feat: resolving issue #8 #9 and #10

backend/.tes_instances

@@ -10,7 +10,6 @@ TESK/Kubernetes @ ELIXIR-CZ (NA),https://tesk-na.cloud.e-infra.cz/
 TESK/Kubernetes @ ELIXIR-DE,https://tesk.elixir-cloud.bi.denbi.de/
 TESK/Kubernetes @ ELIXIR-GR,https://tesk-eu.hypatia-comp.athenarc.gr/
 TESK/OpenShift @ ELIXIR-FI,https://csc-tesk-noauth.rahtiapp.fi/
-TESK North America,https://tesk-na.cloud.e-infra.cz/
 
 # Local Development
 Local TES,http://localhost:8080

backend/routes/instances.py

@@ -28,6 +28,27 @@ def get_healthy_instances_route():
         print(f"❌ Error in get_healthy_instances: {str(e)}")
         return jsonify({'error': str(e)}), 500
 
+@instances_bp.route('/api/instances-with-status', methods=['GET'])
+def get_instances_with_status():
+    """Get all TES instances with their current health status"""
+    try:
+        from utils.tes_utils import load_tes_location_data
+        instances = load_tes_location_data()
+
+        # Fetch status for all instances in parallel
+        with ThreadPoolExecutor(max_workers=8) as pool:
+            results = list(pool.map(fetch_tes_status, instances))
+
+        return jsonify({
+            'instances': results,
+            'count': len(results),
+            'last_updated': datetime.now(timezone.utc).isoformat()
+        })
+
+    except Exception as e:
+        print(f"Error in get_instances_with_status: {str(e)}")
+        return jsonify({'error': str(e)}), 500
+
 @instances_bp.route('/api/tes_locations', methods=['GET'])
 def tes_locations():
     from utils.tes_utils import load_tes_location_data

backend/routes/tasks.py

@@ -4,9 +4,13 @@
 import json
 import time
 import requests
+import shlex
 from services.task_service import get_submitted_tasks, add_task, update_single_task_status
 from utils.tes_utils import load_tes_instances
 from utils.auth_utils import get_instance_credentials
+import logging
+
+logger = logging.getLogger(__name__)
 
 tasks_bp = Blueprint('tasks', __name__)
 
@@ -36,9 +40,38 @@ def submit_task():
                 tes_name = inst['name']
                 break
 
+
+        command_raw = data.get('command', '')
+        if isinstance(command_raw, list):
+            command = command_raw
+        elif command_raw:
+
+            shell_operators = ['&&', '||', '|', '>', '<', '>>', '2>', '&', ';', '$(', '`']
+            needs_shell = any(op in command_raw for op in shell_operators)
+
+            if needs_shell:
+
+                command = ["/bin/sh", "-c", command_raw]
+                print(f"🐚 Command contains shell operators, wrapping in shell: {command}")
+            else:
+
+                try:
+                    command = shlex.split(command_raw)
+                    print(f"📝 Simple command parsed: {command}")
+                except ValueError as e:
+                    logger.error(f"Command parsing error: {e}")
+                    return jsonify({
+                        'success': False,
+                        'error': f'Invalid command syntax: {str(e)}',
+                        'error_type': 'bad_request',
+                        'error_code': 'INVALID_COMMAND'
+                    }), 400
+        else:
+            command = ['echo', 'Hello World']
+
         executor = {
             "image": docker_image,
-            "command": data.get('command') if isinstance(data.get('command'), list) else (data.get('command', '').split() if data.get('command') else ['echo', 'Hello World']),
+            "command": command,
             "workdir": data.get('workdir', '/tmp')
         }
 
@@ -100,13 +133,24 @@ def submit_task():
 
             try:
                 print(f"  Trying service-info: {service_info_url}")
-                test_response = requests.get(service_info_url, timeout=10) 
-                if test_response.status_code in [200, 403]:
+                test_response = requests.get(service_info_url, timeout=10)
+
+                if test_response.status_code == 200:
                     service_is_reachable = True
                     working_endpoint = tasks_url
                     print(f"  ✅ Service reachable at {service_info_url} (status {test_response.status_code})")
                     print(f"  Will use tasks endpoint: {tasks_url}")
                     break
+                elif test_response.status_code in [401, 403]:
+                    # Authentication required - treat as unreachable since we can't use it
+                    print(f"  🔐 Authentication required at {service_info_url} (status {test_response.status_code})")
+                    connectivity_error_info = {
+                        'error_type': 'unauthorized',
+                        'error_code': 'UNAUTHORIZED',
+                        'message': 'Authentication required - TES instance requires credentials',
+                        'reason': 'This TES instance requires authentication. Please configure TESK_PROD_TOKEN or credentials in environment variables.'
+                    }
+                    continue
                 else:
                     print(f"  ⚠️ Service returned status {test_response.status_code}")
 
@@ -199,6 +243,7 @@ def submit_task():
 
         tes_endpoint = working_endpoint
         print(f"🚀 Submitting task to {tes_endpoint}")
+        print(f"📦 Task payload: {json.dumps(tes_task, indent=2)}")
 
         credentials = get_instance_credentials(tes_name, tes_url)
         headers = {
@@ -301,7 +346,7 @@ def submit_task():
         else:
             error_type_map = {
                 400: {'error_type': 'bad_request', 'error_code': 'BAD_REQUEST', 'reason': 'The task specification is invalid or malformed'},
-                401: {'error_type': 'unauthorized', 'error_code': 'UNAUTHORIZED', 'reason': 'Authentication required or credentials are invalid'},
+                401: {'error_type': 'unauthorized', 'error_code': 'UNAUTHORIZED', 'reason': 'Authentication required. Please configure TESK_PROD_TOKEN or TESK_PROD_USER/TESK_PROD_PASSWORD environment variables for this instance.'},
                 403: {'error_type': 'forbidden', 'error_code': 'FORBIDDEN', 'reason': 'You do not have permission to submit tasks to this instance'},
                 404: {'error_type': 'not_found', 'error_code': 'NOT_FOUND', 'reason': 'The TES endpoint was not found. Check if the URL is correct.'},
                 408: {'error_type': 'timeout', 'error_code': 'TIMEOUT', 'reason': 'The request timed out. The TES instance may be overloaded.'},
@@ -319,12 +364,21 @@ def submit_task():
             })
 
             error_msg = f'TES submission failed with status {response.status_code}'
+            print(f"❌ TES returned status {response.status_code}")
+            print(f"Response headers: {dict(response.headers)}")
+            print(f"Response body: {response.text[:500]}")
+
             try:
                 error_data = response.json()
+                print(f"Error data JSON: {error_data}")
                 if error_data.get('message'):
                     error_msg = error_data.get('message')
                 elif error_data.get('error'):
                     error_msg = error_data.get('error')
+                elif error_data.get('detail'):
+                    error_msg = error_data.get('detail')
+                elif error_data.get('title'):
+                    error_msg = error_data.get('title')
                 else:
                     error_msg = f'{error_msg}: {str(error_data)}'
             except:

backend/services/tes_service.py

@@ -28,7 +28,46 @@ def fetch_tes_status(instance):
         r = requests.get(f"{tes_base_url}/ga4gh/tes/v1/service-info", timeout=5)
         latency_ms = int((time.time() - start_time) * 1000)
 
-        status = "healthy" if r.status_code == 200 else "unhealthy"
+        # First check service-info endpoint
+        if r.status_code in [401, 403]:
+            status = "unhealthy"  # Authentication required but not available
+        elif r.status_code != 200:
+            status = "unhealthy"
+        else:
+            # Service-info is accessible, but we need to check if tasks endpoint is usable
+            # Try a HEAD/OPTIONS request to tasks endpoint to see if it requires auth
+            try:
+                instance_name = instance.get("name", "")
+                credentials = get_instance_credentials(instance_name, tes_base_url)
+
+                # Test tasks endpoint with credentials (if available)
+                headers = {'Accept': 'application/json'}
+                auth = None
+                if credentials.get('token'):
+                    headers['Authorization'] = f"Bearer {credentials['token']}"
+                elif credentials.get('user') and credentials.get('password'):
+                    auth = (credentials['user'], credentials['password'])
+
+                # Try to list tasks (with view=MINIMAL to reduce payload)
+                tasks_response = requests.get(
+                    f"{tes_base_url}/ga4gh/tes/v1/tasks?view=MINIMAL",
+                    headers=headers,
+                    auth=auth,
+                    timeout=5
+                )
+
+                # If tasks endpoint returns 401/403, mark as unhealthy (auth required but not configured)
+                if tasks_response.status_code in [401, 403]:
+                    print(f"⚠️ {instance.get('name')} tasks endpoint requires authentication (status {tasks_response.status_code})")
+                    status = "unhealthy"
+                else:
+                    # Tasks endpoint is accessible (200) or returns other non-auth error
+                    status = "healthy"
+            except Exception as tasks_error:
+                print(f"⚠️ Could not check tasks endpoint for {instance.get('name')}: {tasks_error}")
+                # If we can't check tasks endpoint, assume healthy based on service-info
+                status = "healthy"
+
         version = ""
         try:
             version = r.json().get("version", "")

frontend/src/hooks/useInstances.js

@@ -4,6 +4,7 @@ import instanceService from '../services/instanceService';
 const useInstances = () => {
   const [state, setState] = useState({
     instances: [],
+    allInstances: [],
     loading: true,
     error: null,
     lastUpdate: null
@@ -15,7 +16,11 @@ const useInstances = () => {
     };
     instanceService.addListener(handleUpdate);
     const initialState = instanceService.getHealthyInstances();
-    setState(initialState);
+    const allInstancesState = instanceService.getAllInstancesWithStatus();
+    setState({
+      ...initialState,
+      allInstances: allInstancesState.instances
+    });
     return () => {
       instanceService.removeListener(handleUpdate);
     };
@@ -26,6 +31,7 @@ const useInstances = () => {
 
   return {
     instances: state.instances,
+    allInstances: state.allInstances,
     loading: state.loading,
     error: state.error,
     lastUpdate: state.lastUpdate,