", height = "45px", style = "margin-right:10px;"),
+    tags$span(style = "font-size: 24px;", "NEST @ Roche")
+  )
+)
+
+footer <- tags$p(
+  "This teal app is brought to you by the NEST Team at Roche/Genentech.
+        For more information, please visit:",
+  tags$a(href = app_source, target = "_blank", "Source Code"), ", ",
+  tags$a(href = gh_issues_page, target = "_blank", "Report Issues")
+)
+
+app <- init(
+  data = data,
+  filter = teal_slices(
+    teal_slice("ADSL", "SEX"),
+    teal_slice("ADSL", "AGE", selected = c(18L, 65L))
+  ),
+  modules = modules(
+    example_module("Module with transformations", transformers = my_transformers),
+    example_module("Module with only iris transformation", transformers = my_transformers[1]),
+    example_module("Module with no transformations")
+  ),
+  title = build_app_title("Custom Transform Teal App", nest_logo),
+  header = header,
+  footer = footer
+)
+
+shinyApp(app$ui, app$server)

custom-transform/delayed-data.Rproj

@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes