Fix bugs with Sun Grid Engine #382
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WalkthroughThe pull request introduces a new static method Changes
Sequence DiagramsequenceDiagram
participant User
participant SunGridEngineCommands
User->>SunGridEngineCommands: get_job_id_from_output(queue_submit_output)
SunGridEngineCommands-->>User: Returns job ID as integer
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Actionable comments posted: 1
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pysqa/wrapper/sge.py(1 hunks)
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🔇 Additional comments (1)
pysqa/wrapper/sge.py (1)
85-88: Verify consistency with other scheduler implementations.Let's ensure this implementation aligns with other scheduler wrappers and the base class.
✅ Verification successful
Implementation is consistent with scheduler framework
The
get_job_id_from_outputmethod:
- Follows the abstract base class contract
- Uses the same parsing strategy as Slurm for the -terse output format
- Is properly integrated with the job submission workflow
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for similar job ID parsing methods in other scheduler implementations # and verify the -terse flag behavior in SGE documentation. # Check for similar methods in other scheduler implementations echo "Checking for similar methods in other scheduler implementations..." rg -l "job_id.*output" --type py # Look for the base class implementation echo -e "\nChecking base class (SchedulerCommands) implementation..." rg -l "class SchedulerCommands" --type py # Check if other classes parse job IDs differently echo -e "\nChecking for other job ID parsing patterns..." rg "job.*id.*=|jobid.*=|id.*=.*job" --type py # Look for SGE documentation references echo -e "\nChecking for SGE documentation or test files..." fd -e rst -e md -e txt . | xargs rg -l "qsub.*terse"Length of output: 4089
Script:
#!/bin/bash # Check base class and implementations echo "Checking base class for job ID parsing methods..." ast-grep --pattern 'class SchedulerCommands { $$$ get_job_id_from_output($$$) { $$$ } $$$ }' echo -e "\nChecking specific implementations of get_job_id_from_output..." rg "get_job_id_from_output" -B 2 -A 4 --type py echo -e "\nChecking SGE submit command construction..." rg "submit_job_command" -B 2 -A 4 pysqa/wrapper/sge.pyLength of output: 5439
pysqa/wrapper/sge.py
Outdated
| @staticmethod | ||
| def get_job_id_from_output(queue_submit_output: str) -> int: | ||
| """Extracts the job ID from the output of the job submission command.""" | ||
| return int(queue_submit_output.splitlines()[-1].rstrip().lstrip().split()[-1]) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add error handling and simplify the parsing logic.
The current implementation makes assumptions about the output format and lacks error handling. Since the class uses the -terse flag in submit_job_command, the output should contain only the job ID.
Consider this safer implementation:
@staticmethod
def get_job_id_from_output(queue_submit_output: str) -> int:
- """Extracts the job ID from the output of the job submission command."""
+ """Extracts the job ID from the output of the job submission command.
+
+ Args:
+ queue_submit_output: Output string from qsub -terse command
+ containing only the job ID.
+
+ Returns:
+ The extracted job ID as an integer.
+
+ Raises:
+ ValueError: If the output is empty or contains an invalid job ID.
+
+ Example:
+ >>> SunGridEngineCommands.get_job_id_from_output("123456\\n")
+ 123456
+ """
+ if not queue_submit_output:
+ raise ValueError("Empty output from job submission command")
+ try:
+ return int(queue_submit_output.strip())
+ except ValueError as e:
+ raise ValueError(f"Invalid job ID in output: {queue_submit_output!r}") from e📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| @staticmethod | |
| def get_job_id_from_output(queue_submit_output: str) -> int: | |
| """Extracts the job ID from the output of the job submission command.""" | |
| return int(queue_submit_output.splitlines()[-1].rstrip().lstrip().split()[-1]) | |
| @staticmethod | |
| def get_job_id_from_output(queue_submit_output: str) -> int: | |
| """Extracts the job ID from the output of the job submission command. | |
| Args: | |
| queue_submit_output: Output string from qsub -terse command | |
| containing only the job ID. | |
| Returns: | |
| The extracted job ID as an integer. | |
| Raises: | |
| ValueError: If the output is empty or contains an invalid job ID. | |
| Example: | |
| >>> SunGridEngineCommands.get_job_id_from_output("123456\\n") | |
| 123456 | |
| """ | |
| if not queue_submit_output: | |
| raise ValueError("Empty output from job submission command") | |
| try: | |
| return int(queue_submit_output.strip()) | |
| except ValueError as e: | |
| raise ValueError(f"Invalid job ID in output: {queue_submit_output!r}") from e |
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