R/file-tools.R

In Abhi-1U/TexoR: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'

#' @title comment filter for latex lines data
#'
#' @description
#' removes commented latex lines to avoid wrong reference data
#' @param data block of data
#' @keywords internal
#' @return filtered data
#' @noRd
comment_filter <- function(data) {
    comment_break_points <- which(grepl("^%", data))
    for (pos in comment_break_points) {
        data[pos] <- ""
    }
    comment_break_points <- which(grepl("^%%", data))
    for (pos in comment_break_points) {
        data[pos] <- ""
    }
    return(data[nzchar(data)])
}

#' quick function to writelines to a file
#'
#' @param file_path path of text file to write contents to
#' @param mode mode of opening
#' @param raw_text the text/ list of lines to be written
#' @keywords internal
#' @return create/append/write a new file
#' @noRd
write_external_file <- function(file_path, mode, raw_text) {
    file_path <- xfun::normalize_path(file_path)
    write_file <- file(file_path, mode)
    writeLines(raw_text, write_file)
    close(write_file)
}

#' Get the name of the tex file included within wrapper file
#'
#'The wrapper file refers to an external tex file which contains
#'the actual document content.
#' @param article_dir path to the directory which contains tex article
#'
#' @return String name of the tex-file name
#' @export
#' @examples
#' article_dir <- system.file("examples/article",
#'                  package = "texor")
#' dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
#' x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
#' your_article_path <- paste(your_article_folder,"article",sep="/")
#' texor::get_texfile_name(your_article_path)
#' unlink(your_article_folder,recursive = TRUE)
get_texfile_name <- function(article_dir) {
    article_dir <- xfun::normalize_path(article_dir)
    lookup_file <- get_wrapper_type(article_dir)
    if (file.exists(file.path(article_dir,lookup_file))) {
        wrapper_file <- readLines(file.path(article_dir, lookup_file))
    }
    else {
        message("LaTeX file not found !")
        return(FALSE)
    }
    wrapper_file <- stringr::str_subset(wrapper_file, ".+")
    article_start <- which(grepl(
        "^\\s*\\\\begin\\{article\\}",
        wrapper_file))
    pre_marker <- wrapper_file[seq_len(article_start)]
    post_marker <- wrapper_file[seq_len(article_start) + 1]
    source_line <- setdiff(post_marker, pre_marker)
    tex_file <- gsub("[[:space:]]", "",
                     gsub("\\\\input\\{|\\}", "", source_line))
    if (!grepl(".tex$", tex_file)) {
        tex_file <- paste0(tex_file, ".tex")
    }
    return(tex_file)
}

#' get markdown file name
#'
#' @param article_dir path to the directory which contains tex article
#'
#' @return markdown file name
#' @export
#' @examples
#' article_dir <- system.file("examples/article",
#'                  package = "texor")
#' dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
#' x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
#' your_article_path <- paste(your_article_folder,"article",sep="/")
#' texor::get_md_file_name(your_article_path)
#' unlink(your_article_folder,recursive = TRUE)
get_md_file_name <- function(article_dir) {
    article_dir <- xfun::normalize_path(article_dir)
    lookup_file <- get_wrapper_type(article_dir)
    markdown_file <- xfun::with_ext(lookup_file,".md")
    return (markdown_file)
}

#' get Journal details
#'
#' @param article_dir path to the directory which contains tex article
#'
#' @return journal details in an object
#' @export
#' @examples
#' article_dir <- "/home/user/documents/2022-1/2020-36/"
#' texor::get_journal_details(article_dir)
get_journal_details <- function(article_dir) {
    article_dir <- xfun::normalize_path(article_dir)
    journal_details <- list()
    # windows
    if (grepl("\\\\",article_dir)) {
        hierarchy <- str_split(article_dir, "\\\\")[[1]]
    }
    if (grepl("/",article_dir)) {
        hierarchy <- str_split(article_dir, "/")[[1]]
    } else {
        #--pass
    }
    journal_folder <- hierarchy[length(hierarchy) - 1]
    if (journal_folder == "") {
        journal_folder <- hierarchy[length(hierarchy) - 2]
    }
    journal_info <- str_split(journal_folder, "-")[[1]]
    journal_details$volume <- strtoi(journal_info[1],10) - 2008
    journal_details$issue <- strtoi(journal_info[2],10)
    journal_details$slug <- paste("RJ", hierarchy[length(hierarchy)], sep = "-")
    if (is.na(journal_details$issue)) {
        journal_details$sample <- TRUE
        journal_info <- str_split(Sys.Date(), "-")[[1]]
        journal_details$volume <- strtoi(journal_info[1],10) - 2008
        if ( strtoi(journal_info[1],10) < 2022) {
            journal_details$issue <- floor(strtoi(journal_info[2],10) / 6)
        }
        else {
            journal_details$issue <- floor(strtoi(journal_info[2],10) / 3)
            journal_details$slug <- paste('RJ', strtoi(journal_info[1],10), "000", sep = "-")
        }
    } else {
        journal_details$sample <- FALSE
    }
    return(journal_details)
}

#' Copy Supporting Documents like images,bib file,etc.
#'
#' Copies supporting documents like images,pdf,bib files into the output
#' folder for building the HTML version of the R-Markdown file.
#'
#' @param from_path String indicating base path for the working directory
#' @return copies dependency files into the output folder.
#' @export
#' @examples
#' article_dir <- system.file("examples/article", package = "texor")
#' dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
#' x <- file.copy(from = article_dir, to = your_article_folder,recursive = TRUE,)
#' your_article_path <- paste(your_article_folder,"article",sep="/")
#' rmarkdown::pandoc_version()
#' texor::include_style_file(your_article_path)
#' rebib::aggregate_bibliography(your_article_path)
#' texor::copy_other_files(your_article_path)
#' list.files(paste0(your_article_path,"/web/"))
#' unlink(your_article_folder,recursive = TRUE)
copy_other_files <- function(from_path) {
    old_working_directory <- getwd()
    setwd(from_path)
    on.exit(setwd(old_working_directory))
    image_paths <- generate_image_paths(from_path)
    if (! dir.exists("web/")) {
        dir.create("web/", showWarnings = FALSE)
    }
    for (path in image_paths) {
        if(!dir.exists(paste0("web/",dirname(path)))) {
                dir.create(paste0("web/",dirname(path)),showWarnings = TRUE)
        }
        if (!file.exists(path)) {
            # extension naming issue
            if (file.exists(xfun::with_ext(path,".PNG"))){
                path <- xfun::with_ext(path,".PNG")
            }
            if (file.exists(xfun::with_ext(path,".JPG"))) {
                path <- xfun::with_ext(path,".JPG")
            }
            if (file.exists(xfun::with_ext(path,".JPEG"))){
                path <- xfun::with_ext(path,".JPEG")
            }
            if (file.exists(xfun::with_ext(path,"pdf"))){
                convert_to_png(xfun::with_ext(path,"pdf"))
            }
        }
        if (is.null(path)){
            #pass
        }
        else {
            file.copy(path, paste0("web/", path), overwrite = TRUE)
        }
    }
    file_list <- list.files(recursive = FALSE)
    extensions <- c("*.bib$", "*.pdf$", "*.R$", "*.bbl$", "_files$")
    target_files <- unique(grep(paste(
        extensions, collapse = "|"), file_list, value = TRUE))
    file.copy(target_files,
              to = "web/",
              copy.mode = TRUE,
              recursive = TRUE, )

}
copy_to_web <- function(rel_path, ext, article_dir){
    article_dir <- xfun::normalize_path(article_dir)
    if (! grepl(paste0(".",ext,"$"),rel_path)) {
        rel_path <- paste0(rel_path,".",ext)
    }
    web_dir <- paste0(article_dir,"/web")
    if (! dir.exists(web_dir)){
        dir.create(web_dir)
    }
    if (dirname(rel_path) == ".") {
        image_target_file_path <- (paste0(article_dir,"/web/",rel_path))
    } else {
        image_target_file_path <- (paste0(article_dir,"/web/",rel_path))
    }
    image_folder <- paste0(article_dir,"/web/",dirname(rel_path))
    if (! dir.exists(paste0(article_dir,"/web/",dirname(rel_path)))) {
        dir.create(paste0(article_dir,"/web/",dirname(rel_path)))
    }
    file_path <- paste0(article_dir,"/",rel_path)
    web_file_path <- paste0(article_dir,"/web/",rel_path)
    file.copy(file_path, web_file_path)
    png_file <- paste(toString(
        tools::file_path_sans_ext(file_path)), ".png",
        sep = "")

}
#-------------------------------------------------------------------------------

#' generate image paths
#'
#' @param article_dir path to the directory which contains tex article
#'
#' @return list of image paths
#' @noRd
generate_image_paths <- function(article_dir) {
    article_dir <- xfun::normalize_path(article_dir)
    # wrapper file name
    input_file <- get_wrapper_type(article_dir)
    # resource path for pandoc
    input_file_path <- paste(article_dir, input_file, sep = "/")
    abs_file_path <- tools::file_path_as_absolute(input_file_path)
    # markdown equivalent filename
    temp_file <- "temp-native.txt"
    temp_file_path <- paste(article_dir, temp_file, sep = "/")

    image_list_filter <- system.file(
        "image_list_filter.lua", package = "texor")
    pandoc_opt <- c("-s",
                    "--resource-path", abs_file_path,
                    "--lua-filter", image_list_filter)
    if (! pandoc_version_check()){
        message(paste0("pandoc version too old, current-v : ",rmarkdown::pandoc_version()," required-v : >=2.17\n","Please Install a newer version of pandoc to run texor"))
        pdf_image_paths <- NULL
        return(pdf_image_paths)
    }
    else {
        #pass
    }
    rmarkdown::pandoc_convert(input_file_path,
                              from = "latex",
                              to = "native",
                              options = pandoc_opt,
                              output = temp_file_path,
                              verbose = TRUE)
    if (file.exists(paste0(article_dir,"/image_source.txt"))) {
        image_paths <- readLines(paste0(article_dir,"/image_source.txt"))
    } else {
        image_paths <- NULL
    }

    return(image_paths)
}

#' Check article for sub-files
#'
#' There are some articles which include sub-section as seperate files, this
#' function checks for the existence of such files.
#'
#' @param article_dir path to the directory which contains tex article
#'
#' @return TRUE if article has multiple sub files else FALSE
#' @noRd
check_sub_sec_files <- function(article_dir) {
    root_article <- texor::get_texfile_name(article_dir)
    article_data <- readLines(paste0(article_dir,"/",root_article))
    sub_sec_file <- article_data[grepl("\\\\input\\{",article_data)]
    if (length(sub_sec_file) > 0) {
        return(TRUE)
    }
    return(FALSE)
}

#' Ge paths of sub-files from article
#'
#' There are some articles which include sub-section as seperate files, this
#' function fetches the paths of these included files and returns them as a list.
#'
#' @param article_dir path to the directory which contains tex article
#'
#' @return a list of file names/ relative paths of included files
#' @noRd
get_sub_sec_files <- function(article_dir) {
    if (!check_sub_sec_files(article_dir)) {
        return(FALSE)
    }
    root_article <- texor::get_texfile_name(article_dir)
    sub_sec_file <- readLines(paste0(article_dir,"/",root_article))
    sub_sec_file <- sub_sec_file[grepl("\\\\input\\{",sub_sec_file)]
    tex_files <- gsub("[[:space:]]", "",
                     gsub("\\\\input\\{|\\}", "", sub_sec_file))
    for (i in 1:length(tex_files)) {
        if (!grepl(".tex$", tex_files[i])) {
            tex_files[i] <- paste0(tex_files[i], ".tex")
        }
    }
    return(tex_files)
}