Add FileAgent

[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: .github/workflows/test.yml

Rule 1: Do not ignore potential bugs in the code

Details: The change from --only main --extras security to --all-extras could potentially introduce unintended dependencies that might cause conflicts or unexpected behavior in the build process.

Affected Code Snippet:

- run: poetry install --no-interaction --only main --extras security
+ run: poetry install --no-interaction --all-extras

Start Line: 99
End Line: 99

Details: Similar issue with dependency changes in the second location.

Affected Code Snippet:

- run: poetry install --no-interaction --only main
+ run: poetry install --no-interaction --all-extras

Start Line: 154
End Line: 154

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Changing from --only main --extras security to --all-extras removes the explicit security extras specification and could potentially include unnecessary dependencies that might increase the attack surface. Installing all extras instead of only required ones violates the principle of least privilege.

Affected Code Snippet:

- run: poetry install --no-interaction --only main --extras security
+ run: poetry install --no-interaction --all-extras

Start Line: 99
End Line: 99

Details: Second instance of the same security concern.

Affected Code Snippet:

- run: poetry install --no-interaction --only main
+ run: poetry install --no-interaction --all-extras

Start Line: 154
End Line: 154

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

Rule 3: Do not deviate from the original coding standards

Details: The change actually deviates from the established coding style in the project. The original code used multi-line formatting for better readability of the list comprehension. The modification compresses it into a single line, which could potentially reduce code readability, especially for longer header collections. Consider maintaining the original multi-line format for consistency and readability.

Affected Code Snippet:

header_string = "\n".join(f"{key}: {value}" for key, value in headers.items())

Start Line: 94

End Line: 94

Recommendation: Maintain the original multi-line format:

header_string = "\n".join(
    f"{key}: {value}" for key, value in headers.items()
)

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

Rule 1: Do not ignore potential bugs in the code

Details: The code introduces a potential bug in path handling where view_range index validation is missing, which could lead to IndexError exceptions.

Affected Code Snippet:

if view_range:
    lines = content.splitlines()
    start, end = view_range
    content = "\n".join(lines[start - 1 : end])

Start Line: 66
End Line: 69

---

Rule 2: Do not overlook possible security vulnerabilities

Details: The code modification has introduced a path traversal vulnerability by not properly sanitizing the path input before joining it with repo_path.

Affected Code Snippet:

wanted_path = Path(path)
if not Path(path).is_absolute():
    wanted_path = self.repo_path / path

Start Line: 48
End Line: 50

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

Rule 1: Do not ignore potential bugs in the code

Details: Several potential bugs identified in the code:

1. No error handling for file permission issues during directory operations
2. No validation of SQL query before execution
3. No cleanup of temporary database file
4. Potential race condition with database file access

Affected Code Snippet:

def execute(self, files: list[str], query: str) -> str:
    db_path = (Path(self.tmp_path) / "tmp.db").resolve()
    db_url = URL.create(drivername="sqlite", host="/" + str(db_path)).render_as_string()
    
    # No error handling for file operations
    files_to_insert = []
    if db_path.is_file():
        with sqlite3.connect(str(db_path)) as conn:
            for file in files:
                res = conn.execute(
                    f"SELECT 1 from {file.removesuffix('.csv')}",
                )
                if res.fetchone() is None:
                    files_to_insert.append(file)

Start Line: 110
End Line: 124

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Critical security vulnerabilities found:

1. SQL Injection vulnerability in table name construction
2. Unsanitized file paths used in command execution
3. No input validation for SQL query
4. Potential path traversal vulnerability

Affected Code Snippet:

res = conn.execute(
    f"SELECT 1 from {file.removesuffix('.csv')}",  # SQL Injection vulnerability
)

# Unsanitized command execution
p = subprocess.run(
    ["csvsql", *files_to_insert, "--db", db_url, "--insert"], 
    capture_output=True, 
    text=True, 
    cwd=self.path
)

Start Line: 119
End Line: 128

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

Rule 1: Do not ignore potential bugs in the code

Details: The code introduces a silent exception handling block that swallows all exceptions without logging or handling them properly. This could hide critical errors and make debugging difficult.

Affected Code Snippet:

try:
    with path.open("r") as f:
        for i, line in enumerate(f.readlines()):
            if not matcher(line, pattern):
                continue

            content = f"Line {i + 1}: {line}"
            if len(line) > self.__CHAR_LIMIT:
                content = f"Line {i + 1}: {self.__CHAR_LIMIT_TEXT}"

            file_matches[str(path)].append(content)
except Exception as e:
    pass

Start Line: 189
End Line: 201

---

Rule 2: Do not overlook possible security vulnerabilities

Details: The code attempts to open files without any validation of the file type or size, which could lead to potential security issues like:

1. Opening binary files that could contain malicious content
2. Opening very large files that could cause memory exhaustion (readlines() loads entire file)
3. No proper error handling for permission issues

Affected Code Snippet:

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

Start Line: 189
End Line: 190

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

Rule 1: Do not ignore potential bugs in the code

Details: There are a few potential bugs that should be addressed:

1. No error handling for file operations in temporary directory
2. No validation of input parameters
3. Potential race condition with temporary directory usage
4. Unchecked agent_config before accessing tool_set

Affected Code Snippet:

def run(self) -> dict:
    kwargs = self.strat_kwargs
    with tempfile.TemporaryDirectory() as tmpdir:
        agent_config = next(iter(kwargs.get("agent_configs", [])), None)
        agent_config.tool_set = dict(
            find_text=FindTextTool(self.base_path),
            file_view=FileViewTool(self.base_path),
            in2csv_tool=In2CSVTool(self.base_path),
            csvsql_tool=CSVSQLTool(self.base_path, tmpdir),
        )

Start Line: 50
End Line: 59

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Several security concerns identified:

1. Using raw user input in template rendering without sanitization
2. Using Path.cwd() as default base path could allow access outside intended directory
3. No path traversal protection in base_path handling

Affected Code Snippet:

def __init__(self, inputs):
    super().__init__(inputs)
    self.base_path = inputs.get("base_path", str(Path.cwd()))
    data = inputs.get("prompt_value", {})
    task = mustache_render(inputs["task"], data)

Start Line: 16
End Line: 20

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

Rule 1: Do not ignore potential bugs in the code

Details: Potential bug found in class name typo. The class name __ReconcilationAgentRequiredInputs appears to have a spelling error in "Reconcilation" which should be "Reconciliation". This could lead to confusion and maintenance issues.

Affected Code Snippet:

class __ReconcilationAgentRequiredInputs(TypedDict):
    task: str

Start Line: 6
End Line: 7

---

Rule 2: Do not overlook possible security vulnerabilities

Details: Security vulnerability detected in API key handling. The code allows multiple API keys to be passed as configuration, but there's no validation or sanitization of these keys visible in the type definitions. While type definitions alone don't implement security, the structure suggests these keys might be passed around in an insecure manner.

Affected Code Snippet:

    openai_api_key: Annotated[
        str, StepTypeConfig(is_config=True, or_op=["patched_api_key", "google_api_key", "anthropic_api_key"])
    ]
    anthropic_api_key: Annotated[
        str, StepTypeConfig(is_config=True, or_op=["patched_api_key", "google_api_key", "openai_api_key"])
    ]
    google_api_key: Annotated[
        str, StepTypeConfig(is_config=True, or_op=["patched_api_key", "openai_api_key", "anthropic_api_key"])
    ]

Start Line: 13
End Line: 21

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

Rule 1: Do not ignore potential bugs in the code

Details: The removal of List import while still using TypedDict could potentially create a bug if List is used elsewhere in the codebase that imports from this file. Additionally, removing conversation_history and tool_records from GitHubAgentOutputs could cause runtime errors if other parts of the code expect these fields to be present.

Affected Code Snippet:

-from typing_extensions import Annotated, Any, Dict, List, TypedDict
+from typing_extensions import Annotated, Any, Dict, TypedDict

class GitHubAgentOutputs(TypedDict):
-    conversation_history: List[Dict]
-    tool_records: List[Dict]
    request_tokens: int
    response_tokens: int

Start Line: 1

End Line: 27

File Changed: patchwork/steps/__init__.py

Rule 2: Do not overlook possible security vulnerabilities

Details: Potential security concern with the introduction of FileAgent module. The name suggests it handles file operations, which could introduce file system access vulnerabilities if not properly implemented. However, this diff only shows the import and export declarations - a full security assessment would require reviewing the actual FileAgent implementation.

Affected Code Snippet:

from patchwork.steps.FileAgent.FileAgent import FileAgent
...
"FileAgent",

Start Line: 28

End Line: 86

File Changed: pyproject.toml

Rule 2: Do not overlook possible security vulnerabilities

Analysis: The addition of csvkit v2.1.0 introduces a new dependency that deals with CSV file processing. While the package itself is well-maintained, it could potentially expose the application to CSV injection attacks if not used properly. This requires careful implementation review in the actual code using this library.

Details: WARNING: Adding csvkit requires security review for CSV injection prevention patterns in implementation code.

Affected Code Snippet:

csvkit = "^2.1.0"

Start Line: 52

End Line: 52