Log analysis

[CTY-git]

PR Checklist

• The commit message follows our guidelines: Code of conduct
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)
• Does this PR introduce a breaking change?
• Include PR in release notes?

PR Type

• Bugfix
• Feature
• Refactoring
• Build /CI
• Documentation
• Others

What is the current behavior?

Issue Number: N/A

What is the new behavior?

Other information

[patched-admin]

File Changed: patchwork/app.py

Rule 1: Do not ignore potential bugs in the code

Details: The code change moves the Any type import from typing to typing_extensions. While this change appears intentional, it could potentially introduce compatibility issues if the codebase is used with different Python versions where typing_extensions behavior differs from the standard typing module.

Affected Code Snippet:

-from typing import Any
from typing_extensions import Any, Iterable

Start Line: 8
End Line: 11

File Changed: patchwork/common/client/llm/aio.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug found in request_stream method where yield statement is incorrect and could cause unexpected behavior.

Affected Code Snippet:

async def request_stream(
        self,
        messages: list[ModelMessage],
        model_settings: ModelSettings | None,
        model_request_parameters: ModelRequestParameters,
) -> AsyncIterator[StreamedResponse]:
    model = self.__get_model(model_settings)
    if model is None:
        raise ValueError("Model cannot be unset")

    for client in self.__clients:
        if client.is_model_supported(model):
            yield client.request(messages, model_settings, model_request_parameters)
            return

Start Line: 65
End Line: 82

The yield client.request() statement is yielding a coroutine object directly instead of awaiting it first. This should be async for chunk in client.request(...): yield chunk for proper async streaming.

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security vulnerability in error messages exposing internal client names.

Affected Code Snippet:

client_names = [client.__class__.__name__ for client in self.__original_clients]
raise ValueError(
    f"Model {model} is not supported by {client_names} clients. "
    f"Please ensure that the respective API keys are correct."
)

Start Line: 59
End Line: 63

The error message exposes internal implementation details about client names and hints at API keys, which could aid potential attackers. Consider using a more generic error message.

File Changed: patchwork/common/client/llm/anthropic.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug found in request_stream method where yield statement is used incorrectly

Affected Code Snippet:

async def request_stream(
        self,
        messages: list[ModelMessage],
        model_settings: ModelSettings | None,
        model_request_parameters: ModelRequestParameters,
) -> AsyncIterator[StreamedResponse]:
    model = self.__get_pydantic_model(model_settings)
    yield model.request_stream(messages, model_settings, model_request_parameters)

Start Line: 104
End Line: 111

The method uses a single yield statement to yield the entire request_stream call, which is likely incorrect. Instead, it should probably be yielding from the stream using async for:

async for response in model.request_stream(messages, model_settings, model_request_parameters):
    yield response

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security vulnerability in API key handling

Affected Code Snippet:

def __init__(self, api_key: str):
    self.__api_key = api_key

Start Line: 80
End Line: 81

The API key is stored as an instance variable. While it uses double underscore for name mangling, it's still accessible throughout the instance's lifetime. Consider using a more secure credential management system or environment variables.

File Changed: patchwork/common/client/llm/google.py

Rule 1: Do not ignore potential bugs in the code

Details: There are two potential bugs identified in the code:

1. The request_stream method incorrectly uses yield with a direct return value instead of async iteration, which could cause runtime errors.
2. The model_name property returns a hardcoded "Undetermined" value which could lead to unexpected behavior in code relying on this property.

Affected Code Snippet:

async def request_stream(
        self,
        messages: list[ModelMessage],
        model_settings: ModelSettings | None,
        model_request_parameters: ModelRequestParameters,
) -> AsyncIterator[StreamedResponse]:
    model = self.__get_pydantic_model(model_settings)
    yield model.request_stream(messages, model_settings, model_request_parameters)

Start Line: 71
End Line: 77

---

Rule 2: Do not overlook possible security vulnerabilities

Details: The code stores the API key as an instance variable without any encryption or secure storage mechanism. While this is a common practice, it could lead to security issues if the object is serialized or if memory dumps are exposed.

Affected Code Snippet:

def __init__(self, api_key: str):
    self.__api_key = api_key
    generativeai.configure(api_key=api_key)

Start Line: 49
End Line: 51

File Changed: patchwork/common/client/llm/openai_.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug in request_stream method - the yield statement is incorrect and will cause issues.

Affected Code Snippet:

async def request_stream(
        self,
        messages: list[ModelMessage],
        model_settings: ModelSettings | None,
        model_request_parameters: ModelRequestParameters,
) -> AsyncIterator[StreamedResponse]:
    model = self.__get_pydantic_model(model_settings)
    yield model.request_stream(messages, model_settings, model_request_parameters)

Start Line: 75
End Line: 82

The method uses yield with a direct method call instead of async for or awaiting the stream. This will likely cause runtime errors as the stream isn't properly handled.

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security concern with error handling in __get_pydantic_model method where model settings validation could expose sensitive information.

Affected Code Snippet:

def __get_pydantic_model(self, model_settings: ModelSettings | None) -> Model:
    if model_settings is None:
        raise ValueError("Model settings cannot be None")
    model_name = model_settings.get("model")
    if model_name is None:
        raise ValueError("Model must be set cannot be None")

Start Line: 58
End Line: 65

The error messages could potentially expose internal implementation details. Consider using more generic error messages or implementing proper error handling that doesn't leak implementation details.

File Changed: patchwork/common/client/llm/protocol.py

Rule 1: Do not ignore potential bugs in the code

Details: The modification of the return type annotation for remove_not_given method could introduce potential bugs due to incomplete type handling. While the new type annotation Union[None, dict[Any, Any], list[Any], Any] is more specific, it might not cover all edge cases when processing nested structures.

Affected Code Snippet:

@staticmethod
def remove_not_given(obj: Any) -> Union[None, dict[Any, Any], list[Any], Any]:
    if isinstance(obj, NotGiven):
        return None
    if isinstance(obj, dict):
        return {k: NotGiven.remove_not_given(v) for k, v in obj.items()}
    if isinstance(obj, list):
        return [NotGiven.remove_not_given(x) for x in obj]
    return obj

Start Line: 21
End Line: 29

---

Rule 3: Do not deviate from the original coding standards established in the pull request

Details: The code changes maintain consistent coding standards with proper type hints, docstrings, and formatting. The transition from Protocol to Model base class and addition of @AbstractMethod decorators follows good Python practices and enhances the interface definition.

However, there is one minor inconsistency in type hints usage where both typing and typing_extensions are imported for the same types (Dict, List, Any), which could lead to confusion.

Affected Code Snippet:

from typing import Dict, Any, List
...
from typing_extensions import Any, Dict, Iterable, List, Optional, Union

Start Line: 3
Start Line: 14

End Line: 3
End Line: 14

File Changed: patchwork/common/client/llm/utils.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug identified in example list handling where an empty list could cause an IndexError.

Affected Code Snippet:

elif isinstance(example_data_value, list):
    nested_value = example_data_value[0]
    if isinstance(nested_value, dict):
        nested_typing = example_dict_to_base_model(nested_value)
    else:
        nested_typing = type(nested_value)
    value_typing = List[nested_typing]

Start Line: 101
End Line: 107

The code assumes that the list has at least one element when accessing example_data_value[0]. This could raise an IndexError if an empty list is provided. Should add a length check before accessing the first element.

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security vulnerability in JSON parsing without size limits.

Affected Code Snippet:

try:
    example_data = json.loads(json_example)
except Exception as e:
    logger.error(f"Failed to parse example json", e)
    return None

Start Line: 87
End Line: 91

The code accepts arbitrary JSON input without size limits, which could lead to a denial of service attack through memory exhaustion. Should implement size limits for the input JSON.

File Changed: patchwork/common/client/patched.py

Rule 1: Do not ignore potential bugs in the code

Details: Changing the import of Any from typing to typing_extensions could potentially introduce compatibility issues if the codebase is using Python versions where typing_extensions is not available or if there are subtle differences in the implementation between the two modules.

Affected Code Snippet:

-from typing import Any
+from typing_extensions import Any

Start Line: 4
End Line: 4

---

Summary

The code diff shows a single change replacing the import of Any from Python's standard typing module to typing_extensions. While this change maintains coding standards and doesn't introduce security vulnerabilities, it could potentially cause compatibility issues depending on the Python environment and version requirements of the project. It's recommended to:

1. Verify that typing_extensions is properly listed in the project's dependencies
2. Document the minimum Python version requirement if this change is necessary for backward compatibility
3. Add a comment explaining why typing_extensions is preferred over the standard typing module in this case

File Changed: patchwork/common/client/sonar.py

Rule 1: Do not ignore potential bugs in the code

Details: The change from typing to typing_extensions could potentially introduce compatibility issues if the project's environment doesn't have typing_extensions installed or if there are version mismatches. While not a direct bug, this dependency change should be validated.

Affected Code Snippet:

-from typing import Optional, Union
+from typing_extensions import Optional, Union

Start Line: 3
End Line: 3

File Changed: patchwork/common/multiturn_strategy/agentic_strategy.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug in error handling where agents_result dictionary could be empty but accessed without proper validation.

Affected Code Snippet:

if len(agents_result) == 0:
    return dict()

if len(agents_result) == 1:
    final_result = self.__summariser.run_sync(
        "From the actions taken by the assistant. Please give me the result.",
        message_history=next(v for _, v in agents_result.items()).all_messages(),
    )

Start Line: 91
End Line: 97

Details: No proper error handling for agent_output being None after the loop execution.

Affected Code Snippet:

for i in range(limit or self.__limit or sys.maxsize):
    agent_output = agent.run_sync(user_message, message_history=message_history)
    message_history = agent_output.all_messages()
    if getattr(agent_output.data, _COMPLETION_FLAG_ATTRIBUTE, False):
        break
    user_message = "Please continue"
agents_result[index] = agent_output

Start Line: 82
End Line: 89

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potentially unsafe template rendering without proper input validation for template_data dictionary.

Affected Code Snippet:

mustache_render(system_prompt_template, self.__template_data)

Start Line: 56
End Line: 56

Details: API key is passed directly as a parameter without any validation or secure handling.

Affected Code Snippet:

model = AnthropicModel("claude-3-5-sonnet-latest", api_key=api_key)

Start Line: 54
End Line: 54

File Changed: patchwork/common/tools/bash_tool.py

Rule 1: Do not ignore potential bugs in the code

Details: The code changes introduce a potential bug by removing *args and **kwargs from the execute method signature without properly handling any existing calls that might be using positional or keyword arguments. This could cause runtime errors if the method is called with additional arguments elsewhere in the codebase.

Affected Code Snippet:

def execute(
    self,
    command: Optional[str] = None,
) -> str:

Start Line: 38
End Line: 41

---

Rule 2: Do not overlook possible security vulnerabilities

Details: The execute method potentially accepts command input that could be executed in a shell context (based on the method's docstring mentioning "Execute editor commands"). Without proper input validation or sanitization visible in the diff, this could lead to command injection vulnerabilities if the command parameter is user-controlled.

Affected Code Snippet:

def execute(
    self,
    command: Optional[str] = None,
) -> str:

Start Line: 38
End Line: 41

File Changed: patchwork/common/tools/code_edit_tools.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug in code edit tool where modified_files is updated even if command execution fails

Affected Code Snippet:

try:
    abs_path = self.__get_abs_path(path)
    if command == "create":
        result = self.__create(file_text, abs_path)
    elif command == "str_replace":
        result = self.__str_replace(new_str, old_str, abs_path)
    elif command == "insert":
        result = self.__insert(abs_path, file_text, insert_line)
    else:
        return f"Error: Unknown command {command}"
except Exception as e:
    return f"Error: {str(e)}"

self.modified_files.update({abs_path})  # Bug: Updates even after exception

Start Line: 158
End Line: 174

Details: FileViewTool does not properly handle non-text files which could cause crashes

Affected Code Snippet:

if abs_path.is_file():
    with open(abs_path, "r") as f:  # No binary file handling
        content = f.read()

Start Line: 56
End Line: 58

Rule 2: Do not overlook possible security vulnerabilities

Details: Both tools validate path traversal but don't implement file access controls or handle symbolic links securely

Affected Code Snippet:

def __get_abs_path(self, path: str):
    wanted_path = Path(path).resolve()
    if wanted_path.is_relative_to(self.repo_path):
        return wanted_path
    else:
        raise ValueError(f"Path {path} contains illegal path traversal")

Start Line: 45
End Line: 50

Details: FileViewTool lacks input validation for view_range parameters which could lead to index out of bounds

Affected Code Snippet:

if view_range:
    lines = content.splitlines()
    start, end = view_range
    content = "\n".join(lines[start - 1 : end])  # No bounds checking

Start Line: 60
End Line: 63

File Changed: patchwork/common/tools/grep_tool.py

Rule 1: Do not ignore potential bugs in the code

Details: The code contains potential bugs in handling file paths and error handling

Affected Code Snippet:

def execute(
    self,
    path: Optional[Path] = None,
    pattern: Optional[str] = None,
    is_case_sensitive: bool = False,
) -> str:
    if path is None:
        raise ValueError("Path argument is required!")

    path = Path(path).resolve()
    if not path.is_relative_to(self.__working_dir):
        raise ValueError("Path must be relative to working dir")

    with path.open("r") as f:
        for i, line in enumerate(f.readlines()):

Start Line: 152
End Line: 167

Issues:

1. No error handling for file not found or permission issues
2. readlines() loads entire file into memory which could cause problems with large files
3. No encoding specification for file opening which could cause issues with non-ASCII text

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Several security vulnerabilities exist in the code

Affected Code Snippet:

def execute(self, pattern: Optional[str] = None, depth: int = 1, is_case_sensitive: bool = False) -> str:
    if pattern is None:
        raise ValueError("Pattern argument is required!")

    matcher = fnmatch.fnmatch
    if is_case_sensitive:
        matcher = fnmatch.fnmatchcase

    file_matches = []
    dir_matches = []
    for root, dirs, files in os.walk(self.__working_dir):

Start Line: 63
End Line: 73

Issues:

1. No validation of pattern input which could lead to path traversal attacks
2. os.walk() follows symlinks by default which could lead to directory traversal
3. No limit on total matches which could lead to denial of service
4. Path traversal vulnerability in file path handling

File Changed: patchwork/common/tools/tool.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug identified in the type narrowing from 'ToolProtocol' to 'Tool' in get_description and get_parameters methods. This change might break existing code that relies on the broader ToolProtocol type.

Affected Code Snippet:

@staticmethod
-def get_description(tooling: "ToolProtocol") -> str:
+def get_description(tooling: "Tool") -> str:
    return tooling.json_schema.get("description", "")

@staticmethod
-def get_parameters(tooling: "ToolProtocol") -> str:
+def get_parameters(tooling: "Tool") -> str:
    return ", ".join(tooling.json_schema.get("required", []))

Start Line: 43
End Line: 48

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security vulnerability in the new to_pydantic_ai_function_tool method. The method directly uses json_schema data without validation, which could lead to injection vulnerabilities if the schema is manipulated.

Affected Code Snippet:

def to_pydantic_ai_function_tool(self) -> PydanticTool[None]:
    async def _prep(ctx: RunContext[None], tool_def: ToolDefinition) -> ToolDefinition:
        tool_def.parameters_json_schema = self.json_schema.get("input_schema", {})
        return tool_def

Start Line: 50
End Line: 53

File Changed: patchwork/patchflow.py

Rule 1: Do not ignore potential bugs in the code

Details: The change from typing to typing_extensions Type import is a potential source of compatibility issues. While not strictly a bug, it could lead to runtime errors if the typing_extensions package is not properly included in the project dependencies. However, this change is likely intentional to support older Python versions or specific typing features.

Affected Code Snippet:

-from typing import Type
+from typing_extensions import Type

Start Line: 2

End Line: 2

File Changed: patchwork/patchflows/GenerateDocstring/GenerateDocstring.py

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security concern with the yaml import. While not directly related to the diff changes, the presence of yaml.load() (if used in the codebase) without specifying Loader=yaml.SafeLoader could lead to arbitrary code execution vulnerabilities. This should be reviewed in the context of how YAML is used in the codebase.

Affected Code Snippet:

import yaml

Start Line: 5

End Line: 5

File Changed: patchwork/patchflows/LogAnalysis/LogAnalysis.py

Rule 1: Do not ignore potential bugs in the code

Details: The code has potential bugs related to error handling and file access:

1. No error handling for file reading operations
2. No validation of file existence before processing
3. Unbounded iteration potential in nested loops

Affected Code Snippet:

final_inputs = yaml.safe_load(_DEFAULT_INPUT_FILE.read_text()) or dict()

log_filename = "gcp_logs.log"
sentry_filename = "sentry_issues.json"
for i in range(self.inputs.get("analysis_limit") or 5):
    logs_detection_output = AgenticLLM(...)

Start Line: 21
End Line: 38

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Several security concerns are present:

1. Hardcoded file paths for sensitive log files
2. Direct reading of YAML file without safe parsing validation
3. Potential for sensitive data exposure in logs

Affected Code Snippet:

log_filename = "gcp_logs.log"
sentry_filename = "sentry_issues.json"

# Later used in user prompt
user_prompt=f"""\
The log file {log_filename} from GCP and the sentry logs can be found at {sentry_filename}.

Here are some relevant information:
Custom Patchflow Id: 5826
Organisation Id: 301
Repository Id: 456
"""

Start Line: 36
End Line: 54

File Changed: patchwork/steps/AgenticLLM/AgenticLLM.py

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug identified in type conversion and error handling. The code assumes inputs.get("max_agent_calls") will always return a valid integer-convertible string, but no error handling is present for invalid values.

Affected Code Snippet:

self.conversation_limit = int(inputs.get("max_agent_calls", 1))

Start Line: 18
End Line: 18

Rule 2: Do not overlook possible security vulnerabilities

Details: Security vulnerability identified in API key handling. The anthropic_api_key is passed directly from inputs without any validation or secure handling mechanisms.

Affected Code Snippet:

api_key=inputs.get("anthropic_api_key"),

Start Line: 20
End Line: 20

Rule 3: Do not deviate from the original coding standards

Details: Code standards deviation observed in return value structure. The original code returned a dictionary with specific keys ('conversation_history' and 'tool_records'), while the new code directly returns the execute() result without maintaining the same structure.

Affected Code Snippet:

def run(self) -> dict:
    return self.agentic_strategy.execute(limit=self.conversation_limit)

Start Line: 34
End Line: 35

File Changed: patchwork/steps/AgenticLLM/typed.py

Rule 1: Do not ignore potential bugs in the code

Details: The removal of type validation and or_op configuration for API keys could lead to runtime errors if the code still expects these validations elsewhere in the codebase. Additionally, the removal of conversation_history and tool_records from AgenticLLMOutputs TypedDict without replacement could cause TypeErrors if other parts of the code expect these fields.

Affected Code Snippet:

class AgenticLLMOutputs(TypedDict):
    pass

Start Line: 17
End Line: 19

---

Rule 2: Do not overlook possible security vulnerabilities

Details: The removal of the structured API key validation system (or_op and configuration messages) reduces the security controls around API key handling. The new implementation accepts a plain string for anthropic_api_key without any validation or documentation, which could lead to insecure API key handling.

Affected Code Snippet:

    anthropic_api_key: str
    agent_system_prompt: str
    example_json: str

Start Line: 12
End Line: 14

File Changed: patchwork/steps/FixIssue/FixIssue.py

Rule 1: Do not ignore potential bugs in the code

Details: The change involves moving from the standard typing module to typing_extensions. This could potentially introduce compatibility issues if the project runs on different Python versions, as typing_extensions is a backport of newer typing features. However, this appears to be an intentional change and doesn't introduce direct bugs.

Affected Code Snippet:

-from typing import Any, Optional
+from typing_extensions import Any, Optional

Start Line: 3
End Line: 3

File Changed: patchwork/steps/ScanSonar/ScanSonar.py

Rule 1: Do not ignore potential bugs in the code

Details: The change from typing to typing_extensions could potentially introduce compatibility issues if the codebase relies on specific behavior from the standard typing module. However, this is a minor concern as typing_extensions is generally used to backport typing features to older Python versions.

Affected Code Snippet:

-from typing import List
+from typing_extensions import List

Start Line: 1
End Line: 1

---

Summary:
The code diff shows a minor modification to replace the standard typing module with typing_extensions. While this change warrants attention for potential compatibility issues (Rule 1), it does not introduce security vulnerabilities (Rule 2) or violate coding standards (Rule 3). The use of typing_extensions is a common practice for ensuring compatibility across different Python versions.

Recommendation:

• Verify that typing_extensions is listed in the project's dependencies
• Ensure the minimum Python version requirement is documented
• Test the code with all supported Python versions to confirm compatibility

File Changed: pyproject.toml

Rule 1: Do not ignore potential bugs in the code

Details: The dependency updates introduce potential version compatibility issues. The change from pydantic ~2.8.2 to ~2.10.6 and adding pydantic-ai could introduce breaking changes in type validation and model behavior.

Affected Code Snippet:

-pydantic = "~2.8.2"
+pydantic = "~2.10.6"
+pydantic-ai = "^0.0.23"

Start Line: 35
End Line: 37

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Several dependency version updates that could introduce security concerns:

1. requests upgrade to 2.32.3 is a non-standard version (latest stable is 2.31.0)
2. anthropic change from 0.40.0 to ^0.45.2 uses caret (^) instead of tilde () versioning, which could allow broader version updates and potential security risks

Affected Code Snippet:

-requests = "~2.31.0"
+requests = "~2.32.3"
-anthropic = "~0.40.0"
+anthropic = "^0.45.2"

Start Line: 42, 46
End Line: 42, 46