feat: per-caller Bearer token auth and new query tools for MCP server (#984)

Replace the broken GATEWAY_SECRET auth (token was sent as a query
parameter, silently ignored by the gateway) with end-to-end Bearer
token forwarding.  Each MCP caller gets a dedicated WebSocket
authenticated via the gateway's in-band first-frame protocol, with
whoami verification on first connect.

Also fix and extend the tool surface:
- embeddings: accept list of texts (was single string)
- triples_query: use Term wire format with compact keys (was legacy
  Value format), add collection and graph parameters
- sparql_query: new tool for SPARQL SELECT/ASK/CONSTRUCT/DESCRIBE
- graphql_query: new tool for structured data (rows) GraphQL queries
- all tools: add optional workspace parameter

README.md

@@ -11,11 +11,11 @@
 
 <a href="https://trendshift.io/repositories/17291" target="_blank"><img src="https://trendshift.io/api/badge/repositories/17291" alt="trustgraph-ai%2Ftrustgraph | Trendshift" style="width: 250px; height: 55px;" width="250" height="55"/></a>
 
-# The agent runtime platform
+# The semantic deployment platform
 
 </div>
 
-TrustGraph is an agent runtime platform built around context graphs — structured, queryable representations of your domain knowledge that ground every agent query in verified, explainable facts in private deployments with sovereign control. The platform is the full stack for agentic systems: context graphs, memory, retrieval, orchestration, and inference for precision-critical agent workloads.
+TrustGraph is a comprehensive semantic infrastructure for agents built around context graphs — structured, queryable representations of your domain knowledge that ground every agent query in verified, explainable facts in private deployments with sovereign control. The platform is the full stack for agentic systems: context graphs, memory, retrieval, orchestration, and inference for deterministic agent workloads.
 
 The platform:
 - [x] Multi-model and multimodal database system
@@ -99,23 +99,21 @@ For a browser based configuration, try the [Configuration Terminal](https://conf
 - [**Developer APIs and CLI**](https://docs.trustgraph.ai/reference)
 - [**Deployment Guides**](https://docs.trustgraph.ai/deployment)
 
-## Workbench
+## Context Graph UI
 
-The **Workbench** provides tools for all major features of TrustGraph. The **Workbench** is on port `8888` by default.
+<img width="1389" height="961" alt="Image" src="https://github.com/user-attachments/assets/35c9250d-0f01-40cb-9294-1ee8fd9a1b56" />
 
-- **Vector Search**: Search the installed knowledge bases
+The UI provides tools for all major features of TrustGraph. The UI deploys on port `8888` by default.
-- **Agentic, GraphRAG and LLM Chat**: Chat interface for agents, GraphRAG queries, or direct to LLMs
+
-- **Relationships**: Analyze deep relationships in the installed knowledge bases
+- **Agent Console** — Query your agents directly with streaming responses and live explainability event tracking, so you can watch reasoning unfold in real time
-- **Graph Visualizer**: 3D GraphViz of the installed knowledge bases
+- **GraphRAG View** — Interactive graph RAG queries with a visual explainability DAG and inline provenance display, making it easy to see exactly where answers came from
-- **Library**: Staging area for installing knowledge bases
+- **Context Explorer** — An interactive 3D context graph explorer with dynamic graph loading, BFS neighborhood extraction, edge pulse animation, and multiple navigation views
-- **Flow Classes**: Workflow preset configurations
+- **Document Ingestion** — A complete upload and submission workflow with page and chunk inspection and document structure browsing
-- **Flows**: Create custom workflows and adjust LLM parameters during runtime
+- **Ontology Workbench** — A full ontology editor with class and property trees, OWL/XML and Turtle import/export with round-trip fidelity, circular dependency detection, and safe-delete confirmation dialogs
-- **Knowledge Cores**: Manage resuable knowledge bases
+- **Schema Workbench** — Interactive schema management with list, create, edit, and delete operations including field and index management
-- **Prompts**: Manage and adjust prompts during runtime
+- **Flow Management** — Flow creation and detail views with configurable parameters, temperature controls, and grouped storage layout
-- **Schemas**: Define custom schemas for structured data knowledge bases
+- **Workspace UX** — Workspace selection and management surfaced directly in the interface
-- **Ontologies**: Define custom ontologies for unstructured data knowledge bases
+- **Prompt Editor** — A dedicated prompt editing workflow
-- **Agent Tools**: Define tools with collections, knowledge cores, MCP connections, and tool groups
-- **MCP Tools**: Connect to MCP servers
 
 ## TypeScript Library for UIs
 

trustgraph-mcp/trustgraph/mcp_server/tg_socket.py

@@ -1,49 +1,110 @@
 
-from dataclasses import dataclass
 from websockets.asyncio.client import connect
-from urllib.parse import urlencode, urlparse, urlunparse, parse_qs
 import asyncio
 import logging
 import json
 import uuid
-import time
+import hashlib
+
+logger = logging.getLogger(__name__)
+
+
+def _token_key(token):
+    """Derive a dict key from a token without storing the raw secret."""
+    return hashlib.sha256(token.encode()).hexdigest()[:16]
+
 
 class WebSocketManager:
+    """Manages an authenticated WebSocket connection to the TrustGraph
+    gateway on behalf of a single caller.
 
-    def __init__(self, url, token=None):
+    Each caller token gets its own WebSocketManager so that gateway-side
+    identity, workspace, and capability scoping are preserved end-to-end.
+    """
+
+    def __init__(self, url, token):
         self.url = url
+        # ── Security boundary: token storage ──
+        # This is the MCP caller's Bearer token, forwarded verbatim to
+        # the gateway.  It MUST NOT be logged, persisted, or shared
+        # across callers.  It is held only for the lifetime of this
+        # connection so that re-auth (e.g. after a reconnect) is
+        # possible.
         self.token = token
         self.socket = None
-
+        self.identity = None
-    # FIXME: authentication is broken. The /api/v1/socket endpoint uses
+        self.last_used = None
-    # in-band auth (first-frame protocol via the Mux dispatcher), not
-    # query-parameter tokens. This query-string token is silently ignored.
-    # Fix: after connect(), send an auth frame with the bearer token as
-    # the first message, matching the gateway's in-band auth protocol.
-    def _build_url(self):
-        if not self.token:
-            return self.url
-        parsed = urlparse(self.url)
-        params = parse_qs(parsed.query)
-        params["token"] = [self.token]
-        new_query = urlencode(params, doseq=True)
-        return urlunparse(parsed._replace(query=new_query))
 
     async def start(self):
-        self.socket = await connect(self._build_url())
+        """Connect and authenticate via the gateway's in-band auth
+        protocol.  Raises on auth failure."""
+
+        # ── Security boundary: MCP server → gateway ──
+        # The WebSocket connects to the gateway and authenticates using
+        # the caller's Bearer token via the in-band first-frame auth
+        # protocol.  The token belongs to the MCP client — we forward
+        # it as-is and never interpret its contents.
+        self.socket = await connect(self.url)
         self.pending_requests = {}
         self.running = True
+
+        await self._authenticate()
+
         self.reader_task = asyncio.create_task(self.reader())
 
+    async def _authenticate(self):
+        """Send in-band auth frame and wait for auth-ok / auth-failed.
+
+        The gateway expects ``{"type": "auth", "token": "..."}`` as the
+        first frame on a new WebSocket.  Any service frame sent before
+        auth-ok is rejected.
+        """
+        await self.socket.send(json.dumps({
+            "type": "auth",
+            "token": self.token,
+        }))
+
+        response_text = await asyncio.wait_for(self.socket.recv(), 10)
+        response = json.loads(response_text)
+
+        if response.get("type") == "auth-ok":
+            logger.info(
+                "WebSocket authenticated, default workspace: %s",
+                response.get("workspace"),
+            )
+            return
+
+        # Auth failed — close immediately, do not leave an
+        # unauthenticated socket open.
+        await self.socket.close()
+        self.socket = None
+
+        if response.get("type") == "auth-failed":
+            raise RuntimeError(
+                "Gateway rejected the authentication token"
+            )
+
+        raise RuntimeError(
+            f"Unexpected auth response type: {response.get('type')}"
+        )
+
+    async def whoami(self):
+        """Verify the token by calling the gateway's whoami endpoint.
+        Returns the identity dict and caches it on ``self.identity``.
+        """
+        gen = self.request("iam", {"operation": "whoami"}, flow_id=None)
+        async for response in gen:
+            self.identity = response
+            return response
+
     async def stop(self):
         self.running = False
-        await self.reader_task
+        if hasattr(self, "reader_task"):
+            await self.reader_task
 
     async def reader(self):
-        """
+        """Background task: read WebSocket frames and route them to the
-        Background task to read websocket responses and route to correct
+        correct pending-request queue by ``id``."""
-        request
-        """
 
         while self.running:
             try:
@@ -59,23 +120,21 @@ class WebSocketManager:
 
                 request_id = response.get("id")
                 if request_id and request_id in self.pending_requests:
-                    # Put the response in the queue
                     queue = self.pending_requests[request_id]
                     await queue.put(response)
                 else:
-                    logging.warning(
+                    logger.warning(
-                        f"Response for unknown request ID: {request_id}"
+                        "Response for unknown request ID: %s", request_id
                     )
 
             except Exception as e:
 
-                logging.error(f"Error in websocket reader: {e}")
+                logger.error("Error in websocket reader: %s", e)
 
-                # Put error in all pending queues
                 for queue in self.pending_requests.values():
                     try:
                         await queue.put({"error": str(e)})
-                    except:
+                    except Exception:
                         pass
 
                 self.pending_requests.clear()
@@ -86,25 +145,29 @@ class WebSocketManager:
 
     async def request(
             self, service, request_data, flow_id="default",
+            workspace=None,
     ):
-        """
+        """Send a request via WebSocket and yield responses.
-        Send a request via websocket and handle single or streaming responses
+
+        Args:
+            service: Gateway service name (e.g. "graph-rag", "config").
+            request_data: Inner request payload.
+            flow_id: Optional flow identifier.  ``None`` omits the field
+                (workspace-level services don't use flows).
+            workspace: Optional workspace override.  When ``None`` the
+                gateway uses the caller's default workspace.
         """
 
-        # Generate unique request ID
+        import time
+        self.last_used = time.monotonic()
+
         request_id = f"{uuid.uuid4()}"
 
-        # Determine if this service streams responses
-        streaming_services = {"agent"}
-        is_streaming = service in streaming_services
-
-        # Create a queue for all responses (streaming and single)
         response_queue = asyncio.Queue()
         self.pending_requests[request_id] = response_queue
 
         try:
 
-            # Build request message
             message = {
                 "id": request_id,
                 "service": service,
@@ -114,7 +177,16 @@ class WebSocketManager:
             if flow_id is not None:
                 message["flow"] = flow_id
 
-            # Send request
+            # ── Security boundary: workspace scoping ──
+            # When the caller supplies a workspace, we set it on the
+            # message envelope.  The gateway's enforce_workspace()
+            # validates that the authenticated identity is permitted
+            # to access the target workspace — we MUST NOT skip or
+            # override that check.  When workspace is None, the
+            # gateway default-fills from the identity's bound workspace.
+            if workspace is not None:
+                message["workspace"] = workspace
+
             await self.socket.send(json.dumps(message))
 
             while self.running:
@@ -127,19 +199,17 @@ class WebSocketManager:
                     continue
 
                 if "error" in response:
-                    if "message" in response["error"]:
+                    if isinstance(response["error"], dict):
-                        raise RuntimeError(response["error"]["text"])
+                        raise RuntimeError(
+                            response["error"].get("message", str(response["error"]))
+                        )
                     else:
                         raise RuntimeError(str(response["error"]))
 
                 yield response["response"]
 
-                if "complete" in response:
+                if response.get("complete"):
-                    if response["complete"]:
+                    break
-                        break
 
-        except Exception as e:
+        finally:
-            # Clean up on error
             self.pending_requests.pop(request_id, None)
-            raise e
-