code annotations do not work for ojs cells

[homerhanumat]

Bug description

Annotations work for R code cells, but not for ojs code cells.

Steps to reproduce

Render this example .qmd file:

---
code-annotations: hover
---

```{r}
2 + 2   # <1>
cat("hello")  # <2>
```

1. adding
2. greeting

```{ojs}
Inputs.table(olympians)  // <1>
```

1. displaying

Expected behavior

Annotation for ojs cell should show on hover.

Actual behavior

No annotation appears on hover, and the annotation is shown as an ordered list below the cell in the rendered output.

Your environment

• OS: MacOS Ventura 13.5.2
• VS Code 1.84.0

Quarto check output

Quarto 1.4.489
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.8: OK
      Dart Sass version 1.55.0: OK
      Deno version 1.33.4: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.489
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /Library/TeX/texbin
      Version: 2021

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.8
      Path: /usr/local/opt/python@3.10/bin/python3.10
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.3.1
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
      knitr: 1.44
      rmarkdown: 2.25

[✓] Checking Knitr engine render......OK

[cscheid]

@dragonstyle I looked at a filter trace and at the end of the filter chain, to my eye the OJS annotations match the R annotations. I've tagged you here in case you can easily figure out what's happening in the TS side, but I'm happy to pair with you over this as well.

[cderv]

@cscheid I believe this is because of the line counter.

See in the HTML produced, we have for OJS code source cell <span id="annotated-cell-1-5"> but the target annotation does not adapt to that counter

<dl>
<dt data-target-cell="annotated-cell-1" data-target-annotation="1">1</dt>
<dd>
<span data-code-cell="annotated-cell-1" data-code-lines="1" data-code-annotation="1">displaying</span>
</dd>
</dl>

So it will look for <span id="annotated-cell-1-1"> which does not exist.

Not sure exactly why the different counter (as if there was 4 more lines), but I believe this is because OJS does set a startFrom attributes for highlighting, which will make Pandoc creates <span id="annotated-cell-1-5"> on the line

This is the intermediate Markdown

```{.js .cell-code startFrom="5" source-offset="0"}
Inputs.table(olympians)  // <1>
```

Like this one
https://github.com/quarto-dev/quarto-cli/blob/main/src/execute/ojs/compile.ts#L585-L589
Or another startFrom in the file.

I think the annotation processing needs to be aware of this line offsetting

[cderv]

As example to reproduce without OJS, you'll get the same if you apply the offset a the code cell

---
code-annotations: true
---

```{r}
#| code-line-numbers: true
#| attr-source: "startFrom=5"
1 + 1 # <1>
2 + 2
3 + 3 # <2>
```

1. displaying
2. displaying

I think I know where this needs to be taken into account

[cderv]

I have made a PR to fix this specific case.

I believe code annotation and OJS is more complex, because it seems OJS will output results under each line, with no possible grouping.

---
code-annotations: true
---

```{ojs}
1 + 1 // <1>
2 + 2
3 + 3 // <2>
```

1. test
2. test

```{r}
1 + 1 # <1>
2 + 2
3 + 3 # <2>
```

1. test
2. test

but this is another issue because in this case the ordered List is not even processed.