feat: cleanup job definitions

[jakevc]

This PR cleans up job definitions on success and failure

resolves #17

Summary by CodeRabbit

• Refactor
  • Improved the process for cleaning up job resources during job completion or cancellation.
  • Centralized the cleanup steps to ensure consistent deallocation of resources, enhancing overall job management reliability.
  • Enhanced clarity in job status handling with refined control flow.

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes introduce a new method, cleanup_job_resources, in the Executor class of the AWS Batch executor. This method centralizes the logic for terminating and deregistering job resources. It is called in the check_active_jobs method when the job status code is not None and in the cancel_jobs method, replacing direct calls to _terminate_job and _deregister_job. The control flow has been adjusted to yield jobs only when the status code is None, clarifying job status handling.

Changes

File	Changes Summary
snakemake_executor_plugin_aws_batch/__init__.py	Added cleanup_job_resources to centralize job resource cleanup. Updated check_active_jobs to call cleanup when the job status code is set, and modified cancel_jobs to invoke cleanup_job_resources instead of directly calling _terminate_job and _deregister_job.

Sequence Diagram(s)

sequenceDiagram
    participant E as Executor
    participant CAJ as check_active_jobs
    participant CJ as cancel_jobs
    participant CR as cleanup_job_resources
    participant T as _terminate_job
    participant D as _deregister_job

    Note over E, CR: Centralized cleanup flow
    
    E->>CAJ: call check_active_jobs()
    alt Job status code available
        CAJ->>CR: cleanup_job_resources(job)
        CR->>T: _terminate_job(job)
        CR->>D: _deregister_job(job)
    end

    E->>CJ: call cancel_jobs()
    CJ->>CR: cleanup_job_resources(job)
    CR->>T: _terminate_job(job)
    CR->>D: _deregister_job(job)

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 48c7553 and 3b33907.

📒 Files selected for processing (1)

• snakemake_executor_plugin_aws_batch/__init__.py (4 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• snakemake_executor_plugin_aws_batch/init.py

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