From b7550c0d0bf0cc71a8f467ac8c17f5c32d383a14 Mon Sep 17 00:00:00 2001
From: Andy Bayer Roswell <andyroswellrr@gmail.com>
Date: Tue, 23 Jul 2024 23:56:47 +0200
Subject: [PATCH] adding rmd support

---
 vreapis/containerizer/views.py | 9 ++++++++-
 vreapis/requirements.txt       | 1 +
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/vreapis/containerizer/views.py b/vreapis/containerizer/views.py
index d5bd464..22efce6 100644
--- a/vreapis/containerizer/views.py
+++ b/vreapis/containerizer/views.py
@@ -28,6 +28,7 @@
 import jsonschema
 from slugify import slugify
 from github import Github, UnknownObjectException
+import jupytext
 
 from catalog.serializers import CellSerializer
 from containerizer.RContainerizer import RContainerizer
@@ -88,9 +89,15 @@ def get(self, request: Request):
     def post(self, request: Request):
         payload = request.data
         common.logger.debug('ExtractorHandler. payload: ' + json.dumps(payload, indent=4))
+        if 'rmarkdown' in payload:
+            Rmd = jupytext.reads(payload['rmarkdown'], fmt='Rmd')
+            ipynb = jupytext.writes(Rmd, fmt='ipynb')
+            payload['notebook'] = ipynb
         kernel = payload['kernel']
         cell_index = payload['cell_index']
-        notebook = nbformat.reads(json.dumps(payload['notebook']), nbformat.NO_CONVERT)
+        if isinstance(payload['notebook'], dict):
+            payload['notebook'] = json.dumps(payload['notebook'])
+        notebook = nbformat.reads(payload['notebook'], nbformat.NO_CONVERT)
 
         source = notebook.cells[cell_index].source
 
diff --git a/vreapis/requirements.txt b/vreapis/requirements.txt
index 8979a7a..848d433 100644
--- a/vreapis/requirements.txt
+++ b/vreapis/requirements.txt
@@ -22,3 +22,4 @@ pytype
 autopep8
 distro
 pygithub
+jupytext