Inject accessibility #124
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There was a problem hiding this comment. This function isn't working for me. I'm using the same args as for add_tagging and add_alttext, but I get an error I think is about incorrect filepaths ("Error in file(file, "rt") : cannot open the connection"). The error arises at line 73, when add_alttext is called. |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,122 @@ | ||
| #' Add alternative text into latex | ||
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There was a problem hiding this comment. Minor: please change the filetype from .r to .R for consistency |
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| #' | ||
| #' @inheritParams add_accessibility | ||
| #' | ||
| #' @return DRAFT: This function was made to help add in | ||
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There was a problem hiding this comment. Is this still a draft? There was a problem hiding this comment. This is and is outdated somehow after your review which makes no sense because I pushed all of these changes on tuesday |
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| #' alternative text to latex documents generated from | ||
| #' quarto. Quarto does not currently contain a way to | ||
| #' add alternative text to PDF documents, so this function | ||
| #' was developed as a work around. The addition of alternative | ||
| #' text needs to be in the form found in rda files made | ||
| #' from satf plotting functions. If users want to use this | ||
| #' function as a way to add alternative text to all | ||
| #' figures, please leave an issue to request this function. | ||
| #' | ||
| #' @export | ||
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There was a problem hiding this comment. Please add examples if they're absent (I can see an example in Rstudio but not here... ?), and update the example to include the There was a problem hiding this comment. Added on tuesday...not sure why none of my changes are there. Git is telling me that everything is updated |
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| #' | ||
| add_alttext <- function( | ||
| x = list.files(getwd())[grep("skeleton.tex", list.files(getwd()))], | ||
| dir = getwd(), | ||
| rda_dir = getwd(), | ||
| compile = TRUE, | ||
| rename = NULL | ||
| ) { | ||
| # Read latex file | ||
| tex_file <- readLines(file.path(dir, x)) | ||
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| # Check: count instances of pattern | ||
| # sub_count <- length( | ||
| # grep("1", | ||
| # stringr::str_count( | ||
| # tex_file, | ||
| # pattern = stringr::coll("\\pandocbounded{\\includegraphics[")) | ||
| # ) | ||
| # ) | ||
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| # Identify lines with figures | ||
| # this approach allows us to not mistake the replacement for other figures | ||
| fig_lines <- grep("fig-([a-z]+|[a-z]+_[a-z]+)-plot-1.pdf", tex_file) | ||
| # TODO: | ||
| # create check to see if there are any instances where the suffix is not plot-1 | ||
| # Replace instances of macro in the tex file | ||
| # replace_macro <- gsub( | ||
| # "\\pandocbounded", | ||
| # "\\pdftooltip", | ||
| # tex_file | ||
| # ) | ||
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| # Replace pandocbounded with pdftooltip so alt text can be added | ||
| tex_file[fig_lines] <- lapply( | ||
| tex_file[fig_lines], | ||
| function(line) { | ||
| gsub("\\pandocbounded", "\\pdftooltip", line) | ||
| } | ||
| ) | ||
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| # Insert alt text for figures | ||
| # Call alt text in list with names | ||
| obj_files <- list.files(file.path(rda_dir, "rda_files")) | ||
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| # read all files in obj_files and put into list | ||
| alt_text_list <- list() | ||
| for (i in seq_along(obj_files)) { | ||
| load(file.path(rda_dir, "rda_files", obj_files[i])) | ||
| # extract name to add into the list for placement | ||
| rda_name <- stringr::str_replace(obj_files[i], "_figure.rda", "") | ||
| # if name is >1 word then replace the _ with - to follow naming convention for | ||
| # figures in tex file | ||
| if (grepl("_", rda_name)) rda_name <- stringr::str_replace(rda_name, "_", "-") | ||
| # convert to name in tex file to find where the line is located | ||
| tex_name <- glue::glue("fig-{rda_name}-plot-1.pdf") | ||
| # extract alt. text with figure | ||
| alt_text <- rda$alt_text | ||
| # names(alt_text) <- tex_name | ||
| # place obj into list | ||
| alt_text_list[[tex_name]] <- alt_text | ||
| # call tex obj name using names() | ||
| # call alt text using list[[i]] | ||
| # remove rda file to declutter | ||
| rm(rda) | ||
| } | ||
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| # Find where figure is located and append the alt. text | ||
| for (i in seq_along(alt_text_list)) { | ||
| fig_line <- grep(names(alt_text_list[i]), tex_file) | ||
| # Check that line we are adding the alt text to is for correct fig | ||
| if (!grepl(names(alt_text_list[i]), tex_file[fig_line])) { | ||
| warning(glue::glue("Non-matching object name to tex file line.")) | ||
| next | ||
| } | ||
| # Check that selected tex_line contains a marked figure - aka correct placement | ||
| file_name <- stringr::str_remove(x, ".tex") | ||
| if (!grepl(glue::glue("{file_name}_files/figure-pdf/fig-"), tex_file[fig_line])) { | ||
| warning(glue::glue("Improper line for appendment: \n Skipped adding alternative text for {names(alt_text_list[i])}")) | ||
| next | ||
| } | ||
| tex_file[fig_line] <- paste(tex_file[fig_line], "{", alt_text_list[[i]], "}", sep = "") | ||
| # tex_file[fig_line] <- strwrap(paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = "")) # remove strwrap if does not render | ||
| } | ||
| # tex_file[430] <- paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = "") | ||
| # strwrap(paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = ""), width = 80) | ||
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| # Checks | ||
| # add check if there are more plots that did not have alt text added | ||
| # if (length(obj_files) != length(fig_lines)) { | ||
| # # Find which ones were not changed | ||
| # # figs_miss_alt <- | ||
| # warning("Missing alternative text for the followiing figures:") | ||
| # } | ||
| # TODO: test case where additional figure is added into the .tex file that is not included in the rda files | ||
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| # Save overwrite tex file | ||
| write(unlist(tex_file), file = file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x))) | ||
| # utils::capture.output(cat(tex_file), file = file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x)), append = FALSE) | ||
| message("______Alternative text added to tex file.______") | ||
| # Render the .tex file after edits | ||
| if (compile) { | ||
| message("______Compiling in progress - This can take a while...______") | ||
| # test if this can be done when skeleton is in different folder than the wd | ||
| tinytex::lualatex(file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x))) | ||
| message("______Compiling finished______") | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| #' Add tagging structure to latex documents produced from quarto | ||
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There was a problem hiding this comment. Minor: please change the filetype from .r to .R for consistency |
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| #' | ||
| #' @inheritParams add_accessibility | ||
| #' | ||
| #' @return DRAFT: This function was made to help add in | ||
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There was a problem hiding this comment. Is this still a draft? (for this and the other 2 identical comments, please remove "DRAFT: " if it's ready to merge) |
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| #' latex packages and content associated with PDF | ||
| #' tagging. Quarto does not allow the user to edit anything | ||
| #' before documentclass, so this function alters the rendered .tex file. | ||
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There was a problem hiding this comment. Also don't see the example here, but I do see it in my Rstudio file ...? Please update the example to include the fxn's |
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| #' @export | ||
| #' | ||
| add_tagging <- function( | ||
| x = list.files(getwd())[grep("skeleton.tex", list.files(getwd()))], | ||
| dir = getwd(), | ||
| compile = TRUE, | ||
| rename = NULL | ||
| ) { | ||
| # Read latex file | ||
| tex_file <- readLines(file.path(dir, x)) | ||
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| # Identify line where the new accessibility content should be added after | ||
| line_after <- grep("\\PassOptionsToPackage\\{dvipsnames\\,svgnames\\,x11names\\}\\{xcolor\\}", tex_file) | ||
| # Acessibility additions before /documentclass | ||
| line_to_add <- "\\input{accessibility.tex}" | ||
| # Add line into file | ||
| tex_file <- append(line_to_add, tex_file, after = line_after) | ||
| # DO NOT UNCOMMENT FOLLOWING LINES WHEN OPERATING FXN AS A WHOLE | ||
| # We want to keep tex_file open so we can make changes to figures later down the line | ||
| # Export file | ||
| write(tex_file, file = file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x))) | ||
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| # Add accessibility.tex to directory | ||
| accessibility <- paste0( | ||
| "\\DocumentMetadata{%", "\n", | ||
| " ", "% uncompress, %only for debugging!!", "\n", | ||
| " ", "pdfversion=2.0,", "\n", | ||
| " ", "testphase={phase-II, tabular, graphic}%", "\n", | ||
| " ", "% testphase={phase-II,math, tabular, graphic}% TOC Does not work", "\n", | ||
| " ", "% testphase={phase-III,math}% TOC works", "\n", | ||
| "}", "\n", | ||
| "\\tagpdfsetup{activate, tabsorder=structure}", "\n", | ||
| "% Use the following to fix bug in November 2023 download of LaTeX", "\n", | ||
| "\\ExplSyntaxOn", "\n", | ||
| "\\cs_generate_variant:Nn__tag_prop_gput:Nnn{cnx}", "\n", | ||
| "\\ExplSyntaxOff", "\n", | ||
| "%", "\n" | ||
| ) | ||
| # Save accessibility partial | ||
| utils::capture.output(cat(accessibility), file = file.path(dir, "accessibility.tex"), append = FALSE) | ||
| message("______Tagging structure added to tex file.______") | ||
| if (compile) { | ||
| message("______Compiling in progress - This can take a while...______") | ||
| # test if this can be done when skeleton is in different folder than the wd | ||
| tinytex::lualatex(file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x))) | ||
| message("______Compiling finished______") | ||
| } | ||
| } | ||
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Also, meant to mention this: Initially, I had some issues rendering the 08_tables.qmd. Based on conversations from a couple of weeks ago, I'm sure this will be resolved with rebasing (these errors arose for you before, I believe, as explained here: #153 )