diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 16656171..8b987a17 100644 --- a/.github/workflows/deploy.yml +++ b/.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 +67,17 @@ jobs: echo "BRANCH_NAME=main" >> $GITHUB_ENV fi + - name: Check if deployment should be skipped + id: skip_check + run: | + if [[ "${{ matrix.channel }}" == "stable" && ("${{ matrix.directory }}" == "delayed-data" || "${{ matrix.directory }}" == "custom-transform") ]]; then + echo "skip=true" >> $GITHUB_OUTPUT + echo "Skipping deployment for ${{ matrix.directory }} app." + else + echo "skip=false" >> $GITHUB_OUTPUT + echo "Proceeding with deployment for ${{ matrix.directory }} app." + fi + - name: Setup job token 🔑 id: github-token run: | @@ -78,7 +93,7 @@ jobs: - name: Checkout repo 🛎 uses: actions/checkout@v4 with: - ref: "${{ env.BRANCH_NAME }}" + ref: "669_insertUI@dev" token: "${{ steps.github-token.outputs.token }}" - name: Add safe directory in git config @@ -127,6 +142,7 @@ jobs: - name: Update renv.lock file with updated GitHub packages shell: Rscript {0} + if: steps.find-cypress.outputs.has-cypress-tests == 'true' run: | setwd("${{ matrix.directory }}") lockfile <- renv::lockfile_read() @@ -150,6 +166,7 @@ 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 +181,7 @@ 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 +192,14 @@ 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 +220,7 @@ 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" diff --git a/.gitignore b/.gitignore index 5d68b430..50388cd3 100644 --- a/.gitignore +++ b/.gitignore @@ -57,3 +57,9 @@ rsconnect/ # Markdown generated files */README.html + +# Node modules +*/tests/node_modules + +# Teal lock file +*/teal_app.lock diff --git a/README.md b/README.md index 093ae2d5..9ed2a621 100644 --- a/README.md +++ b/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. diff --git a/_internal/quarto/assets/img/custom-transform.gif b/_internal/quarto/assets/img/custom-transform.gif new file mode 100644 index 00000000..7a57b87c Binary files /dev/null and b/_internal/quarto/assets/img/custom-transform.gif differ diff --git a/_internal/quarto/assets/img/custom-transform.png b/_internal/quarto/assets/img/custom-transform.png new file mode 100644 index 00000000..7dbe7e5b Binary files /dev/null and b/_internal/quarto/assets/img/custom-transform.png differ diff --git a/_internal/quarto/assets/img/delayed-data.gif b/_internal/quarto/assets/img/delayed-data.gif new file mode 100644 index 00000000..93a94337 Binary files /dev/null and b/_internal/quarto/assets/img/delayed-data.gif differ diff --git a/_internal/quarto/assets/img/delayed-data.png b/_internal/quarto/assets/img/delayed-data.png new file mode 100644 index 00000000..5aff6625 Binary files /dev/null and b/_internal/quarto/assets/img/delayed-data.png differ diff --git a/_internal/quarto/demo-apps.yml b/_internal/quarto/demo-apps.yml index d19378f5..cdc14714 100644 --- a/_internal/quarto/demo-apps.yml +++ b/_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 diff --git a/custom-transform/.Rprofile b/custom-transform/.Rprofile new file mode 100644 index 00000000..81b960f5 --- /dev/null +++ b/custom-transform/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/custom-transform/README.md b/custom-transform/README.md new file mode 100644 index 00000000..45759696 --- /dev/null +++ b/custom-transform/README.md @@ -0,0 +1,20 @@ + + + +# 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: + + +### Preview the app + +![](../_internal/quarto/assets/img/custom-transform.gif) diff --git a/custom-transform/app.R b/custom-transform/app.R new file mode 100644 index 00000000..bc8125ac --- /dev/null +++ b/custom-transform/app.R @@ -0,0 +1,132 @@ +library(teal) + +my_transformers <- list( + teal_transform_module( + label = "Keep first n-observations 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$ns("merge_b"), selected_b) + ) + }) + + reactive({ + req(input$merge_a, input$merge_b) + new_data <- within( + data(), + ANL <- dplyr::left_join(merge_a, merge_b), + merge_a = as.name(input$merge_a), + merge_b = as.name(input$merge_b) + ) + teal.data::datanames(new_data) <- c(teal.data::datanames(new_data), "ANL") + new_data + }) + }) + } + ) +) + +data <- teal_data() +data <- within(data, { + ADSL <- teal.data::rADSL + ADTTE <- teal.data::rADTTE + iris <- iris + CO2 <- CO2 + factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L)))) + CO2[factors] <- lapply(CO2[factors], as.character) +}) +join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")] +teal.data::datanames(data) <- c("ADSL", "ADTTE", "iris", "CO2") + +nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png" +app_source <- "https://github.com/insightsengineering/teal.gallery/tree/main/basic-teal" +gh_issues_page <- "https://github.com/insightsengineering/teal.gallery/issues" + +header <- tags$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) diff --git a/custom-transform/delayed-data.Rproj b/custom-transform/delayed-data.Rproj new file mode 100644 index 00000000..e83436a3 --- /dev/null +++ b/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 diff 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"Repository": "CRAN", + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + } + } +} diff --git a/custom-transform/renv/.gitignore b/custom-transform/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/custom-transform/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/custom-transform/renv/activate.R b/custom-transform/renv/activate.R new file mode 100644 index 00000000..d13f9932 --- /dev/null +++ b/custom-transform/renv/activate.R @@ -0,0 +1,1220 @@ + +local({ + + # the requested version of renv + version <- "1.0.7" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/custom-transform/renv/settings.json b/custom-transform/renv/settings.json new file mode 100644 index 00000000..ffdbb320 --- /dev/null +++ b/custom-transform/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/custom-transform/tests/cypress.config.js b/custom-transform/tests/cypress.config.js new file mode 100644 index 00000000..17e51ef5 --- /dev/null +++ b/custom-transform/tests/cypress.config.js @@ -0,0 +1,9 @@ +const { defineConfig } = require("cypress"); + +module.exports = defineConfig({ + e2e: { + setupNodeEvents(on, config) {}, + baseUrl: "http://localhost:3333", + supportFile: false, + }, +}); diff --git a/custom-transform/tests/cypress/e2e/app.cy.js b/custom-transform/tests/cypress/e2e/app.cy.js new file mode 100644 index 00000000..6c9c170b --- /dev/null +++ b/custom-transform/tests/cypress/e2e/app.cy.js @@ -0,0 +1,51 @@ +describe("app", () => { + beforeEach(() => { + cy.visit("/"); + }); + + it("Starts", () => {}); + + it("Has 3 tabs", () => { + cy.get(".nav.nav-pills a[data-bs-toggle=tab]", { timeout: 30000 }).should( + "have.length", + 3 + ); + }); + + it('Navigates to all tabs without error', () => { + cy + .get('.nav.nav-pills a[data-bs-toggle=tab]', { timeout: 30000 }) + .each(($el) => { + cy.wrap($el).as('tealTab'); + + cy.get('@tealTab').then(($el2) => { + cy.log(`Navigating to: ${$el2[0].innerText}`); + }); + + cy.get('@tealTab').click(); + + cy.get('@tealTab').invoke('attr', 'href').as('hrefTab'); + + // Make sure that html element does not have a class that indicates + // that shiny is busy + cy.get('html').not('.shiny-busy'); + + cy + .get('@hrefTab') + .then((hrefTab) => { + cy + .get(`${hrefTab}.tab-pane.active`) + .should('be.visible') + .within(() => { + cy + .get('*') + .filter(':visible') + .should('have.length.gte', 1) + .then(($el3) => { + cy.wrap($el3).contains(/.+/); + }); + }); + }); + }); + }); +}); diff --git a/custom-transform/tests/cypress/support/commands.js b/custom-transform/tests/cypress/support/commands.js new file mode 100644 index 00000000..a5ee6857 --- /dev/null +++ b/custom-transform/tests/cypress/support/commands.js @@ -0,0 +1,33 @@ +Cypress.Commands.add( + "waitForStabilityAndCatchError", + (selector, stabilityPeriod = 300) => { + let lastInnerHTML = ""; + let timesRun = 0; + const checkInterval = 100; + const maxTimesRun = stabilityPeriod / checkInterval; + + function checkForChanges() { + cy.get(selector).then(($el) => { + // Check for shiny-output-error class anywhere in the body + if (Cypress.$("body").find(".shiny-output-error").length > 0) { + throw new Error( + "shiny-output-error class detected during stability check" + ); + } + + const currentInnerHTML = $el.prop("innerHTML"); + if (currentInnerHTML !== lastInnerHTML) { + lastInnerHTML = currentInnerHTML; + timesRun = 0; + } else if (timesRun < maxTimesRun) { + timesRun += 1; + } else { + return; + } + cy.wait(checkInterval).then(checkForChanges); + }); + } + + checkForChanges(); + } +); diff --git a/custom-transform/tests/package-lock.json b/custom-transform/tests/package-lock.json new file mode 100644 index 00000000..76601b81 --- /dev/null +++ b/custom-transform/tests/package-lock.json @@ -0,0 +1,3884 @@ +{ + "name": "tests", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "devDependencies": { + "cypress": "^13.13.2", + "start-server-and-test": "^2.0.3" + } + }, + "node_modules/@colors/colors": { + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/@colors/colors/-/colors-1.5.0.tgz", + "integrity": "sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==", + "dev": true, + "optional": true, + "engines": { + 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--- /dev/null +++ b/delayed-data/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/delayed-data/README.md b/delayed-data/README.md new file mode 100644 index 00000000..4b7b517d --- /dev/null +++ b/delayed-data/README.md @@ -0,0 +1,19 @@ + + + +# delayed-data app + +### Run the app yourself + + source("https://raw.github.com/insightsengineering/teal.gallery/main/_internal/utils/sourceme.R") + + # Run the app + restore_and_run("delayed-data", package_repo = "https://insightsengineering.r-universe.dev") + +### View the deployed app + +Deployed app: + +### Preview the app + +![](../_internal/quarto/assets/img/delayed-data.gif) diff --git a/delayed-data/app.R b/delayed-data/app.R new file mode 100644 index 00000000..e02e1d64 --- /dev/null +++ b/delayed-data/app.R @@ -0,0 +1,99 @@ +library(teal) + +data <- teal_data_module( + ui = function(id) { + ns <- NS(id) + fluidPage( + selectInput( + ns("datasets"), + "Choose datasets", + choices = c("iris", "mtcars", "CO2", "airquality"), + selected = c("iris", "mtcars"), + multiple = TRUE + ), + actionButton(ns("load"), "Load Datasets") + ) + }, + server = function(id, ...) { + moduleServer(id, function(input, output, session) { + eventReactive(input$load, { + data <- teal.data::teal_data() |> + within( + { + if ("iris" %in% datasets) { + iris <- iris + } + if ("mtcars" %in% datasets) { + mtcars <- mtcars + } + if ("CO2" %in% datasets) { + CO2 <- CO2 + } + if ("airquality" %in% datasets) { + airquality <- airquality + } + }, + datasets = input$datasets + ) + data + }) + }) + }, + once = FALSE +) + +filters <- teal_slices( + teal_slice(dataname = "mtcars", varname = "gear", multiple = FALSE), + teal_slice(dataname = "iris", varname = "Species"), + teal_slice(dataname = "iris", varname = "Sepal.Length"), + teal_slice( + dataname = "iris", varname = "Species3", + fixed = TRUE, anchored = FALSE + ), + teal_slice( + dataname = "iris", varname = "Species4", + fixed = FALSE, anchored = TRUE, multiple = TRUE + ), + teal_slice( + dataname = "iris", varname = "Species5", + fixed = TRUE, anchored = TRUE + ), + teal_slice( + dataname = "iris", id = "custom_expr", title = "Custom Expression", + expr = "Sepal.Width > 2.5 & Petal.Length > 1.5", + ) +) + +nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png" +app_source <- "https://github.com/insightsengineering/teal.gallery/tree/main/basic-teal" +gh_issues_page <- "https://github.com/insightsengineering/teal.gallery/issues" + +header <- tags$span( + style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;", + tags$span("Teal app with delayed data loading", style = "font-size: 30px;"), + tags$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$a(href = gh_issues_page, target = "_blank", "Report Issues") +) + +app <- init( + data = data, + filter = filters, + modules = modules( + example_module() + ), + title = build_app_title("Delayed Data Teal App", nest_logo), + header = header, + footer = footer +) + +shinyApp(app$ui, app$server) diff --git a/delayed-data/custom-transform.Rproj b/delayed-data/custom-transform.Rproj new file mode 100644 index 00000000..e83436a3 --- /dev/null +++ b/delayed-data/custom-transform.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 diff --git a/delayed-data/renv.lock b/delayed-data/renv.lock new file mode 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+ "grDevices", + "stats", + "tools" + ], + "Hash": "00ce32f398db0415dde61abfef11300c" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "methods", + "rlang" + ], + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + }, + "zip": { + "Package": "zip", + "Version": "2.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + } + } +} diff --git a/delayed-data/renv/.gitignore b/delayed-data/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/delayed-data/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/delayed-data/renv/activate.R b/delayed-data/renv/activate.R new file mode 100644 index 00000000..d13f9932 --- /dev/null +++ b/delayed-data/renv/activate.R @@ -0,0 +1,1220 @@ + +local({ + + # the requested version of renv + version <- "1.0.7" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/delayed-data/renv/settings.json b/delayed-data/renv/settings.json new file mode 100644 index 00000000..ffdbb320 --- /dev/null +++ b/delayed-data/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/delayed-data/tests/cypress.config.js b/delayed-data/tests/cypress.config.js new file mode 100644 index 00000000..17e51ef5 --- /dev/null +++ b/delayed-data/tests/cypress.config.js @@ -0,0 +1,9 @@ +const { defineConfig } = require("cypress"); + +module.exports = defineConfig({ + e2e: { + setupNodeEvents(on, config) {}, + baseUrl: "http://localhost:3333", + supportFile: false, + }, +}); diff --git a/delayed-data/tests/cypress/e2e/app.cy.js b/delayed-data/tests/cypress/e2e/app.cy.js new file mode 100644 index 00000000..4849d63f --- /dev/null +++ b/delayed-data/tests/cypress/e2e/app.cy.js @@ -0,0 +1,67 @@ +describe("app", () => { + beforeEach(() => { + cy.visit("/"); + }); + + it("Starts", () => {}); + + it("Has 2 tabs", () => { + cy.get(".nav.nav-pills a[data-bs-toggle=tab]", { timeout: 30000 }).should( + "have.length", + 2 + ); + }); + + it("Initializes with one disabled module", () => { + cy.get(".nav.nav-pills a:not([data-value=teal_data_module])[disabled=disabled]", { + timeout: 30000, + }).should( + "have.length", + 1 + ); + }); + + it("Should enable the module after successful data pull", () => { + // Cllick the button labled Load Datasets + cy.contains('button', 'Load Datasets').click(); + cy.get(".nav.nav-pills a:not([data-value=teal_data_module])[disabled=disabled]", { + timeout: 30000, + }).should( + "have.length", + 0 + ); + }); + + it("Should be able to navigate to the module after successful data pull", () => { + // Cllick the button labled Load Datasets + cy.contains('button', 'Load Datasets').click(); + cy.contains('.nav.nav-pills a:not([data-value=teal_data_module])', 'example teal module').click(); + + cy.get('.selectize-input').then(($input) => { + const text = $input.text(); + console.log(text); + expect(text).to.include('iris'); + expect(text).to.include('mtacars'); + }); + }); + + it.only("Should be able to update the data using teal_data_module", () => { + // Cllick the button labled Load Datasets + cy.contains('button', 'Load Datasets').click(); + cy.contains('.nav.nav-pills a:not([data-value=teal_data_module])', 'example teal module').click(); + cy.get('.nav.nav-pills a[data-value=teal_data_module]').click(); + cy + .get('#teal-data-content .selectize-input') + .type('{backspace}{backspace}CO2{enter}airquality{enter}mtcars{enter}{esc}'); + cy.contains('button', 'Load Datasets').click(); + cy.contains('.nav.nav-pills a:not([data-value=teal_data_module])', 'example teal module').click(); + + cy.get('.selectize-input').then(($input) => { + const text = $input.text(); + console.log(text); + expect(text).to.include('CO2'); + expect(text).to.include('airquality'); + expect(text).to.include('mtcars'); + }); + }); +}); diff --git a/delayed-data/tests/cypress/support/commands.js b/delayed-data/tests/cypress/support/commands.js new file mode 100644 index 00000000..a5ee6857 --- /dev/null +++ b/delayed-data/tests/cypress/support/commands.js @@ -0,0 +1,33 @@ +Cypress.Commands.add( + "waitForStabilityAndCatchError", + (selector, stabilityPeriod = 300) => { + let lastInnerHTML = ""; + let timesRun = 0; + const checkInterval = 100; + const maxTimesRun = stabilityPeriod / checkInterval; + + function checkForChanges() { + cy.get(selector).then(($el) => { + // Check for shiny-output-error class anywhere in the body + if (Cypress.$("body").find(".shiny-output-error").length > 0) { + throw new Error( + "shiny-output-error class detected during stability check" + ); + } + + const currentInnerHTML = $el.prop("innerHTML"); + if (currentInnerHTML !== lastInnerHTML) { + lastInnerHTML = currentInnerHTML; + timesRun = 0; + } else if (timesRun < maxTimesRun) { + timesRun += 1; + } else { + return; + } + cy.wait(checkInterval).then(checkForChanges); + }); + } + + checkForChanges(); + } +); diff --git a/delayed-data/tests/package-lock.json b/delayed-data/tests/package-lock.json new file mode 100644 index 00000000..76601b81 --- /dev/null +++ b/delayed-data/tests/package-lock.json @@ -0,0 +1,3884 @@ +{ + "name": "tests", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "devDependencies": { + "cypress": "^13.13.2", + "start-server-and-test": "^2.0.3" + } + }, + "node_modules/@colors/colors": { + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/@colors/colors/-/colors-1.5.0.tgz", + "integrity": "sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==", + "dev": true, + "optional": true, + 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