##################

# This code takes a set of Rmd files from a designated git repo and

# 1) knits them to jekyll flavored markdown

# 2) purls them to .R files

# it then cleans up all image directories, etc from the working dir!

# Author: Leah A. Wasser

# last modified:

format(Sys.time(), "%d %h %y @ %H:%M")

##################

require(knitr)

require(rmarkdown)

library(dplyr)

# working directory

options(stringsAsFactors = F)

### Helper function ####

## Helper function - check to see if directory exists and if it doesn't, create it.

check_create_dirs <- function(path_to_check, clean=T){

if (dir.exists(path_to_check)){

# clean out code dir to avoid the issue of duplicate files

if(clean==F){

print(" dir exists")

}else {

print(" dir exists & and has been cleaned ")

unlink(file.path(path_to_check, "/*"), recursive = TRUE)

}

} else {

# create image directory structure

dir.create(path_to_check, recursive=T)

print("new sub dir created.")

}

}

#################### Set up Input Variables #############################

# set working dir - this is where the data are located

wd <- "~/Documents/earth-analytics/"

# where the files to render are

git_repo_base_path <- "~/Documents/Github/earthlab.github.io"

repo_post_path <- "_posts/course-materials"

##### Setup Life ####

# set data working dir

setwd(wd)

# a_dataframe <- all_rmd_files

## subset dataframe to just the files that need a build

# conditions = date modified is not the same OR there is no md file

#file.path(dirname(gsub(".*/_posts","", rmd_files)), gsub(".Rmd$", "", basename(rmd_files)))

populate_all_rmd_df <- function(a_dataframe, all=FALSE){

all_rmd_files_bld <- a_dataframe %>%

mutate(md_files = gsub(".Rmd$", ".md", rmd_files)) %>%

mutate(rmd_modified = file.info(rmd_files)$mtime,

md_modified = file.info(md_files)$mtime) %>%

mutate(base_path = file.path(dirname(gsub(".*/_posts/","", rmd_files)), gsub(".Rmd$", "", basename(rmd_files))),

code_file = gsub(".Rmd$", ".R", (basename(rmd_files))), # create the code name

base_path = sub(".*_posts/", "", base_path),

fig_dir = file.path("images/rfigs", base_path))

# filter the data to just the modified files if it's not a full rebuild

if (all== FALSE) {

all_rmd_files_bld <- all_rmd_files_bld %>%

filter((md_modified < rmd_modified) | is.na(md_modified) == TRUE )

}

return(all_rmd_files_bld)

}

# create code filename

# is it a draft or a final post

# draft_post <- c("_drafts", "_posts")

################# Check For / Set up / Clean out Code and pdf Dir #################

# there is a possibility of duplicate code and image directories here IF there is a file name change. think about this.

#################### Set up Image Directory #############################

# in case you just want to test this function

#rmd_file_df <- all_rmd_files_bld[1, ]

create_markdown <- function(rmd_file_df, wd){

current_file <- rmd_file_df$rmd_files

# copy .Rmd file to data working directory

file.copy(from = current_file, to=wd, overwrite = TRUE)

# check for working dir image dir

check_create_dirs(rmd_file_df$fig_dir)

# check for pdf directory in git repo

pdf_dir <- file.path(git_repo_base_path, "pdf", (sub("[^/]+$", "", rmd_file_df$base_path)))

check_create_dirs(pdf_dir, clean = F)

# set knitr render options.

opts_chunk$set(fig.path = paste0(rmd_file_df$fig_dir,"/"),

fig.cap = " ",

collapse = T,

out.width='100%', dpi=200)

# render jekyll flavor md

render_markdown(strict = FALSE,

fence_char = "`")

# Universal Knitr Config - set the base url for images and links in the md file for website

base_url="{{ site.url }}/"

opts_knit$set(base.url = base_url)

# knit Rmd to jekyll flavored md format, knit to the git repo so don't have to

# move the file

knit(input= basename(current_file),

output = rmd_file_df$md_files,

envir = parent.frame())

# create pdfFile path name

pdf_file <- paste0(pdf_dir, gsub(x=rmd_file_df$code_file, pattern=".R$",".pdf"))

# Universal Knitr Config - set the base url for images and links in the pdf

base_url=""

opts_knit$set(base.url = base_url)

# I ned to replace all instances of {{ site.url }}/images with the path to the image

# turning off pdf - as not sure how to deal with inline images with {{ site.url }} in the path

## clean out the file so we can knit to pdf

rmd_text <- readLines(basename(current_file))

new_rmd_text <- gsub("\\{\\{ site.url \\}\\}/images", paste0(git_repo_base_path,"/images"), rmd_text)

y <- gsub("{% include toc title=\"In This Lesson\" icon=\"file-text\" %}", "", new_rmd_text, fixed="TRUE")

cat(y, file=basename(current_file), sep="\n")

# knit to pdf

#render(basename(current_file),

# output_file = pdf_file,

# output_format = "pdf_document")

if (length(list.files(rmd_file_df$fig_dir)) > 0) {

# create fig dir path

fig_dir_path <- file.path(git_repo_base_path, rmd_file_df$fig_dir)

# make sure image dir exists in git repo

check_create_dirs(fig_dir_path, clean = T)

# copy image directory over to git site if there are images in it

file.copy(rmd_file_df$fig_dir, (sub("[^/]+$", "", fig_dir_path)), recursive=TRUE)

}

# check for code dir in git repo - don't clean out repo

# code path

code_dir <- file.path(git_repo_base_path, "code", (sub("[^/]+$", "", rmd_file_df$base_path)))

check_create_dirs(code_dir, clean=F)

# purl the code to .R format, save in "code" directory

r_file_path <- file.path(code_dir, rmd_file_df$code_file)

purl(basename(current_file), output = r_file_path)

#### Time to clean house

# remove rfigs dir from working directory

unlink(x="images/rfigs/", recursive = T)

# remove rmd file from working directory

unlink(basename(current_file))

}

########################### end script

# create initial list of files

all_rmd_files <- as.data.frame(list.files(file.path(git_repo_base_path, repo_post_path),

pattern="\\.Rmd$",

recursive = T, full.names = T))

names(all_rmd_files) <- "rmd_files"

all_rmd_files_bld <- populate_all_rmd_df(all_rmd_files, all=F)

# just one file

# create_markdown(all_rmd_files_bld[1, ], wd)

## run the function

if ((nrow(all_rmd_files_bld)) > 0){

pb <- txtProgressBar(min = 0, max = nrow(all_rmd_files_bld), style = 3)

for (i in seq(from=1, to=nrow(all_rmd_files_bld))) {

create_markdown(rmd_file_df = all_rmd_files_bld[i, ], wd)

setTxtProgressBar(pb, i)

print(i)

}

}