Migrations: Implement adapter method that copies values between two fields in all documents in a collection

[eecavanna]

In this branch, I implemented an adapter method named copy_value_from_field_to_field_in_each_document, which migrator authors can use to copy all values in one field of a document into another field of that same document (creating the latter field if it doesn't already exist), for every document in a given collection.

Previously, migrator authors could do this by iterating over documents in Python. This new adapter method delegates the iteration to MongoDB.

Fixes #2259

[github-actions]

PR Preview Action v1.4.8
🚀 Deployed preview to https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-2262/
on branch gh-pages at 2024-11-12 22:26 UTC

[kheal]

@eecavanna Did you want to add implementing this method in to https://github.com/microbiomedata/nmdc-schema/blob/main/nmdc_schema/migrators/partials/migrator_from_11_0_3_to_11_1_0/migrator_from_11_0_3_to_11_1_0_part_2.py ? If so, I think doing that in this PR makes sense.

Disregard - I see that this only makes a new field and that you'll need your second adaptor method to delete the contents of the original before implementing.

[kheal]

This all looks good from my perspective, though I am not able to give the most thorough of review since these methods are a bit new to me. All the documentation and doctests make sense to me and match the descriptions.

[eecavanna]

Thanks for reviewing this! That level of review is helpful for me (e.g. in case I made a mistake somewhere while implementing this in haste). Rather than merge this in, I'd prefer to merge the third PR I opened this afternoon, since it includes these changes. That PR is: #2265

[eecavanna]

On second thought, I implemented that third PR in a way where this can be merged in independently. I'll go ahead and merge this in.