Update migration notebook to only dump/restore relevant collections

[eecavanna]

On this branch, I made a performance optimization to the migration notebook used to migrate the Mongo database from nmdc-schema version v11.3.0 to v11.4.0.

Details

I made it so the notebook only dumps and restores the workflow_execution_set collection, since that is the only collection touched by the migrator that the notebook imports from nmdc-schema.

Related issue(s)

Fixes #917

Related subsystem(s)

• Runtime API (except the Minter)
• Minter
• Dagster
• Project documentation (in the docs directory)
• Translators (metadata ingest pipelines)
• MongoDB migrations
• Other

Testing

• I tested these changes (explain below)
• I did not test these changes

I used this optimization when migrating the development Mongo server last week.

Documentation

• I have not checked for relevant documentation yet (e.g. in the docs directory)
• I have updated all relevant documentation so it will remain accurate
• Other (explain below)

Maintainability

• Every Python function I defined includes a docstring (test functions are exempt from this)
• Every Python function parameter I introduced includes a type hint (e.g. study_id: str)
• All "to do" or "fix me" Python comments I added begin with either # TODO or # FIXME
• I used black to format all the Python files I created/modified
• The PR title is in the imperative mood (e.g. "Do X") and not the declarative mood (e.g. "Does X" or "Did X")

[eecavanna]

Merging in before tomorrow's release, during which we'll be running this notebook.