[POST-berkeley-MERGER] Update FunctionalAnnotationAggMember class for compatibility with MetaP Aggregation tables

[kheal]

Description

This PR will

1. Modify the existing FunctionalAnnotationAggMember class to be able to accomodate both annotations from metagenomics and metaproteomics analyses. This is accomplished by exchanging the slot metagenome_anlaysis_id with the existing slot was_generated_by.
2. Implement a migrator to adjust existing records.
3. Deprecate the metagenome_anlaysis_id slot as there are now no classes using this slot.
4. Update tests accordingly
5. Add description to count slot
6. Add a unique_keys to FunctionalAnnotationAggMember class that is a combination of was_generated_byandgene_function_id

This PR will close 1253 and 2155

Reviewers

For review (when out of draft stage):
@mslarae13, @aclum, @SamuelPurvine, @eecavanna
To keep informed:
@naglepuff, @mbthornton-lbl, @corilo, @sujaypatil96, @brynnz22

PR Information

What type of PR is this? (check all applicable)

• Schema change: Structure and content
  • deleted a slot

Related Issues

• Fixes: 1253
• Related Issue(s): #

Did you add/update any tests?

• Yes
  • All example yamls are updated (including invalid examples
  • Doctest for migrator added
  • Added invalid example for FunctionalAnnotationAggMember to check for rule on count slot

Could this schema change make it so any valid data becomes invalid?

• Yes (A migrator is required)

If you answered "Yes", does this PR branch include that migrator?

• Yes

Does this PR have any downstream implications?

• Yes (Explain below)
  We will need to update the aggregation scripts (issue filed here: Update generate_metap_agg.py script to source ids from new slot nmdc-aggregator#13) and the data portal to use the new slot

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://microbiomedata.github.io/berkeley-schema-fy24/pr-preview/pr-242/
on branch gh-pages at 2024-09-11 00:37 UTC

[aclum]

backmerge such that mfmtan is also a valid typecode.

[kheal]

@aclum - you mean "wfmtan", correct? MetatranscriptomeAnnotation class?

[aclum]

can someone remind me the decision on when we'd start using a deprecated.yaml file? @sierra-moxon this pr deprecates quite a bit so it would be nice use.

[mslarae13]

@aclum we decided not to start forcing the use until after berkeley roll out, but there's no reason you can't still put the pieces in the deprecated.yaml.
The only piece we'll be missing is there's supposed to be a release where the item is marked for deprecation. And then after 1 release it's actually moved. So would just skip that preparation step

[kheal]

leaving a note here to make sure @turbomam or @sierra-moxon review this use of unique_keys (in response to microbiomedata#2155)