Add pool_pre_ping option to SQLAlchemy engine configuration

[MichalTorma]

Updated SQLAlchemy engine initialization across multiple files to include the pool_pre_ping option, enhancing connection reliability by preemptively checking for closed connections. This change was made in models.py, sp7_build_models.py, and tests.py, and the SA_POOL_PRE_PING setting was added to the configuration in init.py.

Fixes #

Checklist

• Self-review the PR after opening it to make sure the changes look good and
  self-explanatory (or properly documented)
• Add relevant issue to release milestone
• Add pr to documentation list
• Add automated tests
• Add a reverse migration if a migration is present in the PR
• Add migration function to

  specify7/specifyweb/specify/management/commands/run_key_migration_functions.py

  Line 50 in ea04665

  def fix_schema_config(stdout: WriteToStdOut | None = None):

Testing instructions

Summary by CodeRabbit

• Bug Fixes
  • Improved database connection reliability by checking connections before use and replacing stale connections automatically.
  • Reduced failures caused by connections closed after extended inactivity.

[coderabbitai]

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: abeeb756-5ab8-443b-bf52-7497f978cf21

📥 Commits

Reviewing files that changed from the base of the PR and between 2c3012d and e48c956.

📒 Files selected for processing (4)

• specifyweb/backend/stored_queries/models.py
• specifyweb/backend/stored_queries/sp7_build_models.py
• specifyweb/backend/stored_queries/tests/tests.py
• specifyweb/settings/__init__.py

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📝 Walkthrough

Walkthrough

The change adds SA_POOL_PRE_PING = True and passes it to runtime, generated, and test SQLAlchemy engine constructors.

Changes

SQLAlchemy pool pre-ping

Layer / File(s)	Summary
Pool pre-ping setting specifyweb/settings/__init__.py	Adds SA_POOL_PRE_PING = True and updates the pool configuration comment.
Engine constructor integration specifyweb/backend/stored_queries/models.py, specifyweb/backend/stored_queries/sp7_build_models.py, specifyweb/backend/stored_queries/tests/tests.py	Passes settings.SA_POOL_PRE_PING to runtime, generated, and test SQLAlchemy create_engine calls.

Priority: ⬇️ Low

Change: Feature

Merge Risk: ⚪ Minimal · up to e48c9

This change enables stale-connection checks across runtime, generated, and test engines without an identified merge-blocking risk.

🚥 Pre-merge checks | ✅ 4 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Automatic Tests	⚠️ Warning	The PR adds a new connection-pool behavior, but it adds no automatic test that verifies the behavior. The only test-file change updates the shared setup_sqlalchemy helper to pass pool_pre_ping; it…	Add automatic tests for the new configuration. Assert that the runtime SQLAlchemy engines use settings.SA_POOL_PRE_PING, and add generator coverage that the code produced by gen_sqlalchemy_table_classes_code includes the pool_pre_ping…
Testing Instructions	⚠️ Warning	The PR has no testing instructions. Its ### Testing instructions section contains only the template comments. The diff changes SQLAlchemy engine creation in models.py, generated engine code in `sp…	Add clear testing instructions to the PR description. State the backend test command, including the stored-query tests that exercise setup_sqlalchemy, and state the expected result. Add a check that SA_POOL_PRE_PING is enabled and that …

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: adding the pool_pre_ping option to SQLAlchemy engine configuration.
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.

Full details: Automatic Tests

Explanation

The PR adds a new connection-pool behavior, but it adds no automatic test that verifies the behavior. The only test-file change updates the shared setup_sqlalchemy helper to pass pool_pre_ping; it does not assert the engine configuration. Existing SQLAlchemySetup tests exercise queries, but they do not verify pre-ping, and no test covers the generated engine code in sp7_build_models.py. The contributor checklist also leaves “Add automated tests” unchecked.

Resolution

Add automatic tests for the new configuration. Assert that the runtime SQLAlchemy engines use settings.SA_POOL_PRE_PING, and add generator coverage that the code produced by gen_sqlalchemy_table_classes_code includes the pool_pre_ping setting. Keep the existing query integration tests unchanged as broader regression coverage.

Full details: Testing Instructions

Explanation

The PR has no testing instructions. Its ### Testing instructions section contains only the template comments. The diff changes SQLAlchemy engine creation in models.py, generated engine code in sp7_build_models.py, test-engine setup in tests.py, and adds the SA_POOL_PRE_PING setting. The repository workflow shows a backend test command, but the PR does not state any command, expected result, stale-connection/pre-ping check, or verification for the generated engine code and setting.

Resolution

Add clear testing instructions to the PR description. State the backend test command, including the stored-query tests that exercise setup_sqlalchemy, and state the expected result. Add a check that SA_POOL_PRE_PING is enabled and that the runtime engine uses it. Regenerate or inspect the generated SQLAlchemy model code and confirm that it includes pool_pre_ping=settings.SA_POOL_PRE_PING. If possible, verify that a stale pooled MySQL connection is detected and replaced before a query executes.

• Fix all pre-merge checks with AI

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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