make a start on #37

Author: simon-smart88

R/create_template.R

@@ -328,6 +328,7 @@ create_template <- function(path, name, common_objects, modules, author,
   # Create global ====
 
   full_component_list <- c(components$component, "rep")
+  names(full_component_list) <- c(components$long_component, "Reproduce")
 
   global_params <- c(
     file = system.file("app_skeleton", "global.Rmd", package = "shinyscholar"),

inst/shiny/Rmd/quarto_header.txt

@@ -0,0 +1,20 @@
+---
+format:
+  html:
+    embed-resources: true
+    code-overflow: wrap
+    code-fold: true
+    code-summary: "View code chunk"
+    page-layout: article
+    grid:
+      body-width: 1200px
+fig-format: svg
+execute:
+  warning: false
+  message: false
+theme: spacelab
+---
+
+::: {.panel-tabset}
+
+## Introduction

inst/shiny/Rmd/userReport_intro.Rmd

@@ -1,7 +1,3 @@
----
-title: shinyscholar session `r Sys.Date()`
----
-
 ```{r, include=FALSE}
 library(knitr)
 knit_engines$set(asis = function(options) {
@@ -12,11 +8,11 @@ knitr::opts_chunk$set(message = FALSE, warning = FALSE, eval = FALSE)
 
 Please find below the R code history from your *shinyscholar* v0.4.2 session. 
 
-You can reproduce your session results by running this R Markdown file in RStudio. 
+You can reproduce your session results by running this quarto file in RStudio. 
 
-Each code block is called a "chunk", and you can run them either one-by-one or all at once by choosing an option in the "Run" menu at the top-right corner of the "Source" pane in RStudio. The file can also be rendered into an html file using `rmarkdown::render()` which will contain all of the outputs alongside the code used to generate them.
+Each code block is called a "chunk", and you can run them either one-by-one or all at once by choosing an option in the "Run" menu at the top-right corner of the "Source" pane in RStudio. The file can also be rendered into an html file using `quarto::quarto_render()` which will contain all of the outputs alongside the code used to generate them.
 
-For more detailed information see <http://rmarkdown.rstudio.com>.
+For more detailed information see <https://quarto.org/>.
 
 ### Package installation
 

inst/shiny/global.R

@@ -15,7 +15,7 @@ source("ui_helpers.R")
 
 # The components that have modules. These names must match the values of the
 # tabs of the components in the UI.
-COMPONENTS <- c("select", "plot", "rep", "template")
+COMPONENTS <- c(`Select data` = "select", `Plot data` = "plot", Reproduce = "rep", Template = "template")
 
 # Information about modules that various parts of the app need access to
 COMPONENT_MODULES <- list()

inst/shiny/modules/rep_markdown.R

@@ -1,8 +1,10 @@
 rep_markdown_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
-    selectInput(ns("rmdFileType"), label = "Select download file type",
-                choices = c("Rmd" = ".Rmd", "PDF" = ".pdf", "HTML" = ".html", "Word" = ".docx")),
+    selectInput(ns("file_type"), label = "Select download file type",
+                choices = c("HTML" = ".html", "Quarto" = ".qmd")),
+    conditionalPanel("input.file_type == '.html'",
+                     bslib::input_switch(ns("render"), "Include outputs?", value = TRUE), ns = ns),
     downloadButton(ns("download"), "Download session code")
   )
 }
@@ -44,6 +46,10 @@ rep_markdown_module_server <- function(id, common, parent_session, map, COMPONEN
             )
             module_rmd <- do.call(knitr::knit_expand, knit_params)
 
+            # add a section header to create tabs
+            full_component_name <- names(COMPONENTS[COMPONENTS == component])
+            module_rmd <- c(glue::glue("## {full_component_name}"), module_rmd)
+
             module_rmd_file <- tempfile(pattern = paste0(module$id, "_"),
                                         fileext = ".Rmd")
             writeLines(module_rmd, module_rmd_file)
@@ -67,55 +73,58 @@ rep_markdown_module_server <- function(id, common, parent_session, map, COMPONEN
           lapply(paste, collapse = "\n") |>
           paste(collapse = "\n\n")
 
-        result_file <- tempfile(pattern = "result_", fileext = input$rmdFileType)
-        if (input$rmdFileType == ".Rmd") {
-          combined_rmd <- gsub("``` r", "```{r}", combined_md)
-          combined_rmd <- unlist(strsplit(combined_rmd , "\n"))
+        combined_rmd <- gsub("``` r", "```{r}", combined_md)
+        combined_rmd <- unlist(strsplit(combined_rmd , "\n"))
 
-          # add title section
-          header <- c("---", paste0("title: ", combined_rmd[1]), "---")
-          combined_rmd <- append(combined_rmd, header, after = 0)
-          combined_rmd <- combined_rmd[-c(4, 5)]
+        # remove ## for unused components and duplicates
+        is_tag <- grepl("^## ", combined_rmd)
+        tag_names <- sub("^## ", "", combined_rmd)
+        if (!is.null(names(common$meta))){
+          used_components <- unique(sapply(strsplit(names(common$meta), "_"), function(x) x[1]))
+        } else {
+          used_components <- c()
+        }
+        used_full_components <- names(COMPONENTS[COMPONENTS %in% used_components])
+        lines_to_keep <- (!is_tag) | (tag_names %in% used_full_components & !duplicated(tag_names))
+        combined_rmd <- combined_rmd[lines_to_keep]
 
-          # convert chunk control lines
-          chunk_control_lines <- grep("\\{r,", combined_rmd)
-          if (length(chunk_control_lines) > 0){
-            chunk_starts <- grep("```\\{r\\}", combined_rmd)
-            chunks_to_remove <- NA
-            for (i in seq_along(chunk_control_lines)) {
-              chunks_to_remove[i] <- min(chunk_starts[chunk_starts > chunk_control_lines[i]])
-            }
-            if (any(!is.na(chunks_to_remove))){
-              combined_rmd <- combined_rmd[-chunks_to_remove]
-            }
-            combined_rmd <- gsub("\\{r,", "```{r,", combined_rmd)
-          }
+        # add quarto header
+        quarto_header <- readLines("Rmd/quarto_header.txt")
+        quarto_header <- append(quarto_header, glue::glue("title: shinyscholar Session {Sys.Date()}"), 1)
+        combined_rmd <- c(quarto_header, combined_rmd)
 
-          # fix any very long lines
-          long_lines <- which(nchar(combined_rmd) > 4000)
-          for (l in long_lines){
-            split_lines <- strwrap(combined_rmd[l], 4000)
-            combined_rmd <- combined_rmd[-l]
-            combined_rmd <- append(combined_rmd, split_lines, l-1)
+        # convert chunk control lines
+        chunk_control_lines <- grep("\\{r,", combined_rmd)
+        if (length(chunk_control_lines) > 0){
+          chunk_starts <- grep("```\\{r\\}", combined_rmd)
+          chunks_to_remove <- NA
+          for (i in seq_along(chunk_control_lines)) {
+            chunks_to_remove[i] <- min(chunk_starts[chunk_starts > chunk_control_lines[i]])
+          }
+          if (any(!is.na(chunks_to_remove))){
+            combined_rmd <- combined_rmd[-chunks_to_remove]
           }
+          combined_rmd <- gsub("\\{r,", "```{r,", combined_rmd)
+        }
+
+        # fix any very long lines
+        long_lines <- which(nchar(combined_rmd) > 4000)
+        for (l in long_lines){
+          split_lines <- strwrap(combined_rmd[l], 4000)
+          combined_rmd <- combined_rmd[-l]
+          combined_rmd <- append(combined_rmd, split_lines, l-1)
+        }
 
+        result_file <- paste0("combined", input$file_type)
+        if (input$file_type == ".qmd") {
           writeLines(combined_rmd, result_file, useBytes = TRUE)
         } else {
-          combined_md_file <- tempfile(pattern = "combined_", fileext = ".md")
-          writeLines(combined_md, combined_md_file)
-          rmarkdown::render(
-            input = combined_md_file,
-            output_format =
-              switch(
-                input$rmdFileType,
-                ".pdf" = rmarkdown::pdf_document(),
-                ".html" = rmarkdown::html_document(),
-                ".docx" = rmarkdown::word_document()
-              ),
-            output_file = result_file,
-            clean = TRUE,
-            encoding = "UTF-8"
-          )
+          writeLines(combined_rmd, "combined.qmd")
+          on.exit(unlink("combined.qmd"))
+          quarto::quarto_render(
+            input = "combined.qmd",
+            output_format = "html",
+            execute = input$render)
         }
 
         file.rename(result_file, file)