mirror of
https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git
synced 2025-11-05 13:35:15 +00:00
updates
This commit is contained in:
parent
5f4e1b7207
commit
9cf99ec78d
3
app.py
3
app.py
@ -1905,7 +1905,7 @@ def proxy_hapi(subpath):
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except Exception as e:
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logger.error(f"Unexpected proxy error for {final_url}: {str(e)}", exc_info=True)
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return jsonify({'resourceType': 'OperationOutcome', 'issue': [{'severity': 'error', 'code': 'exception', 'diagnostics': 'An unexpected error occurred within the FHIR proxy.', 'details': {'text': str(e)}}]}), 500
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# --- End of corrected proxy_hapi function ---
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# --- End of corrected proxy_hapi function ---
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@app.route('/api/load-ig-to-hapi', methods=['POST'])
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@ -2338,6 +2338,7 @@ def retrieve_split_data():
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now=datetime.datetime.now(), app_mode=app.config['APP_MODE'],
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api_key=app.config['API_KEY'])
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@app.route('/api/retrieve-bundles', methods=['POST'])
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@csrf.exempt
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@swag_from({
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65
services.py
65
services.py
@ -4583,23 +4583,21 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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else:
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yield json.dumps({"type": "info", "message": "Reference fetching OFF"}) + "\n"
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# Determine Base URL and Headers for Proxy
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base_proxy_url = f"{current_app.config['APP_BASE_URL'].rstrip('/')}/fhir"
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# Determine Base URL and Headers for the requests.
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headers = {'Accept': 'application/fhir+json, application/fhir+xml;q=0.9, */*;q=0.8'}
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is_custom_url = fhir_server_url != '/fhir' and fhir_server_url is not None and fhir_server_url.startswith('http')
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if is_custom_url:
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# NEW: Add the custom URL as a query parameter for the proxy to use.
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# This bypasses issues where reverse proxies might strip custom headers.
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base_proxy_url = f"{base_proxy_url}?proxy-target={fhir_server_url.rstrip('/')}"
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final_base_url = fhir_server_url.rstrip('/') if fhir_server_url else '/fhir'
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if is_custom_url:
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if auth_type in ['bearer', 'basic'] and auth_token:
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auth_display = 'Basic <redacted>' if auth_type == 'basic' else (auth_token[:10] + '...' if len(auth_token) > 10 else auth_token)
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yield json.dumps({"type": "info", "message": f"Using {auth_type} auth with header: Authorization: {auth_display}"}) + "\n"
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headers['Authorization'] = auth_token
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else:
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yield json.dumps({"type": "info", "message": "Using no authentication for custom URL"}) + "\n"
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logger.debug(f"Will use proxy with proxy-target: {fhir_server_url}")
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logger.debug(f"Will send requests directly to: {final_base_url}")
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else:
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yield json.dumps({"type": "info", "message": "Using no authentication for local HAPI server"}) + "\n"
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logger.debug("Will use proxy targeting local HAPI server")
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@ -4607,25 +4605,24 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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# Fetch Initial Bundles
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initial_bundle_files = []
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for resource_type in resources:
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#url = f"{base_proxy_url}/{quote(resource_type)}"
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url = urljoin(base_proxy_url, quote(resource_type))
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yield json.dumps({"type": "progress", "message": f"Fetching bundle for {resource_type} via proxy..."}) + "\n"
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logger.debug(f"Sending GET request to proxy {url} with headers: {json.dumps(headers)}")
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url = f"{final_base_url}/{quote(resource_type)}"
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yield json.dumps({"type": "progress", "message": f"Fetching bundle for {resource_type}..."}) + "\n"
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logger.debug(f"Sending GET request to {url} with headers: {json.dumps(headers)}")
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try:
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response = requests.get(url, headers=headers, timeout=60)
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logger.debug(f"Proxy response for {resource_type}: HTTP {response.status_code}")
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logger.debug(f"Response for {resource_type}: HTTP {response.status_code}")
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if response.status_code != 200:
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error_detail = f"Proxy returned HTTP {response.status_code}."
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error_detail = f"Server returned HTTP {response.status_code}."
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try: error_detail += f" Body: {response.text[:200]}..."
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except: pass
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yield json.dumps({"type": "error", "message": f"Failed to fetch {resource_type}: {error_detail}"}) + "\n"
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logger.error(f"Failed to fetch {resource_type} via proxy {url}: {error_detail}")
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logger.error(f"Failed to fetch {resource_type} at {url}: {error_detail}")
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continue
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try:
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bundle = response.json()
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except ValueError as e:
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yield json.dumps({"type": "error", "message": f"Invalid JSON response for {resource_type}: {str(e)}"}) + "\n"
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logger.error(f"Invalid JSON from proxy for {resource_type} at {url}: {e}, Response: {response.text[:500]}")
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logger.error(f"Invalid JSON from {resource_type} at {url}: {e}, Response: {response.text[:500]}")
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continue
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if not isinstance(bundle, dict) or bundle.get('resourceType') != 'Bundle':
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yield json.dumps({"type": "error", "message": f"Expected Bundle for {resource_type}, got {bundle.get('resourceType', 'unknown')}"}) + "\n"
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@ -4648,8 +4645,8 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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logger.error(f"Failed to write bundle file {output_file}: {e}")
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continue
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except requests.RequestException as e:
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yield json.dumps({"type": "error", "message": f"Error connecting to proxy for {resource_type}: {str(e)}"}) + "\n"
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logger.error(f"Error retrieving bundle for {resource_type} via proxy {url}: {e}")
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yield json.dumps({"type": "error", "message": f"Error connecting to server for {resource_type}: {str(e)}"}) + "\n"
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logger.error(f"Error retrieving bundle for {resource_type} via {url}: {e}")
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continue
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except Exception as e:
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yield json.dumps({"type": "error", "message": f"Unexpected error fetching {resource_type}: {str(e)}"}) + "\n"
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@ -4699,18 +4696,18 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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if ref_type in retrieved_references_or_types:
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continue
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url = f"{base_proxy_url}/{quote(ref_type)}"
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yield json.dumps({"type": "progress", "message": f"Fetching full bundle for type {ref_type} via proxy..."}) + "\n"
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logger.debug(f"Sending GET request for full type bundle {ref_type} to proxy {url} with headers: {json.dumps(headers)}")
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url = f"{final_base_url}/{quote(ref_type)}"
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yield json.dumps({"type": "progress", "message": f"Fetching full bundle for type {ref_type}..."}) + "\n"
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logger.debug(f"Sending GET request for full type bundle {ref_type} to {url} with headers: {json.dumps(headers)}")
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try:
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response = requests.get(url, headers=headers, timeout=180)
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logger.debug(f"Proxy response for {ref_type} bundle: HTTP {response.status_code}")
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logger.debug(f"Response for {ref_type} bundle: HTTP {response.status_code}")
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if response.status_code != 200:
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error_detail = f"Proxy returned HTTP {response.status_code}."
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error_detail = f"Server returned HTTP {response.status_code}."
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try: error_detail += f" Body: {response.text[:200]}..."
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except: pass
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yield json.dumps({"type": "warning", "message": f"Failed to fetch full bundle for {ref_type}: {error_detail}"}) + "\n"
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logger.warning(f"Failed to fetch full bundle {ref_type} via proxy {url}: {error_detail}")
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logger.warning(f"Failed to fetch full bundle {ref_type} via {url}: {error_detail}")
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retrieved_references_or_types.add(ref_type)
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continue
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@ -4718,7 +4715,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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bundle = response.json()
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except ValueError as e:
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yield json.dumps({"type": "warning", "message": f"Invalid JSON for full {ref_type} bundle: {str(e)}"}) + "\n"
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logger.warning(f"Invalid JSON response from proxy for full {ref_type} bundle at {url}: {e}")
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logger.warning(f"Invalid JSON response from {ref_type} bundle at {url}: {e}")
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retrieved_references_or_types.add(ref_type)
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continue
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@ -4742,8 +4739,8 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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logger.error(f"Failed to write full bundle file {output_file}: {e}")
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retrieved_references_or_types.add(ref_type)
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except requests.RequestException as e:
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yield json.dumps({"type": "warning", "message": f"Error connecting to proxy for full {ref_type} bundle: {str(e)}"}) + "\n"
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logger.warning(f"Error retrieving full {ref_type} bundle via proxy: {e}")
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yield json.dumps({"type": "warning", "message": f"Error connecting to server for full {ref_type} bundle: {str(e)}"}) + "\n"
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logger.warning(f"Error retrieving full {ref_type} bundle via: {e}")
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retrieved_references_or_types.add(ref_type)
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except Exception as e:
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yield json.dumps({"type": "warning", "message": f"Unexpected error fetching full {ref_type} bundle: {str(e)}"}) + "\n"
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@ -4765,19 +4762,19 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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ref_type, ref_id = ref_parts
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search_param = quote(f"_id={ref_id}")
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url = f"{base_proxy_url}/{quote(ref_type)}?{search_param}"
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yield json.dumps({"type": "progress", "message": f"Fetching referenced {ref_type}/{ref_id} via proxy..."}) + "\n"
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logger.debug(f"Sending GET request for referenced {ref} to proxy {url} with headers: {json.dumps(headers)}")
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url = f"{final_base_url}/{quote(ref_type)}?{search_param}"
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yield json.dumps({"type": "progress", "message": f"Fetching referenced {ref_type}/{ref_id}..."}) + "\n"
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logger.debug(f"Sending GET request for referenced {ref} to {url} with headers: {json.dumps(headers)}")
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response = requests.get(url, headers=headers, timeout=60)
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logger.debug(f"Proxy response for referenced {ref}: HTTP {response.status_code}")
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logger.debug(f"Response for referenced {ref}: HTTP {response.status_code}")
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if response.status_code != 200:
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error_detail = f"Proxy returned HTTP {response.status_code}."
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error_detail = f"Server returned HTTP {response.status_code}."
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try: error_detail += f" Body: {response.text[:200]}..."
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except: pass
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yield json.dumps({"type": "warning", "message": f"Failed to fetch referenced {ref}: {error_detail}"}) + "\n"
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logger.warning(f"Failed to fetch referenced {ref} via proxy {url}: {error_detail}")
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logger.warning(f"Failed to fetch referenced {ref} via {url}: {error_detail}")
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retrieved_references_or_types.add(ref)
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continue
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@ -4785,7 +4782,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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bundle = response.json()
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except ValueError as e:
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yield json.dumps({"type": "warning", "message": f"Invalid JSON for referenced {ref}: {str(e)}"}) + "\n"
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logger.warning(f"Invalid JSON from proxy for ref {ref} at {url}: {e}")
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logger.warning(f"Invalid JSON from ref {ref} at {url}: {e}")
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retrieved_references_or_types.add(ref)
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continue
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@ -4815,7 +4812,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
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retrieved_references_or_types.add(ref)
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except requests.RequestException as e:
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yield json.dumps({"type": "warning", "message": f"Network error fetching referenced {ref}: {str(e)}"}) + "\n"
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logger.warning(f"Network error retrieving referenced {ref} via proxy: {e}")
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logger.warning(f"Network error retrieving referenced {ref} via: {e}")
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retrieved_references_or_types.add(ref)
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except Exception as e:
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yield json.dumps({"type": "warning", "message": f"Unexpected error fetching referenced {ref}: {str(e)}"}) + "\n"
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@ -27,7 +27,7 @@
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</ul>
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</div>
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{% endif %}
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<form id="retrieveForm" method="POST" enctype="multipart/form-data">
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<form id="retrieveForm" method="POST">
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{{ form.hidden_tag() }}
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<div class="mb-3">
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<label class="form-label fw-bold">FHIR Server</label>
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@ -401,52 +401,35 @@ document.addEventListener('DOMContentLoaded', () => {
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formData.append('fetch_reference_bundles', 'false');
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}
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const currentFhirServerUrl = useLocalHapi ? '/fhir' : fhirServerUrlInput.value.trim();
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if (!useLocalHapi && !currentFhirServerUrl) {
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alert('Custom FHIR Server URL is required.');
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fhirServerUrlInput.classList.add('is-invalid');
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retrieveButton.disabled = false;
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if (spinner) spinner.style.display = 'none';
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if (icon) icon.style.display = 'inline-block';
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return;
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}
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formData.append('fhir_server_url', currentFhirServerUrl);
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const currentFhirServerUrl = useLocalHapi ? null : fhirServerUrlInput.value.trim().replace(/\/+$/, '');
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const authType = authTypeSelect?.value;
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const authHeader = (authType === 'bearer' && bearerTokenInput?.value) ? `Bearer ${bearerTokenInput.value}`
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: (authType === 'basic' && usernameInput?.value && passwordInput?.value) ? `Basic ${btoa(`${usernameInput.value}:${passwordInput.value}`)}`
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: null;
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// Add authentication fields for custom URL
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if (!useLocalHapi && authTypeSelect) {
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const authType = authTypeSelect.value;
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formData.append('auth_type', authType);
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if (authType === 'bearer' && bearerTokenInput) {
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if (!bearerTokenInput.value) {
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alert('Please enter a Bearer Token.');
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retrieveButton.disabled = false;
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if (spinner) spinner.style.display = 'none';
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if (icon) icon.style.display = 'inline-block';
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return;
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}
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formData.append('bearer_token', bearerTokenInput.value);
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} else if (authType === 'basic' && usernameInput && passwordInput) {
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if (!usernameInput.value || !passwordInput.value) {
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alert('Please enter both Username and Password for Basic Authentication.');
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retrieveButton.disabled = false;
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if (spinner) spinner.style.display = 'none';
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if (icon) icon.style.display = 'inline-block';
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return;
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}
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formData.append('username', usernameInput.value);
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formData.append('password', passwordInput.value);
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}
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const url = new URL('/api/stream-retrieve', window.location.origin);
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if (currentFhirServerUrl) {
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url.searchParams.set('proxy-target', currentFhirServerUrl);
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}
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selectedResources.forEach(res => url.searchParams.append('resource_type', res));
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url.searchParams.set('validate_references', formData.get('validate_references'));
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url.searchParams.set('fetch_reference_bundles', formData.get('fetch_reference_bundles'));
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const headers = { 'Accept': 'application/x-ndjson' };
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if (authHeader) {
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headers['Authorization'] = authHeader;
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}
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if (csrfTokenInput) {
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headers['X-CSRFToken'] = csrfTokenInput.value;
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}
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if (apiKey) {
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headers['X-API-Key'] = apiKey;
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}
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const headers = {
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'Accept': 'application/x-ndjson',
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'X-CSRFToken': csrfTokenInput ? csrfTokenInput.value : '',
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'X-API-Key': apiKey
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};
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console.log(`Submitting retrieve request. Server: ${currentFhirServerUrl}, ValidateRefs: ${formData.get('validate_references')}, FetchRefBundles: ${formData.get('fetch_reference_bundles')}, AuthType: ${formData.get('auth_type')}`);
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console.log(`Submitting retrieve request. URL: ${url.toString()}, Headers: ${JSON.stringify(headers)}`);
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try {
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const response = await fetch('/api/retrieve-bundles', { method: 'POST', headers: headers, body: formData });
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const response = await fetch(url.toString(), { method: 'GET', headers: headers });
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if (!response.ok) {
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const errorData = await response.json().catch(() => ({ message: 'Failed to parse error response.' }));
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@ -454,7 +437,6 @@ document.addEventListener('DOMContentLoaded', () => {
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}
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retrieveZipPath = response.headers.get('X-Zip-Path');
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console.log(`Received X-Zip-Path: ${retrieveZipPath}`);
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const reader = response.body.getReader();
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const decoder = new TextDecoder();
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let buffer = '';
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