How to use tinkr to retrieve markdown images insertions in order to convert them into .Rmd code chunks containing a call to knitr::include_graphics() ?

[pokyah]

Hello,

My goal is to convert a markdown document to a Rmarkdown (.Rmd) document where the pictures are inserted using knitr::include_graphics() into a code chunk so that I can knit it back to markdown format where the figures will be numerated. I have easily converted the extension to .Rmd and added the proper yaml header containing the rendering options. Now I'm stuck with the images numeration.

I was thinking of using regex to find and replace all the images insertions but someone suggested me to use tinkr package.

I guess that by parsing the document, I can retrieve all the expressions corresponding to an image insertion and then replace these by a character containing the code chunk.

Here is a reprex :

=====
dummy.md markdown document content :

# This is a dummy markdown document to be parsed

This document contains text and images.

The following picture is the first of the document

![logoR][logoR.jpg]

And here is the second picture of the document : 

![logoTidyverse][logoTidyverse.png]

====

How can I parse this document in order to find all the images insertions :

![logoR][logoR.jpg]
![logoTidyverse][logoTidyverse.png]

and replace these by .Rmd code chunks as follow :

```{r logoR, echo=FALSE, fig.cap="logoR", out.width = '100%'}
knitr::include_graphics("logoR.jpg)
```

```{r logoR, echo=FALSE, fig.cap="logoTidyverse", out.width = '100%'}
knitr::include_graphics("logoTidyverse.png")
```

?

Maybe that tinkr is not the best solution to achieve this. Sorry if this is the case.

Thanks for your support

[maelle]

What I have for now.
Problems

• Not easy to choose where to add the new md.
• The original image doesn't disappear.
  I'll try a bit more.

library("tinkr")
library("xml2")
path <- tempfile()
brio::write_lines(
  c("![logoR](logoR.jpg)", "![logoTidyverse](logoTidyverse.png)"),
  path
)
ex1 <- tinkr::yarn$new(path)
# find all images
images <- xml_find_all(
  x = ex1$body, 
  xpath = ".//md:image", 
  ns = ex1$ns
)

handle_image <- function(image, ex1) {
  destination <- xml2::xml_attr(image, "destination")
  text <- xml2::xml_text(image)
  new_text <- glue::glue(
    '```{r @text$, echo=FALSE, fig.cap="@text$", out.width = "100%"}
 knitr::include_graphics("@destination$")
```\n',
    .open = "@",
    .close = "$"
  )
  # Add new Markdown text
  ex1$add_md(new_text, where = 1L)
  # Remove original image node
  xml2::xml_remove(image)
}
purrr::walk(images, handle_image, ex1 = ex1)
ex1$write(path)
brio::read_lines(path)
#>  [1] "![logoR](logoR.jpg)"                                                              
#>  [2] "![logoTidyverse](logoTidyverse.png)"                                              
#>  [3] ""                                                                                 
#>  [4] "```{r logoTidyverse, echo=FALSE, fig.cap=\"logoTidyverse\", out.width = \"100%\"}"
#>  [5] " knitr::include_graphics(\"logoTidyverse.png\")"                                  
#>  [6] "```"                                                                              
#>  [7] ""                                                                                 
#>  [8] "```{r logoR, echo=FALSE, fig.cap=\"logoR\", out.width = \"100%\"}"                
#>  [9] " knitr::include_graphics(\"logoR.jpg\")"                                          
#> [10] "```"                                                                              
#> [11] ""                                                                                 
#> [12] ""

^{Created on 2021-04-22 by the reprex package (v1.0.0.9001)}

[maelle]

Ah now the image suppression works

library("tinkr")
library("xml2")
path <- tempfile()
brio::write_lines(
  c("![logoR](logoR.jpg)", "![logoTidyverse](logoTidyverse.png)"),
  path
)
ex1 <- tinkr::yarn$new(path)
# find all images
images <- xml_find_all(
  x = ex1$body, 
  xpath = ".//md:image", 
  ns = ex1$ns
)

images_copy <- images
xml2::xml_remove(images)

handle_image <- function(image, ex1) {
  destination <- xml2::xml_attr(image, "destination")
  text <- xml2::xml_text(image)
  new_text <- glue::glue(
    '```{r @text$, echo=FALSE, fig.cap="@text$", out.width = "100%"}
 knitr::include_graphics("@destination$")
```\n',
    .open = "@",
    .close = "$"
  )
  
  # Add new Markdown text
  ex1$add_md(new_text, where = 1L)
}
purrr::walk(images, handle_image, ex1 = ex1)
ex1$write(path)
brio::read_lines(path)
#>  [1] ""                                                                                 
#>  [2] ""                                                                                 
#>  [3] ""                                                                                 
#>  [4] "```{r logoTidyverse, echo=FALSE, fig.cap=\"logoTidyverse\", out.width = \"100%\"}"
#>  [5] " knitr::include_graphics(\"logoTidyverse.png\")"                                  
#>  [6] "```"                                                                              
#>  [7] ""                                                                                 
#>  [8] "```{r logoR, echo=FALSE, fig.cap=\"logoR\", out.width = \"100%\"}"                
#>  [9] " knitr::include_graphics(\"logoR.jpg\")"                                          
#> [10] "```"                                                                              
#> [11] ""                                                                                 
#> [12] ""

^{Created on 2021-04-22 by the reprex package (v1.0.0.9001)}

[maelle]

Now for adding the chunks in the right position I need to find the original position of images. 🤔

[maelle]

I wonder whether tinkr is lacking a feature @zkamvar: maybe something like replace_md where you'd give new text like for add_md, but also a node to replace. 🤔

[pokyah]

Now for adding the chunks in the right position I need to find the original position of images. 🤔

No way to retrieve the position via the "character number" corresponding to the retrived xpath node ?

[maelle]

"character number" corresponding to the retrived xpath node

what do you mean?

[maelle]

This below seems to work but it uses the unexported tinkr:::clean_content() function

library("tinkr")
library("xml2")
path <- tempfile()
brio::write_lines(
  c("![logoR](logoR.jpg)", "something else", "![logoTidyverse](logoTidyverse.png)"),
  path
)
ex1 <- tinkr::yarn$new(path)
# find all images
images <- xml_find_all(
  x = ex1$body, 
  xpath = ".//md:image", 
  ns = ex1$ns
)

handle_image <- function(image, ex1) {
  destination <- xml2::xml_attr(image, "destination")
  text <- xml2::xml_text(image)
  new_text <- glue::glue(
    '\n```{r @text$, echo=FALSE, fig.cap="@text$", out.width = "100%"}
 knitr::include_graphics("@destination$")
```\n',
    .open = "@",
    .close = "$"
  )
  new <- tinkr:::clean_content(new_text)
  new <- commonmark::markdown_xml(new, extensions = TRUE)
  new <- xml2::xml_ns_strip(xml2::read_xml(new))
  xml2::xml_replace(image, new)
}
purrr::walk(images, handle_image, ex1 = ex1)
ex1$write(path)
brio::read_lines(path)
#>  [1] "```{r logoR, echo=FALSE, fig.cap=\"logoR\", out.width = \"100%\"}"                
#>  [2] " knitr::include_graphics(\"logoR.jpg\")"                                          
#>  [3] "```"                                                                              
#>  [4] ""                                                                                 
#>  [5] "something else"                                                                   
#>  [6] "```{r logoTidyverse, echo=FALSE, fig.cap=\"logoTidyverse\", out.width = \"100%\"}"
#>  [7] " knitr::include_graphics(\"logoTidyverse.png\")"                                  
#>  [8] "```"                                                                              
#>  [9] ""                                                                                 
#> [10] ""                                                                                 
#> [11] ""

^{Created on 2021-04-22 by the reprex package (v1.0.0.9001)}

[pokyah]

"character number" corresponding to the retrived xpath node

what do you mean?

By the poition I mean this :

position_exclamation= stringr::str_locate_all(string = "a special character ! in a string", pattern = "!")
> position_exclamation
[[1]]
     start end
[1,]    21  21

[maelle]

ah no the position for xml2 is something different I think :-)

[zkamvar]

Now for adding the chunks in the right position I need to find the original position of images. thinking

No way to retrieve the position via the "character number" corresponding to the retrived xpath node ?

This is what the sourcepos argument is for: https://docs.ropensci.org/tinkr/reference/to_xml.html

I use this to get the line positions of elements in {pegboard}:

# Get the position of an element
get_pos <- function(x, e = 1) {
  as.integer(
    gsub(
      "^(\\d+?):(\\d+?)[-](\\d+?):(\\d)+?$",
      glue::glue("\\{e}"),
      xml2::xml_attr(x, "sourcepos")
    )
  )
}

# helpers for get_pos
get_linestart <- function(x) get_pos(x, e = 1)
get_colstart  <- function(x) get_pos(x, e = 2)
get_lineend   <- function(x) get_pos(x, e = 3)
get_colend    <- function(x) get_pos(x, e = 4)

[maelle]

ooooh that's how it works, thank you @zkamvar!

Now I wonder whether we still need to use replacement instead of adding. 🤔

[zkamvar]

Now I wonder whether we still need to use replacement instead of adding. thinking

I think replacement might still be a worthwhile option.

[maelle]

@pokyah do you have remaining problems?

[pokyah]

Hi @maelle and @zkamvar .

I'm back to this problem.

How could we develop the replace method for the md images as suggested in #41?

Thanks for the support and the investigations :)

[maelle]

👋 @pokyah, could you please comment in that issue as it's still open, with some more context on what you're trying to achieve? Thank you!