R/automation-tools.R
In Abhi-1U/TexoR: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Defines functions
convert_to_html
latex_to_web
Documented in
latex_to_web
#' @title latex to web
#' @description automated function for converting a single RJarticle to web
#' @param dir directory path
#' @param log_steps Enable/Disable Logging of conversion steps
#' @param example for examples only by default keep it FALSE.
#' @param auto_wrapper automatically creates a wrapper if TRUE, else asks user. default value TRUE
#' @param temp_mode temp mode will convert the document in a temporary folder and keep the original
#' article untouched. default value = TRUE
#' @param web_dir option to create a new web directory, default FALSE
#' @param interactive_mode interactive mode for converting articles with options. default FALSE
#' @param autonumber_eq whether to autonumber the equations, default is FALSE
#' @param compile_rmd_in_temp This works only with a forked version of rjtools.
#' @param kable_tab converts to kable table instead of markdown tables, default is FALSE
#' @param fig_in_r whether to include figures in R code chunks, default is FALSE
#' Not recommended to use with CRAN or github version of the rjtools package. (default FALSE)
#' @note Use pandoc version greater than or equal to 3.1
#' @note Do not set example = TRUE param when working with conversions.
#' @note example param is set TRUE in example, to conform with CRAN check restrictions.
#' @return RJweb article document in /web 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="/")
#' texor::latex_to_web(your_article_path,log_steps = FALSE, example = TRUE, temp_mode =FALSE)
#' unlink(your_article_folder, recursive = TRUE)
latex_to_web <- function(dir,log_steps = TRUE, example = FALSE, auto_wrapper = TRUE,
temp_mode = TRUE, web_dir = FALSE, interactive_mode = FALSE,
autonumber_eq = FALSE, compile_rmd_in_temp = !temp_mode,
kable_tab = FALSE, fig_in_r = FALSE) {
message(dir)
if (!pandoc_version_check()) {
warning(paste0("pandoc version too old, current-v : ",rmarkdown::pandoc_version()," required-v : >=3.1"))
return(FALSE)
}
else {
#pass
}
dir <- xfun::normalize_path(dir)
date <- Sys.Date()
wrapper <- get_wrapper_type(dir,
auto_wrapper = auto_wrapper,
interactive_mode = interactive_mode) #wrapper file name
file_name <- get_texfile_name(dir)
# PHINNEY: patch abstract here
patch_rnw_abstract(paste0(dir, "/", file_name))
# temp mode
if (temp_mode) {
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
dir.create(your_article_folder_2 <- paste(your_article_folder, basename(dirname(dir)),sep = '/'))
x <- file.copy(from = dir, to = your_article_folder_2,recursive = TRUE,)
your_article_path <- paste(your_article_folder_2, basename(dir),"",sep = "/")
on.exit(unlink(your_article_folder, recursive = TRUE))
# run latex to web recursively on a temp folder
x <- tryCatch(texor::latex_to_web(your_article_path,
auto_wrapper = auto_wrapper,
temp_mode = FALSE,
web_dir = web_dir,
interactive_mode = interactive_mode,
compile_rmd_in_temp = compile_rmd_in_temp,
kable_tab = kable_tab,
fig_in_r = fig_in_r),
error = function(c) {
warning(c)
})
all_files <- list.files(your_article_path)
exculde_files <- c("*[.]bk$","*[.]tex$","*[.]yaml$","*[.]sty$","*[.]log$","*[.]txt$")
for (exp in exculde_files) {
all_files <- all_files[!grepl(exp,all_files)]
}
y <- file.copy(from = paste(your_article_path,all_files,sep = "/"),
to = xfun::normalize_path(dir),
recursive = TRUE,
)
if (!compile_rmd_in_temp) {
message(paste0("Knitting Rmd to html"))
texor::produce_html(dir, web_dir = web_dir, interactive_mode = interactive_mode)
}
return(TRUE)
}
if (log_steps) {
log_file <- paste0("texor-log-",date,".log")
log_setup(dir, log_file, "texor" ,2)
texor_log(paste0("working directory : ", dir), "info", 2)
texor_log(paste0("file name : ", file_name), "info", 2)
# Step - 0 : Set working directory
# pdf directory
# Step - 1 : Include Meta-fix style file
wrapper <- get_wrapper_type(dir, auto_wrapper = auto_wrapper)
texor_log(paste0("Stage-01 | ", "including Style File to : ", wrapper), "info", 2)
texor_log(paste0("Stage-01 | ", "Style File : Metafix.sty"), "info", 2)
include_style_file(dir)
texor_log(paste0("Stage-01 | ", "Included Style File : Metafix.sty"), "info", 2)
# Step - 2 : Manage Bibliography(ies)
texor_log(paste0("Stage-02 | ", "aggregating Bibliography using : rebib"), "info", 2)
texor_log(paste0("Stage-02 | ", "Check rebib logs for more info"), "info", 2)
rebib::aggregate_bibliography(dir)
log_setup(dir, log_file, "texor", 2)
# Step - 3 : patch code environments to verbatim
texor_log(paste0("Stage-03| ","Patching Code Env"), "info", 2)
patch_code_env(dir)
texor_log(paste0("Stage-03 | ","Patched Code Env"), "info", 2)
# Step - 4 : patch custom table environments to table
texor_log(paste0("Stage-04 | ","Patching Table Env"), "info", 2)
patch_table_env(dir)
texor_log(paste0("Stage-04 | ","Patched Table Env"), "info", 2)
# Step - 5 : Check for PDF and then convert
# PDF to PNG based on condition
texor_log(paste0("Stage-05 | ","converting Images to png"), "info", 2)
data <- handle_figures(dir, file_name)
texor_log(paste0("Stage-05 | ","converted pdf files to png"), "info", 2)
# Step - 5.5 : patch math or latex commands
patch_equations(dir)
# Step - 6 : patch figure environments to figure
texor_log(paste0("Stage-06 | ","Patching Figure Env"), "info", 2)
patch_figure_env(dir)
texor_log(paste0("Stage-06 | ","Patched Figure Env"), "info", 2)
# Step - 7 : Convert to markdown + find package
# references
texor_log(paste0("Stage-07 | ","Converting LaTeX to Markdown"), "info", 2)
meta <- pre_conversion_statistics(dir)
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r)
texor_log(paste0("Stage-07 | ","Converted LaTeX to Markdown"), "info", 2)
# Step - 8 : Create a new directory and copy
# dependent files/folders
texor_log(paste0("Stage-08 | ","Copying Dependencies to /web"), "info", 2)
if (web_dir) {
copy_other_files(dir)
}
texor_log(paste0("Stage-08 | ","Copied Dependencies to /web"), "info", 2)
# Step - 9 : generate R markdown file with
# metadata from DESCRIPTION, tex file
# and file path
# Note : the below function will work on any article, However ideally it needs a
# folder structure similar to RJournal style /YYYY-ZZ/YYYY-MMM where
# YYYY is the year, ZZ is the Journal issue number and MMM is the DOI
# referral(unique article number).
texor_log(paste0("Stage-09 | ","Creating R-markdown File to /web"), "info", 2)
texor::generate_rmd(dir,web_dir = web_dir, interactive_mode = interactive_mode)
texor_log(paste0("Stage-09 | ","Created R-markdown File to /web"), "info", 2)
# Step - 10 : produce html (using rj_web_article) format
if (compile_rmd_in_temp) {
texor_log(paste0("Stage-10 | ","Knitting Rmd to html"), "info", 2)
texor::produce_html(dir, web_dir = web_dir, interactive_mode = interactive_mode)
texor_log(paste0("Stage-10 | ","Knitted Rmd to html"), "info", 2)
}
post_data <- yaml::read_yaml(paste0(dir,"/post-conversion-meta.yaml"))
if (post_data$text$words == 0) {
texor_log(paste0("Pandoc produced an empty file"), "error", 2)
} else {
texor_log(paste0("Conversion Summary | ", "Pre-Conversion ", "Post-Conversion"), "debug", 2)
texor_log(paste0("Tables | ", post_data$table, " ", meta$table), "debug", 2)
texor_log(paste0("Figures | ", post_data$figure, " ", meta$figure), "debug", 2)
texor_log(paste0("Math | ", post_data$math, " ", meta$math), "debug", 2)
texor_log(paste0("Citations | ", post_data$citations, " ", meta$citations), "debug", 2)
texor_log(paste0("Code Inline | ", post_data$code$inline, " ", meta$code$inline), "debug", 2)
texor_log(paste0("Code Block | ", post_data$code$block, " ", meta$code$block), "debug", 2)
}
return(TRUE)
}
else{
wrapper <- get_wrapper_type(dir, auto_wrapper = auto_wrapper) #wrapper file name
include_style_file(dir) # Step 1
rebib::aggregate_bibliography(dir) # Step 2
patch_code_env(dir) # Step 3
patch_table_env(dir) # Step 4
data <- handle_figures(dir, file_name) # Step 5
patch_equations(dir) # Step 5.5
patch_figure_env(dir) # Step 6
meta <- pre_conversion_statistics(dir) # Step 6.5
if (example) {
if (web_dir) {
copy_other_files(dir) # Step 8
}
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r) # Step 7
texor::generate_rmd(dir,web_dir = web_dir) # Step 9
if (compile_rmd_in_temp) {
texor::produce_html(dir,example = TRUE, web_dir = web_dir,
interactive_mode = interactive_mode) # Step 10
}
}
else {
if (web_dir) {
copy_other_files(dir) # Step 8
}
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r) # Step 7
texor::generate_rmd(dir,web_dir = web_dir,
interactive_mode = interactive_mode) # Step 9
if (compile_rmd_in_temp) {
texor::produce_html(dir,web_dir = web_dir,
interactive_mode = interactive_mode) # Step 10
}
}
return(TRUE)
}
}
#' @title conversion function with logging success and failure
#' @description When applied to a list of article_dirs it will also log
#' successful and failed slugs.
#' @param dir absolute path to the article_dir
#' @param log_steps Enable/Disable Logging of conversion steps
#' @return Log file
#' @noRd
convert_to_html <- function(dir,log_steps = TRUE) {
wd <- getwd()
dir <- xfun::normalize_path(dir)
if(log_steps){
texor::log_setup(wd,"texor-conversions.log","texor-stats",2)
}
else{
message("Logging Disabled")
}
x<- FALSE
x<- tryCatch(texor::latex_to_web(dir),
error = function(c) {
c$message <- paste0(c$message, " (in ", basename(dir), ")")
if(log_steps){
logger::log_error(paste("Conversion Failed",basename(dir), sep=" "),namespace = "texor-stats")
logger::log_error(paste(c$message, sep=" "),namespace = "texor-stats")
}
else{
warning(c$message)
}
}
)
if (identical(x,TRUE)) {
if(log_steps){
logger::log_success(paste("Conversion Success", basename(dir), sep=" "),namespace = "texor-stats")
}
else{
message(paste("Conversion Success", basename(dir), sep=" "))
}
}
}
Abhi-1U/TexoR documentation built on June 10, 2025, 2:55 a.m.
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Defines functions convert_to_html latex_to_web
Documented in latex_to_web
#' @title latex to web
#' @description automated function for converting a single RJarticle to web
#' @param dir directory path
#' @param log_steps Enable/Disable Logging of conversion steps
#' @param example for examples only by default keep it FALSE.
#' @param auto_wrapper automatically creates a wrapper if TRUE, else asks user. default value TRUE
#' @param temp_mode temp mode will convert the document in a temporary folder and keep the original
#' article untouched. default value = TRUE
#' @param web_dir option to create a new web directory, default FALSE
#' @param interactive_mode interactive mode for converting articles with options. default FALSE
#' @param autonumber_eq whether to autonumber the equations, default is FALSE
#' @param compile_rmd_in_temp This works only with a forked version of rjtools.
#' @param kable_tab converts to kable table instead of markdown tables, default is FALSE
#' @param fig_in_r whether to include figures in R code chunks, default is FALSE
#' Not recommended to use with CRAN or github version of the rjtools package. (default FALSE)
#' @note Use pandoc version greater than or equal to 3.1
#' @note Do not set example = TRUE param when working with conversions.
#' @note example param is set TRUE in example, to conform with CRAN check restrictions.
#' @return RJweb article document in /web 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="/")
#' texor::latex_to_web(your_article_path,log_steps = FALSE, example = TRUE, temp_mode =FALSE)
#' unlink(your_article_folder, recursive = TRUE)
latex_to_web <- function(dir,log_steps = TRUE, example = FALSE, auto_wrapper = TRUE,
temp_mode = TRUE, web_dir = FALSE, interactive_mode = FALSE,
autonumber_eq = FALSE, compile_rmd_in_temp = !temp_mode,
kable_tab = FALSE, fig_in_r = FALSE) {
message(dir)
if (!pandoc_version_check()) {
warning(paste0("pandoc version too old, current-v : ",rmarkdown::pandoc_version()," required-v : >=3.1"))
return(FALSE)
}
else {
#pass
}
dir <- xfun::normalize_path(dir)
date <- Sys.Date()
wrapper <- get_wrapper_type(dir,
auto_wrapper = auto_wrapper,
interactive_mode = interactive_mode) #wrapper file name
file_name <- get_texfile_name(dir)
# PHINNEY: patch abstract here
patch_rnw_abstract(paste0(dir, "/", file_name))
# temp mode
if (temp_mode) {
dir.create(your_article_folder <- file.path(tempdir(), "tempdir"))
dir.create(your_article_folder_2 <- paste(your_article_folder, basename(dirname(dir)),sep = '/'))
x <- file.copy(from = dir, to = your_article_folder_2,recursive = TRUE,)
your_article_path <- paste(your_article_folder_2, basename(dir),"",sep = "/")
on.exit(unlink(your_article_folder, recursive = TRUE))
# run latex to web recursively on a temp folder
x <- tryCatch(texor::latex_to_web(your_article_path,
auto_wrapper = auto_wrapper,
temp_mode = FALSE,
web_dir = web_dir,
interactive_mode = interactive_mode,
compile_rmd_in_temp = compile_rmd_in_temp,
kable_tab = kable_tab,
fig_in_r = fig_in_r),
error = function(c) {
warning(c)
})
all_files <- list.files(your_article_path)
exculde_files <- c("*[.]bk$","*[.]tex$","*[.]yaml$","*[.]sty$","*[.]log$","*[.]txt$")
for (exp in exculde_files) {
all_files <- all_files[!grepl(exp,all_files)]
}
y <- file.copy(from = paste(your_article_path,all_files,sep = "/"),
to = xfun::normalize_path(dir),
recursive = TRUE,
)
if (!compile_rmd_in_temp) {
message(paste0("Knitting Rmd to html"))
texor::produce_html(dir, web_dir = web_dir, interactive_mode = interactive_mode)
}
return(TRUE)
}
if (log_steps) {
log_file <- paste0("texor-log-",date,".log")
log_setup(dir, log_file, "texor" ,2)
texor_log(paste0("working directory : ", dir), "info", 2)
texor_log(paste0("file name : ", file_name), "info", 2)
# Step - 0 : Set working directory
# pdf directory
# Step - 1 : Include Meta-fix style file
wrapper <- get_wrapper_type(dir, auto_wrapper = auto_wrapper)
texor_log(paste0("Stage-01 | ", "including Style File to : ", wrapper), "info", 2)
texor_log(paste0("Stage-01 | ", "Style File : Metafix.sty"), "info", 2)
include_style_file(dir)
texor_log(paste0("Stage-01 | ", "Included Style File : Metafix.sty"), "info", 2)
# Step - 2 : Manage Bibliography(ies)
texor_log(paste0("Stage-02 | ", "aggregating Bibliography using : rebib"), "info", 2)
texor_log(paste0("Stage-02 | ", "Check rebib logs for more info"), "info", 2)
rebib::aggregate_bibliography(dir)
log_setup(dir, log_file, "texor", 2)
# Step - 3 : patch code environments to verbatim
texor_log(paste0("Stage-03| ","Patching Code Env"), "info", 2)
patch_code_env(dir)
texor_log(paste0("Stage-03 | ","Patched Code Env"), "info", 2)
# Step - 4 : patch custom table environments to table
texor_log(paste0("Stage-04 | ","Patching Table Env"), "info", 2)
patch_table_env(dir)
texor_log(paste0("Stage-04 | ","Patched Table Env"), "info", 2)
# Step - 5 : Check for PDF and then convert
# PDF to PNG based on condition
texor_log(paste0("Stage-05 | ","converting Images to png"), "info", 2)
data <- handle_figures(dir, file_name)
texor_log(paste0("Stage-05 | ","converted pdf files to png"), "info", 2)
# Step - 5.5 : patch math or latex commands
patch_equations(dir)
# Step - 6 : patch figure environments to figure
texor_log(paste0("Stage-06 | ","Patching Figure Env"), "info", 2)
patch_figure_env(dir)
texor_log(paste0("Stage-06 | ","Patched Figure Env"), "info", 2)
# Step - 7 : Convert to markdown + find package
# references
texor_log(paste0("Stage-07 | ","Converting LaTeX to Markdown"), "info", 2)
meta <- pre_conversion_statistics(dir)
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r)
texor_log(paste0("Stage-07 | ","Converted LaTeX to Markdown"), "info", 2)
# Step - 8 : Create a new directory and copy
# dependent files/folders
texor_log(paste0("Stage-08 | ","Copying Dependencies to /web"), "info", 2)
if (web_dir) {
copy_other_files(dir)
}
texor_log(paste0("Stage-08 | ","Copied Dependencies to /web"), "info", 2)
# Step - 9 : generate R markdown file with
# metadata from DESCRIPTION, tex file
# and file path
# Note : the below function will work on any article, However ideally it needs a
# folder structure similar to RJournal style /YYYY-ZZ/YYYY-MMM where
# YYYY is the year, ZZ is the Journal issue number and MMM is the DOI
# referral(unique article number).
texor_log(paste0("Stage-09 | ","Creating R-markdown File to /web"), "info", 2)
texor::generate_rmd(dir,web_dir = web_dir, interactive_mode = interactive_mode)
texor_log(paste0("Stage-09 | ","Created R-markdown File to /web"), "info", 2)
# Step - 10 : produce html (using rj_web_article) format
if (compile_rmd_in_temp) {
texor_log(paste0("Stage-10 | ","Knitting Rmd to html"), "info", 2)
texor::produce_html(dir, web_dir = web_dir, interactive_mode = interactive_mode)
texor_log(paste0("Stage-10 | ","Knitted Rmd to html"), "info", 2)
}
post_data <- yaml::read_yaml(paste0(dir,"/post-conversion-meta.yaml"))
if (post_data$text$words == 0) {
texor_log(paste0("Pandoc produced an empty file"), "error", 2)
} else {
texor_log(paste0("Conversion Summary | ", "Pre-Conversion ", "Post-Conversion"), "debug", 2)
texor_log(paste0("Tables | ", post_data$table, " ", meta$table), "debug", 2)
texor_log(paste0("Figures | ", post_data$figure, " ", meta$figure), "debug", 2)
texor_log(paste0("Math | ", post_data$math, " ", meta$math), "debug", 2)
texor_log(paste0("Citations | ", post_data$citations, " ", meta$citations), "debug", 2)
texor_log(paste0("Code Inline | ", post_data$code$inline, " ", meta$code$inline), "debug", 2)
texor_log(paste0("Code Block | ", post_data$code$block, " ", meta$code$block), "debug", 2)
}
return(TRUE)
}
else{
wrapper <- get_wrapper_type(dir, auto_wrapper = auto_wrapper) #wrapper file name
include_style_file(dir) # Step 1
rebib::aggregate_bibliography(dir) # Step 2
patch_code_env(dir) # Step 3
patch_table_env(dir) # Step 4
data <- handle_figures(dir, file_name) # Step 5
patch_equations(dir) # Step 5.5
patch_figure_env(dir) # Step 6
meta <- pre_conversion_statistics(dir) # Step 6.5
if (example) {
if (web_dir) {
copy_other_files(dir) # Step 8
}
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r) # Step 7
texor::generate_rmd(dir,web_dir = web_dir) # Step 9
if (compile_rmd_in_temp) {
texor::produce_html(dir,example = TRUE, web_dir = web_dir,
interactive_mode = interactive_mode) # Step 10
}
}
else {
if (web_dir) {
copy_other_files(dir) # Step 8
}
convert_to_markdown(dir, autonumber_eq = autonumber_eq, kable_tab = kable_tab, fig_in_r = fig_in_r) # Step 7
texor::generate_rmd(dir,web_dir = web_dir,
interactive_mode = interactive_mode) # Step 9
if (compile_rmd_in_temp) {
texor::produce_html(dir,web_dir = web_dir,
interactive_mode = interactive_mode) # Step 10
}
}
return(TRUE)
}
}
#' @title conversion function with logging success and failure
#' @description When applied to a list of article_dirs it will also log
#' successful and failed slugs.
#' @param dir absolute path to the article_dir
#' @param log_steps Enable/Disable Logging of conversion steps
#' @return Log file
#' @noRd
convert_to_html <- function(dir,log_steps = TRUE) {
wd <- getwd()
dir <- xfun::normalize_path(dir)
if(log_steps){
texor::log_setup(wd,"texor-conversions.log","texor-stats",2)
}
else{
message("Logging Disabled")
}
x<- FALSE
x<- tryCatch(texor::latex_to_web(dir),
error = function(c) {
c$message <- paste0(c$message, " (in ", basename(dir), ")")
if(log_steps){
logger::log_error(paste("Conversion Failed",basename(dir), sep=" "),namespace = "texor-stats")
logger::log_error(paste(c$message, sep=" "),namespace = "texor-stats")
}
else{
warning(c$message)
}
}
)
if (identical(x,TRUE)) {
if(log_steps){
logger::log_success(paste("Conversion Success", basename(dir), sep=" "),namespace = "texor-stats")
}
else{
message(paste("Conversion Success", basename(dir), sep=" "))
}
}
}
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