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@btraven00 btraven00 commented Mar 14, 2025

Initially I was using a simple regex for escaping single quotes; this is copied over from the original apptainer implementation in what I believe it's an attempt at defending against shell injection via provided commands.

It seems shlex.quote is a more robust function call to try to properly parse strings that can be safely used as shell command line.

Do note that shlex.quote() is only designed for POSIX-compliant shells.

Summary by CodeRabbit

  • Refactor
    • Improved the handling of shell commands to securely process special characters, resulting in more robust and reliable command execution.

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coderabbitai bot commented Mar 14, 2025

📝 Walkthrough

Walkthrough

The change updates the decorate_shellcmd method in the ContainerEnv class. The previous manual replacement of single quotes in the command string has been replaced with a call to shlex.quote to ensure proper shell escaping, particularly handling special characters and spaces. An import of the shlex module has also been added to support this functionality.

Changes

File Change Summary
src/snakemake_software_deployment_plugin_container/__init__.py Updated decorate_shellcmd: replaced manual single quote replacement with shlex.quote for safer shell command escaping and added import shlex.

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  • src/snakemake_software_deployment_plugin_container/__init__.py (2 hunks)
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Initially I was using a simple regex for escaping single quotes; this is
copied over from the original apptainer implementation in what I believe
it's an attempt at defending against shell injection via provided
commands.

It seems `shlex.quote` is a more robust function call to try to properly
parse strings that can be safely used as shell command line.

Do note that `shlex.quote()` is only designed for POSIX-compliant
shells.
@btraven00 btraven00 force-pushed the feat/fix-shell-execution branch from 5334701 to ea77d4a Compare March 14, 2025 18:34
@btraven00 btraven00 changed the title bug: use shlex for more robust shell escaping fix: use shlex for more robust shell escaping Mar 14, 2025
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