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Merged
kevinbackhouse merged 3 commits into from
Dec 4, 2025
Merged

Use seclab_taskflow_agent.path_utils #11

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7959cec
Use seclab_taskflow_agent.path_utils
kevinbackhouse Dec 4, 2025
1a1f5cf
Update src/seclab_taskflows/mcp_servers/codeql_python/mcp_server.py
kevinbackhouse Dec 4, 2025
c45e064
Update src/seclab_taskflows/mcp_servers/local_file_viewer.py
kevinbackhouse Dec 4, 2025
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20 changes: 10 additions & 10 deletions src/seclab_taskflows/mcp_servers/codeql_python/mcp_server.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,6 @@


import logging
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s',
filename='logs/mcp_codeql_python.log',
filemode='a'
)
from seclab_taskflow_agent.mcp_servers.codeql.client import run_query, _debug_log
# from seclab_taskflow_agent.path_utils import mcp_data_dir

Expand All @@ -23,14 +17,20 @@
from sqlalchemy.orm import Session
import subprocess
import importlib.resources
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

from .codeql_sqlite_models import Base, Source
from ..utils import process_repo

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")

Expand Down
16 changes: 8 additions & 8 deletions src/seclab_taskflows/mcp_servers/gh_actions.py
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Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -19,7 +12,14 @@
from sqlalchemy import create_engine
from sqlalchemy.orm import Session
from pathlib import Path
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

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
Expand Down Expand Up @@ -49,7 +49,7 @@ 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__])
Expand Down
19 changes: 10 additions & 9 deletions src/seclab_taskflows/mcp_servers/gh_code_scanning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,6 @@
# 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'
)
from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -20,18 +14,25 @@
import zipfile
from sqlalchemy import create_engine
from sqlalchemy.orm import Session
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

from .alert_results_models import AlertResults, AlertFlowGraph, 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:
"""Parse the alert dictionary to extract relevant information."""
Expand Down
17 changes: 9 additions & 8 deletions src/seclab_taskflows/mcp_servers/gh_file_viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -22,6 +15,14 @@
import aiofiles
import zipfile
import tempfile
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

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
Expand All @@ -46,7 +47,7 @@ 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__])
Expand Down
14 changes: 8 additions & 6 deletions src/seclab_taskflows/mcp_servers/ghsa.py
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@@ -1,17 +1,19 @@
import logging
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s',
filename='logs/mcp_ghsa.log',
filemode='a'
)

from fastmcp import FastMCP
from pydantic import Field
import re
import json
from urllib.parse import urlparse, parse_qs
from .gh_code_scanning import call_api
from seclab_taskflow_agent.path_utils import log_file_name

logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s',
filename=log_file_name('mcp_ghsa.log'),
filemode='a'
)

mcp = FastMCP("GitHubRepoAdvisories")

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16 changes: 8 additions & 8 deletions src/seclab_taskflows/mcp_servers/local_file_viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -18,11 +11,18 @@
import aiofiles
import zipfile
import tempfile
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name
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Copilot AI Dec 4, 2025

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Import of 'log_file_name' is not used.

Copilot uses AI. Check for mistakes.

logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s',
filename=log_file_dir('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):
directory_path = Path(directory)
Expand Down
16 changes: 8 additions & 8 deletions src/seclab_taskflows/mcp_servers/local_gh_resources.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -18,15 +11,22 @@
import aiofiles
import zipfile
import tempfile
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

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):
directory_path = Path(directory)
Expand Down
17 changes: 9 additions & 8 deletions src/seclab_taskflows/mcp_servers/repo_context.py
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Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
from pydantic import Field
import httpx
Expand All @@ -19,11 +12,19 @@
from sqlalchemy import create_engine
from sqlalchemy.orm import Session
from pathlib import Path
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

from .repo_context_models import Application, EntryPoint, UserAction, WebEntryPoint, ApplicationIssue, AuditResult, Base
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):
return {
Expand Down
17 changes: 9 additions & 8 deletions src/seclab_taskflows/mcp_servers/report_alert_state.py
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Expand Up @@ -2,13 +2,6 @@
# 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'
)

from fastmcp import FastMCP
import json
from pathlib import Path
Expand All @@ -17,9 +10,17 @@
from sqlalchemy import create_engine
from sqlalchemy.orm import Session
from pydantic import Field
from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name

from .alert_results_models import AlertResults, AlertFlowGraph, 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 {
"canonical_id": result.canonical_id,
Expand Down Expand Up @@ -57,7 +58,7 @@ 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:
def __init__(self, memcache_state_dir: str):
Expand Down