Update services.py

fix context relative path.

app.py

@@ -5,6 +5,7 @@ CURRENT_DIR = os.path.abspath(os.path.dirname(__file__))
 # Introduce app_dir variable that can be overridden by environment
 app_dir = os.environ.get('APP_DIR', CURRENT_DIR)
 sys.path.append(CURRENT_DIR)
+#sys.path.append(os.path.abspath(os.path.dirname(__file__)))
 import datetime
 import shutil
 import queue
@@ -1790,25 +1791,39 @@ def proxy_hapi(subpath):
     logger.debug(f"Proxy received request for path: '/fhir/{subpath}', cleaned subpath: '{clean_subpath}'")
 
     # Determine the target FHIR server base URL
+    # NEW: Check for proxy-target query parameter first
+    target_server_query = request.args.get('proxy-target')
     target_server_header = request.headers.get('X-Target-FHIR-Server')
     final_base_url = None
     is_custom_target = False
 
-    if target_server_header:
+    if target_server_query:
         try:
-             parsed_url = urlparse(target_server_header)
-             if not parsed_url.scheme or not parsed_url.netloc:
-                  raise ValueError("Invalid URL format in X-Target-FHIR-Server header")
-             final_base_url = target_server_header.rstrip('/')
-             is_custom_target = True
-             logger.info(f"Proxy target identified from header: {final_base_url}")
+            parsed_url = urlparse(target_server_query)
+            if not parsed_url.scheme or not parsed_url.netloc:
+                raise ValueError("Invalid URL format in proxy-target query parameter")
+            final_base_url = target_server_query.rstrip('/')
+            is_custom_target = True
+            logger.info(f"Proxy target identified from query parameter: {final_base_url}")
         except ValueError as e:
-             logger.warning(f"Invalid URL in X-Target-FHIR-Server header: '{target_server_header}'. Falling back. Error: {e}")
-             final_base_url = current_app.config['HAPI_FHIR_URL'].rstrip('/')
-             logger.debug(f"Falling back to default local HAPI due to invalid header: {final_base_url}")
+            logger.warning(f"Invalid URL in proxy-target query parameter: '{target_server_query}'. Falling back. Error: {e}")
+            final_base_url = current_app.config['HAPI_FHIR_URL'].rstrip('/')
+            logger.debug(f"Falling back to default local HAPI due to invalid query: {final_base_url}")
+    elif target_server_header:
+        try:
+            parsed_url = urlparse(target_server_header)
+            if not parsed_url.scheme or not parsed_url.netloc:
+                raise ValueError("Invalid URL format in X-Target-FHIR-Server header")
+            final_base_url = target_server_header.rstrip('/')
+            is_custom_target = True
+            logger.info(f"Proxy target identified from header: {final_base_url}")
+        except ValueError as e:
+            logger.warning(f"Invalid URL in X-Target-FHIR-Server header: '{target_server_header}'. Falling back. Error: {e}")
+            final_base_url = current_app.config['HAPI_FHIR_URL'].rstrip('/')
+            logger.debug(f"Falling back to default local HAPI due to invalid header: {final_base_url}")
     else:
         final_base_url = current_app.config['HAPI_FHIR_URL'].rstrip('/')
-        logger.debug(f"No target header found, proxying to default local HAPI: {final_base_url}")
+        logger.debug(f"No target info found, proxying to default local HAPI: {final_base_url}")
 
     # Construct the final URL for the target server request
     # Append the cleaned subpath only if it's not empty
@@ -1890,7 +1905,6 @@ def proxy_hapi(subpath):
     except Exception as e:
          logger.error(f"Unexpected proxy error for {final_url}: {str(e)}", exc_info=True)
          return jsonify({'resourceType': 'OperationOutcome', 'issue': [{'severity': 'error', 'code': 'exception', 'diagnostics': 'An unexpected error occurred within the FHIR proxy.', 'details': {'text': str(e)}}]}), 500
-
 # --- End of corrected proxy_hapi function ---
 
 
@@ -2402,19 +2416,21 @@ def api_retrieve_bundles():
     output_zip = os.path.join(temp_dir, zip_filename)
 
     def generate():
-        try:
-            yield from services.retrieve_bundles(
-                fhir_server_url=fhir_server_url,
-                resources=resources,
-                output_zip=output_zip,
-                validate_references=validate_references,
-                fetch_reference_bundles=fetch_reference_bundles,
-                auth_type=auth_type,
-                auth_token=auth_token
-            )
-        except Exception as e:
-            logger.error(f"Error in retrieve_bundles: {e}", exc_info=True)
-            yield json.dumps({"type": "error", "message": f"Unexpected error: {str(e)}"}) + "\n"
+        # Push the application context manually for the generator's lifetime
+        with app.app_context():
+            try:
+                yield from services.retrieve_bundles(
+                    fhir_server_url=fhir_server_url,
+                    resources=resources,
+                    output_zip=output_zip,
+                    validate_references=validate_references,
+                    fetch_reference_bundles=fetch_reference_bundles,
+                    auth_type=auth_type,
+                    auth_token=auth_token
+                )
+            except Exception as e:
+                logger.error(f"Error in retrieve_bundles: {e}", exc_info=True)
+                yield json.dumps({"type": "error", "message": f"Unexpected error: {str(e)}"}) + "\n"
 
     response = Response(generate(), mimetype='application/x-ndjson')
     response.headers['X-Zip-Path'] = os.path.join('/tmp', zip_filename)

services.py

@@ -11,7 +11,7 @@ from flask import current_app, Blueprint, request, jsonify
 from fhirpathpy import evaluate
 from collections import defaultdict, deque
 from pathlib import Path
-from urllib.parse import quote, urlparse
+from urllib.parse import quote, urlparse, urljoin
 from types import SimpleNamespace
 import datetime
 import subprocess
@@ -4586,16 +4586,20 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
         # Determine Base URL and Headers for Proxy
         base_proxy_url = f"{current_app.config['APP_BASE_URL'].rstrip('/')}/fhir"
         headers = {'Accept': 'application/fhir+json, application/fhir+xml;q=0.9, */*;q=0.8'}
+
         is_custom_url = fhir_server_url != '/fhir' and fhir_server_url is not None and fhir_server_url.startswith('http')
         if is_custom_url:
-            headers['X-Target-FHIR-Server'] = fhir_server_url.rstrip('/')
+            # NEW: Add the custom URL as a query parameter for the proxy to use.
+            # This bypasses issues where reverse proxies might strip custom headers.
+            base_proxy_url = f"{base_proxy_url}?proxy-target={fhir_server_url.rstrip('/')}"
+            
             if auth_type in ['bearer', 'basic'] and auth_token:
                 auth_display = 'Basic <redacted>' if auth_type == 'basic' else (auth_token[:10] + '...' if len(auth_token) > 10 else auth_token)
                 yield json.dumps({"type": "info", "message": f"Using {auth_type} auth with header: Authorization: {auth_display}"}) + "\n"
                 headers['Authorization'] = auth_token
             else:
                 yield json.dumps({"type": "info", "message": "Using no authentication for custom URL"}) + "\n"
-            logger.debug(f"Will use proxy with X-Target-FHIR-Server: {headers['X-Target-FHIR-Server']}")
+            logger.debug(f"Will use proxy with proxy-target: {fhir_server_url}")
         else:
             yield json.dumps({"type": "info", "message": "Using no authentication for local HAPI server"}) + "\n"
             logger.debug("Will use proxy targeting local HAPI server")
@@ -4603,7 +4607,8 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
         # Fetch Initial Bundles
         initial_bundle_files = []
         for resource_type in resources:
-            url = f"{base_proxy_url}/{quote(resource_type)}"
+            #url = f"{base_proxy_url}/{quote(resource_type)}"
+            url = urljoin(base_proxy_url, quote(resource_type))
             yield json.dumps({"type": "progress", "message": f"Fetching bundle for {resource_type} via proxy..."}) + "\n"
             logger.debug(f"Sending GET request to proxy {url} with headers: {json.dumps(headers)}")
             try: