Enhancement: Add Python 3.12 and 3.13

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     if: github.event.pull_request.draft == false
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository

.github/workflows/publish.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.11"
+        python-version: "3.12"
     - name: Bump version
       run: |
         VERSION=$(git describe --tags --abbrev=0)

cookbook/notereader_clinical_coding_fhir.py

@@ -132,7 +132,7 @@ def run_server():
 
     # Create sandbox client for testing
     client = SandboxClient(
-        url="http://localhost:8000/notereader/fhir/",
+        url="http://localhost:8000/notereader/?wsdl",
         workflow="sign-note-inpatient",
         protocol="soap",
     )

healthchain/fhir/readers.py

@@ -6,6 +6,7 @@
 
 import logging
 import importlib
+import re
 
 from typing import Optional, Dict, Any, List
 from fhir.resources.resource import Resource
@@ -14,6 +15,42 @@
 logger = logging.getLogger(__name__)
 
 
+def _fix_timezone_naive_datetimes(data: Any) -> Any:
+    """
+    Recursively fix timezone-naive datetime strings by appending UTC timezone.
+
+    Pydantic v2 requires timezone-aware datetimes. This function walks through
+    nested dicts/lists and adds 'Z' (UTC) to datetime strings that match the
+    pattern YYYY-MM-DDTHH:MM:SS but lack timezone info.
+
+    Args:
+        data: Dict, list, or primitive value to process
+
+    Returns:
+        Processed data with timezone-aware datetime strings
+
+    Example:
+        >>> data = {"start": "2021-04-19T00:00:00", "name": "Test"}
+        >>> _fix_timezone_naive_datetimes(data)
+        {"start": "2021-04-19T00:00:00Z", "name": "Test"}
+    """
+    # Pattern: YYYY-MM-DDTHH:MM:SS optionally followed by microseconds
+    # Must NOT already have timezone (Z or +/-HH:MM)
+    datetime_pattern = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(?:\.\d+)?$")
+
+    if isinstance(data, dict):
+        return {
+            key: _fix_timezone_naive_datetimes(value) for key, value in data.items()
+        }
+    elif isinstance(data, list):
+        return [_fix_timezone_naive_datetimes(item) for item in data]
+    elif isinstance(data, str) and datetime_pattern.match(data):
+        # Add UTC timezone
+        return f"{data}Z"
+    else:
+        return data
+
+
 def create_resource_from_dict(
     resource_dict: Dict, resource_type: str
 ) -> Optional[Resource]:
@@ -99,8 +136,10 @@ def convert_prefetch_to_fhir_objects(
             resource_type = resource_data.get("resourceType")
             if resource_type:
                 try:
+                    # Fix timezone-naive datetimes before validation
+                    fixed_data = _fix_timezone_naive_datetimes(resource_data)
                     resource_class = get_fhir_model_class(resource_type)
-                    result[key] = resource_class(**resource_data)
+                    result[key] = resource_class(**fixed_data)
                 except Exception as e:
                     logger.warning(
                         f"Failed to convert {resource_type} to FHIR object: {e}"

healthchain/gateway/api/app.py

@@ -11,7 +11,6 @@
 from datetime import datetime
 from fastapi import FastAPI, APIRouter, HTTPException, Request
 from fastapi.middleware.cors import CORSMiddleware
-from fastapi.middleware.wsgi import WSGIMiddleware
 from fastapi.exceptions import RequestValidationError
 from fastapi.responses import JSONResponse
 from termcolor import colored
@@ -233,10 +232,10 @@ def _add_component_routes(
         # Case 2: WSGI services (like NoteReaderService) - only for services
         if (
             component_type == "service"
-            and hasattr(component, "create_wsgi_app")
-            and callable(component.create_wsgi_app)
+            and hasattr(component, "create_fastapi_router")
+            and callable(component.create_fastapi_router)
         ):
-            self._register_wsgi_service(
+            self._register_mounted_service(
                 component, component_name, endpoints_registry, path
             )
             return
@@ -249,7 +248,7 @@ def _add_component_routes(
         else:
             logger.warning(
                 f"Service {component_name} does not implement APIRouter or WSGI patterns. "
-                f"Services must either inherit from APIRouter or implement create_wsgi_app()."
+                f"Services must either inherit from APIRouter or implement create_fastapi_router()."
             )
 
     def _register_api_router(
@@ -277,29 +276,42 @@ def _register_api_router(
         else:
             logger.debug(f"Registered {component_name} as router (routes unknown)")
 
-    def _register_wsgi_service(
+    def _register_mounted_service(  # Renamed from _register_wsgi_service
         self,
         service: BaseProtocolHandler,
         service_name: str,
         endpoints_registry: Dict[str, set],
         path: Optional[str] = None,
     ) -> None:
-        """Register a WSGI service."""
-        # Create WSGI app
-        wsgi_app = service.create_wsgi_app()
+        """Register a service with a custom router."""
+        router_or_app = service.create_fastapi_router()
 
-        # Determine mount path with fallback chain
         mount_path = (
             path
             or getattr(service.config, "default_mount_path", None)
             or getattr(service.config, "base_path", None)
             or f"/{service_name.lower().replace('service', '').replace('gateway', '')}"
         )
 
-        # Mount the WSGI app
-        self.mount(mount_path, WSGIMiddleware(wsgi_app))
-        endpoints_registry[service_name].add(f"WSGI:{mount_path}")
-        logger.debug(f"Registered WSGI service {service_name} at {mount_path}")
+        logger.debug(f"🔧 Registering {service_name} at: {mount_path}")
+        logger.debug(f"   Router type: {type(router_or_app)}")
+
+        # Use include_router for APIRouter instances
+        if isinstance(router_or_app, APIRouter):
+            if hasattr(router_or_app, "routes"):
+                logger.debug(f"   Routes in router: {len(router_or_app.routes)}")
+                for route in router_or_app.routes:
+                    if hasattr(route, "methods") and hasattr(route, "path"):
+                        logger.info(f"     - {route.methods} {route.path}")
+
+            self.include_router(router_or_app, prefix=mount_path)
+            endpoints_registry[service_name].add(f"INCLUDED:{mount_path}")
+            logger.info(f"✅ Included router {service_name} at {mount_path}")
+        else:
+            # For FastAPI apps, use mount
+            self.mount(mount_path, router_or_app)
+            endpoints_registry[service_name].add(f"MOUNTED:{mount_path}")
+            logger.info(f"✅ Mounted app {service_name} at {mount_path}")
 
     def register_gateway(
         self,

healthchain/gateway/soap/__init__.py

@@ -1,10 +1,6 @@
-from .notereader import NoteReaderService
-from .utils.epiccds import CDSServices
-from .utils.model import ClientFault, ServerFault
+from .notereader import NoteReaderService, NoteReaderConfig
 
 __all__ = [
     "NoteReaderService",
-    "CDSServices",
-    "ClientFault",
-    "ServerFault",
+    "NoteReaderConfig",
 ]