Implement bypass_cache flag for Tier1 and other fixes

[shuchenliu]

This PR solves tier1 part of #45 and added other fixes

1. Fixed flaky test in metadata_retrieval
   Resolved an issue where stale data in the Redis instance could cause test failures when new indices were deployed.

2. Enabled bypass_cache for get_subclass_mapping
   Added support for the bypass_cache flag in the driver.get_subclass_mapping method to address similar cache-related issues.

3. Implemented query-level bypass_cache support
   Added support for the TRAPI-level bypass_cache flag, allowing clients to purge Elasticsearch’s query, request, and fielddata caches when bypass_cache: true is specified in the original TRAPI query, by updatingdriver.run_query method to accept an additional bypass_cache keyword parameter.

[sentry]

Codecov Report

❌ Patch coverage is 52.00000% with 12 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
.../retriever/data_tiers/tier_1/elasticsearch/meta.py	0.00%	7 Missing ⚠️
...etriever/data_tiers/tier_1/elasticsearch/driver.py	50.00%	2 Missing and 1 partial ⚠️
..._tiers/tier_1/elasticsearch/aggregating_querier.py	83.33%	1 Missing and 1 partial ⚠️

Files with missing lines	Coverage Δ
..._tiers/tier_1/elasticsearch/aggregating_querier.py	32.83% <83.33%> (+9.62%)	⬆️
...etriever/data_tiers/tier_1/elasticsearch/driver.py	50.00% <50.00%> (+4.83%)	⬆️
.../retriever/data_tiers/tier_1/elasticsearch/meta.py	22.64% <0.00%> (-0.29%)	⬇️

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

Adds cache-bypass capabilities to Tier 1 Elasticsearch metadata/subclass-mapping retrieval and query execution, primarily to mitigate stale-cache issues and related test flakiness (Issue #45).

Changes:

• Add bypass_cache support to Tier 1 ES query execution by clearing ES index caches before running queries when requested.
• Add bypass_cache support to ubergraph subclass mapping retrieval (skip Redis metadata cache when requested).
• Update Tier 1 ES driver tests to use cache bypass and add a new cache-bypass test.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
src/retriever/data_tiers/tier_1/elasticsearch/driver.py	Adds bypass_cache handling for query execution and passes bypass flag through subclass-mapping retrieval.
src/retriever/data_tiers/tier_1/elasticsearch/meta.py	Adds bypass_cache option to ubergraph info retrieval to skip cached values when requested.
tests/data_tiers/tier_1/elasticsearch_tests/test_tier1_driver.py	Updates integration tests to bypass cache for metadata/subclass mapping and adds a cache-bypass query test.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

@shuchenliu I've opened a new pull request, #138, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[tokebe]

@shuchenliu Just checking, this now does a timestamp check instead of purging the cache, and is ready for review?

[shuchenliu]

@shuchenliu Just checking, this now does a timestamp check instead of purging the cache, and is ready for review?

Yes, we no longer purge the cache. A timestamp check payload is no added to every query