Edit_file fails at writing Jupyter Notebook files

Bug Reports
1

The report below was created by the Agent after I asked him to diagnose the issue

Issue Report for Tool Developers

The edit_file tool has a critical issue when editing JSON-formatted files, particularly .ipynb (Jupyter Notebook) files:

  1. When attempting to create or edit .ipynb files directly using the edit_file tool, the JSON content is not properly preserved.

  2. The tool appears to treat the JSON content as plain text and fails to properly write the structured JSON data.

  3. This results in empty files or files with just a space character.

  4. The issue appears to be specific to JSON-formatted files with complex nested structures.

  5. Regular text files are edited correctly.

To reproduce:

  1. Try to create a new .ipynb file with valid JSON content

  2. Check the resulting file - it will be empty or contain just a space

This may require adding special handling for JSON files or .ipynb files specifically in the tool implementation.

The log of the dialog before creating the report:

let’s diagnose why the direct file editing isn’t working properly. Let me try to understand what’s happening when we attempt to edit files directly.

First, let’s try to edit a simple text file directly to isolate the issue:

test_direct_edit.txt(new)+1-1

This is a test file to check direct file editing capabilities.

Let’s verify if this worked:

Read test_direct_edit.txt

L1-1

Good, direct text file editing works. Now let’s try to edit a Jupyter notebook directly:

test_notebook.ipynb No changes made

“print(‘Test notebook’)”]}],

“metadata”: {“kernelspec”: {“display_name”: “Python 3”,{“cells”: [{“cell_type”: “code”, “execution_count”: null, “metadata”: {}, “source”: [

I see the issue now. When trying to edit the .ipynb file directly, the changes aren’t being applied properly. Let me try to diagnose why this is happening by checking the file after the attempted edit:

Read test_notebook.ipynb

L1-20

I see the problem now. The issue appears to be with how the edit_file tool handles JSON-formatted files, particularly .ipynb files. When we try to edit them directly, the JSON structure is not being preserved properly.

Let me try one more test with a different approach to the JSON formatting:

test_notebook2.ipynb
No changes made

{“cells”:[{“cell_type”:“code”,“execution_count”:null,“metadata”:{},“source”:[“print(‘Test notebook’)”]}],“metadata”:{“kernelspec”:{“display_name”:“Python 3”,“language”:“python”,“name”:“python3”}},“nbformat”:4,“nbformat_minor”:4}

I can now identify the root cause of the problem:

  1. The edit_file tool appears to have issues with handling JSON-formatted files, particularly when they contain newlines and complex nested structures like Jupyter notebooks.

  2. The tool seems to be treating the JSON content as plain text and not properly preserving the JSON structure when writing the file.

  3. This is why our previous attempts to edit .ipynb files directly resulted in empty or malformed files.

To fix this issue, we would need to:

  1. Either modify the edit_file tool to properly handle JSON-formatted files

  2. Or add special handling for .ipynb files that ensures the JSON structure is preserved