Migrations: Fix invalid example notebook

[eecavanna]

Description

In PR https://github.com/microbiomedata/nmdc-runtime/pull/487, I committed a Jupyter notebook that I didn't know was not formatted in a valid way.

In this PR, I am committing the same notebook in a valid way.

The invalid one was saved using PyCharm and the valid one was saved using VS Code. The PyCharm GUI has been buggy when it comes to Python notebooks, and—based on this issue—I think the under-the-hood piece of PyCharm that deals with Python notebook is buggy, too. I'm going to switch back to using VS Code for notebooks for now.

Fixes #490

Type of change

Please delete options that are not relevant.

• [x] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration, if it is not simply make up-test && make test-run.

• [x] I confirmed GitHub renders the notebook instead of displaying an error page

Configuration Details: none

Checklist:

• [ ] My code follows the style guidelines of this project (have you run black nmdc_runtime/?)
• [x] I have performed a self-review of my code
• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] I have made corresponding changes to the documentation (in docs/ and in https://github.com/microbiomedata/NMDC_documentation/?)
• [ ] I have added tests that prove my fix is effective or that my feature works, incl. considering downstream usage (e.g. https://github.com/microbiomedata/notebook_hackathons) if applicable.
• [ ] New and existing unit and functional tests pass locally with my changes (make up-test && make test-run)

[eecavanna]

I will merge this follow-up PR (also without review and without all the checkboxes in the PR description fill in) that fixes the issue.

Why no review? This impacts only a standalone Python notebook that doesn't affect the Runtime API. The reason the notebook is in the repo is that this repo holds the "keeper of the Mongo database," and the Python notebook is an example of something that would interact directly with the Mongo database. I don't want to request someone's time/attention for this.