Batch-hydrate all nodes and CREs (N+1, supersedes #850)

[northdpole]

Summary

• #850 wanted to kill N+1 in __make_cre_links / __get_all_nodes_and_cres.
• __make_cre_links is already gone: CRE hydration is _hydrate_cres_batch.
• Graph load (with_graph) still called get_cre_by_db_id / get_nodes once per row.
• This PR loads all Node/CRE rows once and hydrates links in bulk (_hydrate_nodes_batch + existing _hydrate_cres_batch).

Original review credit: @shiwani42 (#850). Do not land #850 as-is.

Test plan

• python -m unittest application.tests.db_test.TestDB.test_get_all_nodes_and_cres_does_not_use_per_id_lookups
• …test_get_all_nodes_and_cres_cres_only_skips_nodes
• …test_get_all_nodes_and_cres_hydrates_same_as_per_id
• …test_export

Supersedes #850

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Summary by CodeRabbit

• Performance

  • Improved loading of nodes and CREs by processing records in batches, reducing repeated database lookups.
  • Batch-loaded results preserve existing filtering, link handling, and validation behavior.

• Bug Fixes

  • Ensured CRE-only results still include their associated non-CRE links.

• Tests

  • Added coverage verifying batch results match existing per-record results and avoid unnecessary lookups.

Walkthrough

The database collection now batch-hydrates all nodes and CREs. Node links and referenced CREs use batched queries. Tests verify lookup avoidance, CRE-only results, link hydration, and parity with per-id hydration.

Changes

Batch hydration

Layer / File(s)	Summary
Batch hydration implementation application/database/db.py	__get_all_nodes_and_cres uses batch hydration for nodes and CREs. _hydrate_nodes_batch loads links and referenced CREs with batched queries, preserves filtering, and raises an assertion for missing CRE links.
Batch hydration validation application/tests/db_test.py	Tests verify that per-id helpers are not called, cres_only=True excludes nodes while retaining links, and batch CRE results match per-id results.

Priority: ⬇️ Low

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Refactor

Merge Risk: 🟡 Moderate · up to c9ee5

Fully linked graphs still perform redundant bulk queries after their rows have already been loaded, undermining the intended graph-loading performance improvement. Reuse the loaded rows and links before merging.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 22.22% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 9 functions across 2 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the main change: batch hydration of nodes and CREs to address N+1 lookups. It is concise and specific.
Description check	✅ Passed	The description directly explains the N+1 problem, the batch-loading implementation, the superseded PR, and the related tests.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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• Commit unit tests in branch maintainer/batch-hydrate-all-docs

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Actionable comments posted: 1

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Inline comments:
In `@application/database/db.py`:
- Around line 1507-1508: Update __get_all_nodes_and_cres to load Links and
InternalLinks once and build shared Node, CRE, and link maps, then pass those
maps to _hydrate_nodes_batch and _hydrate_cres_batch so graph hydration reuses
the loaded rows without repeated SELECTs or link scans. Preserve the existing
query behavior in both hydrators when shared maps are not provided.

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