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Fix T201: replace print() with logging; remove global suppression #253

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Fix T201: replace print() with logging; remove global suppression #253

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Copilot Jun 1, 2026
f79999e
Fix T201 linter errors and remove global suppression from pyproject.toml
Copilot Jun 1, 2026
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3 changes: 2 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,6 @@ ignore = [
"EM101", # Exception string literals
"EM102", # Exception f-strings
"G004", # Logging f-strings
"T201", # print() used for user output
"TRY003", # Raise with inline message strings

# Backwards-compatibility suppressions for existing code
Expand Down Expand Up @@ -264,3 +263,5 @@ ignore = [

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["S101", "PLR2004"]
"release_tools/*" = ["T201"]
"scripts/*" = ["T201"]
40 changes: 21 additions & 19 deletions src/seclab_taskflow_agent/mcp_servers/codeql/client.py
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Expand Up @@ -22,6 +22,8 @@

WAIT_INTERVAL = 0.1

logger = logging.getLogger(__name__)

@p- p- Jun 1, 2026

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Logging should be configured here (similar as to our other MCP servers, but with a different file name)
e.g.
https://github.com/GitHubSecurityLab/seclab-taskflows/blob/1eafe13b91b5fa717f96625b24badac9cb4ffe48/src/seclab_taskflows/mcp_servers/gh_file_viewer.py#L21



# for when our stdout goes into the void
def _debug_log(msg):
Expand All @@ -30,7 +32,7 @@ def _debug_log(msg):


def shell_command_to_string(cmd):
print(f"Executing: {cmd}")
logger.debug(f"Executing: {cmd}")
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
stdout, stderr = p.communicate()
p.wait()
Expand Down Expand Up @@ -88,7 +90,7 @@ def _server_start(self):

# set some default callbacks for common notifications
def _handle_ql_progressUpdated(params):
print(f">> Progress: {params.get('step')}/{params.get('maxStep')} status: {params.get('message')}")
logger.debug(f">> Progress: {params.get('step')}/{params.get('maxStep')} status: {params.get('message')}")

ql_progressUpdated = "ql/progressUpdated"
if ql_progressUpdated not in self.method_handlers:
Expand Down Expand Up @@ -150,7 +152,7 @@ def _callback(err: Exception, res: str | None = None):
if err:
raise err
self.active_database = database
print(f"++ {rpc_method}: {res}")
logger.debug(f"++ {rpc_method}: {res}")

return self._server_rpc_call(
rpc_method,
Expand All @@ -168,7 +170,7 @@ def _callback(err: Exception, res: str | None = None):
if err:
raise err
self.active_database = None
print(f"++ {rpc_method}: {res}")
logger.debug(f"++ {rpc_method}: {res}")

return self._server_rpc_call(
rpc_method,
Expand Down Expand Up @@ -232,25 +234,25 @@ def _check_runquery_result_for_errors(params: dict):
case 0:
return False, ""
case 1:
print(f"xx ERROR Other: {message}")
logger.error(f"xx ERROR Other: {message}")
return True, message
case 2:
print(f"xx ERROR Compilation: {message}")
logger.error(f"xx ERROR Compilation: {message}")
return True, message
case 3:
print(f"xx ERROR OOM: {message}")
logger.error(f"xx ERROR OOM: {message}")
return True, message
case 4:
print(f"xx ERROR Query Canceled: {message}")
logger.error(f"xx ERROR Query Canceled: {message}")
return True, message
case 5:
print(f"xx ERROR DB Scheme mismatch: {message}")
logger.error(f"xx ERROR DB Scheme mismatch: {message}")
return True, message
case 6:
print(f"xx ERROR DB Scheme no upgrade found: {message}")
logger.error(f"xx ERROR DB Scheme no upgrade found: {message}")
return True, message
case _:
print(f"xx ERROR: unknown result type {result_type}: {message}")
logger.error(f"xx ERROR: unknown result type {result_type}: {message}")
return True, message
else:
return False, ""
Expand All @@ -260,7 +262,7 @@ def _check_runquery_result_for_errors(params: dict):
else:
self.active_query_error = (True, f"Unknown result state: {res}")
self.active_query_id = None
print(f"++ {rpc_method}: {res}")
logger.debug(f"++ {rpc_method}: {res}")
if err:
raise err

Expand All @@ -284,7 +286,7 @@ def _search_paths_from_codeql_config(self, config="~/.config/codeql/config"):
if match and match.group(2):
return match.group(2).split(":")
except FileNotFoundError as e:
print(f"Error: {e}")
logger.error(f"Error: {e}")
return []

def _lang_server_contact(self):
Expand All @@ -310,7 +312,7 @@ def _resolve_library_paths(self, query_path):
args = ["resolve", "library-path"]
args += ["-v", "--log-to-stderr", "--format=json"]
if search_path:
print(f"Using search path: {search_path}")
logger.debug(f"Using search path: {search_path}")
args += [f'--additional-packs="{search_path}"']
args += [f"--query={query_path}"]
return json.loads(shell_command_to_string(self.codeql_cli + args))
Expand Down Expand Up @@ -364,7 +366,7 @@ def _bqrs_to_csv(self, bqrs_path, entities=""):
with open(csv_out) as f:
return f.read()
except RuntimeError as e:
print(f"Could not decode {bqrs_path} to {csv_out}: {e}")
logger.error(f"Could not decode {bqrs_path} to {csv_out}: {e}")
return ""

def _bqrs_to_json(self, bqrs_path, entities):
Expand All @@ -377,7 +379,7 @@ def _bqrs_to_json(self, bqrs_path, entities):
with open(json_out) as f:
return f.read()
except RuntimeError as e:
print(f"Could not decode {bqrs_path} to {json_out}: {e}")
logger.error(f"Could not decode {bqrs_path} to {json_out}: {e}")
return ""

def _bqrs_to_sarif(self, bqrs_path, query_info, max_paths=10):
Expand All @@ -401,7 +403,7 @@ def _bqrs_to_sarif(self, bqrs_path, query_info, max_paths=10):
):
with open(sarif_out) as f:
return f.read()
print(f"Could not decode {bqrs_path} to {sarif_out}")
logger.error(f"Could not decode {bqrs_path} to {sarif_out}")
return ""


Expand All @@ -417,12 +419,12 @@ def __enter__(self):
return _ACTIVE_CODEQL_SERVERS[self.database]
if not self.active_connection:
self._server_start()
print("Waiting for server start ...")
logger.info("Waiting for server start ...")
while not self.active_connection:
time.sleep(WAIT_INTERVAL)
if not self.active_database:
self._server_register_database(self.database)
print("Waiting for database registration ...")
logger.info("Waiting for database registration ...")
while not self.active_database:
time.sleep(WAIT_INTERVAL)
if self.keep_alive:
Expand Down
4 changes: 3 additions & 1 deletion src/seclab_taskflow_agent/render_utils.py
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Expand Up @@ -5,6 +5,7 @@

import asyncio
import logging
import sys

from .path_utils import log_file_name

Expand Down Expand Up @@ -44,4 +45,5 @@ async def render_model_output(data: str, log: bool = True, async_task: bool = Fa
if data:
if log:
render_logger.info(data)
print(data, end="", flush=True)
sys.stdout.write(data)

@p- p- Jun 1, 2026

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I think a single line linter suppression is better here than using sys.stdout

sys.stdout.flush()