Fix job deletion error handling with specific JobDeletedException

[Copilot]

Problem

The system was using generic ValueError to signal job deletion in the user-facing API, which is too generic and might hide other errors. Additionally, RDSJobQueue.handle_timeouts was not handling deletion errors gracefully, causing crashes when jobs were deleted by users.

Solution

This PR introduces a specific JobDeletedException for job deletion scenarios and updates all relevant code to handle it gracefully.

Key Changes

1. New Exception Class: Created JobDeletedException in workerfacing_api/exceptions.py with job ID tracking and descriptive error messages.

2. Updated Error Handling:

   • job_tracking.update_job now raises JobDeletedException instead of ValueError on 404 responses
   • RDSJobQueue._update_job_status catches and re-raises the specific exception
   • RDSJobQueue.handle_timeouts gracefully handles deletion errors by skipping status updates
   • RDSJobQueue.pop gracefully handles deletion errors by returning False
   • API endpoints catch the specific exception maintaining 404 behavior

3. Improved Robustness: The timeout handling mechanism now continues processing other jobs even when some jobs are deleted, preventing system crashes.

Example

Before:

# Generic ValueError could hide other issues
except ValueError as e:
    # Could be job deletion OR other validation error
    pass

After:

# Specific exception for job deletion
except JobDeletedException:
    # Definitely a job deletion - handle gracefully
    pass

Testing

• Added comprehensive unit tests for the new exception handling
• Verified existing queue functionality remains intact
• Confirmed graceful handling of deletion scenarios in timeout processing

This change improves error specificity and system reliability while maintaining backward compatibility.

Fixes #67.

Warning

Firewall rules blocked me from connecting to one or more addresses

I tried to connect to the following addresses, but was blocked by firewall rules:

• cognito-idp.eu-central-1.amazonaws.com
  • Triggering command: /home/REDACTED/work/DECODE_Cloud_WorkerAPI/DECODE_Cloud_WorkerAPI/.venv/bin/python -m pytest tests/integration/endpoints/test_jobs.py::TestJobs::test_put_job_status_canceled -v (dns block)

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---

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[Copilot]

Just as a heads up, I was blocked by some firewall rules while working on your feedback. Expand below for details.

Warning

Firewall rules blocked me from connecting to one or more addresses

I tried to connect to the following addresses, but was blocked by firewall rules:

• install.python-poetry.org
  • Triggering command: curl -sSL REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to my firewall allow list

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
workerfacing_api
__init__.py	0	0	100%
dependencies.py	48	16	67%	32, 48–53, 72–90
exceptions.py	4	0	100%
main.py	28	11	61%	36–45, 50
settings.py	28	5	82%	8–11, 30
tags.py	1	0	100%
workerfacing_api/core
__init__.py	0	0	100%
filesystem.py	73	5	93%	17, 23, 27, 33, 108
queue.py	292	28	90%	77, 82, 87, 101, 106, 141, 173, 247–248, 275–276, 282, 299–300, 358–362, 367, 401, 461–463, 482, 556–558, 568–570
workerfacing_api/crud
__init__.py	0	0	100%
job_tracking.py	11	1	91%	26
workerfacing_api/endpoints
__init__.py	0	0	100%
access.py	9	1	89%	24
files.py	23	1	96%	24
jobs.py	67	12	82%	73–74, 95–96, 149–150, 154–155, 175–176, 180–181
jobs_post.py	9	0	100%
workerfacing_api/schemas
__init__.py	0	0	100%
files.py	6	0	100%
queue_jobs.py	52	0	100%
rds_models.py	32	0	100%
TOTAL	683	80	88%

Tests	Skipped	Failures	Errors	Time
123	0 💤	0 ❌	0 🔥	16m 21s ⏱️

[Copilot]

Just as a heads up, I was blocked by some firewall rules while working on your feedback. Expand below for details.

Warning

Firewall rules blocked me from connecting to one or more addresses

I tried to connect to the following addresses, but was blocked by firewall rules:

• install.python-poetry.org
  • Triggering command: curl -sSL REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to my firewall allow list

[nolan1999]

poetry run ruff format --check . is failing. Please correct the formatting (you can run poetry run ruff format --fix . .