Overwrites the original file

[drtoche]

This project was very promising. But unfortunately it overwrites the original file. I wasn't in the mood to check if the notebook looked good...

[ricoperdiz]

The same just happened to me.

[mariusbommert]

It seems to be beneficial to add a parameter for the name of the output file similar to the following code:

rmd2jupyter <- function(x, out, force = FALSE) {
  if(!file.exists(out) || force) {
    con <- file(x)
    x <- readLines(con, warn = FALSE)
    close(con)
    ## strip yaml
    if (grepl("^---", x[1])) {
      yaml_end <- grep("^---", x)[2]
      x <- x[(yaml_end + 1L):length(x)]
    }
    chunks <- grep("^```", x)
    if (length(chunks) == 0L) {
      lns <- c(1L, length(x))
      chunks <- matrix(lns, ncol = 2, byrow = TRUE)
      chunks <- data.frame(chunks)
      names(chunks) <- c("start", "end")
      chunks$cell_type <- "markdown"
    } else {
      lns <- sort(c(
        1L, length(x), chunks,
        chunks[seq(1, length(chunks), 2)] - 1L,
        chunks[seq(2, length(chunks), 2)] + 1L
      ))
      lns <- lns[lns > 0 & lns <= length(x)]
      if (chunks[length(chunks)] == length(x)) {
        lns <- lns[-length(lns)]
      }
      if (chunks[1L] == 1L) {
        lns <- lns[-1]
      }
      chunks <- matrix(lns, ncol = 2, byrow = TRUE)
      chunks <- data.frame(chunks)
      names(chunks) <- c("start", "end")
      codes <- grep("^```", x)
      codes <- codes[seq(1, length(codes), 2)]
      chunks$cell_type <- ifelse(chunks$start %in% codes, "code", "markdown")
      x <- gsub("^```.*", "", x)
    }
    for (i in seq_len(nrow(chunks))) {
      s <- paste0(x[(chunks$start[i]):(chunks$end[i])], "\n")
      ## trim top and bottom blank lines
      while (s[1] == "\n" & length(s) > 2L) {
        s <- s[-1]
      }
      while (s[length(s)] == "\n" & length(s) > 2L) {
        s <- s[-length(s)]
      }
      chunks$source[i] <- I(list(s))
    }
    cells <- Map(format_cell, chunks$cell_type, chunks$source)
    x <- jsonlite::prettify(format_cells(cells))
    x <- gsub("count\": \"\"", "count\": null", x)
    x <- gsub("metadata\": \"\"", "metadata\": {}", x)
    x <- gsub("outputs\": \"\"", "outputs\": []", x)
    cat(x, file = out)
    message(paste("file saved as", out))
  } else {
    warning(paste0("File ", out, " already exists. Use force = TRUE to force writing.")) 
  }
}

As out something like "file.ipynb" can be used and there is a warning if the file already exists. Setting force = TRUE overwrites the existing file.