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patched-codes / patchwork

Automate development gruntwork like code reviews, patching and documentation with LLM workflows.
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PatchWork AutoFix #622

Closed patched-admin closed 3 weeks ago

patched-admin commented 3 weeks ago

This pull request from patched fixes 3 issues.

* File changed: [patchwork/app.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-839e90b808d34e4cf447eff0896161788ccfc6e1f2970be2e551b64ba413a503)
Fix vulnerability by avoiding untrusted user input in `importlib.import_module()` Avoid using `importlib.import_module()` with untrusted user input by using `importlib.util.spec_from_file_location` and `importlib.util.module_from_spec` instead.
* File changed: [patchwork/common/utils/step_typing.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-4490efb269fda5b75b1edc5f5fa275d34675bca1ffbb22e06829384e562205ff)
Fix vulnerability by avoiding dynamic values in importlib.import_module() Removed dynamic values in importlib.import_module() to prevent running untrusted code.
* File changed: [patchwork/common/utils/dependency.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-6ad070db06c1de59a1e0b0b199944f057089f121f94abdf817a0845e3c5d81f6)
Fix untrusted user input vulnerability in importlib.import_module() Avoid using dynamic values in importlib.import_module() by validating user input against a whitelist before importing modules.
codelion commented 3 weeks ago

Make the sure all new methods have docstrings.

And make sure that we have type annotations as much as possible.

patched-admin commented 3 weeks ago
The pull request review discusses various code modifications across different files, addressing security vulnerabilities, functionality enhancements, bug fixes, and coding standard adherence. The removal of importlib.import_module() in patchwork/app.py for security reasons is commendable, and the introduction of `limit` parameter in GitHub and GitLab classes for improved functionality is positive but requires some corrections for consistency. The addition of `VALID_MODULES` set for validation in `import_with_dependency_group` function is a good practice, while changes in `CallLLM.py` for log message sanitization are aligned with security best practices. It is noted that some changes may introduce potential bugs, such as in `ModifyCodePB.py`, and require adjustments for correctness. Overall, the review emphasizes maintaining code quality, security, and consistency with original coding standards. ------
* File changed: [patchwork/app.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-839e90b808d34e4cf447eff0896161788ccfc6e1f2970be2e551b64ba413a503) The code modification in patchwork/app.py removes the usage of importlib.import_module(), which previously could have introduced a security vulnerability by allowing untrusted user input. The new approach of using importlib.util.spec_from_file_location and importlib.util.module_from_spec is a more secure alternative. This change aligns with the effort to avoid running untrusted code and adheres to better coding practices by reducing the risk of potential security vulnerabilities.
* File changed: [patchwork/common/client/scm.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-a4a0213f577e66fc33444faad6c1991a8c60deb8fc7d5b5527069a66f59804f5) The addition of the 'limit' parameter in the 'find_prs' method for both the Github and Gitlab classes seem to be a good enhancement in terms of functionality and flexibility. However, there are some issues in the implementation: 1. In the Github section, the 'page_list' should be initialized as a list instead of an empty list, and it should be extended with 'pages' not 'prs' to maintain consistency. Also, when creating 'rv_list', the 'itertools.chain' should be corrected to 'itertools.chain.from_iterable'. 2. In the Gitlab section, the 'page_list' should also be initialized as a list instead of an empty list, and should be appended with 'mrs_instance' not 'mrs'. Similar to the Github section, when creating 'rv_list', use 'itertools.chain.from_iterable' instead of 'itertools.chain'. These corrections will ensure the expected behavior of limiting the results based on the specified parameter.
* File changed: [patchwork/common/utils/dependency.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-6ad070db06c1de59a1e0b0b199944f057089f121f94abdf817a0845e3c5d81f6) The addition of the `VALID_MODULES` set to store the keys of `__DEPENDENCY_GROUPS` for validation is a good approach to validate user input against a whitelist before importing modules in the `import_with_dependency_group` function. This change helps prevent untrusted user input vulnerabilities when using `importlib.import_module()`. However, it would be beneficial to also provide a more detailed comment explaining the purpose of the `VALID_MODULES` set in the code for better code readability and maintenance.
* File changed: [patchwork/common/utils/step_typing.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-4490efb269fda5b75b1edc5f5fa275d34675bca1ffbb22e06829384e562205ff) The diff in patchwork/common/utils/step_typing.py seems to just change the formatting of strings from using double quotes with html encoding to using double quotes directly. The modification does not introduce any potential bugs, new vulnerabilities, or deviate from the original coding standards in the pull request.
* File changed: [patchwork/logger.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-20f986b5bd504db976ce63bea58d28a56004397cc82fddf3e2230f3a7c53b8c6) The change in patchwork/logger.py introduces a modification to the Live object initialization by setting vertical_overflow="visible" instead of vertical_overflow="crop". This change may impact the display of the progress bar in the panel. It is recommended to verify if setting vertical_overflow to "visible" aligns with the original design and functionality of the progress bar.
* File changed: [patchwork/steps/CallLLM/CallLLM.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-06684f9c0b7bb0e746ea0a10fd6f7cbe2e671ff44a4069e16cdf4faae231c409) The code modifications in the `CallLLM.py` file introduce the use of `rich.markup.escape` from the `rich` library to escape special characters in log messages. This change is relevant for preventing any potential injection attacks through the logged messages. It's a good practice to sanitize input data before including it in log messages to prevent any unintended interpretation of the injected content. This enhancement aligns with security best practices and doesn't deviate from the original coding standards set in the pull request.
* File changed: [patchwork/steps/Combine/Combine.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-1d0f83176b7971ff9e383e557947e5792f3e279885d52ffeeda9106a778e8644) The code modification in Combine.py seems fine. It simplifies the return statement by removing the unnecessary 'dict' function around the dictionary merge operation.
* File changed: [patchwork/steps/JoinListPB/JoinListPB.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-e4133732e0f6fe1802d805c41ab0991e6d546a590cea6d606dbdb71b87adbd1c) The code modification in JoinListPB.py appears to be fixing a bug where the 'list' key was not correctly extracted from each item. The change now correctly assigns 'item.get(self.key)' to 'join_list' instead of the previous 'item'. This fix should provide the expected behavior as intended.
* File changed: [patchwork/steps/ModifyCode/ModifyCode.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-10e9c07de238f7931e667c3d1d277b8b9ba8850bbeced487eb2de77ae6edc278) The code modifications in patchwork/steps/ModifyCode/ModifyCode.py seem well-handled. The addition of `from pathlib import Path` for handling file paths is a good improvement. The `replace_code_in_file` function now checks if the file path exists before reading it, which is a good defensive programming practice. The code now allows for None values for start_line and end_line, providing more flexibility. The use of `pathlib` is a good practice for file operations. Overall, the changes align with the original coding standards and do not introduce new security vulnerabilities.
* File changed: [patchwork/steps/ModifyCodePB/ModifyCodePB.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-91ead4cc2c45643d0995f496ccdddbfd5f8c5b9d72aab0b93ff49a6eb0dcc2af) The code modifications in `ModifyCodePB.py` appear to accurately reflect the input changes and adjustments made to `files_with_patch`. However, there is one potential issue: The return statement at the end of the `run` function is attempting to access a key in `modified_code_files` by index, which might be incorrect. It's recommended to review the changes in `run` method to ensure the correct key is being accessed for returning the modified code files. Additionally, the changes seem to adhere to the original coding standards in the pull request.
* File changed: [patchwork/steps/ModifyCodePB/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-c86d4b11855ae4336541cca428905fb74724376897064079f4f058e976144a23) The code modifications in patchwork/steps/ModifyCodePB/typed.py rename the class 'FileWithPatch' to 'ModifyCodePBInputs'. This change seems fine and does not introduce any new bugs or vulnerabilities. However, it would be more consistent if the previous definition of 'ModifyCodePBInputs' inside the same file was also removed to avoid confusion and adhere to coding standards.
* File changed: [patchwork/steps/PR/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-7314b3f35a75a646a72bd4fee80989b2deef7d1729f3ac1f916f1d22818f7448) The code modifications in patchwork/steps/PR/typed.py should follow the naming convention of using snake_case for variable names. The new variables 'commit_message' and 'patch_message' should be in lower case like 'commit_message' and 'patch_message' to adhere to the original coding standards established in the pull request.
* File changed: [patchwork/steps/PRPB/PRPB.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-a40b0df7f656f8452dac88be8472924312df4a46ea78b2a701dc7dde4849f8dc) The code modifications appear to be adding a new Step class 'PRPB' in the file 'PRPB.py'. The new code seems to be correctly structured and in line with the existing coding standards. The class defines an '__init__' method to initialize the inputs and a 'run' method that creates and runs a 'PR' instance with modified code files. However, it would be beneficial to include type hints in the method signatures for better code readability and maintainability.
* File changed: [patchwork/steps/PRPB/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-b5b5620287eba41f5b657e7546b262d28c1403666971c7d34abd5477ec35e365) The code modifications in `patchwork/steps/PRPB/typed.py` seem to be adding new type definitions for inputs and outputs related to PRPB (Pull Request Process Builder). The changes include defining specific types for inputs and outputs, along with adding annotations for StepTypeConfig. It appears that the code aligns with the original coding standards and does not introduce any potential bugs or security vulnerabilities based on the provided information.
* File changed: [patchwork/steps/ReadFile/ReadFile.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-278f5372ad6c85629c7e029f8479ab37b57f955ebb26fcefd68079f464aaf52a) The code modification in 'ReadFile.py' seems to be correct. The change from 'open_with_chardet("r", self.file)' to 'open_with_chardet(self.file, 'r')' appears to fix the parameter order issue. No potential bugs or new security vulnerabilities introduced by this change. The modification adheres to the original coding standards in the pull request.
* File changed: [patchwork/steps/ReadPRDiffsPB/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-089bf4a815f7dd204cffec1404b405531959bdaae5b76d59f096f5a4450c582d) The code changes in the pull request have renamed the class from `ReadPRDiffsOutputs` to `ReadPRDiffsPBOutputs`. This seems like a reasonable change and adheres to the original coding standards in the pull request.
* File changed: [patchwork/steps/ReadPRs/ReadPRs.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-28214f6c6e7457a73649d1d3df3e08b1716a0b3a136330f3c22c30b742ce8578) The code modifications in patchwork/steps/ReadPRs/ReadPRs.py look fine overall. The addition of 'self.limit = inputs.get("limit", 50)' ensures a default value is set for 'limit' if not provided. The change in 'run' method to return a dictionary instead of a list and renaming 'def run(self) -> List[DataPoint]:' to 'def run(self) -> DataPoint:' does not adhere to original coding standards where 'run' method was expected to return a list of DataPoint. It's recommended to maintain consistency with the existing coding standards.
* File changed: [patchwork/steps/ReadPRs/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-efbaea9043a9cee1d66c81dddb4480a3b2382eca5023a9c29dd9e840fa8a382e) The code modifications in the pull request removed the `Diff` typed dictionary and replaced it with `pr_texts: List[ReadPRDiffsPBOutputs]`. This change could potentially introduce bugs if there are other parts of the codebase that relied on the previous structure of `Diff`. It would be helpful to ensure that all references to `Diff` are appropriately updated to `pr_texts`. Additionally, it's important to verify if this change aligns with the original coding standards of the project.
* File changed: [patchwork/steps/SimplifiedLLMOnce/SimplifiedLLMOnce.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-afe4ee83eab4a19914ecfb9495e7627ef4c98a8a07d19af6e22a8fbdf9cc8fa0) The code modification in the `SimplifiedLLMOnce.py` file seems to be incorrect. The original import statements for `SimplifiedLLM` and `SimplifiedLLMOnce` are commented out but not replaced with the correct path for the imports. This could potentially cause import errors and should be corrected before merging the code.
* File changed: [patchwork/steps/SimplifiedLLMOncePB/SimplifiedLLMOncePB.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-f9e84fdd8dc3a5f5c47cf44a6330e11a12c50fa420c6c95d6dd8d85843337077) The code modifications in the pull request appear to be in a file `SimplifiedLLMOncePB.py` under the path `patchwork/steps/SimplifiedLLMOncePB/SimplifiedLLMOncePB.py`. Here are some potential issues identified in the code: 1. The method `__json_schema_as_suffix` is implemented to add a prompt to a given JSON schema, but the implementation of this method seems to be incomplete as it uses a placeholder `{prompt}` without actually replacing it with the provided `prompt` parameter. This could lead to unexpected behavior or errors in the generated JSON schema. 2. It would be beneficial to ensure that the input provided to `__json_schema_as_suffix` is properly escaped to prevent any injection attacks, especially if the `prompt` string comes from user input. This is important for maintaining security and preventing vulnerabilities. 3. The code modifications do not adhere to the original coding standards in the pull request as the method implementation is incomplete and lacks proper substitution of placeholders.
* File changed: [patchwork/steps/SimplifiedLLMOncePB/typed.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-9ce10c0e15676a3cb8cddbcc4ce8db1971ab1b2e67ec019db7794cb801026d12) The code modifications in `typed.py` seem to be adding new configurations for `SimplifiedLLMOncePB`. It is recommended to ensure that the additional configurations, especially related to API keys like `patched_api_key`, `google_api_key`, `openai_api_key`, and `anthropic_api_key`, are properly secured and validated. It's also important to make sure that the added code aligns with the original coding standards set in the pull request.
* File changed: [patchwork/steps/__init__.py](https://github.com/patched-codes/patchwork/pull/622/files#diff-f31de71df95e57998018a4108a0780a90d8e790683810803959e17e72412f513) The code modifications in the pull request seem to add new modules like 'PRPB', 'ReadFile', 'SimplifiedLLMOnce', and 'SimplifiedLLMOncePB' to the 'steps' package. It is essential to ensure that the new modules adhere to the established coding standards and do not introduce any potential bugs or security vulnerabilities. A thorough code review should be conducted to verify the quality and integrity of these additions.
* File changed: [pyproject.toml](https://github.com/patched-codes/patchwork/pull/622/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711) The version of pydantic library has been updated from ~2.6.4 to ~2.8.2 in pyproject.toml. This change is acceptable as it keeps the package up to date with the latest version which may include bug fixes and new features. No issues found in this change.