Merge pull request #140 from NIFU-NO/dev

Dev

R/download_zip_to_folder.R

@@ -42,12 +42,12 @@ download_zip_to_folder <-
     zip_temp_path <- zip::unzip(zipfile = zip_path, files = files, exdir = tmpfolder, junkpaths = FALSE, overwrite = TRUE)
     folder_in_temp_path <- fs::dir_ls(path = tmpfolder, recurse = FALSE, type = "directory")
     new_files <- fs::dir_ls(folder_in_temp_path, recurse = TRUE, type = "file", all = TRUE)
-    new_files <- gsub(x = new_files, pattern = folder_in_temp_path, replacement = "")
-    new_files <- gsub(x = new_files, pattern = "^/", replacement = "")
+    new_files <- stringi::stri_replace_first_fixed(new_files, pattern = folder_in_temp_path, replacement = "")
+    new_files <- stringi::stri_replace_first_regex(new_files, pattern = "^/", replacement = "")
     dir.create(out_path, showWarnings = FALSE, recursive = TRUE)
     old_files <- fs::dir_ls(out_path, recurse = TRUE, type = "file", all = TRUE)
-    old_files <- gsub(x = old_files, pattern = out_path, replacement = "")
-    old_files <- gsub(x = old_files, pattern = "^/", replacement = "")
+    old_files <- stringi::stri_replace_first_fixed(old_files, pattern = out_path, replacement = "")
+    old_files <- stringi::stri_replace_first_regex(old_files, pattern = "^/", replacement = "")
     intersects <- new_files[new_files %in% old_files]
     if (isTRUE(prompt) && length(intersects) > 0 && isTRUE(overwrite)) {
       cli::cli_inform(intersects)

R/draft_report.R

@@ -77,6 +77,12 @@
 #'   To turn off, set `pdf=FALSE`.
 #'
 #'
+#' @param report_includes_files *Whether report.qmd includes \{\{< include chapter.qmd >\}\}*
+#'
+#'   `scalar<logical>` // *default:* `FALSE`
+#'
+#'   Useful to have in mesos reports. However, bear in mind that including other qmd files with conflicting YAML-headers might be risky.
+#'
 #' @param chapter_qmd_start_section_filepath,chapter_qmd_end_section_filepath,index_qmd_start_section_filepath,index_qmd_end_section_filepath,report_qmd_start_section_filepath,report_qmd_end_section_filepath, *Path to qmd-bit for start/end of each qmd*
 #'
 #'   `scalar<character>` // *default:* `NULL` (`optional`)
@@ -212,6 +218,7 @@ draft_report <-
            report_yaml_file = NULL,
            report_qmd_start_section_filepath = NULL,
            report_qmd_end_section_filepath = NULL,
+           report_includes_files = FALSE,
            ignore_heading_for_group = c(
              ".template_name",
              ".variable_type_dep",
@@ -281,6 +288,7 @@ draft_report <-
           qmd_start_section_filepath = args$report_qmd_start_section_filepath,
           qmd_end_section_filepath = args$report_qmd_end_section_filepath,
           chapter_structure = args$chapter_structure,
+          include_files = if (isTRUE(args$report_includes_files)) sort(basename(chapter_filepaths)),
           title = args$title,
           authors = all_authors,
           output_formats = NULL,
@@ -301,7 +309,7 @@ draft_report <-
         title = args$title,
         authors = all_authors,
         output_formats = if (!is.null(args$report_yaml_file)) find_yaml_formats(args$report_yaml_file),
-        output_filename = args$report_filename,
+        output_filename = stringi::stri_replace_first_regex(str = args$report_filename, pattern = "^_", replacement = ""),
         call = rlang::caller_env()
       )
     processed_files <- c(processed_files, index_filepath)

R/filename_sanitizer.R

@@ -20,27 +20,36 @@ filename_sanitizer <- function(x,
                                valid_obj = FALSE,
                                to_lower = FALSE,
                                make_unique = TRUE) {
-
-  pattern <- if(isTRUE(accept_hyphen)) "[^[:alnum:]-+]+" else "[^[:alnum:]+]+"
+  pattern <- if (isTRUE(accept_hyphen)) "[^[:alnum:]-+]+" else "[^[:alnum:]+]+"
   out <-
     stringi::stri_replace_all_regex(x,
-                                    pattern = pattern,
-                                    replacement = sep)
-  if(isTRUE(valid_obj)) {
+      pattern = pattern,
+      replacement = sep
+    )
+  if (isTRUE(valid_obj)) {
     out <-
       stringi::stri_replace_all_regex(out, pattern = "^[^[:alpha:]]+", replacement = "")
   }
 
-  out <- iconv(out, from ="UTF-8", to="ASCII//TRANSLIT", sub='')
+  out <- iconv(out, from = "UTF-8", to = "ASCII//TRANSLIT", sub = "")
 
-  if(isTRUE(to_lower)) out <- tolower(out)
+  if (isTRUE(to_lower)) out <- tolower(out)
 
-  out <- truncator(x=out, max_chars = max_chars)
-  if(isTRUE(make_unique)) out <- make.unique(out, sep=sep)
+  out <- truncator(x = out, max_chars = max_chars)
+  out <- avoid_ending_with_specials(out)
+  if (isTRUE(make_unique)) out <- make.unique(out, sep = sep)
   out
 }
 
 truncator <- function(x, max_chars = NA_integer_) {
-  if(!(is.na(max_chars) || is.null(max_chars)) &&
-     length(x)>0) stringi::stri_sub(x, from = 1, to = max_chars) else x
+  if (!(is.na(max_chars) || is.null(max_chars)) &&
+    length(x) > 0) {
+    stringi::stri_sub(x, from = 1, to = max_chars)
+  } else {
+    x
+  }
+}
+
+avoid_ending_with_specials <- function(x) {
+  stringi::stri_replace_last_regex(x, pattern = "[^[:alnum:]]+$", replacement = "")
 }

R/gen_qmd_file.R

@@ -1,5 +1,3 @@
-
-
 #' Generate Quarto Index File That Merges All Chapters
 #'
 #' This function creates an index Quarto file (QMD) that merges all chapters in the specified order. It can also include optional title and author(s) information.
@@ -18,97 +16,113 @@
 #' @return A string containing the filepath to the generated Quarto report file.
 #' @keywords internal
 gen_qmd_file <-
-  function(
-    path = NULL,
-    filename = "report",
-    yaml_file = NULL,
-    qmd_start_section_filepath = NULL,
-    qmd_end_section_filepath = NULL,
-    chapter_structure = NULL,
-    title = NULL,
-    authors = NULL,
-    output_formats = NULL,
-    output_filename = NULL,
-    call = rlang::caller_env()) {
-
-    check_string(path, n = 1, null.ok = TRUE,  call = call)
-    check_string(filename, n = 1, null.ok = TRUE,  call = call)
+  function(path = NULL,
+           filename = "report",
+           yaml_file = NULL,
+           qmd_start_section_filepath = NULL,
+           qmd_end_section_filepath = NULL,
+           chapter_structure = NULL,
+           include_files = NULL,
+           title = NULL,
+           authors = NULL,
+           output_formats = NULL,
+           output_filename = NULL,
+           call = rlang::caller_env()) {
+    check_string(path, n = 1, null.ok = TRUE, call = call)
+    check_string(filename, n = 1, null.ok = TRUE, call = call)
     check_string(yaml_file, n = 1, null.ok = TRUE, call = call)
     check_string(qmd_start_section_filepath, n = 1, null.ok = TRUE, call = call)
     check_string(qmd_end_section_filepath, n = 1, null.ok = TRUE, call = call)
     check_string(title, n = 1, null.ok = TRUE, call = call)
     check_string(authors, n = NULL, null.ok = TRUE, call = call)
     check_string(output_formats, n = NULL, null.ok = TRUE, call = call)
     check_string(output_filename, n = 1, null.ok = TRUE, call = call)
-    if(is.null(title) && is.null(filename)) {
+    if (is.null(title) && is.null(filename)) {
       cli::cli_abort("{.arg filename} and {.arg title} cannot be both `NULL`.")
     }
 
     yaml_section <-
-      process_yaml(yaml_file = yaml_file,
-                   title = title,
-                   authors = authors[!is.na(authors)])
+      process_yaml(
+        yaml_file = yaml_file,
+        title = title,
+        authors = authors[!is.na(authors)]
+      )
 
 
     report_links <-
-      if(is.character(output_filename) &&
-         is.character(output_formats)) {
-
+      if (is.character(output_filename) &&
+        is.character(output_formats)) {
         stringi::stri_c(
-        lapply(output_formats, function(frmt) {
-          if(frmt == "typst") frmt <- "pdf"
+          lapply(output_formats, function(frmt) {
+            if (frmt == "typst") frmt <- "pdf"
 
-          stringi::stri_c("-\t[(", toupper(frmt), ")](", output_filename, ".", frmt, ")")
-        }), collapse="\n")
+            stringi::stri_c("-\t[(", toupper(frmt), ")](", output_filename, ".", frmt, ")")
+          }),
+          collapse = "\n"
+        )
       }
 
-    if(inherits(chapter_structure, "data.frame")) {
+    if (inherits(chapter_structure, "data.frame")) {
       chapter_structure_simplified <-
         collapse_chapter_structure_to_chr(chapter_structure)
     }
 
     qmd_start_section <-
-      if(!is.null(qmd_start_section_filepath)) {
-        out <- stringi::stri_c(collapse="\n",
-                               ignore_null=TRUE,
-                               readLines(con = qmd_start_section_filepath)
-                               )
-        if(inherits(chapter_structure, "data.frame")) {
+      if (!is.null(qmd_start_section_filepath)) {
+        out <- stringi::stri_c(
+          collapse = "\n",
+          ignore_null = TRUE,
+          readLines(con = qmd_start_section_filepath)
+        )
+        if (inherits(chapter_structure, "data.frame")) {
           tryCatch(glue::glue_data(chapter_structure_simplified, out, .na = ""),
-                   error = function(cnd) glue_err(cnd=cnd, arg_name=paste0(filename, "_qmd_start_section")))
-        } else out
+            error = function(cnd) glue_err(cnd = cnd, arg_name = paste0(filename, "_qmd_start_section"))
+          )
+        } else {
+          out
+        }
       }
     qmd_end_section <-
-      if(!is.null(qmd_end_section_filepath)) {
+      if (!is.null(qmd_end_section_filepath)) {
         out <-
-          stringi::stri_c(collapse="\n",
-                          ignore_null=TRUE,
-                          readLines(con = qmd_end_section_filepath)
-                          )
-        if(inherits(chapter_structure, "data.frame")) {
+          stringi::stri_c(
+            collapse = "\n",
+            ignore_null = TRUE,
+            readLines(con = qmd_end_section_filepath)
+          )
+        if (inherits(chapter_structure, "data.frame")) {
           tryCatch(glue::glue_data(chapter_structure_simplified, out, .na = ""),
-                   error = function(cnd) glue_err(cnd=cnd, arg_name=paste0(filename, "_qmd_end_section")))
-        } else out
+            error = function(cnd) glue_err(cnd = cnd, arg_name = paste0(filename, "_qmd_end_section"))
+          )
+        } else {
+          out
+        }
       }
-
+    if (!is.null(include_files)) {
+      include_files <-
+        paste0('{{< include "', include_files, '">}}', collapse = "\n\n")
+    }
 
     out <-
-      c(yaml_section, "\n",
+      c(
+        yaml_section, "\n",
         qmd_start_section,
         report_links,
-        qmd_end_section)
+        include_files,
+        qmd_end_section
+      )
     out <- stringi::stri_remove_na(out)
-    out <- stringi::stri_c(out, collapse="\n", ignore_null=TRUE)
+    out <- stringi::stri_c(out, collapse = "\n", ignore_null = TRUE)
     out <- stringi::stri_replace_all_regex(out,
-                                           pattern = "\n{3,}",
-                                           replacement = "\n\n\n")
+      pattern = "\n{3,}",
+      replacement = "\n\n\n"
+    )
     filepath <-
-      if(is.character(filename)) {
+      if (is.character(filename)) {
         file.path(path, stringi::stri_c(filename, ".qmd"))
-      } else if(is.null(filename)) { # Produce unique report file name based on title
+      } else if (is.null(filename)) { # Produce unique report file name based on title
         file.path(path, stringi::stri_c("0_", filename_sanitizer(title), ".qmd", ignore_null = TRUE))
       }
     cat(out, file = filepath, append = FALSE)
     filepath
   }
-

R/process_yaml.R

@@ -51,16 +51,20 @@ process_yaml <- function(yaml_file = NULL,
   )
 
   if (add_fences) {
-    yaml_section <- stringi::stri_c("---",
-      yaml_section,
-      "---",
-      sep = "\n",
-      ignore_null = TRUE
-    )
+    yaml_section <- add_yaml_fences(yaml_section)
   }
   yaml_section
 }
 
+add_yaml_fences <- function(x) {
+  stringi::stri_c("---",
+    x,
+    "---",
+    sep = "\n",
+    ignore_null = TRUE
+  )
+}
+
 
 find_yaml_formats <- function(yaml_file) {
   x <- yaml::read_yaml(file = yaml_file)