feat: fall back on scrambled password #11
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📝 WalkthroughWalkthroughThe changes modify the iRODS storage plugin for Snakemake, focusing on improving password management for iRODS sessions. The modifications introduce a more flexible approach to handling authentication credentials by allowing password retrieval from the Changes
Sequence DiagramsequenceDiagram
participant Settings as StorageProviderSettings
participant Provider as StorageProvider
participant File as ~/.irods/.irodsA
Settings->>Provider: Initialize with settings
alt Password provided in settings
Provider->>Provider: Use provided password
else No password in settings
Provider->>File: Attempt to read scrambled password
alt File accessible
File->>Provider: Return scrambled password
Provider->>Provider: Decode password
else File not accessible
Provider->>Provider: Raise authentication error
end
end
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Actionable comments posted: 1
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snakemake_storage_plugin_irods/__init__.py(5 hunks)
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snakemake_storage_plugin_irods/__init__.py (1)
Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
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🪛 Ruff (0.8.2)
snakemake_storage_plugin_irods/__init__.py
248-251: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
(B904)
🔇 Additional comments (4)
snakemake_storage_plugin_irods/__init__.py (4)
9-9: Import statement is appropriate.
No issues found with importing password_obfuscation.
38-41: Clear and descriptive help text.
Including a fallback mechanism message in the help text is helpful for administrators.
73-75: Optional password improves flexibility.
Changing this field to not be strictly required aligns with the new fallback mechanism.
97-98: Documentation clarity.
Adding the fallback note in the authentication_scheme field’s help text is beneficial, so users understand the interplay between this scheme and the fallback password usage.
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snakemake_storage_plugin_irods/__init__.py (2)
240-254: LGTM: Robust implementation of password fallback mechanismThe implementation correctly handles the password fallback logic, properly uses the official
password_obfuscationmodule, and maintains good error handling.Consider adding debug logging to improve operational transparency:
if self.settings.password is None: + logger.debug("No password provided in settings, attempting to use ~/.irods/.irodsA") irodsA = os.path.expanduser("~/.irods/.irodsA") try: with open(irodsA, "r") as r: scrambled_password = r.read() password = password_obfuscation.decode(scrambled_password) authentication_scheme = "native" + logger.debug("Successfully retrieved password from ~/.irods/.irodsA") except OSError as err:
240-251: Consider additional security measures for password handlingWhile the implementation is functionally correct, consider these security enhancements:
- Verify file permissions are restricted (600 or similar)
- Clear password from memory after use
Add permission check:
irodsA = os.path.expanduser("~/.irods/.irodsA") try: + # Verify file permissions + stat = os.stat(irodsA) + if stat.st_mode & 0o077: + raise Exception("Insecure file permissions on ~/.irods/.irodsA. Please chmod 600.") with open(irodsA, "r") as r: scrambled_password = r.read() password = password_obfuscation.decode(scrambled_password) authentication_scheme = "native" + # Clear sensitive data + del scrambled_password
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Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.
🔇 Additional comments (2)
snakemake_storage_plugin_irods/__init__.py (2)
9-9: LGTM: Import added for password decoding functionality
The addition of password_obfuscation import is appropriate for implementing the fallback authentication mechanism.
38-41: LGTM: Clear documentation of password fallback behavior
The help text effectively communicates the authentication fallback mechanism, and the password field is correctly marked as optional since it can now be retrieved from ~/.irods/.irodsA.
Also applies to: 73-75
If no password is provided in the settings or environment file, try to fall back on native authentication using the scrambled password in ~/.irods/.irodsA
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If no password is provided in the settings or environment file, try to fall back on native authentication using the scrambled password in ~/.irods/.irodsA
Summary by CodeRabbit
New Features
Bug Fixes