Merge main branch with path_utils changes and apply linter fixes

Co-authored-by: kevinbackhouse <4358136+kevinbackhouse@users.noreply.github.com>

Author: Copilot

src/seclab_taskflows/mcp_servers/codeql_python/mcp_server.py

@@ -2,37 +2,34 @@
 # SPDX-License-Identifier: MIT
 
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_codeql_python.log",
-    filemode="a",
-)
 import csv
 import importlib.resources
 import json
+import logging
 import os
 import subprocess
 from pathlib import Path
 
 # from mcp.server.fastmcp import FastMCP, Context
 from fastmcp import FastMCP  # use FastMCP 2.0
-
-# from seclab_taskflow_agent.path_utils import mcp_data_dir
 from pydantic import Field
 from seclab_taskflow_agent.mcp_servers.codeql.client import _debug_log, run_query
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 from ..utils import process_repo
 from .codeql_sqlite_models import Base, Source
 
-MEMORY = Path(os.getenv("DATA_DIR", default="/app/data"))
-CODEQL_DBS_BASE_PATH = Path(os.getenv("CODEQL_DBS_BASE_PATH", default="/app/data"))
-# MEMORY =  mcp_data_dir('seclab-taskflows', 'codeql', 'DATA_DIR')
-# CODEQL_DBS_BASE_PATH =  mcp_data_dir('seclab-taskflows', 'codeql', 'CODEQL_DBS_BASE_PATH')
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_codeql_python.log"),
+    filemode="a",
+)
+
+MEMORY = mcp_data_dir("seclab-taskflows", "codeql", "DATA_DIR")
+CODEQL_DBS_BASE_PATH = mcp_data_dir("seclab-taskflows", "codeql", "CODEQL_DBS_BASE_PATH")
 
 mcp = FastMCP("CodeQL-Python")
 

src/seclab_taskflows/mcp_servers/gh_actions.py

@@ -1,26 +1,25 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_gh_actions.log",
-    filemode="a",
-)
-
 import json
+import logging
 import os
-from pathlib import Path
 
 import httpx
 import yaml
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import DeclarativeBase, Mapped, Session, mapped_column
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_gh_actions.log"),
+    filemode="a",
+)
+
 
 class Base(DeclarativeBase):
     pass
@@ -56,7 +55,7 @@ def __repr__(self):
 if not GITHUB_PERSONAL_ACCESS_TOKEN:
     GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("COPILOT_TOKEN")
 
-ACTIONS_DB_DIR = Path(os.getenv("ACTIONS_DB_DIR", default="/app/my_data"))
+ACTIONS_DB_DIR = mcp_data_dir("seclab-taskflows", "gh_actions", "ACTIONS_DB_DIR")
 
 engine = create_engine(f"sqlite:///{os.path.abspath(ACTIONS_DB_DIR)}/actions.db", echo=False)
 Base.metadata.create_all(engine, tables=[WorkflowUses.__table__])

src/seclab_taskflows/mcp_servers/gh_code_scanning.py

@@ -1,15 +1,8 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_gh_code_scanning.log",
-    filemode="a",
-)
 import json
+import logging
 import os
 import re
 import zipfile
@@ -20,20 +13,27 @@
 import httpx
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 from .alert_results_models import AlertFlowGraph, AlertResults, Base
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_gh_code_scanning.log"),
+    filemode="a",
+)
+
 mcp = FastMCP("GitHubCodeScanning")
 
 GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("GITHUB_PERSONAL_ACCESS_TOKEN", default="")
 if not GITHUB_PERSONAL_ACCESS_TOKEN:
     GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("COPILOT_TOKEN")
 
-CODEQL_DBS_BASE_PATH = Path(os.getenv("CODEQL_DBS_BASE_PATH", default="/app/my_data"))
-
-ALERT_RESULTS_DIR = Path(os.getenv("ALERT_RESULTS_DIR", default="/app/my_data"))
+CODEQL_DBS_BASE_PATH = mcp_data_dir("seclab-taskflows", "codeql", "CODEQL_DBS_BASE_PATH")
+ALERT_RESULTS_DIR = mcp_data_dir("seclab-taskflows", "gh_code_scanning", "ALERT_RESULTS_DIR")
 
 
 def parse_alert(alert: dict) -> dict:

src/seclab_taskflows/mcp_servers/gh_file_viewer.py

@@ -1,16 +1,8 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_gh_file_viewer.log",
-    filemode="a",
-)
-
 import json
+import logging
 import os
 import tempfile
 import zipfile
@@ -20,9 +12,17 @@
 import httpx
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import DeclarativeBase, Mapped, Session, mapped_column
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_gh_file_viewer.log"),
+    filemode="a",
+)
+
 
 class Base(DeclarativeBase):
     pass
@@ -51,7 +51,7 @@ def __repr__(self):
 if not GITHUB_PERSONAL_ACCESS_TOKEN:
     GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("COPILOT_TOKEN")
 
-SEARCH_RESULT_DIR = Path(os.getenv("SEARCH_RESULTS_DIR", default="/app/my_data"))
+SEARCH_RESULT_DIR = mcp_data_dir("seclab-taskflows", "gh_file_viewer", "SEARCH_RESULTS_DIR")
 
 engine = create_engine(f"sqlite:///{os.path.abspath(SEARCH_RESULT_DIR)}/search_result.db", echo=False)
 Base.metadata.create_all(engine, tables=[SearchResults.__table__])

src/seclab_taskflows/mcp_servers/ghsa.py

@@ -1,18 +1,21 @@
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG, format="%(asctime)s - %(levelname)s - %(message)s", filename="logs/mcp_ghsa.log", filemode="a"
-)
-
 import json
+import logging
 import re
 from urllib.parse import parse_qs, urlparse
 
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name
 
 from .gh_code_scanning import call_api
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_ghsa.log"),
+    filemode="a",
+)
+
 mcp = FastMCP("GitHubRepoAdvisories")
 
 

src/seclab_taskflows/mcp_servers/local_file_viewer.py

@@ -1,26 +1,26 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_local_file_viewer.log",
-    filemode="a",
-)
-
 import json
+import logging
 import os
 import zipfile
 from pathlib import Path
 
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
+
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_local_file_viewer.log"),
+    filemode="a",
+)
 
 mcp = FastMCP("LocalFileViewer")
 
-LOCAL_GH_DIR = Path(os.getenv("LOCAL_GH_DIR", default="/app/my_data"))
+LOCAL_GH_DIR = mcp_data_dir("seclab-taskflows", "local_file_viewer", "LOCAL_GH_DIR")
 
 
 def is_subdirectory(directory, potential_subdirectory):

src/seclab_taskflows/mcp_servers/local_gh_resources.py

@@ -1,30 +1,30 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_local_gh_resources.log",
-    filemode="a",
-)
-
 import json
+import logging
 import os
 from pathlib import Path
 
 import aiofiles
 import httpx
 from fastmcp import FastMCP
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
+
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_local_gh_resources.log"),
+    filemode="a",
+)
 
 mcp = FastMCP("LocalGHResources")
 
 GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("GITHUB_PERSONAL_ACCESS_TOKEN")
 if not GITHUB_PERSONAL_ACCESS_TOKEN:
     GITHUB_PERSONAL_ACCESS_TOKEN = os.getenv("COPILOT_TOKEN")
 
-LOCAL_GH_DIR = Path(os.getenv("LOCAL_GH_DIR", default="/app/my_data"))
+LOCAL_GH_DIR = mcp_data_dir("seclab-taskflows", "local_gh_resources", "LOCAL_GH_DIR")
 
 
 def is_subdirectory(directory, potential_subdirectory):

src/seclab_taskflows/mcp_servers/repo_context.py

@@ -1,28 +1,27 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_repo_context.log",
-    filemode="a",
-)
-
 import json
-import os
+import logging
 from pathlib import Path
 
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 from .repo_context_models import Application, ApplicationIssue, AuditResult, Base, EntryPoint, UserAction, WebEntryPoint
 from .utils import process_repo
 
-MEMORY = Path(os.getenv("REPO_CONTEXT_DIR", default="/app/my_data"))
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_repo_context.log"),
+    filemode="a",
+)
+
+MEMORY = mcp_data_dir("seclab-taskflows", "repo_context", "REPO_CONTEXT_DIR")
 
 
 def app_to_dict(result):

src/seclab_taskflows/mcp_servers/report_alert_state.py

@@ -1,27 +1,26 @@
 # SPDX-FileCopyrightText: 2025 GitHub
 # SPDX-License-Identifier: MIT
 
-import logging
-
-logging.basicConfig(
-    level=logging.DEBUG,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-    filename="logs/mcp_report_alert_state.log",
-    filemode="a",
-)
-
 import json
-import os
+import logging
 from pathlib import Path
 from typing import Any
 
 from fastmcp import FastMCP
 from pydantic import Field
+from seclab_taskflow_agent.path_utils import log_file_name, mcp_data_dir
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 from .alert_results_models import AlertFlowGraph, AlertResults, Base
 
+logging.basicConfig(
+    level=logging.DEBUG,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+    filename=log_file_name("mcp_report_alert_state.log"),
+    filemode="a",
+)
+
 
 def result_to_dict(result):
     return {
@@ -62,7 +61,7 @@ def remove_line_numbers(location: str) -> str:
     return ":".join(parts[:-4])
 
 
-MEMORY = Path(os.getenv("ALERT_RESULTS_DIR", default="/app/my_data"))
+MEMORY = mcp_data_dir("seclab-taskflows", "report_alert_state", "ALERT_RESULTS_DIR")
 
 
 class ReportAlertStateBackend: