Detect dev/prod & data updates

DESCRIPTION

@@ -12,3 +12,11 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+Imports: 
+    dplyr,
+    gh,
+    golem,
+    lubridate,
+    renv,
+    rmarkdown,
+    usethis

NAMESPACE

@@ -1,9 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
 export(make_child_app)
+export(run_data_prep_local_data_folder)
 export(use_batch_jobs)
+importFrom(dplyr,filter)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,mutate)
+importFrom(gh,gh)
 importFrom(golem,create_golem)
+importFrom(lubridate,ymd_hms)
 importFrom(renv,scaffold)
-importFrom(rhino,init)
+importFrom(rmarkdown,render)
 importFrom(usethis,use_package)
 importFrom(usethis,write_union)

R/data_prep_update.R

@@ -0,0 +1,68 @@
+## Handle local data in `data folder`
+
+
+get_updated_time <- function(data_loc) {
+  current_files <- list.files(file.path(data_loc))
+
+  current_data_info <- file.info(file.path(data_loc, current_files))
+  current_data_info$file_name <- current_files
+
+  rownames(current_data_info) <- NULL
+  current_data_info <- current_data_info[, c("file_name", "mtime")]
+
+  return(current_data_info)
+}
+
+#' @export
+run_data_prep_local_data_folder <- function(dev_data_loc) {
+
+  if (length(list.files(dev_data_loc)) == 0) {
+    message("There is no data. Skipping data processing")
+    return(invisible(NULL))
+  }
+
+  # Look for the file that has file name & last updated
+  data_update_log <- file.path("jobs", "data_update_log.csv")
+
+  # If not exist, make one
+  if (!file.exists(data_update_log)) {
+    curr_data_info <- get_updated_time(dev_data_loc)
+    write.csv(curr_data_info, data_update_log, row.names = FALSE)
+  }
+
+  data_update_log <- read.csv(data_update_log)
+
+  # Pull the current information in the data folder to compare against log
+  current_data_info <- get_updated_time(dev_data_loc)
+
+  # Conditionally run data prep
+  if (nrow(current_data_info) > nrow(data_update_log)) {
+    message("New data has been added! Running data prep")
+    rmarkdown::render("jobs/data_prep.Rmd")
+  } else if (nrow(current_data_info) < nrow(data_update_log)) {
+    message("Data has been removed! Running data prep")
+    rmarkdown::render("jobs/data_prep.Rmd")
+  } else {
+    joined <- data_update_log |>
+      dplyr::inner_join(current_data_info, by = "file_name")
+
+    n_updates <- joined |>
+      dplyr::mutate(
+        mtime.x = lubridate::ymd_hms(mtime.x),
+        mtime.y = lubridate::ymd_hms(mtime.y)
+      ) |>
+      dplyr::filter(mtime.x < mtime.y) |>
+      nrow()
+
+    if (n_updates > 0) {
+      message("Data has been updated! Running data prep")
+      rmarkdown::render("jobs/data_prep.Rmd")
+      write.csv(current_data_info, "jobs/data_update_log.csv")
+    } else {
+      message("No change in data, skipping data prep")
+    }
+  }
+  return(invisible(NULL))
+}
+
+

R/dependencies.R

@@ -1,7 +1,10 @@
 #' @importFrom golem create_golem
-#' @importFrom rhino init
 #' @importFrom renv scaffold
 #' @importFrom usethis use_package write_union
+#' @importFrom gh gh
+#' @importFrom dplyr inner_join mutate filter
+#' @importFrom lubridate ymd_hms
+#' @importFrom rmarkdown render
 #'
 #'
 NULL

R/make_child_app.R

@@ -1,6 +1,6 @@
 #' Make Child app from Parent app with modules
 #'
-#' @param parent_app_dir `character` Path to existing parent app, including the parent app directory
+#' @param parent_github_repo `character` github repo of the parent in the form of "parent/repo"
 #' @param child_app_dir `character` Path to new child app, including the child app directory
 #' @param include_renv `logical` Include `renv` structure in child app or now. Default is `FALSE`
 #' @param copy_jobs_dir `logical` Copy the `jobs` directory from the parent app (`TRUE`)
@@ -14,25 +14,20 @@
 #'
 #' @examples
 #' \dontrun{
-#' make_child_app(parent_app_dir = "inst/parentApp",
-#'                child_app_dir = "~/childTest")
-#'
-#'
-#' make_child_app(parent_app_dir = "inst/parentApp",
-#'                child_app_dir = "~/childTest2",
-#'                copy_jobs_dir = FALSE,
-#'                include_renv = TRUE)
-#'
-#' make_child_app(parent_app_dir = "inst/parentApp",
-#'                child_app_dir = "~/childTest3",
-#'                include_renv = TRUE,
-#'                framework = "golem")
+#'  make_child_app(parent_github_repo = "atorus-research/matteParentPkg",
+#'                 child_app_dir = "~/childTest",
+#'                 copy_jobs_dir = TRUE,
+#'                 include_renv = FALSE,
+#'                 include_meta_yaml = TRUE,
+#'                 job_file_type = "Rmd",
+#'                 overwrite = FALSE,
+#'                 framework = "none")
 #' }
 #'
 
 # TODO: add logging
 
-make_child_app <- function(parent_app_dir,
+make_child_app <- function(parent_github_repo,
                            child_app_dir,
                            include_renv = FALSE,
                            copy_jobs_dir = FALSE,
@@ -50,28 +45,31 @@ make_child_app <- function(parent_app_dir,
     stop("`framework` must be one of: 'none', 'golem' or 'rhino'")
   }
 
+  top_level_files <- gh::gh("/repos/:owner/:repo/contents", owner = "atorus-research", repo = "matteParentPkg")
+  r_folder_files <- gh::gh("/repos/:owner/:repo/contents/R", owner = "atorus-research", repo = "matteParentPkg")
+  jobs_folder_files <- gh::gh("/repos/:owner/:repo/contents/jobs", owner = "atorus-research", repo = "matteParentPkg")
+
   ##create the child app path dir (if it doesn't exist)
-  parent_app_dir_ <- normalizePath(parent_app_dir, winslash = "/")
-  child_app_dir_ <-
-    normalizePath(child_app_dir, winslash = "/") %>% suppressWarnings()
+  parent_pkg_name <- strsplit(parent_github_repo, "/")[[1]][[2]]
+  child_app_dir_ <- normalizePath(child_app_dir, winslash = "/") |> suppressWarnings()
 
   ## make sure all needed files/directories exist in parent_app
-  if (!file.exists(file.path(parent_app_dir_, "app.R")) ||
-      !file.exists(file.path(parent_app_dir_, "R", "app_ui.R")) ||
-      !file.exists(file.path(parent_app_dir_, "R", "app_server.R"))) {
+  if (length(Filter(function(x){x$name == "app.R"}, top_level_files)) == 0 ||
+      length(Filter(function(x){x$name == "app_ui.R"}, r_folder_files)) == 0 ||
+      length(Filter(function(x){x$name == "app_server.R"}, r_folder_files)) == 0) {
     stop(
       sprintf(
         "%s must contain app.R, R/app_ui.R and R/app_server.R in order to be duplicated",
-        basename(parent_app_dir_)
+        parent_pkg_name
       )
     )
   }
 
-  if (copy_jobs_dir && !file.exists(file.path(parent_app_dir_, "jobs"))) {
+  if (copy_jobs_dir && length(Filter(function(x){x$name == "jobs"}, top_level_files)) == 0) {
     stop(
       sprintf(
         "%s must contain jobs folder when copy_jobs_dir = TRUE",
-        basename(parent_app_dir_)
+        parent_pkg_name
       )
     )
   }
@@ -96,12 +94,49 @@ make_child_app <- function(parent_app_dir,
     golem::create_golem(child_app_dir_, open = FALSE)
   }
   else if (framework == "rhino") {
-    rhino::init(child_app_dir_)
+    # rhino::init(child_app_dir_)
   }
   else {
     dir.create(child_app_dir_)
   }
 
+  ## create Rproj
+  rproj_file <- paste0(child_app_dir_, "/", basename(child_app_dir), ".Rproj")
+  if (!file.exists(rproj_file)) {
+    file.create(rproj_file)
+    fileCon <- file(rproj_file)
+    writeLines(c("Version: 1.0",
+                 "RestoreWorkspace: No",
+                 "SaveWorkspace: No",
+                 "AlwaysSaveHistory: Default",
+                 "EnableCodeIndexing: Yes",
+                 "UseSpacesForTab: Yes",
+                 "NumSpacesForTab: 2",
+                 "Encoding: UTF-8",
+                 "RnwWeave: Sweave",
+                 "LaTeX: pdfLaTeX",
+                 "AutoAppendNewline: Yes",
+                 "StripTrailingWhitespace: Yes",
+                 "LineEndingConversion: Posix",
+                 "BuildType: Package",
+                 "PackageUseDevtools: Yes",
+                 "PackageInstallArgs: --no-multiarch --with-keep.source",
+                 "PackageRoxygenize: rd,collate,namespace"),
+               con = fileCon)
+    close(fileCon)
+  }
+
+  ## create Renviron (dev/prod detection)
+  renviron_file <- paste0(child_app_dir_, "/", ".Renviron")
+  if (!file.exists(renviron_file)) {
+    file.create(renviron_file)
+    fileCon <- file(renviron_file)
+    writeLines(c("DEVELOPMENT_ENVIRONMENT=DEV",
+                 "DEVELOPMENT_DATA_LOCATION_TYPE=LOCAL",
+                 "DEVELOPMENT_DATA_LOCATION=data"),
+               con = fileCon)
+    close(fileCon)
+  }
 
   ## create R folder
   if (!file.exists(paste0(child_app_dir_, "/R"))) {
@@ -110,31 +145,51 @@ make_child_app <- function(parent_app_dir,
 
 
   ## start copying over all of the needed files from parent_app or templates
+  ## We're going to download from github into a temp location and copy it over
+
+
+  ## Pull parent repo info from github
+  tmp_folder <- tempdir()
+
+  download.file("https://raw.githubusercontent.com/atorus-research/matteParentPkg/main/R/app_ui.R", file.path(tmp_folder, "app_ui.R"))
   file.copy(
-    from = file.path(parent_app_dir_, "R", "app_ui.R"),
+    from = file.path(tmp_folder, "app_ui.R"),
     to   = file.path(child_app_dir_, "R", "app_ui.R"),
     overwrite = TRUE
   )
+
+  download.file("https://raw.githubusercontent.com/atorus-research/matteParentPkg/main/R/app_server.R", file.path(tmp_folder, "app_server.R"))
   file.copy(
-    from = file.path(parent_app_dir_, "R", "app_server.R"),
+    from = file.path(tmp_folder, "app_server.R"),
     to   = file.path(child_app_dir_, "R", "app_server.R"),
     overwrite = TRUE
   )
-  if (file.exists(file.path(parent_app_dir_, "manifest.json"))) {
+
+
+  if (length(Filter(function(x){x$name == "manifest.json"}, top_level_files)) == 1) {
+
+    download.file("https://raw.githubusercontent.com/atorus-research/matteParentPkg/main/manifest.json", file.path(tmp_folder, "manifest.json"))
     file.copy(
-      from = file.path(parent_app_dir_, "manifest.json"),
+      from = file.path(tmp_folder, "manifest.json"),
       to   = file.path(child_app_dir_, "manifest.json"),
       overwrite = TRUE
     )
   }
   ## add the app.R templates
   if (framework != "rhino") {
+
     file.copy(
       from = system.file(paste0("app_template_",framework,".R"),
                          package = "matte"),
       to   = file.path(child_app_dir_, "app.R"),
       overwrite = TRUE
     )
+
+    # app.R installs parent package
+    file_content <- readLines(file.path(child_app_dir_, "app.R"))
+    file_content <- gsub("PARENT_PACKAGE_REPO", parent_github_repo, file_content)
+    file_content <- gsub("PARENT_PACKAGE", parent_pkg_name, file_content)
+    writeLines(file_content, file.path(child_app_dir_, "app.R"))
   }
   ## add the main.R template for rhino
   else {
@@ -149,12 +204,19 @@ make_child_app <- function(parent_app_dir,
   ## create jobs directory
   if (copy_jobs_dir) {
     dir.create(paste0(child_app_dir_, "/jobs"))
-    file.copy(
-      from = paste0(parent_app_dir_, "/jobs"),
-      to = child_app_dir_,
-      recursive = TRUE,
-      overwrite = overwrite
-    )
+
+    dir.create(file.path(tmp_folder, "jobs"))
+
+    for (jobs_file in jobs_folder_files) {
+      download.file(jobs_file$download_url, file.path(tmp_folder, "jobs", jobs_file$name))
+
+      file.copy(
+        from = file.path(tmp_folder, "jobs", jobs_file$name),
+        to = file.path(child_app_dir_, "jobs"),
+        recursive = TRUE,
+        overwrite = overwrite
+      )
+    }
   }
   else{
     dir.create(paste0(child_app_dir_, "/jobs"))
@@ -171,7 +233,7 @@ make_child_app <- function(parent_app_dir,
   }
 
   ## if they want a meta yaml file, but do not have one in the parent app jobs folder, copy it from template
-  if (include_meta_yaml && all(!grepl(".yaml", list.files(paste0(parent_app_dir_, "/jobs"))))) {
+  if (include_meta_yaml && length(Filter(function(x){grepl(".yaml", x$name)}, jobs_folder_files)) == 0) {
     file.copy(
       from = system.file("meta_template.yaml",
                          package = "matte"),
@@ -189,7 +251,7 @@ make_child_app <- function(parent_app_dir,
 
   #create dependencies.R
   fileCon <- file(file.path(child_app_dir_, "R", "dependencies.R"))
-  writeLines(c(paste("#' @import", basename(parent_app_dir_)),
+  writeLines(c(paste("#' @import", parent_pkg_name),
                "#'",
                "NULL"),
              con = fileCon)

inst/app_template_none.R

@@ -1,4 +1,15 @@
+## install parent package
+if (!require(PARENT_PACKAGE, quietly = TRUE)) {
+  remotes::install_github("PARENT_PACKAGE_REPO")
+}
+
+## install matte
+if (!require(matte, quietly = TRUE)) {
+  remotes::install_github("atorus-research/matte@data-dev-prod")
+}
+
 ## Launch the ShinyApp
+source("R/app_ui.R")
+source("R/app_server.R")
 
-shinyApp(ui = app_ui,
-         server = app_server)
+shiny::shinyApp(ui = app_ui, server = app_server)