[feat] Add functionality to rename legacy figure/table docs

R/create_template.R

@@ -586,40 +586,7 @@ create_template <- function(
       }
     } # close check for previous files & respective copying
 
-    # Handle legacy document order and migration
-    # TODO: Not sure how setting this to rerender = FALSE always impacts this feature
-    # Maybe this should go through deprecation in x amnt of time?
-    fig_info <- migrate_legacy_docs(subdir, doc_type = "figures", rerender_skeleton = FALSE)
-    tbl_info <- migrate_legacy_docs(subdir, doc_type = "tables", rerender_skeleton = FALSE)
-
-    renamed_tables_doc <- FALSE
-    if (can_rename_legacy_doc(tbl_info)) {
-      from <- fs::path(subdir, tbl_info$legacy_name)
-      to <- fs::path(subdir, tbl_info$current_name)
-      if (!identical(from, to) && file.exists(from)) {
-        renamed_tables_doc <- file.rename(from = from, to = to)
-      }
-    }
-
-    renamed_figures_doc <- FALSE
-    if (can_rename_legacy_doc(fig_info)) {
-      from <- fs::path(subdir, fig_info$legacy_name)
-      to <- fs::path(subdir, fig_info$current_name)
-      if (!identical(from, to) && file.exists(from)) {
-        renamed_figures_doc <- file.rename(from = from, to = to)
-      }
-    }
-
-    if (renamed_figures_doc || renamed_tables_doc) {
-      renamed_docs <- c(
-        if (renamed_figures_doc) paste0("{.file ", fig_info$current_name, "}"),
-        if (renamed_tables_doc) paste0("{.file ", tbl_info$current_name, "}")
-      )
-      cli::cli_alert_info("Detected legacy figure/table document order in the skeleton.")
-      cli::cli_alert_info("asar switched to {toString(renamed_docs)}.")
-    }
-
-    # Created tables doc
+    # Create tables doc
     tables_doc_name <- switch(
       type,
       "nemt" = "06_tables.qmd",
@@ -651,6 +618,14 @@ create_template <- function(
         to = fs::path(subdir, figures_doc_name)
       )
     }
+
+    # rename tables doc
+    if (tables_doc_name != "09_tables.qmd") {
+      file.rename(
+        from = fs::path(subdir, "09_tables.qmd"),
+        to = fs::path(subdir, tables_doc_name)
+      )
+    }
 
     # Part I
     # Create a report template file to render for the region and species

R/rerender_skeleton.R

@@ -531,4 +531,35 @@ rerender_skeleton <- function(
   }
   # Print message
   cli::cli_alert_success("Updated report skeleton in directory {file_dir}.")
+
+
+  # Handle legacy document order and migration
+  fig_doc <- list.files(file_dir, pattern = "figures.qmd")
+  tbl_doc <- list.files(file_dir, pattern = "tables.qmd")
+
+  # if the number preceding the figures.qmd is higher than the number preceding the tables.qmd, then rename the files to match the new order
+  fig_num <- as.numeric(stringr::str_extract(fig_doc, "(?<=^)[0-9]+"))
+  tbl_num <- as.numeric(stringr::str_extract(tbl_doc, "(?<=^)[0-9]+"))
+
+  if (!is.na(fig_num) && !is.na(tbl_num) && fig_num > tbl_num) {
+    cli::cli_alert_info("Detected legacy figure/table document order in the skeleton.")
+
+    # Rename the files to match the new order
+    file.rename(
+      from = fs::path(file_dir, fig_doc),
+      to = fs::path(file_dir,
+                    paste0(stringi::stri_pad_left(tbl_num, 2, "0"),
+                           "_figures.qmd")
+                    )
+    )
+    file.rename(
+      from = fs::path(file_dir, tbl_doc),
+      to = fs::path(file_dir, 
+                    paste0(stringi::stri_pad_left(fig_num, 2, "0"),
+                           "_tables.qmd")
+                    )
+    )
+    cli::cli_alert_success("Changed order to match the new skeleton.")
+
+  }
 }