Merge pull request #24 from Sudo-JHare/V4-Alpha

V4.1 - Merge release

app.py

@@ -48,7 +48,9 @@ from services import (
     import_manual_package_and_dependencies,
     parse_and_list_igs, 
     generate_ig_yaml,
-    apply_and_validate
+    apply_and_validate,
+    run_validator_cli,
+    uuid
 )
 from forms import IgImportForm, ManualIgImportForm, ValidationForm, FSHConverterForm, TestDataUploadForm, RetrieveSplitDataForm, IgYamlForm
 from wtforms import SubmitField
@@ -70,11 +72,16 @@ app.config['FHIR_PACKAGES_DIR'] = os.path.join(instance_path, 'fhir_packages')
 app.config['API_KEY'] = os.environ.get('API_KEY', 'your-fallback-api-key-here')
 app.config['VALIDATE_IMPOSED_PROFILES'] = True
 app.config['DISPLAY_PROFILE_RELATIONSHIPS'] = True
+app.config['LATEST_BUILD_URL'] = "http://build.fhir.org/ig/qas.json"
+app.config['VALIDATION_LOG_DIR'] = os.path.join(app.instance_path, 'validation_logs')
+os.makedirs(app.config['VALIDATION_LOG_DIR'], exist_ok=True)
 app.config['UPLOAD_FOLDER'] = os.path.join(CURRENT_DIR, 'static', 'uploads')  # For GoFSH output
 app.config['APP_BASE_URL'] = os.environ.get('APP_BASE_URL', 'http://localhost:5000')
 app.config['HAPI_FHIR_URL'] = os.environ.get('HAPI_FHIR_URL', 'http://localhost:8080/fhir')
 CONFIG_PATH = os.environ.get('CONFIG_PATH', '/usr/local/tomcat/conf/application.yaml')
 
+
+
 # Basic Swagger configuration
 app.config['SWAGGER'] = {
     'title': 'FHIRFLARE IG Toolkit API',
@@ -1765,6 +1772,157 @@ csrf.exempt(api_push_ig)   # Add this line
 # Exempt the entire API blueprint (for routes defined IN services.py, like /api/validate-sample)
 csrf.exempt(services_bp) # Keep this line for routes defined in the blueprint
 
+@app.route('/validate-sample', methods=['GET'])
+def validate_resource_page():
+    """Renders the validation form page."""
+    form = ValidationForm()
+    # Fetch list of packages to populate the dropdown
+    packages = current_app.config.get('MANUAL_PACKAGE_CACHE', [])
+    return render_template('validate_sample.html', form=form, packages=packages)
+
+@app.route('/api/validate', methods=['POST'])
+@swag_from({
+    'tags': ['Validation'],
+    'summary': 'Starts a validation process for a FHIR resource or bundle.',
+    'description': 'Starts a validation task and immediately returns a task ID for polling. The actual validation is run in a separate thread to prevent timeouts.',
+    'security': [{'ApiKeyAuth': []}],
+    'consumes': ['application/json'],
+    'parameters': [
+        {
+            'name': 'validation_payload',
+            'in': 'body',
+            'required': True,
+            'schema': {
+                'type': 'object',
+                'required': ['package_name', 'version', 'fhir_resource'],
+                'properties': {
+                    'package_name': {'type': 'string', 'example': 'hl7.fhir.us.core'},
+                    'version': {'type': 'string', 'example': '6.1.0'},
+                    'fhir_resource': {'type': 'string', 'description': 'A JSON string of the FHIR resource or Bundle to validate.'},
+                    'fhir_version': {'type': 'string', 'example': '4.0.1'},
+                    'do_native': {'type': 'boolean', 'default': False},
+                    'hint_about_must_support': {'type': 'boolean', 'default': False},
+                    'assume_valid_rest_references': {'type': 'boolean', 'default': False},
+                    'no_extensible_binding_warnings': {'type': 'boolean', 'default': False},
+                    'show_times': {'type': 'boolean', 'default': False},
+                    'allow_example_urls': {'type': 'boolean', 'default': False},
+                    'check_ips_codes': {'type': 'boolean', 'default': False},
+                    'allow_any_extensions': {'type': 'boolean', 'default': False},
+                    'tx_routing': {'type': 'boolean', 'default': False},
+                    'snomed_ct_version': {'type': 'string', 'default': ''},
+                    'profiles': {'type': 'string', 'description': 'Comma-separated list of profile URLs.'},
+                    'extensions': {'type': 'string', 'description': 'Comma-separated list of extension URLs.'},
+                    'terminology_server': {'type': 'string', 'description': 'URL of an alternate terminology server.'}
+                }
+            }
+        }
+    ],
+    'responses': {
+        '202': {'description': 'Validation process started successfully, returns a task_id.'},
+        '400': {'description': 'Invalid request (e.g., missing fields, invalid JSON).'}
+    }
+})
+def validate_resource():
+    """API endpoint to run validation on a FHIR resource."""
+    try:
+        # Get data from the JSON payload
+        data = request.get_json()
+        if not data:
+            return jsonify({'status': 'error', 'message': 'Invalid JSON: No data received.'}), 400
+            
+        fhir_resource_text = data.get('fhir_resource')
+        fhir_version = data.get('fhir_version')
+        package_name = data.get('package_name')
+        version = data.get('version')
+        profiles = data.get('profiles')
+        extensions = data.get('extensions')
+        terminology_server = data.get('terminology_server')
+        snomed_ct_version = data.get('snomed_ct_version')
+        
+        # Build the list of IGs from the package name and version
+        igs = [f"{package_name}#{version}"] if package_name and version else []
+        
+        flags = {
+            'doNative': data.get('do_native'),
+            'hintAboutMustSupport': data.get('hint_about_must_support'),
+            'assumeValidRestReferences': data.get('assume_valid_rest_references'),
+            'noExtensibleBindingWarnings': data.get('no_extensible_binding_warnings'),
+            'showTimes': data.get('show_times'),
+            'allowExampleUrls': data.get('allow_example_urls'),
+            'checkIpsCodes': data.get('check_ips_codes'),
+            'allowAnyExtensions': data.get('allow_any_extensions'),
+            'txRouting': data.get('tx_routing'),
+        }
+
+        # Check for empty resource
+        if not fhir_resource_text:
+            return jsonify({'status': 'error', 'message': 'No FHIR resource provided.'}), 400
+        
+        try:
+            # Generate a unique task ID
+            task_id = str(uuid.uuid4())
+            
+            # Store a pending status in the global cache
+            with services.cache_lock:
+                services.validation_results_cache[task_id] = {"status": "pending"}
+            
+            # Start the validation process in a new thread
+            app_context = app.app_context()
+            thread = threading.Thread(
+                target=services.validate_in_thread,
+                args=(app_context, task_id, fhir_resource_text, fhir_version, igs, profiles, extensions, terminology_server, flags, snomed_ct_version),
+                daemon=True
+            )
+            thread.start()
+            
+            logger.info(f"Validation task {task_id} started in background thread.")
+            
+            return jsonify({"status": "accepted", "message": "Validation started", "task_id": task_id}), 202
+
+        except Exception as e:
+            logger.error(f"Error starting validation thread: {e}", exc_info=True)
+            return jsonify({'status': 'error', 'message': f'An internal server error occurred while starting the validation: {e}'}), 500
+
+    except Exception as e:
+        logger.error(f"Validation API error: {e}")
+        return jsonify({'status': 'error', 'message': f'An internal server error occurred: {e}'}), 500
+
+@app.route('/api/check-validation-status/<task_id>', methods=['GET'])
+@swag_from({
+    'tags': ['Validation'],
+    'summary': 'Check the status of a validation task.',
+    'description': 'Polls for the result of a validation task by its ID. Returns the full validation report when the task is complete.',
+    'security': [{'ApiKeyAuth': []}],
+    'parameters': [
+        {'name': 'task_id', 'in': 'path', 'type': 'string', 'required': True, 'description': 'The unique ID of the validation task.'}
+    ],
+    'responses': {
+        '200': {'description': 'Returns the full validation report if the task is complete.'},
+        '202': {'description': 'The validation task is still in progress.'},
+        '404': {'description': 'The specified task ID was not found.'}
+    }
+})
+def check_validation_status(task_id):
+    """
+    This GET endpoint is polled by the frontend to check the status of a validation task.
+    """
+    with services.cache_lock:
+        task_result = services.validation_results_cache.get(task_id)
+
+    if task_result is None:
+        return jsonify({"status": "error", "message": "Task not found."}), 404
+        
+    if task_result["status"] == "pending":
+        return jsonify({"status": "pending", "message": "Validation is still in progress."}), 202
+
+    # Remove the result from the cache after it has been retrieved to prevent a memory leak
+    with services.cache_lock:
+        del services.validation_results_cache[task_id]
+
+    return jsonify({"status": "complete", "result": task_result["result"]}), 200
+
+
+
 def create_db():
     logger.debug(f"Attempting to create database tables for URI: {app.config['SQLALCHEMY_DATABASE_URI']}")
     try:

docker-compose.yml

@@ -17,5 +17,5 @@ services:
       - NODE_PATH=/usr/lib/node_modules
       - APP_MODE=standalone
       - APP_BASE_URL=http://localhost:5000
-      - HAPI_FHIR_URL=https://fhir.hl7.org.au/aucore/fhir/DEFAULT/
+      - HAPI_FHIR_URL=https://smile.sparked-fhir.com/aucore/fhir/DEFAULT/
     command: supervisord -c /etc/supervisord.conf

forms.py

@@ -311,4 +311,59 @@ class FhirRequestForm(FlaskForm):
 class IgYamlForm(FlaskForm):
     """Form to select IGs for YAML generation."""
     igs = SelectMultipleField('Select IGs to include', validators=[DataRequired()])
-    generate_yaml = SubmitField('Generate YAML')
+    generate_yaml = SubmitField('Generate YAML')
+
+# --- New ValidationForm class for the new page ---
+class ValidationForm(FlaskForm):
+    """Form for validating a single FHIR resource with various options."""
+    # Added fields to match the HTML template
+    package_name = StringField('Package Name', validators=[Optional()])
+    version = StringField('Package Version', validators=[Optional()])
+    
+    # Main content fields
+    fhir_resource = TextAreaField('FHIR Resource (JSON or XML)', validators=[InputRequired()],
+                                  render_kw={'placeholder': 'Paste your FHIR JSON here...'})
+    fhir_version = SelectField('FHIR Version', choices=[
+        ('4.0.1', 'R4 (4.0.1)'),
+        ('3.0.2', 'STU3 (3.0.2)'),
+        ('5.0.0', 'R5 (5.0.0)')
+    ], default='4.0.1', validators=[DataRequired()])
+    
+    # Flags and options from validator settings.pdf
+    do_native = BooleanField('Native Validation (doNative)')
+    hint_about_must_support = BooleanField('Must Support (hintAboutMustSupport)')
+    assume_valid_rest_references = BooleanField('Assume Valid Rest References (assumeValidRestReferences)')
+    no_extensible_binding_warnings = BooleanField('Extensible Binding Warnings (noExtensibleBindingWarnings)')
+    show_times = BooleanField('Show Times (-show-times)')
+    allow_example_urls = BooleanField('Allow Example URLs (-allow-example-urls)')
+    check_ips_codes = BooleanField('Check IPS Codes (-check-ips-codes)')
+    allow_any_extensions = BooleanField('Allow Any Extensions (-allow-any-extensions)')
+    tx_routing = BooleanField('Show Terminology Routing (-tx-routing)')
+    
+    # SNOMED CT options
+    snomed_ct_version = SelectField('Select SNOMED Version', choices=[
+        ('', '-- No selection --'),
+        ('intl', 'International edition (900000000000207008)'),
+        ('us', 'US edition (731000124108)'),
+        ('uk', 'United Kingdom Edition (999000041000000102)'),
+        ('es', 'Spanish Language Edition (449081005)'),
+        ('nl', 'Netherlands Edition (11000146104)'),
+        ('ca', 'Canadian Edition (20611000087101)'),
+        ('dk', 'Danish Edition (554471000005108)'),
+        ('se', 'Swedish Edition (45991000052106)'),
+        ('au', 'Australian Edition (32506021000036107)'),
+        ('be', 'Belgium Edition (11000172109)')
+    ], validators=[Optional()])
+    
+    # Text input fields
+    profiles = StringField('Profiles',
+                           validators=[Optional()],
+                           render_kw={'placeholder': 'e.g. http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient'})
+    extensions = StringField('Extensions',
+                             validators=[Optional()],
+                             render_kw={'placeholder': 'e.g. http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace'})
+    terminology_server = StringField('Terminology Server',
+                                     validators=[Optional()],
+                                     render_kw={'placeholder': 'e.g. http://tx.fhir.org'})
+    
+    submit = SubmitField('Validate')

services.py

@@ -198,6 +198,203 @@ def safe_parse_version(v_str):
          logger.error(f"Unexpected error in safe_parse_version for '{v_str}': {e}")
          return pkg_version.parse("0.0.0a0") # Fallback
 
+# --- New Function to run the FHIR Validator CLI ---
+def run_validator_cli(resource_text, fhir_version, igs, profiles, extensions, terminology_server, flags, snomed_ct_version, app_config):
+    """
+    Constructs and runs the Java FHIR Validator CLI command.
+
+    Args:
+        resource_text (str): The FHIR resource/bundle as a string.
+        fhir_version (str): The FHIR version to validate against.
+        igs (list): List of selected IG canonical URLs.
+        profiles (str): Comma-separated list of profile URLs.
+        extensions (str): Comma-separated list of extension URLs.
+        terminology_server (str): The URL of the terminology server.
+        flags (dict): Dictionary of boolean flags for validation.
+        snomed_ct_version (str): The SNOMED CT version to use.
+        app_config (dict): The Flask application configuration.
+
+    Returns:
+        dict: A dictionary containing the validation output and status.
+    """
+    temp_dir = tempfile.mkdtemp(dir=app_config['VALIDATION_LOG_DIR'])
+    
+    # Store the temp directory in the app config for the download endpoint to find it.
+    app_config['VALIDATION_TEMP_DIR'] = temp_dir
+    
+    temp_resource_path = os.path.join(temp_dir, f'resource_{uuid.uuid4()}.json')
+    try:
+        with open(temp_resource_path, 'w', encoding='utf-8') as f:
+            f.write(resource_text)
+    except Exception as e:
+        shutil.rmtree(temp_dir)
+        return {'status': 'error', 'message': f'Failed to write temporary resource file: {e}'}
+
+    output_json_path = os.path.join(temp_dir, 'validation-report.json')
+    output_html_path = os.path.join(temp_dir, 'validation-report.html')
+    
+    command = [
+        'java',
+        '-jar', os.environ.get('JAVA_VALIDATOR_PATH', '/app/validator_cli/validator_cli.jar'),
+        temp_resource_path,
+        '-version', fhir_version,
+        '-output', output_json_path,
+        '-html-output', output_html_path,
+    ]
+
+    # Add flags
+    if flags.get('doNative'):
+        command.append('-do-native')
+    if flags.get('hintAboutMustSupport'):
+        command.append('-hint-about-must-support')
+    if flags.get('assumeValidRestReferences'):
+        command.append('-assume-valid-rest-references')
+    if flags.get('noExtensibleBindingWarnings'):
+        command.append('-no-extensible-binding-warnings')
+    if flags.get('showTimes'):
+        command.append('-show-times')
+    if flags.get('allowExampleUrls'):
+        command.append('-allow-example-urls')
+    if flags.get('checkIpsCodes'):
+        command.append('-check-ips-codes')
+    if flags.get('allowAnyExtensions'):
+        command.append('-allow-any-extensions')
+    if flags.get('txRouting'):
+        command.append('-tx-routing')
+    
+    # Add other options
+    if igs:
+        for ig in igs:
+            command.extend(['-ig', ig])
+    if profiles:
+        command.extend(['-profile', profiles])
+    if extensions:
+        command.extend(['-extension', extensions])
+    if terminology_server:
+        command.extend(['-tx', terminology_server])
+    if snomed_ct_version:
+        command.extend(['-sct', snomed_ct_version])
+
+    logger.info(f"Running validator with command: {' '.join(command)}")
+
+    try:
+        result = subprocess.run(
+            command,
+            capture_output=True,
+            text=True,
+            check=False,
+            timeout=300,
+        )
+        
+        stdout = result.stdout
+        stderr = result.stderr
+        
+        logger.debug(f"Validator stdout:\n{stdout}")
+        logger.debug(f"Validator stderr:\n{stderr}")
+
+        # Check for errors in the stdout and stderr
+        if result.returncode != 0 and not os.path.exists(output_json_path):
+            return_dict = {
+                'status': 'error',
+                'output': stderr or "Validation process failed with an unknown error.",
+                'file_paths': {},
+                'errors': [stderr or "Validation process failed with an unknown error."],
+                'warnings': [],
+                'summary': {'error_count': 1, 'warning_count': 0},
+                'results': {}
+            }
+            return return_dict
+        
+        # Now, try to read the JSON file produced by the validator
+        if os.path.exists(output_json_path):
+            with open(output_json_path, 'r', encoding='utf-8') as f:
+                json_report = json.load(f)
+            
+            # Process the JSON report to get a structured summary
+            error_count = 0
+            warning_count = 0
+            errors_list = []
+            warnings_list = []
+            detailed_results = {}
+            is_valid = True
+
+            for issue in json_report.get('issue', []):
+                severity = issue.get('severity')
+                diagnostics = issue.get('diagnostics') or issue.get('details', {}).get('text') or 'No details provided.'
+                resource_expression = issue.get('expression', ['unknown'])[0]
+                
+                # Determine the resource ID and type from the expression, e.g., "AllergyIntolerance" or "AllergyIntolerance[0].extension[0]"
+                resource_id = resource_expression.split('[')[0].split('.')[0]
+                
+                if resource_id not in detailed_results:
+                    detailed_results[resource_id] = {'valid': True, 'details': []}
+                
+                detail = {
+                    'issue': diagnostics,
+                    'severity': severity,
+                    'description': issue.get('details', {}).get('text', diagnostics)
+                }
+                detailed_results[resource_id]['details'].append(detail)
+                
+                if severity == 'error':
+                    error_count += 1
+                    errors_list.append(diagnostics)
+                    is_valid = False
+                    detailed_results[resource_id]['valid'] = False
+                elif severity == 'warning':
+                    warning_count += 1
+                    warnings_list.append(diagnostics)
+
+            # Determine the overall status
+            status = 'success'
+            if error_count > 0:
+                status = 'error'
+            elif warning_count > 0:
+                status = 'warning'
+
+            # Build the final return dictionary
+            return_dict = {
+                'status': status,
+                'valid': is_valid,
+                'output': stdout,
+                'file_paths': {
+                    'json': output_json_path,
+                    'html': output_html_path
+                },
+                'errors': errors_list,
+                'warnings': warnings_list,
+                'summary': {
+                    'error_count': error_count,
+                    'warning_count': warning_count
+                },
+                'results': detailed_results
+            }
+            return return_dict
+        else:
+            # Fallback if validator completed but didn't produce a file
+            return_dict = {
+                'status': 'error',
+                'valid': False,
+                'output': stdout,
+                'file_paths': {},
+                'errors': ["Validator failed to produce the expected output files."],
+                'warnings': [],
+                'summary': {'error_count': 1, 'warning_count': 0},
+                'results': {}
+            }
+            return return_dict
+
+    except FileNotFoundError:
+        return {'status': 'error', 'message': 'Java command or validator JAR not found. Please check paths.'}
+    except subprocess.TimeoutExpired:
+        return {'status': 'error', 'message': 'Validation timed out.'}
+    except Exception as e:
+        return {'status': 'error', 'message': f'An unexpected error occurred during validation: {e}'}
+    finally:
+        # NOTE: We no longer delete the temporary directory here.
+        # It is the responsibility of the `clear-validation-results` endpoint.
+        pass
+
 # --- MODIFIED FUNCTION with Enhanced Logging ---
 def get_additional_registries():
     """Fetches the list of additional FHIR IG registries from the master feed."""
@@ -1108,15 +1305,16 @@ validation_results_cache = {}
 # Thread lock to safely manage access to the cache
 cache_lock = threading.Lock()
 
-def validate_in_thread(app_context, task_id, package_name, version, sample_data):
+def validate_in_thread(app_context, task_id, fhir_resource_text, fhir_version, igs, profiles, extensions, terminology_server, flags, snomed_ct_version):
     """
     Wrapper function to run the blocking validator in a separate thread.
     It acquires an app context and then calls the main validation logic.
     """
     with app_context:
         logger.info(f"Starting validation thread for task ID: {task_id}")
-        # Call the core blocking validation function
-        result = run_java_validator(package_name, version, sample_data)
+        
+        # Call the core blocking validation function, passing all arguments
+        result = run_validator_cli(fhir_resource_text, fhir_version, igs, profiles, extensions, terminology_server, flags, snomed_ct_version, current_app.config)
         
         # Safely update the shared cache with the final result
         with cache_lock:

templates/cp_downloaded_igs.html

@@ -40,7 +40,7 @@
 
     <div class="row g-4">
         <!-- LEFT: Downloaded Packages -->
-        <div class="col-md-6">
+        <div class="col-md-5">
             <div class="card h-100">
                 <div class="card-header"><i class="bi bi-folder-symlink me-1"></i> Downloaded Packages ({{ packages|length }})</div>
                 <div class="card-body">
@@ -65,20 +65,20 @@
                                             </td>
                                             <td>{{ pkg.version }}</td>
                                             <td>
-                                                <div class="btn-group btn-group-sm">
+                                                <div class="btn-group-vertical btn-group-sm w-80">
                                                     {% if is_processed %}
                                                         <span class="btn btn-success disabled"><i class="bi bi-check-lg"></i> Processed</span>
                                                     {% else %}
                                                         <form method="POST" action="{{ url_for('process_ig') }}" style="display:inline;">
                                                             {{ form.csrf_token }}
                                                             <input type="hidden" name="filename" value="{{ pkg.filename }}">
-                                                            <button type="submit" class="btn btn-outline-primary"><i class="bi bi-gear"></i> Process</button>
+                                                            <button type="submit" class="btn btn-outline-primary w-80"><i class="bi bi-gear"></i> Process</button>
                                                         </form>
                                                     {% endif %}
                                                     <form method="POST" action="{{ url_for('delete_ig') }}" style="display:inline;">
                                                         {{ form.csrf_token }}
                                                         <input type="hidden" name="filename" value="{{ pkg.filename }}">
-                                                        <button type="submit" class="btn btn-outline-danger" onclick="return confirm('Are you sure you want to delete {{ pkg.name }}#{{ pkg.version }}?');"><i class="bi bi-trash"></i> Delete</button>
+                                                        <button type="submit" class="btn btn-outline-danger w-80" onclick="return confirm('Are you sure you want to delete {{ pkg.name }}#{{ pkg.version }}?');"><i class="bi bi-trash"></i> Delete</button>
                                                     </form>
                                                 </div>
                                             </td>
@@ -105,7 +105,7 @@
         </div>
 
         <!-- RIGHT: Processed Packages -->
-        <div class="col-md-6">
+        <div class="col-md-7">
             <div class="card h-100">
                 <div class="card-header"><i class="bi bi-check-circle me-1"></i> Processed Packages ({{ processed_list|length }})</div>
                 <div class="card-body">
@@ -139,12 +139,12 @@
                                                 {% endif %}
                                             </td>
                                             <td>
-                                                <div class="btn-group-vertical btn-group-sm w-100">
-                                                    <a href="{{ url_for('view_ig', processed_ig_id=processed_ig.id) }}" class="btn btn-outline-info w-100" title="View Details"><i class="bi bi-search"></i> View</a>
+                                                <div class="btn-group-vertical btn-group-sm w-80">
+                                                    <a href="{{ url_for('view_ig', processed_ig_id=processed_ig.id) }}" class="btn btn-outline-info w-80" title="View Details"><i class="bi bi-search"></i> View</a>
                                                     <form method="POST" action="{{ url_for('unload_ig') }}" style="display:inline;">
                                                         {{ form.csrf_token }}
                                                         <input type="hidden" name="ig_id" value="{{ processed_ig.id }}">
-                                                        <button type="submit" class="btn btn-outline-warning w-100 mt-1" onclick="return confirm('Are you sure you want to unload {{ processed_ig.package_name }}#{{ processed_ig.version }}?');"><i class="bi bi-x-lg"></i> Unload</button>
+                                                        <button type="submit" class="btn btn-outline-warning w-80 mt-1" onclick="return confirm('Are you sure you want to unload {{ processed_ig.package_name }}#{{ processed_ig.version }}?');"><i class="bi bi-x-lg"></i> Unload</button>
                                                     </form>
                                                 </div>
                                             </td>

templates/fhir_ui.html

@@ -6,7 +6,7 @@
     <h1 class="display-5 fw-bold text-body-emphasis">FHIR API Explorer</h1>
     <div class="col-lg-6 mx-auto">
         <p class="lead mb-4">
-            Interact with FHIR servers using GET, POST, PUT, or DELETE requests. Toggle between local Fhir Server or a custom server to explore resources or perform searches.
+            Interact with FHIR servers using GET, POST, PUT, or DELETE requests. Toggle between local HAPI or a custom server to explore resources or perform searches.
         </p>
     </div>
 </div>
@@ -21,11 +21,11 @@
                     <label class="form-label">FHIR Server</label>
                     <div class="input-group">
                         <button type="button" class="btn btn-outline-primary" id="toggleServer">
-                            <span id="toggleLabel">Use Local </span>
+                            <span id="toggleLabel">Use Local Server</span>
                         </button>
                         <input type="text" class="form-control" id="fhirServerUrl" name="fhir_server_url" placeholder="e.g., https://hapi.fhir.org/baseR4" style="display: none;" aria-describedby="fhirServerHelp">
                     </div>
-                    <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local (http://localhost:8080/fhir) or enter a custom FHIR server URL.</small>
+                    <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local HAPI (http://localhost:8080/fhir) or enter a custom FHIR server URL.</small>
                 </div>
                 <div class="mb-3" id="authSection" style="display: none;">
                     <label class="form-label">Authentication</label>
@@ -126,7 +126,7 @@ document.addEventListener('DOMContentLoaded', function() {
     const authSection = document.getElementById('authSection');
     const authTypeSelect = document.getElementById('authType');
     const authInputsGroup = document.getElementById('authInputsGroup');
-    const bearerTokenInput = document.getElementById('bearerToken');
+    const bearerTokenInput = document.getElementById('bearerTokenInput');
     const basicAuthInputs = document.getElementById('basicAuthInputs');
     const usernameInput = document.getElementById('username');
     const passwordInput = document.getElementById('password');
@@ -141,7 +141,6 @@ document.addEventListener('DOMContentLoaded', function() {
 
     // --- State Variable ---
     let useLocalHapi = true;
-    let localHapiBaseUrl = ''; // New variable to store the fetched URL
 
     // --- Get App Mode from Flask Context ---
     const appMode = '{{ app_mode | default("standalone") | lower }}';
@@ -194,22 +193,6 @@ document.addEventListener('DOMContentLoaded', function() {
         } catch (err) { console.error('Copy failed:', err); }
     }
 
-    async function fetchLocalUrlAndSetUI() {
-        try {
-            const response = await fetch('/api/get-local-server-url');
-            if (!response.ok) throw new Error('Failed to fetch local server URL.');
-            const data = await response.json();
-            localHapiBaseUrl = data.url;
-            console.log(`Local HAPI URL fetched: ${localHapiBaseUrl}`);
-        } catch (error) {
-            console.error(error);
-            localHapiBaseUrl = '/fhir'; // Fallback to proxy
-            alert('Could not fetch local HAPI server URL. Falling back to proxy.');
-        } finally {
-            updateServerToggleUI();
-        }
-    }
-
     function updateServerToggleUI() {
         if (appMode === 'lite') {
             useLocalHapi = false;
@@ -229,7 +212,7 @@ document.addEventListener('DOMContentLoaded', function() {
             toggleServerButton.style.pointerEvents = 'auto';
             toggleServerButton.removeAttribute('aria-disabled');
             toggleServerButton.title = "Toggle between Local HAPI and Custom URL";
-            toggleLabel.textContent = useLocalHapi ? 'Using Local HAPI' : 'Using Custom URL';
+            toggleLabel.textContent = useLocalHapi ? 'Using Local Server' : 'Using Custom URL';
             fhirServerUrlInput.style.display = useLocalHapi ? 'none' : 'block';
             fhirServerUrlInput.placeholder = "e.g., https://hapi.fhir.org/baseR4";
             fhirServerUrlInput.required = !useLocalHapi;
@@ -261,7 +244,8 @@ document.addEventListener('DOMContentLoaded', function() {
             fhirServerUrlInput.value = '';
         }
         updateServerToggleUI();
-        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local HAPI' : 'Custom URL'}`);
+        updateAuthInputsUI();
+        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local Server' : 'Custom URL'}`);
     }
 
     function updateRequestBodyVisibility() {
@@ -277,7 +261,7 @@ document.addEventListener('DOMContentLoaded', function() {
     }
 
     // --- Initial Setup ---
-    fetchLocalUrlAndSetUI(); // Fetch the URL and then set up the UI
+    updateServerToggleUI();
     updateRequestBodyVisibility();
 
     // --- Event Listeners ---
@@ -312,7 +296,7 @@ document.addEventListener('DOMContentLoaded', function() {
         const customUrl = fhirServerUrlInput.value.trim();
         let body = undefined;
         const authType = authTypeSelect ? authTypeSelect.value : 'none';
-        const bearerToken = bearerTokenInput ? bearerTokenInput.value.trim() : '';
+        const bearerToken = document.getElementById('bearerToken').value.trim();
         const username = usernameInput ? usernameInput.value.trim() : '';
         const password = passwordInput ? passwordInput.value : '';
 
@@ -329,30 +313,14 @@ document.addEventListener('DOMContentLoaded', function() {
             sendButton.textContent = 'Send Request';
             return;
         }
-
-        // --- Determine Final URL & Headers ---
-        const cleanedPath = cleanFhirPath(path);
-        const headers = { 'Accept': 'application/fhir+json, application/fhir+xml;q=0.9, */*;q=0.8' };
-        let finalFetchUrl;
-
-        if (useLocalHapi) {
-            if (!localHapiBaseUrl) {
-                alert('Local HAPI URL not available. Please refresh the page.');
-                sendButton.disabled = false;
-                sendButton.textContent = 'Send Request';
-                return;
-            }
-            // Direct request to the local URL
-            finalFetchUrl = `${localHapiBaseUrl.replace(/\/+$/, '')}/${cleanedPath}`;
-        } else {
-            // Use the proxy for custom URLs
-            if (!customUrl) {
-                alert('Please enter a custom FHIR Server URL.');
-                fhirServerUrlInput.classList.add('is-invalid');
-                sendButton.disabled = false;
-                sendButton.textContent = 'Send Request';
-                return;
-            }
+        if (!useLocalHapi && !customUrl) {
+            alert('Please enter a custom FHIR Server URL.');
+            fhirServerUrlInput.classList.add('is-invalid');
+            sendButton.disabled = false;
+            sendButton.textContent = 'Send Request';
+            return;
+        }
+        if (!useLocalHapi && customUrl) {
             try { new URL(customUrl); }
             catch (_) {
                 alert('Invalid custom FHIR Server URL format.');
@@ -361,19 +329,27 @@ document.addEventListener('DOMContentLoaded', function() {
                 sendButton.textContent = 'Send Request';
                 return;
             }
-            finalFetchUrl = '/fhir/' + cleanedPath;
-            headers['X-Target-FHIR-Server'] = customUrl.replace(/\/+$/, '');
-            console.log("Adding header X-Target-FHIR-Server:", headers['X-Target-FHIR-Server']);
-            if (authType === 'bearer') {
-                headers['Authorization'] = `Bearer ${bearerToken}`;
-                console.log("Adding header Authorization: Bearer <truncated>");
-            } else if (authType === 'basic') {
-                const credentials = btoa(`${username}:${password}`);
-                headers['Authorization'] = `Basic ${credentials}`;
-                console.log("Adding header Authorization: Basic <redacted>");
+        }
+
+        // --- Validate Authentication ---
+        if (!useLocalHapi) {
+            if (authType === 'bearer' && !bearerToken) {
+                alert('Please enter a Bearer Token.');
+                document.getElementById('bearerToken').classList.add('is-invalid');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
+            }
+            if (authType === 'basic' && (!username || !password)) {
+                alert('Please enter both Username and Password for Basic Authentication.');
+                if (!username) usernameInput.classList.add('is-invalid');
+                if (!password) passwordInput.classList.add('is-invalid');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
             }
         }
-        
+
         // --- Validate & Get Body ---
         if (method === 'POST' || method === 'PUT') {
             body = validateRequestBody(method, path);
@@ -386,6 +362,31 @@ document.addEventListener('DOMContentLoaded', function() {
             if (body === '') body = '';
         }
 
+        // --- Determine Fetch URL and Headers ---
+        const cleanedPath = cleanFhirPath(path);
+        const finalFetchUrl = '/fhir/' + cleanedPath;
+        const headers = { 'Accept': 'application/fhir+json, application/fhir+xml;q=0.9, */*;q=0.8' };
+
+        if (body !== undefined) {
+            if (body.trim().startsWith('{')) { headers['Content-Type'] = 'application/fhir+json'; }
+            else if (body.trim().startsWith('<')) { headers['Content-Type'] = 'application/fhir+xml'; }
+            else if (method === 'POST' && path.endsWith('_search') && body && !body.trim().startsWith('{') && !body.trim().startsWith('<')) { headers['Content-Type'] = 'application/x-www-form-urlencoded'; }
+            else if (body) { headers['Content-Type'] = 'application/fhir+json'; }
+        }
+
+        if (!useLocalHapi && customUrl) {
+            headers['X-Target-FHIR-Server'] = customUrl.replace(/\/+$/, '');
+            console.log("Adding header X-Target-FHIR-Server:", headers['X-Target-FHIR-Server']);
+            if (authType === 'bearer') {
+                headers['Authorization'] = `Bearer ${bearerToken}`;
+                console.log("Adding header Authorization: Bearer <truncated>");
+            } else if (authType === 'basic') {
+                const credentials = btoa(`${username}:${password}`);
+                headers['Authorization'] = `Basic ${credentials}`;
+                console.log("Adding header Authorization: Basic <redacted>");
+            }
+        }
+
         const csrfTokenInput = form.querySelector('input[name="csrf_token"]');
         const csrfToken = csrfTokenInput ? csrfTokenInput.value : null;
         if (useLocalHapi && ['POST', 'PUT', 'DELETE', 'PATCH'].includes(method) && csrfToken) {
@@ -453,7 +454,7 @@ document.addEventListener('DOMContentLoaded', function() {
         } catch (error) {
             console.error('Fetch error:', error);
             responseCard.style.display = 'block';
-            responseStatus.textContent = `Network Error`;
+            responseStatus.textContent = 'Network Error';
             responseStatus.className = 'badge bg-danger';
             responseHeaders.textContent = 'N/A';
             let errorDetail = `Error: ${error.message}\n\n`;

templates/fhir_ui_operations.html

@@ -114,14 +114,7 @@
         <p class="lead mb-4">
             Explore FHIR server operations by selecting resource types or system operations. Toggle between local Server or a custom server to interact with FHIR metadata, resources, and server-wide operations.
         </p>
-        <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
-        <div class="d-grid gap-2 d-sm-flex justify-content-sm-center">
-            <a href="{{ url_for('index') }}" class="btn btn-primary btn-lg px-4 gap-3">Back to Home</a>
-            <a href="{{ url_for('fhir_ui') }}" class="btn btn-outline-secondary btn-lg px-4">FHIR API Explorer</a>
-            <a href="{{ url_for('validate_sample') }}" class="btn btn-outline-secondary btn-lg px-4">Validate FHIR Sample</a>
         </div>
-        ------------------------------------------------------------------------------------------------------------------------------------------>
-    </div>
 </div>
 
 <div class="container mt-4">
@@ -134,11 +127,12 @@
                     <label class="form-label fw-bold">FHIR Server</label>
                     <div class="input-group">
                         <button type="button" class="btn btn-outline-primary" id="toggleServer">
-                            <span id="toggleLabel">Use Local </span>
+                            <span id="toggleLabel">Use Local Server</span>
                         </button>
                         <input type="text" class="form-control" id="fhirServerUrl" name="fhir_server_url" placeholder="Enter FHIR Base URL e.g., https://hapi.fhir.org/baseR4" style="display: none;" aria-describedby="fhirServerHelp">
                     </div>
                     <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local Fhir Server (/fhir proxy) or enter a custom FHIR server URL.</small>
+                    <small id="fhirServerHelp1" class="form-text text-muted">To enable the input fields you will have to toggle the server button when changing options (Issue Raised)</small>                    
                 </div>
                 <div class="mb-3" id="authSection" style="display: none;">
                     <label class="form-label fw-bold">Authentication</label>
@@ -367,7 +361,8 @@ document.addEventListener('DOMContentLoaded', () => {
     const authSection = document.getElementById('authSection');
     const authTypeSelect = document.getElementById('authType');
     const authInputsGroup = document.getElementById('authInputsGroup');
-    const bearerTokenInput = document.getElementById('bearerToken');
+    const bearerTokenInput = document.getElementById('bearerTokenInput');
+    const basicAuthInputs = document.getElementById('basicAuthInputs');
     const usernameInput = document.getElementById('username');
     const passwordInput = document.getElementById('password');
     if (!toggleServerButton || !toggleLabel || !fhirServerUrlInput || !authSection || !authTypeSelect) {
@@ -413,9 +408,14 @@ function updateAuthInputsUI() {
     authInputsGroup.style.display = (authType === 'bearer' || authType === 'basic') ? 'block' : 'none';
     bearerTokenInput.style.display = authType === 'bearer' ? 'block' : 'none';
     basicAuthInputs.style.display = authType === 'basic' ? 'block' : 'none';
-    if (authType !== 'bearer' && bearerTokenInput) bearerTokenInput.value = '';
-    if (authType !== 'basic' && usernameInput) usernameInput.value = '';
-    if (authType !== 'basic' && passwordInput) passwordInput.value = '';
+    if (authType !== 'bearer') {
+        const tokenInput = document.getElementById('bearerToken');
+        if (tokenInput) tokenInput.value = '';
+    }
+    if (authType !== 'basic') {
+        if (usernameInput) usernameInput.value = '';
+        if (passwordInput) passwordInput.value = '';
+    }
     console.log(`[updateAuthInputsUI] authInputsGroup display: ${authInputsGroup.style.display}, bearer: ${bearerTokenInput.style.display}, basic: ${basicAuthInputs.style.display}`);
 }
 
@@ -445,7 +445,7 @@ function updateAuthInputsUI() {
             toggleServerButton.style.pointerEvents = 'auto';
             toggleServerButton.removeAttribute('aria-disabled');
             toggleServerButton.title = "";
-            toggleLabel.textContent = isUsingLocalHapi ? 'Use Local HAPI' : 'Use Custom URL';
+            toggleLabel.textContent = isUsingLocalHapi ? 'Use Local Server' : 'Use Custom URL';
             fhirServerUrlInput.style.display = isUsingLocalHapi ? 'none' : 'block';
             fhirServerUrlInput.placeholder = "Enter FHIR Base URL e.g., https://hapi.fhir.org/baseR4";
             authSection.style.display = isUsingLocalHapi ? 'none' : 'block';
@@ -533,6 +533,7 @@ function updateAuthInputsUI() {
 
         isUsingLocalHapi = !isUsingLocalHapi;
         updateServerToggleUI();
+        updateAuthInputsUI();
 
         if (isUsingLocalHapi && fhirServerUrlInput) {
             fhirServerUrlInput.value = '';
@@ -543,7 +544,7 @@ function updateAuthInputsUI() {
         fetchedMetadataCache = null;
         availableSystemOperations = [];
         operationDefinitionCache = {};
-        console.log(`Server toggled (Standalone): Now using ${isUsingLocalHapi ? 'Local HAPI' : 'Custom URL'}`);
+        console.log(`Server toggled (Standalone): Now using ${isUsingLocalHapi ? 'Use Local Server' : 'Use Custom URL'}`);
     }
 
     if (toggleServerButton) {
@@ -1068,7 +1069,7 @@ function updateAuthInputsUI() {
                      </div>
                      <div class="opblock-section responses-section">
                           <div class="opblock-section-header"><h4>Example Response / Schema</h4></div><table class="responses-table"><thead><tr class="responses-header"><td class="response-col_status">Code</td><td class="response-col_description">Description</td></tr></thead><tbody><tr class="response" data-code="200"><td class="response-col_status">200</td><td class="response-col_description"><div class="response-col_description__inner"><div class="renderedMarkdown"><p>Success</p></div></div><section class="response-controls mb-2"><div class="row g-2 align-items-center mb-1">
-                          <div class="col-auto"><label for="${blockId}-example-media-type" class="response-control-media-type__title mb-0">Example Format:</label></div><div class="col-auto"><div class="content-type-wrapper"><select id="${blockId}-example-media-type" aria-label="Example Media Type" class="content-type example-media-type-select form-select form-select-sm" style="width: auto;"><option value="application/fhir+json">JSON</option><option value="application/fhir+xml">XML</option></select></div></div><div class="col"><small class="response-control-media-type__accept-message text-muted">Controls example/schema format.</small></div></div></section><div class="model-example"><ul class="tab list-unstyled ps-0 mb-2" role="tablist"><li class="tabitem active"><button class="tablinks badge active" data-name="example">Example Value</button></li><li class="tabitem"><button class="tablinks badge" data-name="schema">Schema</button></li></ul><div class="example-panel" style="display: block;"><div class="highlight-code"><pre class="example-code-display"><code class="language-json">${query.example && typeof query.example === 'string' ? query.example : '{}'}</code></pre></div></div><div class="schema-panel" style="display: none;"><div class="highlight-code"><pre class="schema-code-display"><code class="language-json">${JSON.stringify(query.schema || {}, null, 2)}</code></pre></div></div></div></td></tr><tr class="response" data-code="4xx/5xx"><td class="response-col_status">4xx/5xx</td><td class="response-col_description"><p>Error (e.g., Not Found, Server Error)</p></td></tr></tbody></table>
+                          <div class="col-auto"><label for="${blockId}-example-media-type" class="response-control-media-type__title mb-0">Example Format:</label></div><div class="col-auto"><div class="content-type-wrapper"><select id="${blockId}-example-media-type" aria-label="Example Media Type" class="content-type example-media-type-select form-select form-select-sm" style="width: auto;"><option value="application/fhir+json">JSON</option><option value="application/fhir+xml">XML</option></select></div></div><div class="col"><small class="response-control-media-type__accept-message text-muted">Controls example/schema format.</small></div></div></section><div class="model-example"><ul class="tab list-unstyled ps-0 mb-2" role="tablist"><li class="tabitem active"><button class="tablinks badge active" data-name="example">Example Value</button></li><li class="tabitem"><button class="tablinks badge" data-name="schema">Schema</button></li></ul><div class="example-panel" style="display: block;"><div class="highlight-code"><pre class="request-example-code"><code class="language-json">${query.example && typeof query.example === 'string' ? query.example : '{}'}</code></pre></div></div><div class="schema-panel" style="display: none;"><div class="highlight-code"><pre class="schema-code-display"><code class="language-json">${JSON.stringify(query.schema || {}, null, 2)}</code></pre></div></div></div></td></tr><tr class="response" data-code="4xx/5xx"><td class="response-col_status">4xx/5xx</td><td class="response-col_description"><p>Error (e.g., Not Found, Server Error)</p></td></tr></tbody></table>
                      </div>
                  </div>`;
              queryListContainer.appendChild(block);
@@ -1090,20 +1091,19 @@ function updateAuthInputsUI() {
             const curlOutput = executeWrapper?.querySelector('.curl-output code');
             const copyCurlButton = executeWrapper?.querySelector('.copy-curl-btn');
             const copyRespButton = executeWrapper?.querySelector('.copy-response-btn');
-            const downloadRespButton = executeWrapper?.querySelector('.download-response-btn');
+            const downloadRespButton = executeWrapper?.querySelector('.copy-response-btn');
             const exampleMediaTypeSelect = block.querySelector('.example-media-type-select');
             const exampleTabs = block.querySelectorAll('.responses-section .tablinks.badge');
             const examplePanel = block.querySelector('.responses-section .example-panel');
             const schemaPanel = block.querySelector('.responses-section .schema-panel');
 
-
             if (opblockSummary) {
-                 opblockSummary.addEventListener('click', (e) => {
+                opblockSummary.addEventListener('click', (e) => {
                     if (e.target.closest('button, a, input, select')) return;
                     const wasOpen = block.classList.contains('is-open');
                     block.classList.toggle('is-open', !wasOpen);
                     if(opblockBody) opblockBody.style.display = wasOpen ? 'none' : 'block';
-                 });
+                });
             }
 
             if (tryButton && executeButton) {
@@ -1113,22 +1113,22 @@ function updateAuthInputsUI() {
                     paramInputs.forEach(input => {
                         input.disabled = !enable;
                         if (!enable) {
-                             input.classList.remove('is-invalid');
-                             if (input.type === 'checkbox') {
-                                 input.checked = false;
-                             } else if (input.tagName === 'SELECT') {
-                                  const exampleValue = input.dataset.example;
-                                  if (exampleValue && input.querySelector(`option[value="${exampleValue}"]`)) { input.value = exampleValue; }
-                                  else if (input.options.length > 0) { input.selectedIndex = 0; }
-                             } else {
-                                  input.value = input.dataset.example || '';
-                             }
+                            input.classList.remove('is-invalid');
+                            if (input.type === 'checkbox') {
+                                input.checked = false;
+                            } else if (input.tagName === 'SELECT') {
+                                const exampleValue = input.dataset.example;
+                                if (exampleValue && input.querySelector(`option[value="${exampleValue}"]`)) { input.value = exampleValue; }
+                                else if (input.options.length > 0) { input.selectedIndex = 0; }
+                            } else {
+                                input.value = input.dataset.example || '';
+                            }
                         }
                     });
                     if (reqBodyTextarea) reqBodyTextarea.disabled = !enable;
                     if (reqContentTypeSelect) reqContentTypeSelect.disabled = !enable;
                     if (!enable && reqBodyTextarea && !query.parameters.some(p => p.in === 'body (Parameters)')) {
-                         reqBodyTextarea.value = (query.method === 'POST' && query.path.endsWith('_search')) ? query.example : '';
+                        reqBodyTextarea.value = (query.method === 'POST' && query.path.endsWith('_search')) ? query.example : '';
                     }
                     tryButton.textContent = enable ? 'Cancel' : 'Try it out';
                     tryButton.classList.toggle('cancel', enable);
@@ -1151,9 +1151,9 @@ function updateAuthInputsUI() {
             }
 
             if (reqContentTypeSelect && reqBodyTextarea && tryButton) {
-                 const reqExampleCode = block.querySelector('.request-example-code code');
-                 const reqExampleContainer = block.querySelector('.request-body-example');
-                 reqContentTypeSelect.addEventListener('change', () => {
+                const reqExampleCode = block.querySelector('.request-example-code code');
+                const reqExampleContainer = block.querySelector('.request-body-example');
+                reqContentTypeSelect.addEventListener('change', () => {
                     const type = reqContentTypeSelect.value;
                     const isFormUrlEncoded = type === 'application/x-www-form-urlencoded';
                     const isJsonParams = type === 'application/fhir+json' && query.parameters.some(p => p.in === 'body (Parameters)');
@@ -1177,8 +1177,8 @@ function updateAuthInputsUI() {
                             reqExampleCode.className = 'language-xml'; reqExampleCode.textContent = jsonToFhirXml(jsonExample); Prism.highlightElement(reqExampleCode);
                         }
                     }
-                 });
-                 reqContentTypeSelect.dispatchEvent(new Event('change'));
+                });
+                reqContentTypeSelect.dispatchEvent(new Event('change'));
             }
 
             if (executeButton && executeWrapper && respStatusDiv && reqUrlOutput && curlOutput && respFormatSelect && copyRespButton && downloadRespButton && respOutputCode && respNarrativeDiv && respOutputPre) {
@@ -1223,14 +1223,30 @@ function updateAuthInputsUI() {
                     
                     if (!isUsingLocalHapi) {
                         const authType = authTypeSelect.value;
-                        const bearerToken = bearerTokenInput.value.trim();
-                        const username = usernameInput.value.trim();
-                        const password = passwordInput.value;
+                        const bearerTokenValue = document.getElementById('bearerToken').value.trim();
+                        const usernameValue = document.getElementById('username').value.trim();
+                        const passwordValue = document.getElementById('password').value;
+
                         if (authType === 'bearer') {
-                            headers['Authorization'] = `Bearer ${bearerToken}`;
+                            if (!bearerTokenValue) {
+                                alert('Please enter a Bearer Token.');
+                                document.getElementById('bearerToken').classList.add('is-invalid');
+                                executeButton.disabled = false;
+                                executeButton.textContent = 'Execute';
+                                return;
+                            }
+                            headers['Authorization'] = `Bearer ${bearerTokenValue}`;
                             console.log("Adding header Authorization: Bearer <truncated>");
                         } else if (authType === 'basic') {
-                            headers['Authorization'] = `Basic ${btoa(`${username}:${password}`)}`;
+                            if (!usernameValue || !passwordValue) {
+                                alert('Please enter both Username and Password for Basic Authentication.');
+                                if (!usernameValue) document.getElementById('username').classList.add('is-invalid');
+                                if (!passwordValue) document.getElementById('password').classList.add('is-invalid');
+                                executeButton.disabled = false;
+                                executeButton.textContent = 'Execute';
+                                return;
+                            }
+                            headers['Authorization'] = `Basic ${btoa(`${usernameValue}:${passwordValue}`)}`;
                             console.log("Adding header Authorization: Basic <redacted>");
                         }
                     }
@@ -1618,8 +1634,8 @@ function updateAuthInputsUI() {
                 url = '/fhir/metadata';
                 headers['X-Target-FHIR-Server'] = customUrl;
                 const authType = authTypeSelect.value;
-                if (authType === 'bearer' && bearerTokenInput && bearerTokenInput.value) {
-                    headers['Authorization'] = `Bearer ${bearerTokenInput.value}`;
+                if (authType === 'bearer' && document.getElementById('bearerToken') && document.getElementById('bearerToken').value) {
+                    headers['Authorization'] = `Bearer ${document.getElementById('bearerToken').value}`;
                 } else if (authType === 'basic' && usernameInput && passwordInput && usernameInput.value && passwordInput.value) {
                     const credentials = btoa(`${usernameInput.value}:${passwordInput.value}`);
                     headers['Authorization'] = `Basic ${credentials}`;
@@ -1700,7 +1716,7 @@ function updateAuthInputsUI() {
              if (diagnostics) {
                 html += `<p class="mb-0 mt-1 small"><em>Diagnostics: ${diagnostics}</em></p>`;
             }
-            html += `</li>`;
+            html += '</li>';
         });
 
         html += '</ul>';

templates/retrieve_split_data.html

@@ -32,7 +32,7 @@
                     <label class="form-label fw-bold">FHIR Server</label>
                     <div class="input-group">
                         <button type="button" class="btn btn-outline-primary" id="toggleServer">
-                            <span id="toggleLabel">Use Local </span>
+                            <span id="toggleLabel">Use Local Server</span>
                         </button>
                         {{ form.fhir_server_url(class="form-control", id="fhirServerUrl", style="display: none;", placeholder="e.g., https://fhir.hl7.org.au/aucore/fhir/DEFAULT", **{'aria-describedby': 'fhirServerHelp'}) }}
                     </div>
@@ -162,7 +162,7 @@ document.addEventListener('DOMContentLoaded', () => {
     const authSection = document.getElementById('authSection');
     const authTypeSelect = document.getElementById('authType');
     const authInputsGroup = document.getElementById('authInputsGroup');
-    const bearerTokenInput = document.getElementById('bearerToken');
+    const bearerTokenInput = document.getElementById('bearerTokenInput');
     const basicAuthInputs = document.getElementById('basicAuthInputs');
     const usernameInput = document.getElementById('username');
     const passwordInput = document.getElementById('password');
@@ -221,7 +221,7 @@ document.addEventListener('DOMContentLoaded', () => {
             toggleServerButton.classList.remove('disabled');
             toggleServerButton.style.pointerEvents = 'auto';
             toggleServerButton.removeAttribute('aria-disabled');
-            toggleLabel.textContent = useLocalHapi ? 'Using Local HAPI' : 'Using Custom URL';
+            toggleLabel.textContent = useLocalHapi ? 'Use Local Server' : 'Use Custom URL';
             fhirServerUrlInput.style.display = useLocalHapi ? 'none' : 'block';
             fhirServerUrlInput.placeholder = "e.g., https://hapi.fhir.org/baseR4";
             fhirServerUrlInput.required = !useLocalHapi;
@@ -237,9 +237,15 @@ document.addEventListener('DOMContentLoaded', () => {
         authInputsGroup.style.display = (authType === 'bearer' || authType === 'basic') ? 'block' : 'none';
         bearerTokenInput.style.display = authType === 'bearer' ? 'block' : 'none';
         basicAuthInputs.style.display = authType === 'basic' ? 'block' : 'none';
-        if (authType !== 'bearer' && bearerTokenInput) bearerTokenInput.value = '';
-        if (authType !== 'basic' && usernameInput) usernameInput.value = '';
-        if (authType !== 'basic' && passwordInput) passwordInput.value = '';
+        if (authType !== 'bearer') {
+            // Correctly reference the input element by its ID
+            const tokenInput = document.getElementById('bearerToken');
+            if (tokenInput) tokenInput.value = '';
+        }
+        if (authType !== 'basic') {
+            if (usernameInput) usernameInput.value = '';
+            if (passwordInput) passwordInput.value = '';
+        }
     }
     function toggleFetchReferenceBundles() {
         if (validateReferencesCheckbox && fetchReferenceBundlesGroup) {
@@ -260,6 +266,7 @@ document.addEventListener('DOMContentLoaded', () => {
         useLocalHapi = !useLocalHapi;
         if (useLocalHapi) fhirServerUrlInput.value = '';
         updateServerToggleUI();
+        updateAuthInputsUI();
         resourceTypesDiv.style.display = 'none';
         fetchedMetadataCache = null;
         console.log(`Server toggled: useLocalHapi=${useLocalHapi}`);
@@ -308,8 +315,8 @@ document.addEventListener('DOMContentLoaded', () => {
                 fetchUrl = `${customUrl}/metadata`;
                 // Add authentication headers for the direct request to the custom server
                 const authType = authTypeSelect.value;
-                if (authType === 'bearer' && bearerTokenInput && bearerTokenInput.value) {
-                    headers['Authorization'] = `Bearer ${bearerTokenInput.value}`;
+                if (authType === 'bearer' && document.getElementById('bearerToken') && document.getElementById('bearerToken').value) {
+                    headers['Authorization'] = `Bearer ${document.getElementById('bearerToken').value}`;
                 } else if (authType === 'basic' && usernameInput && passwordInput && usernameInput.value && passwordInput.value) {
                     const credentials = btoa(`${usernameInput.value}:${passwordInput.value}`);
                     headers['Authorization'] = `Basic ${credentials}`;
@@ -404,15 +411,16 @@ document.addEventListener('DOMContentLoaded', () => {
         if (!useLocalHapi && authTypeSelect) {
             const authType = authTypeSelect.value;
             formData.append('auth_type', authType);
-            if (authType === 'bearer' && bearerTokenInput) {
-                if (!bearerTokenInput.value) {
+            if (authType === 'bearer') {
+                const bearerToken = document.getElementById('bearerToken').value.trim();
+                if (!bearerToken) {
                     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);
+                formData.append('bearer_token', bearerToken);
             } else if (authType === 'basic' && usernameInput && passwordInput) {
                 if (!usernameInput.value || !passwordInput.value) {
                     alert('Please enter both Username and Password for Basic Authentication.');

templates/validate_sample.html

@@ -22,8 +22,9 @@
     <div class="card">
         <div class="card-header">Validation Form</div>
         <div class="card-body">
-            <form id="validationForm">
-                {{ form.hidden_tag() }}
+            <form id="validationForm" method="POST" action="/api/validate">
+                {{ form.csrf_token }}
+
                 <div class="mb-3">
                     <small class="form-text text-muted">
                         Select a package from the list below or enter a new one (e.g., <code>hl7.fhir.us.core</code>).
@@ -46,6 +47,7 @@
                         <div class="text-danger">{{ error }}</div>
                     {% endfor %}
                 </div>
+
                 <div class="mb-3">
                     <label for="{{ form.version.id }}" class="form-label">Package Version</label>
                     {{ form.version(class="form-control", id=form.version.id) }}
@@ -53,36 +55,111 @@
                         <div class="text-danger">{{ error }}</div>
                     {% endfor %}
                 </div>
+
+                <hr class="my-4">
+
+                <!-- New Fields from ValidationForm -->
                 <div class="mb-3">
-                    <label for="{{ form.include_dependencies.id }}" class="form-label">Include Dependencies</label>
-                    <div class="form-check">
-                        {{ form.include_dependencies(class="form-check-input") }}
-                        {{ form.include_dependencies.label(class="form-check-label") }}
+                    <label for="fhir_resource" class="form-label">FHIR Resource (JSON or XML)</label>
+                    {{ form.fhir_resource(class="form-control", rows=10, placeholder="Paste your FHIR JSON here...") }}
+                </div>
+
+                <div class="row g-3">
+                    <div class="col-md-6">
+                        <label for="fhir_version" class="form-label">FHIR Version</label>
+                        {{ form.fhir_version(class="form-select") }}
                     </div>
                 </div>
-                <div class="mb-3">
-                    <label for="{{ form.mode.id }}" class="form-label">Validation Mode</label>
-                    {{ form.mode(class="form-select") }}
+
+                <hr class="my-4">
+
+                <h5>Validation Flags</h5>
+                <div class="row g-3">
+                    <div class="col-md-6">
+                        <div class="form-check">
+                            {{ form.do_native(class="form-check-input") }}
+                            <label class="form-check-label" for="do_native">{{ form.do_native.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.hint_about_must_support(class="form-check-input") }}
+                            <label class="form-check-label" for="hint_about_must_support">{{ form.hint_about_must_support.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.assume_valid_rest_references(class="form-check-input") }}
+                            <label class="form-check-label" for="assume_valid_rest_references">{{ form.assume_valid_rest_references.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.no_extensible_binding_warnings(class="form-check-input") }}
+                            <label class="form-check-label" for="no_extensible_binding_warnings">{{ form.no_extensible_binding_warnings.label }}</label>
+                        </div>
+                    </div>
+                    <div class="col-md-6">
+                        <div class="form-check">
+                            {{ form.show_times(class="form-check-input") }}
+                            <label class="form-check-label" for="show_times">{{ form.show_times.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.allow_example_urls(class="form-check-input") }}
+                            <label class="form-check-label" for="allow_example_urls">{{ form.allow_example_urls.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.check_ips_codes(class="form-check-input") }}
+                            <label class="form-check-label" for="check_ips_codes">{{ form.check_ips_codes.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.allow_any_extensions(class="form-check-input") }}
+                            <label class="form-check-label" for="allow_any_extensions">{{ form.allow_any_extensions.label }}</label>
+                        </div>
+                        <div class="form-check">
+                            {{ form.tx_routing(class="form-check-input") }}
+                            <label class="form-check-label" for="tx_routing">{{ form.tx_routing.label }}</label>
+                        </div>
+                    </div>
                 </div>
-                <div class="mb-3">
-                    <label for="{{ form.sample_input.id }}" class="form-label">Sample FHIR Resource/Bundle (JSON)</label>
-                    {{ form.sample_input(class="form-control", rows=10, placeholder="Paste your FHIR JSON here...") }}
-                    {% for error in form.sample_input.errors %}
-                        <div class="text-danger">{{ error }}</div>
-                    {% endfor %}
+
+                <hr class="my-4">
+
+                <h5>Other Settings</h5>
+                <div class="row g-3">
+                    <div class="col-md-6">
+                        <label for="profiles" class="form-label">{{ form.profiles.label }}</label>
+                        {{ form.profiles(class="form-control") }}
+                        <small class="form-text text-muted">Comma-separated URLs, e.g., url1,url2</small>
+                    </div>
+                    <div class="col-md-6">
+                        <label for="extensions" class="form-label">{{ form.extensions.label }}</label>
+                        {{ form.extensions(class="form-control") }}
+                        <small class="form-text text-muted">Comma-separated URLs, e.g., url1,url2</small>
+                    </div>
+                    <div class="col-md-6">
+                        <label for="terminology_server" class="form-label">{{ form.terminology_server.label }}</label>
+                        {{ form.terminology_server(class="form-control") }}
+                        <small class="form-text text-muted">e.g., http://tx.fhir.org</small>
+                    </div>
+                    <div class="col-md-6">
+                        <label for="snomed_ct_version" class="form-label">{{ form.snomed_ct_version.label }}</label>
+                        {{ form.snomed_ct_version(class="form-select") }}
+                        <small class="form-text text-muted">Select a SNOMED CT edition.</small>
+                    </div>
                 </div>
-                <div class="d-flex justify-content-between">
-                    <button type="button" class="btn btn-primary" id="validateButton">Validate</button>
-                    <button type="button" class="btn btn-secondary d-none" id="clearResultsButton">Clear Results</button>
+
+                <div class="mt-4 text-center">
+                    <button type="submit" id="validateButton" class="btn btn-primary btn-lg">
+                        Validate Resource
+                    </button>
+                    <button type="button" id="clearResultsButton" class="btn btn-secondary btn-lg d-none">
+                        Clear Results
+                    </button>
                 </div>
             </form>
         </div>
     </div>
-
-    <div class="card mt-4" id="validationResult" style="display: none;">
-        <div class="card-header">Validation Report</div>
+    
+    <div id="validationResult" class="card mt-4" style="display: none;">
+        <div class="card-header">Validation Results</div>
         <div class="card-body" id="validationContent">
-            </div>
+            <!-- Results will be displayed here -->
+        </div>
     </div>
 </div>
 
@@ -94,6 +171,7 @@
     const spinnerOverlay = document.getElementById('spinner-overlay');
     const spinnerMessage = document.getElementById('spinner-message');
     const spinnerContainer = document.getElementById('spinner-animation');
+    const perPage = 10;
     
     // Function to load the Lottie animation based on theme
     function loadLottieAnimation(theme) {
@@ -136,17 +214,18 @@
 
     // --- Frontend logic starts here
     document.addEventListener('DOMContentLoaded', function() {
-        const packageSelect = document.getElementById('packageSelect');
-        const packageNameInput = document.getElementById('{{ form.package_name.id }}');
-        const versionInput = document.getElementById('{{ form.version.id }}');
+        const form = document.getElementById('validationForm');
         const validateButton = document.getElementById('validateButton');
         const clearResultsButton = document.getElementById('clearResultsButton');
-        const sampleInput = document.getElementById('{{ form.sample_input.id }}');
         const validationResult = document.getElementById('validationResult');
         const validationContent = document.getElementById('validationContent');
         const csrfToken = document.querySelector('input[name="csrf_token"]').value;
-        const perPage = 10;
-
+        const packageSelect = document.getElementById('packageSelect');
+        const packageNameInput = document.getElementById('{{ form.package_name.id }}');
+        const versionInput = document.getElementById('{{ form.version.id }}');
+        const fhirResourceInput = document.getElementById('fhir_resource');
+        
+        // Function to update package fields when a package is selected from the dropdown
         function updatePackageFields(select) {
             const value = select.value;
             if (!packageNameInput || !versionInput) return;
@@ -164,38 +243,8 @@
                 versionInput.value = '';
             }
         }
-
-        if (packageNameInput.value && versionInput.value) {
-            const currentValue = `${packageNameInput.value}#${versionInput.value}`;
-            const optionExists = Array.from(packageSelect.options).some(opt => opt.value === currentValue);
-            if (optionExists) {
-                packageSelect.value = currentValue;
-            }
-        }
-
-        if (packageSelect) {
-            packageSelect.addEventListener('change', function() {
-                updatePackageFields(this);
-            });
-        }
-
-        if (sampleInput) {
-            sampleInput.addEventListener('input', function() {
-                try {
-                    if (this.value.trim()) {
-                        JSON.parse(this.value);
-                        this.classList.remove('is-invalid');
-                        this.classList.add('is-valid');
-                    } else {
-                        this.classList.remove('is-valid', 'is-invalid');
-                    }
-                } catch (e) {
-                    this.classList.remove('is-valid');
-                    this.classList.add('is-invalid');
-                }
-            });
-        }
-
+        
+        // Sanitize text to prevent XSS
         function sanitizeText(text) {
             const div = document.createElement('div');
             div.textContent = text;
@@ -226,7 +275,7 @@
                 li.innerHTML = `
                     <div class="alert alert-${isWarnings ? 'warning' : 'danger'}">
                         ${sanitizeText(typeof item === 'string' ? item : item.message || item.issue)}
-                        ${isWarnings && item.includes('Must Support') ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
+                        ${isWarnings && (item.issue && item.issue.includes('Must Support')) ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
                     </div>
                 `;
                 ul.appendChild(li);
@@ -246,7 +295,7 @@
                     li.innerHTML = `
                         <div class="alert alert-${isWarnings ? 'warning' : 'danger'}">
                             ${sanitizeText(typeof item === 'string' ? item : item.message || item.issue)}
-                            ${isWarnings && item.includes('Must Support') ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
+                            ${isWarnings && (item.issue && item.issue.includes('Must Support')) ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
                         </div>
                     `;
                     remainingUl.appendChild(li);
@@ -275,7 +324,7 @@
             clearResultsButton.classList.remove('d-none');
 
             if (data.file_paths) {
-                // Fix: Extract just the filename to construct the download URL
+                // Use the paths returned from the server to create download links
                 const jsonFileName = data.file_paths.json.split('/').pop();
                 const htmlFileName = data.file_paths.html.split('/').pop();
                 const downloadDiv = document.createElement('div');
@@ -364,7 +413,7 @@
                 new bootstrap.Tooltip(el);
             });
         }
-
+        
         function checkValidationStatus(taskId) {
             fetch(`/api/check-validation-status/${taskId}`)
                 .then(response => {
@@ -398,10 +447,11 @@
                 });
         }
         
-        function runBlockingValidation() {
-            const packageName = packageNameInput.value;
-            const version = versionInput.value;
-            const sampleData = sampleInput.value.trim();
+        function runBlockingValidation(e) {
+            e.preventDefault(); // This is the crucial line to prevent default form submission
+            const packageName = document.getElementById('{{ form.package_name.id }}').value;
+            const version = document.getElementById('{{ form.version.id }}').value;
+            const sampleData = document.getElementById('fhir_resource').value.trim();
             const csrfToken = document.querySelector('input[name="csrf_token"]').value;
 
             if (!packageName || !version) {
@@ -412,31 +462,40 @@
 
             if (!sampleData) {
                 validationResult.style.display = 'block';
-                validationContent.innerHTML = '<div class="alert alert-danger">Please provide FHIR sample JSON.</div>';
+                validationContent.innerHTML = '<div class="alert alert-danger">Please provide FHIR sample JSON or XML.</div>';
                 return;
             }
-
-            try {
-                JSON.parse(sampleData);
-            } catch (e) {
-                validationResult.style.display = 'block';
-                validationContent.innerHTML = '<div class="alert alert-danger">Invalid JSON: ' + sanitizeText(e.message) + '</div>';
-                return;
-            }
-
+            
             toggleSpinner(true, "Running FHIR Validator (This may take up to 5 minutes on the first run).");
             
-            fetch('/api/validate-sample', {
+            // Collect all form data including the new fields
+            const data = {
+                package_name: packageName,
+                version: version,
+                fhir_resource: sampleData,
+                fhir_version: document.getElementById('fhir_version').value,
+                do_native: document.getElementById('do_native').checked,
+                hint_about_must_support: document.getElementById('hint_about_must_support').checked,
+                assume_valid_rest_references: document.getElementById('assume_valid_rest_references').checked,
+                no_extensible_binding_warnings: document.getElementById('no_extensible_binding_warnings').checked,
+                show_times: document.getElementById('show_times').checked,
+                allow_example_urls: document.getElementById('allow_example_urls').checked,
+                check_ips_codes: document.getElementById('check_ips_codes').checked,
+                allow_any_extensions: document.getElementById('allow_any_extensions').checked,
+                tx_routing: document.getElementById('tx_routing').checked,
+                snomed_ct_version: document.getElementById('snomed_ct_version').value,
+                profiles: document.getElementById('profiles').value,
+                extensions: document.getElementById('extensions').value,
+                terminology_server: document.getElementById('terminology_server').value
+            };
+
+            fetch('/api/validate', {
                 method: 'POST',
                 headers: {
                     'Content-Type': 'application/json',
                     'X-CSRFToken': csrfToken
                 },
-                body: JSON.stringify({
-                    package_name: packageName,
-                    version: version,
-                    sample_data: sampleData
-                })
+                body: JSON.stringify(data)
             })
             .then(response => {
                 if (response.status === 202) {
@@ -462,9 +521,9 @@
                 toggleSpinner(false);
                 console.error('Validation failed:', error);
                 validationResult.style.display = 'block';
-                validationContent.innerHTML = `<div class="alert alert-danger">An unexpected error occurred: ${sanitizeText(error.message)}</div>`;
+                validationContent.innerHTML = `<div class="alert alert-danger">An unexpected error occurred during validation: ${sanitizeText(error.message)}</div>`;
             });
-        }
+        };
         
         clearResultsButton.addEventListener('click', function() {
             fetch('/api/clear-validation-results', {
@@ -487,9 +546,40 @@
             });
         });
 
+        if (packageSelect) {
+            packageSelect.addEventListener('change', function() {
+                updatePackageFields(this);
+            });
+        }
+        
         if (validateButton) {
-            validateButton.addEventListener('click', function() {
-                runBlockingValidation();
+            validateButton.addEventListener('click', function(e) {
+                runBlockingValidation(e);
+            });
+        }
+        
+        if (packageNameInput.value && versionInput.value) {
+            const currentValue = `${packageNameInput.value}#${versionInput.value}`;
+            const optionExists = Array.from(packageSelect.options).some(opt => opt.value === currentValue);
+            if (optionExists) {
+                packageSelect.value = currentValue;
+            }
+        }
+
+        if (fhirResourceInput) {
+            fhirResourceInput.addEventListener('input', function() {
+                try {
+                    if (this.value.trim()) {
+                        JSON.parse(this.value);
+                        this.classList.remove('is-invalid');
+                        this.classList.add('is-valid');
+                    } else {
+                        this.classList.remove('is-valid', 'is-invalid');
+                    }
+                } catch (e) {
+                    this.classList.remove('is-valid');
+                    this.classList.add('is-invalid');
+                }
             });
         }
     });