fix : Workflows are not terminated if errors are detected

[asterisk-ragavan]

• Added error raising on line 108 to halt workflow execution when an error occurs.

• Implemented level 2 logging for the initial error.

• Captured and logged the first line of the error at level 0 for user visibility.

• Ensures workflow termination and proper error reporting.

• This will resolve issue Workflows are not terminated if errors are detected #154

Summary by CodeRabbit

• Bug Fixes
  • Improved error handling by ensuring that failures during command execution are now explicitly reported, preventing silent failures.
  • Refined error logging to show concise, first-line error messages for clearer and more effective troubleshooting.

[coderabbitai]

Walkthrough

This pull request updates error handling in two workflow components. In the CommandExecutor, the run_command method now raises a RuntimeError when a shell command fails (detecting stderr output or a non-zero return code) instead of just logging the error. In the WorkflowManager, the error logging within the workflow process has been modified to output only the first line of an exception message, resulting in more concise error reporting.

Changes

File	Change Summary
src/.../CommandExecutor.py	Updated run_command to raise a RuntimeError with a detailed error message instead of solely logging errors when a command fails.
src/.../WorkflowManager.py	Modified workflow_process to log only the first line of any exception, streamlining error reporting by trimming redundant information.

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant CommandExecutor
    participant Shell
    Caller->>CommandExecutor: run_command(command)
    CommandExecutor->>Shell: Execute command
    Shell-->>CommandExecutor: (stdout, stderr, returnCode)
    alt Error detected (stderr exists or non-zero return code)
        CommandExecutor->>Caller: raise RuntimeError("Process failed: ...")
    else No error
        CommandExecutor->>Caller: Return command output
    end

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sequenceDiagram
    participant Caller
    participant WorkflowManager
    participant Logger
    Caller->>WorkflowManager: workflow_process()
    WorkflowManager->>WorkflowManager: Process workflow
    alt Exception occurs
        WorkflowManager->>Logger: log(first line of error message)
    else No exception
        WorkflowManager->>Caller: Continue processing
    end

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Poem

I'm a rabbit on a hop so bright,
With errors caught, I leap with delight.
Exceptions now ring like a crisp bell,
Logging trimmed to keep things well.
Code carrots crunch in the digital night—
Hopping through changes, everything's just right!

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📜 Recent review details

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Review profile: CHILL
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📥 Commits

Reviewing files that changed from the base of the PR and between 75fa783 and d1b92be.

📒 Files selected for processing (2)

• src/workflow/CommandExecutor.py (1 hunks)
• src/workflow/WorkflowManager.py (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (3)

• GitHub Check: build-openms
• GitHub Check: build-simple-app
• GitHub Check: build-full-app

🔇 Additional comments (2)

src/workflow/WorkflowManager.py (1)

53-53: Improvement to error message readability

This change enhances user experience by displaying only the first line of error messages, which often contains the most relevant information. Long stack traces can be overwhelming to users, so showing just the essential error information is a good practice.

For debugging purposes, consider adding a more detailed log at level 2 (similar to what CommandExecutor does), so developers can access the full error information when needed.

src/workflow/CommandExecutor.py (1)

108-108:

✅ Verification successful

Good fix for proper error propagation

This is a critical fix that ensures workflow execution stops when errors are detected in command execution. Previously, errors were only logged but not raised, which could lead to workflows continuing to run with incorrect or incomplete data.

The raised exception will propagate to the workflow_process method in WorkflowManager, where it's caught and logged, effectively terminating the workflow as intended.

---

🏁 Script executed:

#!/bin/bash
# Verify that the error propagation chain works correctly
# Looking for calls to run_command to ensure they're handling the potential exception

# Find direct calls to run_command within the codebase
echo "Checking direct calls to run_command method:"
rg "run_command\(" --type py -A 2 -B 2

Length of output: 1936

---

Verified: Error propagation is correctly implemented

The raised exception in src/workflow/CommandExecutor.py is now effectively halting workflow execution when errors occur. The verification output confirms that calls to run_command—including those from the main workflow and other helper methods—are consistent with the intended error propagation. No further modifications are needed on this front.

• Error propagation via raise RuntimeError(...) is in place.
• All invocations of run_command properly align with the updated error-handling strategy.

✨ Finishing Touches

• 📝 Generate Docstrings

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