fix: implement SQLite partial unique indexes to prevent session_id co…

[Tharickv75]

Type of Change

What type of change does this PR introduce? Mark all that apply:

• 🐛 Bug Fix
• 🚀 Feature Request
• 🔄 Refactor
• 📖 Documentation Update
• 🔧 Other (Please specify):

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Summary

What does this PR address?

This PR implements SQLite support for partial unique indexes and auto-repairing existing non-partial unique indexes on session_id. It prevents INSERT OR REPLACE operations from accidentally deleting Interaction rows when they share a context.session_id with a Conversation node.

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Description

Bug Fixes:

• Description: Saving/updating nodes in SQLite caused Interaction rows to be deleted when sharing context.session_id with Conversation nodes (resulting in empty orchestrator history on SQLite).
• Root Cause: SQLiteDB.create_index ignored Mongo-style partialFilterExpression / partial_filter_expression kwargs, creating global unique indexes across shared node collections instead of scoped/partial ones.
• Resolution:
  1. Implemented translation of Mongo-style partial filter expressions (equality, $eq, $gt, $exists) into SQLite WHERE clauses.
  2. Added a connect-time self-healing repair step (_repair_non_partial_unique_indexes) that automatically drops legacy non-partial unique indexes on session_id missing a WHERE clause so they can be recreated properly on subsequent ensure_indexes calls.
  3. Ensured untranslatable partial filter expressions raise a ValueError rather than silently falling back to a global unique index.

Refactor Request:

• Area Refactored: jvspatial/db/sqlite.py and jvspatial/db/_sqlite_translate.py.
• Improvements: Changed logger level for partial-index repair from WARNING to INFO to reduce one-shot migration noise. Addressed ruff (SIM110) and mypy type-narrowing warnings. Updated .pre-commit-config.yaml hooks (pre-commit-hooks to v6.0.0).

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Changes Made

High-Level Summary:

1. Partial Index Translation: Added translate_partial_filter_expression in _sqlite_translate.py to translate supported filter shapes into SQLite WHERE clauses.
2. Connect-time Repair: Added _repair_non_partial_unique_indexes on SQLite database initialization to automatically clean up legacy global unique indexes on context.session_id.
3. Index Re-creation & Enforcement: Updated create_index to drop and rebuild existing indexes lacking a required WHERE clause and raise errors on untranslatable expressions.
4. Changelog & Maintenance: Updated CHANGELOG.md with fix details and updated .pre-commit-config.yaml.

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Checklist

Mark all that apply:

• Code follows the project’s coding guidelines.
• Tests have been added or updated for new functionality.
• Documentation has been updated (if applicable).
• Existing tests pass locally with these changes.
• Any dependencies introduced are justified and documented.

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Steps to Test

Provide a clear set of steps for testing the changes introduced in this PR:

1. Run the new and updated SQLite partial index unit tests:

   pytest tests/db/test_sqlite_partial_index.py

[github-actions]

Benchmark comparison

Threshold: ±25% (informational, does not block merge)

benchmark	baseline (s)	current (s)	delta	status
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_deferred_save_batched_100	0.037906	0.051476	+35.8%	REGRESSION (+35.8%)
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_immediate_save_100	0.036936	0.052643	+42.5%	REGRESSION (+42.5%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_batched_saves_500	0.391694	0.470958	+20.2%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_empty_query	0.831736	1.024797	+23.2%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_filtered	0.987921	1.152109	+16.6%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_find_filtered	0.757607	0.884308	+16.7%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_save_throughput	0.001448	0.001631	+12.7%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_empty	0.257901	0.352040	+36.5%	REGRESSION (+36.5%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_fallback_via_regex	0.303311	0.404884	+33.5%	REGRESSION (+33.5%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_pushdown	0.264607	0.372038	+40.6%	REGRESSION (+40.6%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_fallback_via_regex	0.275229	0.389850	+41.6%	REGRESSION (+41.6%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_pushdown	0.228907	0.346233	+51.3%	REGRESSION (+51.3%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_sort_limit_pushdown	0.289700	0.414773	+43.2%	REGRESSION (+43.2%)

[github-actions]

Benchmark comparison

Threshold: ±25% (informational, does not block merge)

benchmark	baseline (s)	current (s)	delta	status
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_deferred_save_batched_100	0.038482	0.037605	-2.3%	OK
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_immediate_save_100	0.036431	0.038430	+5.5%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_batched_saves_500	0.733649	0.411107	-44.0%	IMPROVED (-44.0%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_empty_query	1.679002	0.854325	-49.1%	IMPROVED (-49.1%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_filtered	1.366763	0.991088	-27.5%	IMPROVED (-27.5%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_find_filtered	0.924655	0.753134	-18.5%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_save_throughput	0.002665	0.001424	-46.6%	IMPROVED (-46.6%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_empty	0.233810	0.238306	+1.9%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_fallback_via_regex	0.276695	0.302858	+9.5%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_pushdown	0.253736	0.266389	+5.0%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_fallback_via_regex	0.275249	0.285807	+3.8%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_pushdown	0.240668	0.228285	-5.1%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_sort_limit_pushdown	0.274896	0.267216	-2.8%	OK

[github-actions]

Benchmark comparison

Threshold: ±25% (informational, does not block merge)

benchmark	baseline (s)	current (s)	delta	status
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_deferred_save_batched_100	0.038482	0.037288	-3.1%	OK
tests/benchmarks/test_deferred_save_benchmarks.py::test_bench_immediate_save_100	0.036431	0.037752	+3.6%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_batched_saves_500	0.733649	0.383856	-47.7%	IMPROVED (-47.7%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_empty_query	1.679002	0.840647	-49.9%	IMPROVED (-49.9%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_count_filtered	1.366763	1.022743	-25.2%	IMPROVED (-25.2%)
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_find_filtered	0.924655	0.753649	-18.5%	OK
tests/benchmarks/test_jsondb_benchmarks.py::test_bench_jsondb_save_throughput	0.002665	0.001447	-45.7%	IMPROVED (-45.7%)
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_empty	0.233810	0.228872	-2.1%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_fallback_via_regex	0.276695	0.286191	+3.4%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_count_pushdown	0.253736	0.260239	+2.6%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_fallback_via_regex	0.275249	0.281979	+2.4%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_find_pushdown	0.240668	0.225849	-6.2%	OK
tests/benchmarks/test_sqlite_benchmarks.py::test_bench_sqlite_sort_limit_pushdown	0.274896	0.283927	+3.3%	OK