Use omics_processing_output_association for data object queries

[naglepuff]

No description provided.

[Copilot]

Pull Request Overview

This PR migrates the codebase from using a direct foreign key relationship between DataObject and OmicsProcessing to using a many-to-many association table called omics_processing_output_association. This change allows data objects to be associated with multiple omics processing records instead of just one.

Key changes:

• Replace direct foreign key queries with association table joins in query and aggregation functions
• Update the data ingestion pipeline to populate the new association table
• Remove the legacy data generation relation update function

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
nmdc_server/query.py	Updates data object filter queries to use association table joins
nmdc_server/models.py	Adds new many-to-many relationship using association table
nmdc_server/ingest/pipeline.py	Populates association table during data ingestion
nmdc_server/ingest/data_object.py	Removes legacy foreign key update function
nmdc_server/ingest/all.py	Removes call to legacy foreign key update function
nmdc_server/crud.py	Updates to use new relationship property
nmdc_server/aggregations.py	Updates aggregation queries to use association table
tests/test_download.py	Adds test data to populate new relationship

[naglepuff]

I'm over-assigning reviewers to this one in an effort to get eyes on it ASAP. I believe the changes here are straightforward but I'm happy to add details if needed. @aclum this should address the data object aggregation issue on the bulk download widget, as well as some other things that needed to be changed for the bulk download workflow to accommodate the data model changes in #1701.

[eecavanna]

From skimming the diff, I think this PR does the following:

• Updates some SQLAlchemy queries that used to involve the DataObject model, so that they now involve the omics_processing_output_association table
• Updates an attribute access to get the first "omics_processing" from a list, instead of getting the "omics_processing" from a scalar variable
• Removes code that would update references between the "data object" and "data generation" tables during ingest. Adds ingest code that establishes those references in a different way.
• Defines an omics_processings relationship (model)
• Adds something to a test (this change, I don't really understand)

[eecavanna]

I approved in the interest of facilitating a merge once the changes are finalized (e.g. when the tests are passing). I am not familiar with the code that was changed and so my approval represents me saying, "I looked at all the changes and didn't see anything that looks to me like it was done by mistake."