Timer bug

R/config_repo.R

@@ -175,14 +175,28 @@ config_repo_files <- function(config_path) {
   file.path(config_path, c("logo.png", "options.yaml", "checklists"))
 }
 
-#' @importFrom cli cli_alert_success
-#' @importFrom cli cli_blockquote
-custom_options_found <- function(yaml_path) {
-  content <- tryCatch({
+ghqcapp_repo <- function(config_path = ghqc_config_path()) {
+  if (!fs::dir_exists(config_path)) cli::cli_abort("Custom configuration repository is not found locally at {config_path}. The repository from which to install ghqc.app cannot be determined without the repository downloaded.")
+  yaml_path <- file.path(config_path, "options.yaml")
+  if (!fs::file_exists(yaml_path)) return(list("unset" = TRUE, "url"="https://a2-ai.r-universe.dev"))
+  options <- read_custom_options(yaml_path)
+  if (is.null(options)) cli::cli_abort("{yaml_path} could not be read. Please verify proper structure.")
+  if (!("ghqc.app_repository" %in% names(options))) return(list("unset" = TRUE, "url"="https://a2-ai.r-universe.dev"))
+  list("unset" = FALSE, "url" = options["ghqc.app_repository"])
+}
+
+read_custom_options <- function(yaml_path) {
+  tryCatch({
     unlist(yaml::yaml.load_file(yaml_path))
   }, error = function(e) {
     NULL
   })
+}
+
+#' @importFrom cli cli_alert_success
+#' @importFrom cli cli_blockquote
+custom_options_found <- function(yaml_path) {
+  content <- read_custom_options(yaml_path)
   if (is.null(content)) {
     cli::cli_alert_danger(paste0(cli::col_blue("{basename(yaml_path)}"), " could not be read"))
     return()
@@ -204,6 +218,7 @@ custom_options_found <- function(yaml_path) {
   sapply(names(content), function(x) switch(x,
                                      "prepended_checklist_note" = note_found(content[x]),
                                      "checklist_display_name_var" = checklist_display_name_found(content[x]),
+                                     "ghqc.app_repository" = ghqcapp_repository_found(content[x]),
                                      cli::cli_alert_info("{x} is not a recognized custom option.")))
   cli::cli_end(ul)
   if (!("prepended_checklist_note" %in% names(content))) cli::cli_inform("")
@@ -218,6 +233,10 @@ checklist_display_name_found <- function(checklist_disp_name) {
   cli::cli_alert_success("{names(checklist_disp_name)}: {checklist_disp_name}")
 }
 
+ghqcapp_repository_found <- function(repo_url) {
+  cli::cli_alert_success("{names(repo_url)}: {repo_url}")
+}
+
 #' @importFrom cli cli_alert_success
 #' @importFrom cli cli_h3
 checklists_found <- function(config_path) {

R/download_packages.R

@@ -25,7 +25,7 @@ install_ghqcapp_dependencies <- function(lib_path = ghqc_libpath(),
 
     if (use_pak) {
       res <- withr::with_options(list("pkg.sysreqs" = FALSE, repos = setup_rpsm_url(ghqc_depends_snapshot_date)),
-                                 pak::pkg_install(pkgs, lib = lib_path, upgrade = TRUE, ask = FALSE)) #blow cache, run this, check description file
+                                 pak::pkg_install(pkgs, lib = lib_path, upgrade = TRUE, ask = FALSE))
 
     } else {
       if (rlang::is_installed("pak")) cli::cli_alert_warning("pak is installed, but input `use_pak` was set to FALSE. Set `use_pak` to TRUE for better performance.")
@@ -87,11 +87,11 @@ setup_rpsm_url <- function(snapshot_date) {
       system_info <- processx::run(cmd$cmd, args = cmd$args)$stdout
       system_info <- gsub(" ", replacement = "_", system_info)
       ubuntu_codename <- regmatches(system_info, regexec("\nCodename:\t(.*?)\n", system_info))[[1]][2]
+      repo <- file.path("https://packagemanager.posit.co/cran/__linux__", tolower(ubuntu_codename),snapshot_date)
     }, error = function(e) {
-      cli::cli_abort(message = "Failed to detect codename via lsb_release")
+      repo <- file.path("https://packagemanager.posit.co/cran", snapshot_date)
     }
   )
-  repo <- file.path("https://packagemanager.posit.co/cran/__linux__", tolower(ubuntu_codename),snapshot_date)
   if (rlang::is_installed("pak")) {
     repo_status <- withr::with_options(list(repos = repo), pak::repo_status(bioc = FALSE, cran_mirror = repo))$ok
   } else {
@@ -102,11 +102,35 @@ setup_rpsm_url <- function(snapshot_date) {
       repo_status = FALSE
     })
   }
-  if (!repo_status) cli::cli_abort(message = sprintf("Posit package manager for snapshot date %s and os %s is not available", snapshot_date, ubuntu_codename))
+  if (!repo_status) cli::cli_abort(message = "{repo} is not available. Verify snapshot date and/or operating system is valid.")
 
   c("CRAN" = repo)
 }
 
+install_ghqcapp <- function(lib_path = ghqc_libpath(),
+                            repo = ghqcapp_repo()$url,
+                            use_pak = TRUE) {
+  if (!(all(ghqc_depends %in% utils::installed.packages(lib_path)))) cli::cli_abort("All package dependencies for ghqc.app are not found in {lib_path}. Run `check_ghqcapp_dependencies` before continuing.")
+
+  if (!rlang::is_installed("pak") && use_pak) rlang::abort("pak is not installed. Install pak for better performance. If pak cannot be installed, set `use_pak` = FALSE in `install_ghqcapp_dependencies()` function call")
+
+  cli::cli_inform("Installing ghqc.app...")
+  tryCatch({
+    if (use_pak) {
+      res <- withr::with_options(list("pkg.sysreqs" = FALSE, repos = repo),
+                                 pak::pkg_install("ghqc.app", lib = lib_path, dependencies = FALSE, ask = FALSE))
+
+    } else {
+      if (rlang::is_installed("pak")) cli::cli_alert_warning("pak is installed, but input `use_pak` was set to FALSE. Set `use_pak` to TRUE for better performance.")
+      res <- utils::install.packages("ghqc.app", lib = lib_path, repos = repo, dependencies = FALSE)
+    }
+    cli::cli_alert_success("ghqc.app successfully installed")
+  }, error = function(e) {
+    cli::cli_alert_danger(c("ghqc.app did not install. Failure due to: ", e$message))
+  })
+  invisible(res)
+}
+
 
 #' @importFrom rlang is_installed
 #' @importFrom rlang abort

R/helper.R

@@ -109,7 +109,7 @@ run_app <- function(app_name, qc_dir, lib_path, config_path) {
       counter <- counter + 1
       Sys.sleep(1)
     }
-    if (counter > 19) cli::cli_alert_danger("Shiny app could not be started due to timeout or error")
+    if (counter > 100) cli::cli_alert_danger("Shiny app could not be started due to timeout or error")
 
 
     rstudioapi::viewer(url)

R/interactive_setup.R

@@ -1,3 +1,5 @@
+.pe <- new.env()
+
 #' Interactive function to set up the ghqc environment, including writing to the .Renviron, custom configuration repository download, and ghqc.app dependency installation/linking, for use of the ghqc application suite
 #'
 #' @importFrom cli cli_abort
@@ -10,7 +12,7 @@ setup_ghqc <- function() {
   }
 
   renv_text <- interactive_renviron()
-  interactive_config_download()
+  if (!exists("no_config_repo", envir = .pe)) interactive_config_download()
   check_res <- interactive_depends()
 }
 
@@ -28,23 +30,57 @@ interactive_renviron <- function() {
 #' @importFrom glue glue
 interactive_info <- function(renv_text) {
   config <- parse_renviron("GHQC_CONFIG_REPO", renv_text)
-  if (config$val == "") {
-    cli::cli_inform(c(" ", "GHQC_CONFIG_REPO is not set in your ~/.Renviron"))
-    config_read <- readline("Provide the URL to the custom configuration repository: ")
-  } else {
-    cli::cli_inform(c(" ", "GHQC_CONFIG_REPO is set to {config$val} in your ~/.Renviron"))
-    config_read <- readline(glue::glue("Custom Configuration Repository ({config$val}) "))
-    if (config_read == "") config_read <- config$val
+  val <- if (config$val == "") renviron_not_set() else renviron_set(config$val)
+  if (!exists("no_config_repo", envir = .pe)) renv_text <- renviron_edit("GHQC_CONFIG_REPO", val, renv_text)
+  renv_text
+}
+
+renviron_set <- function(config_url) {
+  cli::cli_inform(c(" ", "GHQC_CONFIG_REPO is set to {config_url} in your ~/.Renviron. Would you like to: ",
+                    " " = "1. Proceed",
+                    " " = "2. Replace",
+                    # " " = "3. Delete", Potentially add later
+                    " " = "3. Abort with error"))
+  input <- readline_and_verify("Input: ", 1:3)
+  if (input == "3") cli::cli_abort("GHQC_CONFIG_REPO is set in ~/.Renviron. Aborting...")
+  if (input == "2") return(readline_and_verify_config())
+  if (input == "1") return(config_url)
+}
+
+renviron_not_set <- function() {
+  cli::cli_inform(c(" ", "GHQC_CONFIG_REPO is not set in your ~/.Renviron. Would you like to: ",
+                    " " = "1. Set value",
+                    " " = "2. Proceed without setting",
+                    " " = "3. Abort with error"))
+  input <- readline_and_verify("Input: ", 1:3)
+  if (input == "3") cli::cli_abort("GHQC_CONFIG_REPO not set in ~/.Renviron. Aborting...")
+  if (input == "2") {
+    cli::cli_alert_danger("GHQC_CONFIG_REPO not set in ~/.Renviron. The ghqc shiny apps will not function.")
+    assign("no_config_repo", FALSE, .pe)
   }
+  if (input == "1") readline_and_verify_config()
+}
+
+readline_and_verify_config <- function() {
+  input <- readline("Provide the URL to the custom configuration repository: ")
   repeat {
-    config_read <- gsub('\"', "", config_read)
-    if (grepl("^https:", config_read)) {
-      config$val <- config_read
-      break
-    }
-    config_read <- readline(glue::glue("GHQC_CONFIG_REPO does not start with 'https:'. Please provide a valid URL: "))
+    input <- gsub('\"', "", input)
+    if (grepl("^https://", input)) break
+    input <- readline(glue::glue("'{input}' does not start with 'https://'. Please provide a valid URL: "))
   }
-  renviron_edit("GHQC_CONFIG_REPO", config$val, renv_text)
+  input
+}
+
+readline_and_verify <- function(message, input_options) {
+  if (!is.character(input_options)) input_options <- as.character(input_options)
+  input <- readline(message)
+  repeat {
+    input <- gsub('\"', "", input)
+    if (input %in% input_options) break
+    io_str <- paste0(paste0(input_options[-length(input_options)], collapse = ", "), ", or ", input_options[length(input_options)])
+    input <- readline(glue::glue("Input value of '{input}' is not valid. Please enter {io_str}: "))
+  }
+  input
 }
 
 write_renv_text <- function(renv_text, val, var_name) {
@@ -70,12 +106,40 @@ interactive_config_download <- function() {
     install.packages("gert")
   }
 
-  cli::cli_inform(" ")
-  config_path <- gsub('\"', "", readline(glue::glue("Path to download the custom configuration repository ({ghqc_config_path()}) ")))
-  if (config_path == "") config_path <- ghqc_config_path()
+  determine_ghqc_config_download()
+}
 
-  cli::cli_inform(" ")
-  check_ghqc_configuration(config_path = config_path)
+determine_ghqc_config_download <- function() {
+  cli::cli_inform(c(" ", "Would you like to download the custom configuration repository to the default location ({ghqc_config_path()})? ",
+                    " " = "1. yes, absolutely!",
+                    " " = "2. can I check the contents in the default location first?",
+                    " " = "3. no, I have other plans and want to specify a different location",
+                    " " = "4. no, I don't want to download right now",
+                    " " = "5. Abort with error"))
+  input <- readline_and_verify("Input: ", 1:5)
+  if (input == "5") cli::cli_abort("Custom configuration repository is not downloaded. Aborting...")
+  if (input == "4") {
+    cli::cli_alert_danger("Cannot verify custom configuration repository is downloaded. Please ensure before running any ghqc shiny apps")
+    assign("no_config_repo", TRUE, .pe)
+  }
+  if (input == "3") {
+    cli::cli_alert_warning("NOTE: This is a non-standard option. Please ensure you have an understanding of the effects before continuing.")
+    yN <- readline_and_verify("Would you like to continue (y/N)? ", c("y", "N"))
+    if (yN == "N") {
+      determine_ghqc_config_download()
+      return(invisible())
+    }
+    path <- gsub('\"', "", readline("Provide the path to install the custom configuration repository: "))
+    assign("config_path", path, .pe)
+    download_ghqc_configuration(config_path = path, .force = TRUE)
+  }
+  assign("config_path", ghqc_config_path(), .pe)
+  if (input == "2") {
+    check_ghqc_configuration()
+  }
+  if (input == "1") {
+    download_ghqc_configuration()
+  }
 }
 
 #' @importFrom cli cli_h1
@@ -88,43 +152,67 @@ interactive_depends <- function() {
                     "1. INSTALL",
                     "2. LINK",
                     "3. Neither"))
-  inst_method <- readline("Input: ")
-
-  repeat {
-    inst_method <- gsub('\"', "", inst_method)
-    if ((inst_method %in% c("1", "2", "3"))) break
-    inst_method <- readline(glue::glue("Input of {inst_method} is not a valid input. Please enter 1, 2, or 3: "))
-  }
+  inst_method <- readline_and_verify("Input: ", 1:3)
 
   if (inst_method == "3") {
     cli::cli_alert_warning("Ensure that ghqc.app and its dependencies are installed into an isolated ghqc package library path before using any of the ghqc ecosystem apps.")
     return(invisible())
   }
 
-  if (inst_method == "1") return(interactive_install())
-  if (inst_method == "2") return(interactive_link())
+  if (inst_method == "1") res <- list("install_results" = interactive_install())
+  if (inst_method == "2") res <- list("link_results" = interactive_link())
+  if (!exists("no_config_repo", envir = .pe)) {
+    list(res, "ghqcapp_results" = interactive_ghqcapp_install())
+  } else {
+    cli::cli_alert_warning("The repository from which to install ghqc.app cannot be determined without the custom configuration repository being downloaded.")
+  }
 }
 
-#' @importFrom rlang is_installed
-#' @importFrom utils install.packages
-#' @importFrom cli cli_inform
-#' @importFrom fs file_exists
-#' @importFrom fs dir_create
-interactive_install <- function() {
+interactive_use_pak <- function() {
   use_pak <- TRUE
   if (!rlang::is_installed("pak")) {
     cli::cli_inform(" ")
     yN <- gsub('\"', "", readline("Package `pak` is not found in your project package library. To improve performance, would you like to install pak? (y/N) "))
     if (yN == "y" || yN == "") utils::install.packages("pak") else use_pak <- FALSE
   }
+  use_pak
+}
 
-  cli::cli_inform(" ")
-  lib_path <- gsub('\"', "", readline("Path to install the ghqc.app dependencies (~/.local/share/ghqc/rpkgs) "))
-  if (lib_path == "") lib_path <- ghqc_libpath()
-  if (!fs::file_exists(lib_path)) fs::dir_create(lib_path)
+#' @importFrom rlang is_installed
+#' @importFrom utils install.packages
+#' @importFrom cli cli_inform
+#' @importFrom fs file_exists
+#' @importFrom fs dir_create
+interactive_install <- function() {
+  use_pak <- interactive_use_pak()
+  assign("use_pak", use_pak, .pe)
 
-  cli::cli_inform(" ")
-  check_ghqcapp_dependencies(lib_path = lib_path, use_pak = use_pak)
+  cli::cli_inform(c(" ", "Would you like to install the ghqc.app dependencies to the default location ({ghqc_libpath()})?",
+                    " " = "1. yes, absolutely!",
+                    " " = "2. can I check the contents in the default location first?",
+                    " " = "3. no, I have other plans and want to specify a different location",
+                    " " = "4. Abort with error"))
+  input <- readline_and_verify("Input: ", 1:4)
+
+  if (input == "4") cli::cli_abort("Dependency packages not installed. Aborting...")
+  if (input == "3") {
+    cli::cli_alert_warning("NOTE: This is a non-standard option. Please ensure you have an understanding of the effects before continuing.")
+    yN <- readline_and_verify("Would you like to continue (y/N)? ", c("y", "N"))
+    if (yN == "N") {
+      interactive_install()
+      return(invisible())
+    }
+    path <- gsub('\"', "", readline("Provide the path to install the dependency packages: "))
+    assign("lib_path", path, .pe)
+    install_ghqcapp_dependencies(lib_path = path, use_pak = use_pak)
+  }
+  assign("lib_path", ghqc_libpath(), .pe)
+  if (input == "2") {
+    check_ghqcapp_dependencies()
+  }
+  if (input == "1") {
+    install_ghqcapp_dependencies()
+  }
 }
 
 #' @importFrom cli cli_inform
@@ -142,10 +230,43 @@ interactive_link <- function() {
     return(invisible())
   })
 
-  lib_path <- gsub('\"', "", readline("Path to link the ghqc.app dependencies (~/.local/share/ghqc/rpkgs) "))
-  if (lib_path == "") lib_path <- ghqc_libpath()
-  if (!fs::file_exists(lib_path)) fs::dir_create(lib_path)
+  cli::cli_inform(c(" ", "Would you like to link the ghqc.app dependencies to the default location ({ghqc_libpath()})?",
+                  " " = "1. yes, absolutely!",
+                  " " = "2. no, I have other plans and want to specify a different location",
+                  " " = "3. Abort with error"))
+  input <- readline_and_verify("Input: ", 1:3)
+  if (input == 3) cli::cli_abort("Dependency packages not symlinked. Aborting...")
+  if (input == 2) {
+    cli::cli_alert_warning("NOTE: This is a non-standard option. Please ensure you have an understanding of the effects before continuing.")
+    yN <- readline_and_verify("Would you like to continue (y/N)? ", c("y", "N"))
+    if (yN == "N") {
+      interactive_install()
+      return(invisible())
+    }
+    path <- gsub('\"', "", readline("Provide the path to symlink the dependency packages to: "))
+  }
+  if (input == 1) path <- ghqc_libpath()
+  assign("lib_path", path, .pe)
+  link_ghqcapp_dependencies(link_path, path)
+}
+
+interactive_ghqcapp_install <- function() {
+  #FOR DEV
+  # assign("lib_path", ghqc_libpath(), .pe)
+  # assign("config_path", ghqc_config_path(), .pe)
 
-  cli::cli_inform(" ")
-  link_ghqcapp_dependencies(link_path = link_path, lib_path = lib_path)
+  cli::cli_h1("GHQC.APP INSTALLATION")
+  repo <- ghqcapp_repo(config_path = .pe$config_path)
+  specified <- NULL
+  if (!repo$unset) specified <- "specified "
+  cli::cli_inform("ghqc.app will install from {specified}repository: {repo$url}")
+  yN <- tolower(readline(glue::glue("Would you like to install ghqc.app to {(.pe$lib_path)} (y/N)? ")))
+
+  if (yN == "n") {
+    cli::cli_alert_danger("Please install ghqc.app to {.pe$lib_path} before running any ghqc apps")
+    return(invisible())
+  }
+
+  if (!exists("use_pak", envir = .pe)) assign("use_pak", interactive_use_pak(), .pe)
+  install_ghqcapp(lib_path = .pe$lib_path, repo = repo$url, use_pak = .pe$use_pak)
 }