Standardize logging config

healthchain/__init__.py

@@ -1,17 +1,13 @@
-import logging
 import warnings
 
-from .utils.logger import add_handlers
+from .utils.logger import get_logger
 from .config.base import ConfigManager, ValidationLevel
 
 
 # Enable deprecation warnings
 warnings.filterwarnings("always", category=DeprecationWarning, module="healthchain")
 
-logger = logging.getLogger(__name__)
-
-add_handlers(logger)
-logger.setLevel(logging.INFO)
+logger = get_logger(__name__)
 
 # Export them at the top level
 __all__ = ["ConfigManager", "ValidationLevel", "api", "ehr", "sandbox"]

healthchain/config/base.py

@@ -1,10 +1,10 @@
 import yaml
-import logging
+from healthchain.utils.logger import get_logger
 import os
 from pathlib import Path
 from typing import Dict, Any, Optional, List
 
-log = logging.getLogger(__name__)
+log = get_logger(__name__)
 
 
 def _deep_merge(target: Dict, source: Dict) -> None:

healthchain/config/validators.py

@@ -4,11 +4,11 @@
 This module provides validation models and utilities for configuration files.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 from pydantic import BaseModel, ValidationError, field_validator, ConfigDict
 from typing import Dict, List, Any, Optional, Type, Union
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 #
 # Base Models

healthchain/fhir/dataframe.py

@@ -7,7 +7,7 @@
 """
 
 import pandas as pd
-import logging
+from healthchain.utils.logger import get_logger
 
 from typing import Any, Dict, List, Union, Optional, Literal
 from collections import defaultdict
@@ -20,7 +20,7 @@
     encode_gender,
 )
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 # Resource handler registry

healthchain/fhir/elementhelpers.py

@@ -4,7 +4,7 @@
 as building blocks within FHIR resources (e.g., CodeableConcept, Attachment, Coding).
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 import base64
 import datetime
 
@@ -13,7 +13,7 @@
 if TYPE_CHECKING:
     from healthchain.fhir.version import FHIRVersion
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 def create_single_codeable_concept(

healthchain/fhir/readers.py

@@ -4,15 +4,15 @@
 and reading data from FHIR resources.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 import importlib
 import re
 
 from typing import Optional, Dict, Any, List
 from fhir.resources.resource import Resource
 from fhir.resources.documentreference import DocumentReference
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 def _fix_timezone_naive_datetimes(data: Any) -> Any:

healthchain/fhir/resourcehelpers.py

@@ -10,7 +10,7 @@
 Parameters marked REQUIRED are required by FHIR specification.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 import datetime
 
 from typing import List, Optional, Dict, Any, Union, TYPE_CHECKING
@@ -29,7 +29,7 @@
 if TYPE_CHECKING:
     from healthchain.fhir.version import FHIRVersion
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 def create_condition(

healthchain/fhir/version.py

@@ -23,12 +23,12 @@
 """
 
 import importlib
-import logging
+from healthchain.utils.logger import get_logger
 from contextlib import contextmanager
 from enum import Enum
 from typing import Any, Generator, Optional, Type, Union
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRVersion(str, Enum):

healthchain/gateway/api/app.py

@@ -5,7 +5,7 @@
 healthcare-specific gateways, routes, middleware, and capabilities.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 
 from contextlib import asynccontextmanager
 from datetime import datetime
@@ -21,7 +21,7 @@
 from healthchain.gateway.events.dispatcher import EventDispatcher
 from healthchain.gateway.api.dependencies import get_app
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class HealthChainAPI(FastAPI):

healthchain/gateway/base.py

@@ -5,7 +5,7 @@
 architecture of the gateway system.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 import asyncio
 
 from abc import ABC
@@ -16,7 +16,7 @@
 from healthchain.gateway.api.protocols import EventDispatcherProtocol
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 # Type variables for self-referencing return types and generic gateways

healthchain/gateway/cds/__init__.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 
 from typing import Any, Callable, Dict, List, Optional, TypeVar, Union
 
@@ -14,7 +14,7 @@
 from healthchain.sandbox.workflows import UseCaseMapping
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 # Type variable for self-referencing return types
 T = TypeVar("T", bound="CDSHooksService")

healthchain/gateway/clients/auth.py

@@ -5,7 +5,7 @@
 management and refresh.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 import os
 import uuid
 import asyncio
@@ -17,7 +17,7 @@
 from pydantic import BaseModel
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class OAuth2Config(BaseModel):

healthchain/gateway/clients/fhir/aio/client.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 import httpx
 
 from typing import Any, Dict, Type, Union
@@ -11,7 +11,7 @@
 from healthchain.gateway.clients.fhir.base import FHIRAuthConfig, FHIRServerInterface
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class AsyncFHIRClient(FHIRServerInterface):

healthchain/gateway/clients/fhir/base.py

@@ -1,5 +1,5 @@
 import json
-import logging
+from healthchain.utils.logger import get_logger
 import httpx
 
 from abc import ABC, abstractmethod
@@ -15,7 +15,7 @@
 from pydantic import BaseModel
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRClientError(Exception):

healthchain/gateway/clients/fhir/sync/client.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 import httpx
 
 from typing import Any, Dict, Type, Union
@@ -11,7 +11,7 @@
 from healthchain.gateway.clients.fhir.base import FHIRAuthConfig, FHIRServerInterface
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRClient(FHIRServerInterface):

healthchain/gateway/clients/fhir/sync/connection.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 import urllib.parse
 
 from typing import Dict
@@ -7,7 +7,7 @@
 from healthchain.gateway.fhir.errors import FHIRConnectionError
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRConnectionManager:

healthchain/gateway/events/dispatcher.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 import asyncio
 from enum import Enum
 from pydantic import BaseModel
@@ -10,7 +10,7 @@
 from fastapi_events.middleware import EventHandlerASGIMiddleware
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class EHREventType(Enum):

healthchain/gateway/fhir/aio.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 
 from contextlib import asynccontextmanager
 from typing import Any, Dict, Optional, Type
@@ -15,7 +15,7 @@
 from healthchain.fhir import add_provenance_metadata
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class AsyncFHIRGateway(BaseFHIRGateway):

healthchain/gateway/fhir/base.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 import inspect
 import warnings
 
@@ -14,7 +14,7 @@
 from healthchain.gateway.base import BaseGateway
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 # Type variable for FHIR Resource

healthchain/gateway/fhir/errors.py

@@ -5,10 +5,10 @@
 including status code mapping, error formatting, and exception types.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 from typing import Optional
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRConnectionError(Exception):

healthchain/gateway/fhir/sync.py

@@ -1,4 +1,4 @@
-import logging
+from healthchain.utils.logger import get_logger
 
 from typing import Any, Dict, Type, Optional
 
@@ -13,7 +13,7 @@
 from healthchain.fhir import add_provenance_metadata
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class FHIRGateway(BaseFHIRGateway):

healthchain/gateway/soap/fastapiserver.py

@@ -5,10 +5,10 @@
 from healthchain.models.requests.cdarequest import CdaRequest
 from healthchain.models.responses.cdaresponse import CdaResponse
 import base64
-import logging
+from healthchain.utils.logger import get_logger
 from pathlib import Path
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 # SOAP namespace for envelope
 SOAP_NS = "http://schemas.xmlsoap.org/soap/envelope/"

healthchain/gateway/soap/notereader.py

@@ -5,7 +5,7 @@
 Epic's CDA document processing services.
 """
 
-import logging
+from healthchain.utils.logger import get_logger
 
 from typing import Any, Callable, Dict, Optional, TypeVar, Union
 
@@ -19,7 +19,7 @@
 from healthchain.models.responses.cdaresponse import CdaResponse
 from healthchain.gateway.soap.fastapiserver import create_fastapi_soap_router
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 # Type variable for self-referencing return types

healthchain/interop/__init__.py

@@ -13,7 +13,7 @@
 from .generators.cda import CDAGenerator
 from .generators.fhir import FHIRGenerator
 
-import logging
+from healthchain.utils.logger import get_logger
 from pathlib import Path
 from typing import Optional, Union
 
@@ -106,7 +106,7 @@ def create_interop(
     Raises:
         ValueError: If config_dir doesn't exist or if validation_level/environment has invalid values
     """
-    logger = logging.getLogger(__name__)
+    logger = get_logger(__name__)
 
     if config_dir is None:
         # Use bundled configs as default