Add standalone JSON logging (cre_logging)

Makefile

@@ -162,7 +162,7 @@ lint:
 	[ -d "./venv" ] && . ./venv/bin/activate && black . && yarn lint && make openapi-guardrail
 
 mypy:
-	[ -d "./venv" ] && . ./venv/bin/activate &&  mypy --ignore-missing-imports --implicit-reexport --no-strict-optional --strict application
+	[ -d "./venv" ] && . ./venv/bin/activate &&  mypy --ignore-missing-imports --implicit-reexport --no-strict-optional --strict application cre_logging
 
 frontend:
 	yarn build

application/__init__.py

@@ -1,4 +1,8 @@
 # type:ignore
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import string
 from typing import Any
 from sqlalchemy import MetaData

application/cmd/__init__.py

@@ -0,0 +1,3 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)

application/cmd/cre_main.py

@@ -1,8 +1,11 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import re
 import time
 import argparse
 import json
-import logging
 import os
 import shutil
 import tempfile
@@ -29,9 +32,6 @@
 if TYPE_CHECKING:
     from application.prompt_client import prompt_client as prompt_client
 
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
 
 app = None
 

application/config.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 
 basedir = os.path.abspath(os.path.dirname(__file__))

application/database/__init__.py

@@ -0,0 +1,3 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)

application/database/db.py

@@ -1,15 +1,17 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from sqlalchemy import CheckConstraint
 import networkx as nx
 import uuid
 import neo4j
 import os
-import logging
 import re
 import time
 import yaml
 
 from datetime import datetime, timezone
-from pprint import pprint
 
 from collections import Counter, defaultdict
 from itertools import permutations
@@ -54,10 +56,6 @@
 
 from .. import sqla  # type: ignore
 
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
-
 
 BaseModel: DefaultMeta = sqla.Model
 

application/database/inmemory_graph.py

@@ -1,15 +1,13 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import sys
-import logging
 import networkx as nx
 from typing import List, Tuple
 from application.defs import cre_defs as defs
 
 
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
-
-
 class CycleDetectedError(Exception):
     def __init__(self, message):
         super().__init__(message)

application/database/pgvector_utils.py

@@ -12,6 +12,10 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 from typing import Any, Iterable, Optional, Sequence, Set, Tuple
 
@@ -53,9 +57,7 @@ class PgVectorUnavailableError(RuntimeError):
 
 
 def _exit_with_message(msg: str) -> None:
-    import logging
-
-    logging.getLogger(__name__).error(msg)
+    logger.error(msg)
     raise SystemExit(msg)
 
 

application/defs/__init__.py

@@ -0,0 +1,3 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)

application/defs/cheatsheet_defs.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from dataclasses import dataclass, field
 from typing import Dict, List
 

application/defs/cre_defs.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import re
 import json
 from copy import copy

application/defs/cre_exceptions.py

@@ -1,3 +1,8 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
+
 class DocumentFormatException(Exception):
     pass
 

application/defs/osib_defs.py

@@ -1,6 +1,8 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import networkx as nx
-from pprint import pprint
-import logging
 import os
 import re
 import warnings
@@ -22,10 +24,6 @@
     from_dict,
 )
 
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
-
 
 # used for serialising and deserialising yaml OSIB documents
 

application/feature_flags.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 
 try:

application/mcp/__init__.py

@@ -1,5 +1,9 @@
 """Local stdio MCP server exposing public OpenCRE REST reads (issue #1003 v1)."""
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from application.mcp.catalog import PUBLIC_TOOLS, get_tool, list_tool_names
 
 __all__ = ["PUBLIC_TOOLS", "get_tool", "list_tool_names"]

application/mcp/__main__.py

@@ -2,17 +2,15 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import asyncio
-import logging
-import sys
 
 
 def main() -> None:
-    logging.basicConfig(
-        level=logging.INFO,
-        stream=sys.stderr,
-        format="%(levelname)s %(name)s: %(message)s",
-    )
+    logger.info("starting OpenCRE MCP stdio server")
     from application.mcp.server import run_stdio
 
     asyncio.run(run_stdio())

application/mcp/catalog.py

@@ -5,6 +5,10 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from dataclasses import dataclass
 from typing import Dict, List, Tuple
 

application/mcp/openapi_loader.py

@@ -6,6 +6,10 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import copy
 import os
 from functools import lru_cache

application/mcp/rest_client.py

@@ -6,8 +6,11 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import json
-import logging
 import os
 import re
 from dataclasses import dataclass
@@ -22,7 +25,6 @@
 from application.mcp.catalog import ToolSpec, get_tool
 from application.mcp.openapi_loader import operation_input_schema
 
-logger = logging.getLogger(__name__)
 
 DEFAULT_BASE_URL = "http://127.0.0.1:5000"
 DEFAULT_TIMEOUT_SECONDS = 30.0

application/mcp/server.py

@@ -2,8 +2,11 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import json
-import logging
 from typing import Any, Dict, Optional
 
 import mcp.types as types
@@ -19,7 +22,6 @@
     RestResponseError,
 )
 
-logger = logging.getLogger(__name__)
 
 SERVER_NAME = "opencre"
 SERVER_VERSION = "0.1.0"

application/prompt_client/embed_alignment.py

@@ -8,16 +8,18 @@
 
 from __future__ import annotations
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import json
-import logging
 import os
 import re
 from dataclasses import dataclass
 from typing import Any, Dict, List, Optional, Set, Tuple
 from urllib.parse import urldefrag
 from pydantic import BaseModel, ConfigDict, Field, ValidationError
 
-logger = logging.getLogger(__name__)
 
 SMART_EXTRACT_POLICY_VERSION = os.environ.get("CRE_EMBED_SMART_POLICY_VERSION", "1")
 

application/prompt_client/llm_error_utils.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from typing import Any
 
 

application/prompt_client/prompt_client.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from application.database import db
 from application.defs import cre_defs
 from datetime import datetime
@@ -12,7 +16,6 @@
 from typing import Dict, List, Any, Tuple, Optional
 from pydantic import ValidationError
 from jinja2 import Environment, FileSystemLoader, StrictUndefined
-import logging
 
 try:
     from pypdf import PdfReader
@@ -25,9 +28,6 @@
 import requests
 import time
 
-logging.basicConfig()
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
 
 SIMILARITY_THRESHOLD = float(os.environ.get("CHATBOT_SIMILARITY_THRESHOLD", "0.7"))
 PROMPT_TEMPLATES_DIR = os.path.join(os.path.dirname(__file__), "templates")

application/tests/__init__.py

@@ -0,0 +1,3 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)

application/tests/admin_imports_api_test.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 import unittest
 from unittest.mock import patch

application/tests/ai_exchange_csv_test.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 import unittest
 

application/tests/auth_routes_test.py

@@ -5,6 +5,10 @@
 the NO_LOGIN dev bypass. OpenAPI documentation is intentionally out of scope here.
 """
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import os
 import unittest
 from typing import Any

application/tests/capec_parser_test.py

@@ -1,3 +1,7 @@
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 from application.defs import cre_defs as defs
 import unittest
 from application import create_app, sqla  # type: ignore

application/tests/ccmv4_parser_test.py

@@ -1,5 +1,9 @@
 # Tests disabled as importer disabled
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 # from pathlib import Path
 # from tempfile import mkdtemp, mkstemp
 # import zipfile

application/tests/chat_completion_test.py

@@ -1,5 +1,9 @@
 """Tests for /rest/v1/completion (chatbot) error handling."""
 
+from cre_logging import get_logger
+
+logger = get_logger(__name__)
+
 import json
 import os
 import unittest