Sudo-JHare/FHIRFLARE-IG-Toolkit
Sudo-JHare/FHIRFLARE-IG-Toolkit
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Code Issues Packages Projects Releases 6 Wiki Activity

updates

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This commit is contained in:
Joshua Hare 2025-08-12 21:55:28 +10:00
parent 5f4e1b7207
commit 9cf99ec78d
3 changed files with 58 additions and 78 deletions
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3
app.py
View File

@ -1905,7 +1905,7 @@ def proxy_hapi(subpath):
except Exception as e: except Exception as e:
logger.error(f"Unexpected proxy error for {final_url}: {str(e)}", exc_info=True) 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 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 --- # --- End of corrected proxy_hapi function ---
@app.route('/api/load-ig-to-hapi', methods=['POST']) @app.route('/api/load-ig-to-hapi', methods=['POST'])
@ -2338,6 +2338,7 @@ def retrieve_split_data():
now=datetime.datetime.now(), app_mode=app.config['APP_MODE'], now=datetime.datetime.now(), app_mode=app.config['APP_MODE'],
api_key=app.config['API_KEY']) api_key=app.config['API_KEY'])
@app.route('/api/retrieve-bundles', methods=['POST']) @app.route('/api/retrieve-bundles', methods=['POST'])
@csrf.exempt @csrf.exempt
@swag_from({ @swag_from({

65
services.py
View File

@ -4583,23 +4583,21 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
else: else:
yield json.dumps({"type": "info", "message": "Reference fetching OFF"}) + "\n" yield json.dumps({"type": "info", "message": "Reference fetching OFF"}) + "\n"
# Determine Base URL and Headers for Proxy # Determine Base URL and Headers for the requests.
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'} 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') is_custom_url = fhir_server_url != '/fhir' and fhir_server_url is not None and fhir_server_url.startswith('http')
if is_custom_url:
# 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('/')}"
final_base_url = fhir_server_url.rstrip('/') if fhir_server_url else '/fhir'
if is_custom_url:
if auth_type in ['bearer', 'basic'] and auth_token: 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) 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" yield json.dumps({"type": "info", "message": f"Using {auth_type} auth with header: Authorization: {auth_display}"}) + "\n"
headers['Authorization'] = auth_token headers['Authorization'] = auth_token
else: else:
yield json.dumps({"type": "info", "message": "Using no authentication for custom URL"}) + "\n" yield json.dumps({"type": "info", "message": "Using no authentication for custom URL"}) + "\n"
logger.debug(f"Will use proxy with proxy-target: {fhir_server_url}") logger.debug(f"Will send requests directly to: {final_base_url}")
else: else:
yield json.dumps({"type": "info", "message": "Using no authentication for local HAPI server"}) + "\n" yield json.dumps({"type": "info", "message": "Using no authentication for local HAPI server"}) + "\n"
logger.debug("Will use proxy targeting local HAPI server") logger.debug("Will use proxy targeting local HAPI server")
@ -4607,25 +4605,24 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
# Fetch Initial Bundles # Fetch Initial Bundles
initial_bundle_files = [] initial_bundle_files = []
for resource_type in resources: for resource_type in resources:
#url = f"{base_proxy_url}/{quote(resource_type)}" url = f"{final_base_url}/{quote(resource_type)}"
url = urljoin(base_proxy_url, quote(resource_type)) yield json.dumps({"type": "progress", "message": f"Fetching bundle for {resource_type}..."}) + "\n"
yield json.dumps({"type": "progress", "message": f"Fetching bundle for {resource_type} via proxy..."}) + "\n" logger.debug(f"Sending GET request to {url} with headers: {json.dumps(headers)}")
logger.debug(f"Sending GET request to proxy {url} with headers: {json.dumps(headers)}")
try: try:
response = requests.get(url, headers=headers, timeout=60) response = requests.get(url, headers=headers, timeout=60)
logger.debug(f"Proxy response for {resource_type}: HTTP {response.status_code}") logger.debug(f"Response for {resource_type}: HTTP {response.status_code}")
if response.status_code != 200: if response.status_code != 200:
error_detail = f"Proxy returned HTTP {response.status_code}." error_detail = f"Server returned HTTP {response.status_code}."
try: error_detail += f" Body: {response.text[:200]}..." try: error_detail += f" Body: {response.text[:200]}..."
except: pass except: pass
yield json.dumps({"type": "error", "message": f"Failed to fetch {resource_type}: {error_detail}"}) + "\n" yield json.dumps({"type": "error", "message": f"Failed to fetch {resource_type}: {error_detail}"}) + "\n"
logger.error(f"Failed to fetch {resource_type} via proxy {url}: {error_detail}") logger.error(f"Failed to fetch {resource_type} at {url}: {error_detail}")
continue continue
try: try:
bundle = response.json() bundle = response.json()
except ValueError as e: except ValueError as e:
yield json.dumps({"type": "error", "message": f"Invalid JSON response for {resource_type}: {str(e)}"}) + "\n" yield json.dumps({"type": "error", "message": f"Invalid JSON response for {resource_type}: {str(e)}"}) + "\n"
logger.error(f"Invalid JSON from proxy for {resource_type} at {url}: {e}, Response: {response.text[:500]}") logger.error(f"Invalid JSON from {resource_type} at {url}: {e}, Response: {response.text[:500]}")
continue continue
if not isinstance(bundle, dict) or bundle.get('resourceType') != 'Bundle': if not isinstance(bundle, dict) or bundle.get('resourceType') != 'Bundle':
yield json.dumps({"type": "error", "message": f"Expected Bundle for {resource_type}, got {bundle.get('resourceType', 'unknown')}"}) + "\n" yield json.dumps({"type": "error", "message": f"Expected Bundle for {resource_type}, got {bundle.get('resourceType', 'unknown')}"}) + "\n"
@ -4648,8 +4645,8 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
logger.error(f"Failed to write bundle file {output_file}: {e}") logger.error(f"Failed to write bundle file {output_file}: {e}")
continue continue
except requests.RequestException as e: except requests.RequestException as e:
yield json.dumps({"type": "error", "message": f"Error connecting to proxy for {resource_type}: {str(e)}"}) + "\n" yield json.dumps({"type": "error", "message": f"Error connecting to server for {resource_type}: {str(e)}"}) + "\n"
logger.error(f"Error retrieving bundle for {resource_type} via proxy {url}: {e}") logger.error(f"Error retrieving bundle for {resource_type} via {url}: {e}")
continue continue
except Exception as e: except Exception as e:
yield json.dumps({"type": "error", "message": f"Unexpected error fetching {resource_type}: {str(e)}"}) + "\n" yield json.dumps({"type": "error", "message": f"Unexpected error fetching {resource_type}: {str(e)}"}) + "\n"
@ -4699,18 +4696,18 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
if ref_type in retrieved_references_or_types: if ref_type in retrieved_references_or_types:
continue continue
url = f"{base_proxy_url}/{quote(ref_type)}" url = f"{final_base_url}/{quote(ref_type)}"
yield json.dumps({"type": "progress", "message": f"Fetching full bundle for type {ref_type} via proxy..."}) + "\n" yield json.dumps({"type": "progress", "message": f"Fetching full bundle for type {ref_type}..."}) + "\n"
logger.debug(f"Sending GET request for full type bundle {ref_type} to proxy {url} with headers: {json.dumps(headers)}") logger.debug(f"Sending GET request for full type bundle {ref_type} to {url} with headers: {json.dumps(headers)}")
try: try:
response = requests.get(url, headers=headers, timeout=180) response = requests.get(url, headers=headers, timeout=180)
logger.debug(f"Proxy response for {ref_type} bundle: HTTP {response.status_code}") logger.debug(f"Response for {ref_type} bundle: HTTP {response.status_code}")
if response.status_code != 200: if response.status_code != 200:
error_detail = f"Proxy returned HTTP {response.status_code}." error_detail = f"Server returned HTTP {response.status_code}."
try: error_detail += f" Body: {response.text[:200]}..." try: error_detail += f" Body: {response.text[:200]}..."
except: pass except: pass
yield json.dumps({"type": "warning", "message": f"Failed to fetch full bundle for {ref_type}: {error_detail}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Failed to fetch full bundle for {ref_type}: {error_detail}"}) + "\n"
logger.warning(f"Failed to fetch full bundle {ref_type} via proxy {url}: {error_detail}") logger.warning(f"Failed to fetch full bundle {ref_type} via {url}: {error_detail}")
retrieved_references_or_types.add(ref_type) retrieved_references_or_types.add(ref_type)
continue continue
@ -4718,7 +4715,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
bundle = response.json() bundle = response.json()
except ValueError as e: except ValueError as e:
yield json.dumps({"type": "warning", "message": f"Invalid JSON for full {ref_type} bundle: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Invalid JSON for full {ref_type} bundle: {str(e)}"}) + "\n"
logger.warning(f"Invalid JSON response from proxy for full {ref_type} bundle at {url}: {e}") logger.warning(f"Invalid JSON response from {ref_type} bundle at {url}: {e}")
retrieved_references_or_types.add(ref_type) retrieved_references_or_types.add(ref_type)
continue continue
@ -4742,8 +4739,8 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
logger.error(f"Failed to write full bundle file {output_file}: {e}") logger.error(f"Failed to write full bundle file {output_file}: {e}")
retrieved_references_or_types.add(ref_type) retrieved_references_or_types.add(ref_type)
except requests.RequestException as e: except requests.RequestException as e:
yield json.dumps({"type": "warning", "message": f"Error connecting to proxy for full {ref_type} bundle: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Error connecting to server for full {ref_type} bundle: {str(e)}"}) + "\n"
logger.warning(f"Error retrieving full {ref_type} bundle via proxy: {e}") logger.warning(f"Error retrieving full {ref_type} bundle via: {e}")
retrieved_references_or_types.add(ref_type) retrieved_references_or_types.add(ref_type)
except Exception as e: except Exception as e:
yield json.dumps({"type": "warning", "message": f"Unexpected error fetching full {ref_type} bundle: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Unexpected error fetching full {ref_type} bundle: {str(e)}"}) + "\n"
@ -4765,19 +4762,19 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
ref_type, ref_id = ref_parts ref_type, ref_id = ref_parts
search_param = quote(f"_id={ref_id}") search_param = quote(f"_id={ref_id}")
url = f"{base_proxy_url}/{quote(ref_type)}?{search_param}" url = f"{final_base_url}/{quote(ref_type)}?{search_param}"
yield json.dumps({"type": "progress", "message": f"Fetching referenced {ref_type}/{ref_id} via proxy..."}) + "\n" yield json.dumps({"type": "progress", "message": f"Fetching referenced {ref_type}/{ref_id}..."}) + "\n"
logger.debug(f"Sending GET request for referenced {ref} to proxy {url} with headers: {json.dumps(headers)}") logger.debug(f"Sending GET request for referenced {ref} to {url} with headers: {json.dumps(headers)}")
response = requests.get(url, headers=headers, timeout=60) response = requests.get(url, headers=headers, timeout=60)
logger.debug(f"Proxy response for referenced {ref}: HTTP {response.status_code}") logger.debug(f"Response for referenced {ref}: HTTP {response.status_code}")
if response.status_code != 200: if response.status_code != 200:
error_detail = f"Proxy returned HTTP {response.status_code}." error_detail = f"Server returned HTTP {response.status_code}."
try: error_detail += f" Body: {response.text[:200]}..." try: error_detail += f" Body: {response.text[:200]}..."
except: pass except: pass
yield json.dumps({"type": "warning", "message": f"Failed to fetch referenced {ref}: {error_detail}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Failed to fetch referenced {ref}: {error_detail}"}) + "\n"
logger.warning(f"Failed to fetch referenced {ref} via proxy {url}: {error_detail}") logger.warning(f"Failed to fetch referenced {ref} via {url}: {error_detail}")
retrieved_references_or_types.add(ref) retrieved_references_or_types.add(ref)
continue continue
@ -4785,7 +4782,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
bundle = response.json() bundle = response.json()
except ValueError as e: except ValueError as e:
yield json.dumps({"type": "warning", "message": f"Invalid JSON for referenced {ref}: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Invalid JSON for referenced {ref}: {str(e)}"}) + "\n"
logger.warning(f"Invalid JSON from proxy for ref {ref} at {url}: {e}") logger.warning(f"Invalid JSON from ref {ref} at {url}: {e}")
retrieved_references_or_types.add(ref) retrieved_references_or_types.add(ref)
continue continue
@ -4815,7 +4812,7 @@ def retrieve_bundles(fhir_server_url, resources, output_zip, validate_references
retrieved_references_or_types.add(ref) retrieved_references_or_types.add(ref)
except requests.RequestException as e: except requests.RequestException as e:
yield json.dumps({"type": "warning", "message": f"Network error fetching referenced {ref}: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Network error fetching referenced {ref}: {str(e)}"}) + "\n"
logger.warning(f"Network error retrieving referenced {ref} via proxy: {e}") logger.warning(f"Network error retrieving referenced {ref} via: {e}")
retrieved_references_or_types.add(ref) retrieved_references_or_types.add(ref)
except Exception as e: except Exception as e:
yield json.dumps({"type": "warning", "message": f"Unexpected error fetching referenced {ref}: {str(e)}"}) + "\n" yield json.dumps({"type": "warning", "message": f"Unexpected error fetching referenced {ref}: {str(e)}"}) + "\n"

62
templates/retrieve_split_data.html
View File

@ -27,7 +27,7 @@
</ul> </ul>
</div> </div>
{% endif %} {% endif %}
<form id="retrieveForm" method="POST" enctype="multipart/form-data"> <form id="retrieveForm" method="POST">
{{ form.hidden_tag() }} {{ form.hidden_tag() }}
<div class="mb-3"> <div class="mb-3">
<label class="form-label fw-bold">FHIR Server</label> <label class="form-label fw-bold">FHIR Server</label>
@ -401,52 +401,35 @@ document.addEventListener('DOMContentLoaded', () => {
formData.append('fetch_reference_bundles', 'false'); formData.append('fetch_reference_bundles', 'false');
} }
const currentFhirServerUrl = useLocalHapi ? '/fhir' : fhirServerUrlInput.value.trim(); const currentFhirServerUrl = useLocalHapi ? null : fhirServerUrlInput.value.trim().replace(/\/+$/, '');
if (!useLocalHapi && !currentFhirServerUrl) { const authType = authTypeSelect?.value;
alert('Custom FHIR Server URL is required.'); const authHeader = (authType === 'bearer' && bearerTokenInput?.value) ? `Bearer ${bearerTokenInput.value}`
fhirServerUrlInput.classList.add('is-invalid'); : (authType === 'basic' && usernameInput?.value && passwordInput?.value) ? `Basic ${btoa(`${usernameInput.value}:${passwordInput.value}`)}`
retrieveButton.disabled = false; : null;
if (spinner) spinner.style.display = 'none';
if (icon) icon.style.display = 'inline-block';
return;
}
formData.append('fhir_server_url', currentFhirServerUrl);
// Add authentication fields for custom URL const url = new URL('/api/stream-retrieve', window.location.origin);
if (!useLocalHapi && authTypeSelect) { if (currentFhirServerUrl) {
const authType = authTypeSelect.value; url.searchParams.set('proxy-target', currentFhirServerUrl);
formData.append('auth_type', authType);
if (authType === 'bearer' && bearerTokenInput) {
if (!bearerTokenInput.value) {
alert('Please enter a Bearer Token.');
retrieveButton.disabled = false;
if (spinner) spinner.style.display = 'none';
if (icon) icon.style.display = 'inline-block';
return;
} }
formData.append('bearer_token', bearerTokenInput.value); selectedResources.forEach(res => url.searchParams.append('resource_type', res));
} else if (authType === 'basic' && usernameInput && passwordInput) { url.searchParams.set('validate_references', formData.get('validate_references'));
if (!usernameInput.value || !passwordInput.value) { url.searchParams.set('fetch_reference_bundles', formData.get('fetch_reference_bundles'));
alert('Please enter both Username and Password for Basic Authentication.');
retrieveButton.disabled = false; const headers = { 'Accept': 'application/x-ndjson' };
if (spinner) spinner.style.display = 'none'; if (authHeader) {
if (icon) icon.style.display = 'inline-block'; headers['Authorization'] = authHeader;
return;
} }
formData.append('username', usernameInput.value); if (csrfTokenInput) {
formData.append('password', passwordInput.value); headers['X-CSRFToken'] = csrfTokenInput.value;
} }
if (apiKey) {
headers['X-API-Key'] = apiKey;
} }
const headers = { console.log(`Submitting retrieve request. URL: ${url.toString()}, Headers: ${JSON.stringify(headers)}`);
'Accept': 'application/x-ndjson',
'X-CSRFToken': csrfTokenInput ? csrfTokenInput.value : '',
'X-API-Key': apiKey
};
console.log(`Submitting retrieve request. Server: ${currentFhirServerUrl}, ValidateRefs: ${formData.get('validate_references')}, FetchRefBundles: ${formData.get('fetch_reference_bundles')}, AuthType: ${formData.get('auth_type')}`);
try { try {
const response = await fetch('/api/retrieve-bundles', { method: 'POST', headers: headers, body: formData }); const response = await fetch(url.toString(), { method: 'GET', headers: headers });
if (!response.ok) { if (!response.ok) {
const errorData = await response.json().catch(() => ({ message: 'Failed to parse error response.' })); const errorData = await response.json().catch(() => ({ message: 'Failed to parse error response.' }));
@ -454,7 +437,6 @@ document.addEventListener('DOMContentLoaded', () => {
} }
retrieveZipPath = response.headers.get('X-Zip-Path'); retrieveZipPath = response.headers.get('X-Zip-Path');
console.log(`Received X-Zip-Path: ${retrieveZipPath}`); console.log(`Received X-Zip-Path: ${retrieveZipPath}`);
const reader = response.body.getReader(); const reader = response.body.getReader();
const decoder = new TextDecoder(); const decoder = new TextDecoder();
let buffer = ''; let buffer = '';