feat: Allow outputting of rendered yte config in Datavzrd wrapper #5
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Clone of the PR snakemake/snakemake-wrappers#3123 |
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Review Summary by Korbit AI
Code Execution Comments
- Add error handling and check
snakemake.outputlength to prevent errors during file operations whenoutput_configis True.
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| if output_config: | ||
| shutil.copy(processed.name, snakemake.output[1]) |
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The new feature to output the rendered yte config is a great addition. However, there's a potential issue with the implementation. When 'output_config' is True, the code assumes that snakemake.output[1] exists. This might not always be the case, which could lead to an IndexError. Consider adding a check to ensure snakemake.output has at least two elements before attempting to copy the processed file. For example:
if output_config:
if len(snakemake.output) > 1:
shutil.copy(processed.name, snakemake.output[1])
else:
print("Warning: output_config is True but no second output file specified.")This change will make the code more robust and prevent potential runtime errors.
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| if output_config: | ||
| shutil.copy(processed.name, snakemake.output[1]) |
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Consider adding error handling around the shutil.copy() operation when copying the temporary file to the output. If an error occurs during the file copy, it should be caught and handled appropriately to ensure the stability and reliability of the code. You can use a try-except block to catch any exceptions that may be raised and log the error or provide a fallback behavior.
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QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
Description by Korbit AI
What change is being made?
Add functionality to the Datavzrd wrapper to optionally output the rendered YTE configuration file.
Why are these changes being made?
This change allows users to save the intermediate YTE configuration file for debugging or record-keeping purposes, enhancing the transparency and traceability of the data processing workflow. The approach uses a simple flag (
output_config) to control this behavior, ensuring backward compatibility and minimal disruption to existing workflows.