feat: Add option to modify how a query is printed #54
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WalkthroughThe changes introduced in this pull request involve enhancements to the handling of query strings in the Changes
Possibly related PRs
Recent review detailsConfiguration used: CodeRabbit UI Files selected for processing (2)
Files skipped from review as they are similar to previous changes (1)
Additional context usedPath-based instructions (1)
Ruff
Additional comments not posted (8)
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Actionable comments posted: 7
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Files selected for processing (2)
- snakemake_interface_storage_plugins/storage_object.py (5 hunks)
- snakemake_interface_storage_plugins/storage_provider.py (1 hunks)
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Path-based instructions (2)
snakemake_interface_storage_plugins/storage_provider.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.snakemake_interface_storage_plugins/storage_object.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 theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
Ruff
snakemake_interface_storage_plugins/storage_object.py
147-147: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
154-154: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
161-161: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
193-193: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
200-200: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
223-223: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
Additional comments not posted (2)
snakemake_interface_storage_plugins/storage_provider.py (1)
144-150: Excellent addition for enhancing security!The new
safe_printmethod provides a valuable mechanism for storage providers to remove potentially sensitive information from queries before printing them. This is particularly useful for URL-like queries that may contain authentication tokens, usernames, or passwords.By default, the method simply returns the original query, allowing storage providers to opt-in to this feature and implement their own custom logic for removing sensitive data. This approach maintains backward compatibility while encouraging better security practices.
This addition aligns well with the PR objective of enhancing the handling of query outputs to improve security and privacy.
snakemake_interface_storage_plugins/storage_object.py (1)
71-71: LGTM!The addition of the
print_queryattribute aligns with the PR objective of allowing storage providers to customize how a query is printed. It is assigned the value returned byself.provider.safe_print(self.query), which is expected to return a sanitized version of the query, potentially removing sensitive information.
| @@ -173,7 +174,7 @@ async def managed_retrieve(self): | |||
| else: | |||
| os.remove(local_path) | |||
| raise WorkflowError( | |||
| f"Failed to retrieve storage object from {self.query}", e | |||
| f"Failed to retrieve storage object from {self.print_query}", e | |||
There was a problem hiding this comment.
Use raise ... from e for consistency with the previous instances.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
For consistency with the previous instances, use raise ... from e to distinguish the exception from errors in exception handling:
- f"Failed to retrieve storage object from {self.print_query}", e
+ f"Failed to retrieve storage object from {self.print_query}") from eCommittable 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.
| f"Failed to retrieve storage object from {self.print_query}", e | |
| f"Failed to retrieve storage object from {self.print_query}") from e |
| @@ -143,21 +144,21 @@ | |||
| async with self._rate_limiter(Operation.SIZE): | |||
| return self.size() | |||
| except Exception as e: | |||
| raise WorkflowError(f"Failed to get size of {self.query}", e) | |||
| raise WorkflowError(f"Failed to get size of {self.print_query}", e) | |||
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to get size of {self.print_query}", e)
+ raise WorkflowError(f"Failed to get size of {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to get size of {self.print_query}", e) | |
| raise WorkflowError(f"Failed to get size of {self.print_query}") from e |
Tools
Ruff
147-147: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
| @@ -219,4 +220,4 @@ | |||
| async with self._rate_limiter(Operation.TOUCH): | |||
| self.touch() | |||
| except Exception as e: | |||
| raise WorkflowError(f"Failed to touch storage object {self.query}", e) | |||
| raise WorkflowError(f"Failed to touch storage object {self.print_query}", e) | |||
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to touch storage object {self.print_query}", e)
+ raise WorkflowError(f"Failed to touch storage object {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to touch storage object {self.print_query}", e) | |
| raise WorkflowError(f"Failed to touch storage object {self.print_query}") from e |
Tools
Ruff
223-223: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
| @@ -189,14 +190,14 @@ | |||
| async with self._rate_limiter(Operation.REMOVE): | |||
| self.remove() | |||
| except Exception as e: | |||
| raise WorkflowError(f"Failed to remove storage object {self.query}", e) | |||
| raise WorkflowError(f"Failed to remove storage object {self.print_query}", e) | |||
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to remove storage object {self.print_query}", e)
+ raise WorkflowError(f"Failed to remove storage object {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to remove storage object {self.print_query}", e) | |
| raise WorkflowError(f"Failed to remove storage object {self.print_query}") from e |
Tools
Ruff
193-193: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
|
|
||
| async def managed_store(self): | ||
| try: | ||
| async with self._rate_limiter(Operation.STORE): | ||
| self.store_object() | ||
| except Exception as e: | ||
| raise WorkflowError(f"Failed to store output in storage {self.query}", e) | ||
| raise WorkflowError(f"Failed to store output in storage {self.print_query}", e) |
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to store output in storage {self.print_query}", e)
+ raise WorkflowError(f"Failed to store output in storage {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to store output in storage {self.print_query}", e) | |
| raise WorkflowError(f"Failed to store output in storage {self.print_query}") from e |
Tools
Ruff
200-200: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
|
|
||
| async def managed_exists(self) -> bool: | ||
| try: | ||
| async with self._rate_limiter(Operation.EXISTS): | ||
| return self.exists() | ||
| except Exception as e: | ||
| raise WorkflowError(f"Failed to check existence of {self.query}", e) | ||
| raise WorkflowError(f"Failed to check existence of {self.print_query}", e) |
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to check existence of {self.print_query}", e)
+ raise WorkflowError(f"Failed to check existence of {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to check existence of {self.print_query}", e) | |
| raise WorkflowError(f"Failed to check existence of {self.print_query}") from e |
Tools
Ruff
161-161: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
|
|
||
| async def managed_mtime(self) -> float: | ||
| try: | ||
| async with self._rate_limiter(Operation.MTIME): | ||
| return self.mtime() | ||
| except Exception as e: | ||
| raise WorkflowError(f"Failed to get mtime of {self.query}", e) | ||
| raise WorkflowError(f"Failed to get mtime of {self.print_query}", e) |
There was a problem hiding this comment.
Use raise ... from e to distinguish the exception from errors in exception handling.
The change from self.query to self.print_query in the error message is consistent with the PR objective of using the safe representation of the query in exception handling scenarios.
To improve the clarity of the exception, use raise ... from e as suggested by the static analysis hint:
- raise WorkflowError(f"Failed to get mtime of {self.print_query}", e)
+ raise WorkflowError(f"Failed to get mtime of {self.print_query}") from eCommittable 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.
| raise WorkflowError(f"Failed to get mtime of {self.print_query}", e) | |
| raise WorkflowError(f"Failed to get mtime of {self.print_query}") from e |
Tools
Ruff
154-154: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
This adds an attribute to
storage_objectcalledprint_querywhich allows a storage provider to change how a query is printed (e.g. removing senstitive information) through a new methodsafe_print()which by default just returns the query.Related to issue snakemake/snakemake#3087 and required for PR snakemake/snakemake#3089.
Summary by CodeRabbit
safe_printmethod to enhance security by processing query strings to remove sensitive information.