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 semantic deployment platform
+# The agent runtime platform
 
 </div>
 
-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.
+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.
 
 The platform:
 - [x] Multi-model and multimodal database system
@@ -99,21 +99,23 @@ 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)
 
-## Context Graph UI
+## Workbench
 
-<img width="1389" height="961" alt="Image" src="https://github.com/user-attachments/assets/35c9250d-0f01-40cb-9294-1ee8fd9a1b56" />
+The **Workbench** provides tools for all major features of TrustGraph. The **Workbench** is on port `8888` by default.
 
-The UI provides tools for all major features of TrustGraph. The UI deploys on port `8888` by default.
-
-- **Agent Console** — Query your agents directly with streaming responses and live explainability event tracking, so you can watch reasoning unfold in real time
-- **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
-- **Context Explorer** — An interactive 3D context graph explorer with dynamic graph loading, BFS neighborhood extraction, edge pulse animation, and multiple navigation views
-- **Document Ingestion** — A complete upload and submission workflow with page and chunk inspection and document structure browsing
-- **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
-- **Schema Workbench** — Interactive schema management with list, create, edit, and delete operations including field and index management
-- **Flow Management** — Flow creation and detail views with configurable parameters, temperature controls, and grouped storage layout
-- **Workspace UX** — Workspace selection and management surfaced directly in the interface
-- **Prompt Editor** — A dedicated prompt editing workflow
+- **Vector Search**: Search the installed knowledge bases
+- **Agentic, GraphRAG and LLM Chat**: Chat interface for agents, GraphRAG queries, or direct to LLMs
+- **Relationships**: Analyze deep relationships in the installed knowledge bases
+- **Graph Visualizer**: 3D GraphViz of the installed knowledge bases
+- **Library**: Staging area for installing knowledge bases
+- **Flow Classes**: Workflow preset configurations
+- **Flows**: Create custom workflows and adjust LLM parameters during runtime
+- **Knowledge Cores**: Manage resuable knowledge bases
+- **Prompts**: Manage and adjust prompts during runtime
+- **Schemas**: Define custom schemas for structured data knowledge bases
+- **Ontologies**: Define custom ontologies for unstructured data knowledge bases
+- **Agent Tools**: Define tools with collections, knowledge cores, MCP connections, and tool groups
+- **MCP Tools**: Connect to MCP servers
 
 ## TypeScript Library for UIs
 

tests/unit/test_base/test_cassandra_config.py

@@ -409,57 +409,4 @@ class TestEdgeCases:
         
         assert hosts == ['mixed-host']
         assert username is None  # Stays None
-        assert password == 'mixed-pass'
-
-
-class TestReplicationFactorParamPath:
-
-    def test_explicit_kwarg(self):
-        with patch.dict(os.environ, {}, clear=True):
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=3,
-            )
-            assert rf == 3
-
-    def test_kwarg_overrides_env(self):
-        with patch.dict(os.environ, {'CASSANDRA_REPLICATION_FACTOR': '5'}, clear=True):
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=3,
-            )
-            assert rf == 3
-
-    def test_env_fallback_when_kwarg_none(self):
-        with patch.dict(os.environ, {'CASSANDRA_REPLICATION_FACTOR': '5'}, clear=True):
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=None,
-            )
-            assert rf == 5
-
-    def test_default_when_no_kwarg_no_env(self):
-        with patch.dict(os.environ, {}, clear=True):
-            _, _, _, _, rf = resolve_cassandra_config()
-            assert rf == 1
-
-    def test_params_dict_path(self):
-        with patch.dict(os.environ, {}, clear=True):
-            params = {'cassandra_replication_factor': 3}
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=params.get('cassandra_replication_factor'),
-            )
-            assert rf == 3
-
-    def test_params_dict_overrides_env(self):
-        with patch.dict(os.environ, {'CASSANDRA_REPLICATION_FACTOR': '5'}, clear=True):
-            params = {'cassandra_replication_factor': 3}
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=params.get('cassandra_replication_factor'),
-            )
-            assert rf == 3
-
-    def test_params_dict_missing_falls_to_env(self):
-        with patch.dict(os.environ, {'CASSANDRA_REPLICATION_FACTOR': '5'}, clear=True):
-            params = {}
-            _, _, _, _, rf = resolve_cassandra_config(
-                replication_factor=params.get('cassandra_replication_factor'),
-            )
-            assert rf == 5
+        assert password == 'mixed-pass'

tests/unit/test_base/test_qdrant_config.py

@@ -1,136 +0,0 @@
-
-import os
-import pytest
-from unittest.mock import patch
-
-from trustgraph.base.qdrant_config import (
-    get_qdrant_defaults,
-    resolve_qdrant_config,
-)
-
-
-class TestGetQdrantDefaults:
-
-    def test_defaults_with_no_env_vars(self):
-        with patch.dict(os.environ, {}, clear=True):
-            defaults = get_qdrant_defaults()
-            assert defaults['url'] == 'http://localhost:6333'
-            assert defaults['api_key'] is None
-            assert defaults['replication_factor'] == 1
-            assert defaults['shard_number'] == 1
-
-    def test_defaults_from_env(self):
-        env = {
-            'QDRANT_URL': 'http://qdrant:6333',
-            'QDRANT_API_KEY': 'secret',
-            'QDRANT_REPLICATION_FACTOR': '3',
-            'QDRANT_SHARD_NUMBER': '5',
-        }
-        with patch.dict(os.environ, env, clear=True):
-            defaults = get_qdrant_defaults()
-            assert defaults['url'] == 'http://qdrant:6333'
-            assert defaults['api_key'] == 'secret'
-            assert defaults['replication_factor'] == 3
-            assert defaults['shard_number'] == 5
-
-
-class TestResolveQdrantConfig:
-
-    def test_defaults(self):
-        with patch.dict(os.environ, {}, clear=True):
-            url, api_key, rf, sn = resolve_qdrant_config()
-            assert url == 'http://localhost:6333'
-            assert api_key is None
-            assert rf == 1
-            assert sn == 1
-
-    def test_explicit_kwargs(self):
-        with patch.dict(os.environ, {}, clear=True):
-            url, api_key, rf, sn = resolve_qdrant_config(
-                url='http://custom:6333',
-                api_key='key',
-                replication_factor=3,
-                shard_number=5,
-            )
-            assert url == 'http://custom:6333'
-            assert api_key == 'key'
-            assert rf == 3
-            assert sn == 5
-
-    def test_kwargs_override_env(self):
-        env = {
-            'QDRANT_URL': 'http://env:6333',
-            'QDRANT_REPLICATION_FACTOR': '10',
-            'QDRANT_SHARD_NUMBER': '10',
-        }
-        with patch.dict(os.environ, env, clear=True):
-            url, _, rf, sn = resolve_qdrant_config(
-                url='http://explicit:6333',
-                replication_factor=3,
-                shard_number=5,
-            )
-            assert url == 'http://explicit:6333'
-            assert rf == 3
-            assert sn == 5
-
-    def test_env_fallback_when_kwargs_none(self):
-        env = {
-            'QDRANT_URL': 'http://env:6333',
-            'QDRANT_REPLICATION_FACTOR': '3',
-            'QDRANT_SHARD_NUMBER': '5',
-        }
-        with patch.dict(os.environ, env, clear=True):
-            url, _, rf, sn = resolve_qdrant_config()
-            assert url == 'http://env:6333'
-            assert rf == 3
-            assert sn == 5
-
-    def test_params_dict_path(self):
-        with patch.dict(os.environ, {}, clear=True):
-            params = {
-                'store_uri': 'http://params:6333',
-                'api_key': 'pkey',
-                'qdrant_replication_factor': 3,
-                'qdrant_shard_number': 5,
-            }
-            url, api_key, rf, sn = resolve_qdrant_config(
-                url=params.get('store_uri'),
-                api_key=params.get('api_key'),
-                replication_factor=params.get('qdrant_replication_factor'),
-                shard_number=params.get('qdrant_shard_number'),
-            )
-            assert url == 'http://params:6333'
-            assert api_key == 'pkey'
-            assert rf == 3
-            assert sn == 5
-
-    def test_params_dict_overrides_env(self):
-        env = {
-            'QDRANT_REPLICATION_FACTOR': '10',
-            'QDRANT_SHARD_NUMBER': '10',
-        }
-        with patch.dict(os.environ, env, clear=True):
-            params = {
-                'qdrant_replication_factor': 3,
-                'qdrant_shard_number': 5,
-            }
-            _, _, rf, sn = resolve_qdrant_config(
-                replication_factor=params.get('qdrant_replication_factor'),
-                shard_number=params.get('qdrant_shard_number'),
-            )
-            assert rf == 3
-            assert sn == 5
-
-    def test_params_dict_missing_falls_to_env(self):
-        env = {
-            'QDRANT_REPLICATION_FACTOR': '3',
-            'QDRANT_SHARD_NUMBER': '5',
-        }
-        with patch.dict(os.environ, env, clear=True):
-            params = {}
-            _, _, rf, sn = resolve_qdrant_config(
-                replication_factor=params.get('qdrant_replication_factor'),
-                shard_number=params.get('qdrant_shard_number'),
-            )
-            assert rf == 3
-            assert sn == 5

tests/unit/test_decoding/test_pdf_decoder.py

@@ -49,7 +49,7 @@ class TestPdfDecoderProcessor(IsolatedAsyncioTestCase):
     async def test_on_message_success(self, mock_pdf_loader_class, mock_producer, mock_consumer):
         """Test successful PDF processing"""
         # Mock PDF content
-        pdf_content = b"%PDF-1.7\nfake pdf content"
+        pdf_content = b"fake pdf content"
         pdf_base64 = base64.b64encode(pdf_content).decode('utf-8')
 
         # Mock PyPDFLoader
@@ -88,55 +88,13 @@ class TestPdfDecoderProcessor(IsolatedAsyncioTestCase):
         # Verify triples were sent for each page (provenance)
         assert mock_triples_flow.send.call_count == 2
 
-    @patch('trustgraph.base.librarian_client.Consumer')
-    @patch('trustgraph.base.librarian_client.Producer')
-    @patch('trustgraph.decoding.pdf.pdf_decoder.PyPDFLoader')
-    @patch('trustgraph.base.async_processor.AsyncProcessor', MockAsyncProcessor)
-    async def test_on_message_rejects_librarian_content_that_is_not_pdf(self, mock_pdf_loader_class, mock_producer, mock_consumer):
-        """Test rejecting non-PDF content before invoking the PDF loader"""
-        html_content = b"<html><body>Not found</body></html>"
-        html_base64 = base64.b64encode(html_content)
-
-        mock_metadata = Metadata(id="test-doc")
-        mock_document = Document(metadata=mock_metadata, document_id="doc-123")
-        mock_msg = MagicMock()
-        mock_msg.value.return_value = mock_document
-
-        mock_output_flow = AsyncMock()
-        mock_triples_flow = AsyncMock()
-        mock_flow = MagicMock(side_effect=lambda name: {
-            "output": mock_output_flow,
-            "triples": mock_triples_flow,
-        }.get(name))
-        mock_flow.librarian.fetch_document_metadata = AsyncMock(
-            return_value=MagicMock(kind="application/pdf")
-        )
-        mock_flow.librarian.fetch_document_content = AsyncMock(
-            return_value=html_base64
-        )
-        mock_flow.librarian.save_child_document = AsyncMock()
-
-        config = {
-            'id': 'test-pdf-decoder',
-            'taskgroup': AsyncMock()
-        }
-
-        processor = Processor(**config)
-
-        await processor.on_message(mock_msg, None, mock_flow)
-
-        mock_pdf_loader_class.assert_not_called()
-        mock_output_flow.send.assert_not_called()
-        mock_triples_flow.send.assert_not_called()
-        mock_flow.librarian.save_child_document.assert_not_called()
-
     @patch('trustgraph.base.librarian_client.Consumer')
     @patch('trustgraph.base.librarian_client.Producer')
     @patch('trustgraph.decoding.pdf.pdf_decoder.PyPDFLoader')
     @patch('trustgraph.base.async_processor.AsyncProcessor', MockAsyncProcessor)
     async def test_on_message_empty_pdf(self, mock_pdf_loader_class, mock_producer, mock_consumer):
         """Test handling of empty PDF"""
-        pdf_content = b"%PDF-1.7\nfake pdf content"
+        pdf_content = b"fake pdf content"
         pdf_base64 = base64.b64encode(pdf_content).decode('utf-8')
 
         mock_loader = MagicMock()
@@ -168,7 +126,7 @@ class TestPdfDecoderProcessor(IsolatedAsyncioTestCase):
     @patch('trustgraph.base.async_processor.AsyncProcessor', MockAsyncProcessor)
     async def test_on_message_unicode_content(self, mock_pdf_loader_class, mock_producer, mock_consumer):
         """Test handling of unicode content in PDF"""
-        pdf_content = b"%PDF-1.7\nfake pdf content"
+        pdf_content = b"fake pdf content"
         pdf_base64 = base64.b64encode(pdf_content).decode('utf-8')
 
         mock_loader = MagicMock()

tests/unit/test_query/test_rows_cassandra_query.py

@@ -333,8 +333,8 @@ class TestUnifiedTableQueries:
     """Test queries against the unified rows table"""
 
     @pytest.mark.asyncio
-    @patch('trustgraph.query.rows.cassandra.service.async_execute_paged', new_callable=AsyncMock)
-    async def test_query_with_index_match(self, mock_async_execute_paged):
+    @patch('trustgraph.query.rows.cassandra.service.async_execute', new_callable=AsyncMock)
+    async def test_query_with_index_match(self, mock_async_execute):
         """Test query execution with matching index"""
         processor = MagicMock()
         processor.session = MagicMock()
@@ -344,10 +344,10 @@ class TestUnifiedTableQueries:
         processor.find_matching_index = Processor.find_matching_index.__get__(processor, Processor)
         processor.query_cassandra = Processor.query_cassandra.__get__(processor, Processor)
 
-        # Mock async_execute_paged to return test data (list of pages)
+        # Mock async_execute to return test data
         mock_row = MagicMock()
         mock_row.data = {"id": "123", "name": "Test Product", "category": "electronics"}
-        mock_async_execute_paged.return_value = [[mock_row]]
+        mock_async_execute.return_value = [mock_row]
 
         schema = RowSchema(
             name="products",
@@ -370,10 +370,10 @@ class TestUnifiedTableQueries:
 
         # Verify Cassandra was connected and queried
         processor.connect_cassandra.assert_called_once()
-        mock_async_execute_paged.assert_called_once()
+        mock_async_execute.assert_called_once()
 
         # Verify query structure - should query unified rows table
-        call_args = mock_async_execute_paged.call_args
+        call_args = mock_async_execute.call_args
         query = call_args[0][1]
         params = call_args[0][2]
 
@@ -394,8 +394,8 @@ class TestUnifiedTableQueries:
         assert results[0]["category"] == "electronics"
 
     @pytest.mark.asyncio
-    @patch('trustgraph.query.rows.cassandra.service.async_scan', new_callable=AsyncMock)
-    async def test_query_without_index_match(self, mock_async_scan):
+    @patch('trustgraph.query.rows.cassandra.service.async_execute', new_callable=AsyncMock)
+    async def test_query_without_index_match(self, mock_async_execute):
         """Test query execution without matching index (scan mode)"""
         processor = MagicMock()
         processor.session = MagicMock()
@@ -406,10 +406,12 @@ class TestUnifiedTableQueries:
         processor._matches_filters = Processor._matches_filters.__get__(processor, Processor)
         processor.query_cassandra = Processor.query_cassandra.__get__(processor, Processor)
 
-        # Mock async_scan to return filtered test data
+        # Mock async_execute to return test data
         mock_row1 = MagicMock()
         mock_row1.data = {"id": "1", "name": "Product A", "price": "100"}
-        mock_async_scan.return_value = [mock_row1]
+        mock_row2 = MagicMock()
+        mock_row2.data = {"id": "2", "name": "Product B", "price": "200"}
+        mock_async_execute.return_value = [mock_row1, mock_row2]
 
         schema = RowSchema(
             name="products",
@@ -430,16 +432,13 @@ class TestUnifiedTableQueries:
             limit=10
         )
 
-        # Verify async_scan was called
-        mock_async_scan.assert_called_once()
-
-        # Verify query structure
-        call_args = mock_async_scan.call_args
+        # Query should use ALLOW FILTERING for scan
+        call_args = mock_async_execute.call_args
         query = call_args[0][1]
 
         assert "ALLOW FILTERING" in query
 
-        # Should return filtered results
+        # Should post-filter results
         assert len(results) == 1
         assert results[0]["name"] == "Product A"
 

tests/unit/test_reliability/test_null_embedding_protection.py

@@ -259,8 +259,6 @@ class TestGraphEmbeddingsNullProtection:
         proc.collection_exists = MagicMock(return_value=True)
         proc._cache_lock = asyncio.Lock()
         proc._known_collections = set()
-        proc.replication_factor = 1
-        proc.shard_number = 1
 
         msg = MagicMock()
         msg.metadata.collection = "graphs"

trustgraph-base/trustgraph/base/cassandra_config.py

@@ -103,19 +103,35 @@ def resolve_cassandra_config(
     host: Optional[str] = None,
     username: Optional[str] = None,
     password: Optional[str] = None,
-    default_keyspace: Optional[str] = None,
-    replication_factor: Optional[int] = None,
+    default_keyspace: Optional[str] = None
 ) -> Tuple[List[str], Optional[str], Optional[str], Optional[str], int]:
+    """
+    Resolve Cassandra configuration from various sources.
+
+    Can accept either argparse args object or explicit parameters.
+    Converts host string to list format for Cassandra driver.
+
+    Args:
+        args: Optional argparse namespace with cassandra_host, cassandra_username, cassandra_password, cassandra_keyspace, cassandra_replication_factor
+        host: Optional explicit host parameter (overrides args)
+        username: Optional explicit username parameter (overrides args)
+        password: Optional explicit password parameter (overrides args)
+        default_keyspace: Optional default keyspace if not specified elsewhere
+
+    Returns:
+        tuple: (hosts_list, username, password, keyspace, replication_factor)
+    """
+    # If args provided, extract values
     keyspace = None
+    replication_factor = 1
     if args is not None:
         host = host or getattr(args, 'cassandra_host', None)
         username = username or getattr(args, 'cassandra_username', None)
         password = password or getattr(args, 'cassandra_password', None)
         keyspace = getattr(args, 'cassandra_keyspace', None)
-        replication_factor = replication_factor or getattr(
-            args, 'cassandra_replication_factor', None
-        )
+        replication_factor = getattr(args, 'cassandra_replication_factor', 1)
 
+    # Apply defaults if still None
     defaults = get_cassandra_defaults()
     host = host or defaults['host']
     username = username or defaults['username']

trustgraph-base/trustgraph/base/qdrant_config.py

@@ -1,87 +0,0 @@
-
-import os
-import argparse
-from typing import Optional, Any, Tuple
-
-
-def get_qdrant_defaults() -> dict:
-    return {
-        'url': os.getenv('QDRANT_URL', 'http://localhost:6333'),
-        'api_key': os.getenv('QDRANT_API_KEY'),
-        'replication_factor': int(os.getenv('QDRANT_REPLICATION_FACTOR', '1')),
-        'shard_number': int(os.getenv('QDRANT_SHARD_NUMBER', '1')),
-    }
-
-
-def add_qdrant_args(parser: argparse.ArgumentParser) -> None:
-    defaults = get_qdrant_defaults()
-
-    url_help = f"Qdrant URL (default: {defaults['url']})"
-    if 'QDRANT_URL' in os.environ:
-        url_help += " [from QDRANT_URL]"
-
-    api_key_help = "Qdrant API key"
-    if defaults['api_key']:
-        api_key_help += " (default: <set>)"
-        if 'QDRANT_API_KEY' in os.environ:
-            api_key_help += " [from QDRANT_API_KEY]"
-
-    replication_help = f"Qdrant collection replication factor (default: {defaults['replication_factor']})"
-    if 'QDRANT_REPLICATION_FACTOR' in os.environ:
-        replication_help += " [from QDRANT_REPLICATION_FACTOR]"
-
-    shard_help = f"Qdrant collection shard number (default: {defaults['shard_number']})"
-    if 'QDRANT_SHARD_NUMBER' in os.environ:
-        shard_help += " [from QDRANT_SHARD_NUMBER]"
-
-    parser.add_argument(
-        '--store-uri',
-        default=defaults['url'],
-        help=url_help,
-    )
-
-    parser.add_argument(
-        '--api-key',
-        default=defaults['api_key'],
-        help=api_key_help,
-    )
-
-    parser.add_argument(
-        '--qdrant-replication-factor',
-        type=int,
-        default=defaults['replication_factor'],
-        help=replication_help,
-    )
-
-    parser.add_argument(
-        '--qdrant-shard-number',
-        type=int,
-        default=defaults['shard_number'],
-        help=shard_help,
-    )
-
-
-def resolve_qdrant_config(
-    args: Optional[Any] = None,
-    url: Optional[str] = None,
-    api_key: Optional[str] = None,
-    replication_factor: Optional[int] = None,
-    shard_number: Optional[int] = None,
-) -> Tuple[str, Optional[str], int, int]:
-    if args is not None:
-        url = url or getattr(args, 'store_uri', None)
-        api_key = api_key or getattr(args, 'api_key', None)
-        replication_factor = replication_factor or getattr(
-            args, 'qdrant_replication_factor', None
-        )
-        shard_number = shard_number or getattr(
-            args, 'qdrant_shard_number', None
-        )
-
-    defaults = get_qdrant_defaults()
-    url = url or defaults['url']
-    api_key = api_key or defaults['api_key']
-    replication_factor = replication_factor or defaults['replication_factor']
-    shard_number = shard_number or defaults['shard_number']
-
-    return url, api_key, replication_factor, shard_number

trustgraph-cli/trustgraph/cli/load_structured_data.py

@@ -78,7 +78,7 @@ def load_structured_data(
         logger.info("Step 1: Analyzing data to discover best matching schema...")
         
         # Step 1: Auto-discover schema (reuse discover_schema logic)
-        discovered_schema = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, token=token, workspace=workspace)
+        discovered_schema = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, workspace=workspace)
         if not discovered_schema:
             logger.error("Failed to discover suitable schema automatically")
             print("❌ Could not automatically determine the best schema for your data.")
@@ -90,7 +90,7 @@ def load_structured_data(
         
         # Step 2: Auto-generate descriptor
         logger.info("Step 2: Generating descriptor configuration...")
-        auto_descriptor = _auto_generate_descriptor(api_url, input_file, discovered_schema, sample_chars, flow, logger, token=token, workspace=workspace)
+        auto_descriptor = _auto_generate_descriptor(api_url, input_file, discovered_schema, sample_chars, flow, logger, workspace=workspace)
         if not auto_descriptor:
             logger.error("Failed to generate descriptor automatically")
             print("❌ Could not automatically generate descriptor configuration.")
@@ -172,7 +172,7 @@ def load_structured_data(
         logger.info(f"Sample chars: {sample_chars} characters")
         
         # Use the helper function to discover schema (get raw response for display)
-        response = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, return_raw_response=True, token=token, workspace=workspace)
+        response = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, return_raw_response=True, workspace=workspace)
         
         if response:
             # Debug: print response type and content 
@@ -203,7 +203,7 @@ def load_structured_data(
         # If no schema specified, discover it first
         if not schema_name:
             logger.info("No schema specified, auto-discovering...")
-            schema_name = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, token=token, workspace=workspace)
+            schema_name = _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, workspace=workspace)
             if not schema_name:
                 print("Error: Could not determine schema automatically.")
                 print("Please specify a schema using --schema-name or run --discover-schema first.")
@@ -213,7 +213,7 @@ def load_structured_data(
             logger.info(f"Target schema: {schema_name}")
         
         # Generate descriptor using helper function
-        descriptor = _auto_generate_descriptor(api_url, input_file, schema_name, sample_chars, flow, logger, token=token, workspace=workspace)
+        descriptor = _auto_generate_descriptor(api_url, input_file, schema_name, sample_chars, flow, logger, workspace=workspace)
         
         if descriptor:
             # Output the generated descriptor
@@ -603,7 +603,7 @@ def _send_to_trustgraph(rows, api_url, flow, batch_size=1000, token=None, worksp
 
 
 # Helper functions for auto mode
-def _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, return_raw_response=False, token=None, workspace="default"):
+def _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, return_raw_response=False, workspace="default"):
     """Auto-discover the best matching schema for the input data
     
     Args:
@@ -626,7 +626,7 @@ def _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, retur
         # Import API modules
         from trustgraph.api import Api
         from trustgraph.api.types import ConfigKey
-        api = Api(api_url, token=token, workspace=workspace)
+        api = Api(api_url, workspace=workspace)
         config_api = api.config()
         
         # Get available schemas
@@ -707,7 +707,7 @@ def _auto_discover_schema(api_url, input_file, sample_chars, flow, logger, retur
         return None
 
 
-def _auto_generate_descriptor(api_url, input_file, schema_name, sample_chars, flow, logger, token=None, workspace="default"):
+def _auto_generate_descriptor(api_url, input_file, schema_name, sample_chars, flow, logger, workspace="default"):
     """Auto-generate descriptor configuration for the discovered schema"""
     try:
         # Read sample data
@@ -717,7 +717,7 @@ def _auto_generate_descriptor(api_url, input_file, schema_name, sample_chars, fl
         # Import API modules
         from trustgraph.api import Api
         from trustgraph.api.types import ConfigKey
-        api = Api(api_url, token=token, workspace=workspace)
+        api = Api(api_url, workspace=workspace)
         config_api = api.config()
         
         # Get schema definition

trustgraph-flow/trustgraph/config/service/service.py

@@ -83,8 +83,7 @@ class Processor(AsyncProcessor):
             host=cassandra_host,
             username=cassandra_username,
             password=cassandra_password,
-            default_keyspace="config",
-            replication_factor=params.get("cassandra_replication_factor"),
+            default_keyspace="config"
         )
 
         # Store resolved configuration

trustgraph-flow/trustgraph/cores/service.py

@@ -61,8 +61,7 @@ class Processor(WorkspaceProcessor):
             host=cassandra_host,
             username=cassandra_username,
             password=cassandra_password,
-            default_keyspace="knowledge",
-            replication_factor=params.get("cassandra_replication_factor"),
+            default_keyspace="knowledge"
         )
 
         self.cassandra_host = hosts

trustgraph-flow/trustgraph/decoding/pdf/pdf_decoder.py

@@ -32,10 +32,6 @@ logger = logging.getLogger(__name__)
 default_ident = "document-decoder"
 
 
-def _looks_like_pdf(content):
-    return content.lstrip().startswith(b"%PDF-")
-
-
 class Processor(FlowProcessor):
 
     def __init__(self, **params):
@@ -98,37 +94,33 @@ class Processor(FlowProcessor):
                 )
                 return
 
-        # Check if we should fetch from librarian or use inline data
-        if v.document_id:
-            # Fetch from librarian via Pulsar
-            logger.info(f"Fetching document {v.document_id} from librarian...")
-
-            content = await flow.librarian.fetch_document_content(
-                document_id=v.document_id,
-
-            )
-
-            # Content is base64 encoded
-            if isinstance(content, str):
-                content = content.encode('utf-8')
-            decoded_content = base64.b64decode(content)
-
-            logger.info(f"Fetched {len(decoded_content)} bytes from librarian")
-        else:
-            # Use inline data (backward compatibility)
-            decoded_content = base64.b64decode(v.data)
-
-        if not _looks_like_pdf(decoded_content):
-            logger.error(
-                f"Document {v.metadata.id} is not valid PDF content. "
-                f"Ignoring document."
-            )
-            return
-
-        with tempfile.NamedTemporaryFile(delete=False, suffix='.pdf') as fp:
+        with tempfile.NamedTemporaryFile(delete_on_close=False, suffix='.pdf') as fp:
             temp_path = fp.name
-            fp.write(decoded_content)
-            fp.close()
+
+            # Check if we should fetch from librarian or use inline data
+            if v.document_id:
+                # Fetch from librarian via Pulsar
+                logger.info(f"Fetching document {v.document_id} from librarian...")
+                fp.close()
+
+                content = await flow.librarian.fetch_document_content(
+                    document_id=v.document_id,
+    
+                )
+
+                # Content is base64 encoded
+                if isinstance(content, str):
+                    content = content.encode('utf-8')
+                decoded_content = base64.b64decode(content)
+
+                with open(temp_path, 'wb') as f:
+                    f.write(decoded_content)
+
+                logger.info(f"Fetched {len(decoded_content)} bytes from librarian")
+            else:
+                # Use inline data (backward compatibility)
+                fp.write(base64.b64decode(v.data))
+                fp.close()
 
             global PyPDFLoader
             if PyPDFLoader is None:

trustgraph-flow/trustgraph/direct/cassandra_kg.py

@@ -6,7 +6,7 @@ import logging
 from cassandra.cluster import Cluster
 from cassandra.auth import PlainTextAuthProvider
 from cassandra.query import BatchStatement, SimpleStatement
-import ssl
+from ssl import SSLContext, PROTOCOL_TLSv1_2
 
 from ..tables.cassandra_async import async_execute
 
@@ -41,15 +41,13 @@ class KnowledgeGraph:
 
     def __init__(
             self, hosts=None,
-            keyspace="trustgraph", username=None, password=None,
-            replication_factor=1,
+            keyspace="trustgraph", username=None, password=None
     ):
 
         if hosts is None:
             hosts = ["localhost"]
 
         self.keyspace = keyspace
-        self.replication_factor = replication_factor
         self.username = username
 
         # 7-table schema for quads with full query pattern support
@@ -70,7 +68,7 @@ class KnowledgeGraph:
         self.collection_metadata_table = "collection_metadata"
 
         if username and password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(username=username, password=password)
             self.cluster = Cluster(hosts, auth_provider=auth_provider, ssl_context=ssl_context)
         else:
@@ -94,7 +92,7 @@ class KnowledgeGraph:
             create keyspace if not exists {self.keyspace}
                 with replication = {{
                    'class' : 'SimpleStrategy',
-                   'replication_factor' : {self.replication_factor}
+                   'replication_factor' : 1
                 }};
         """)
 
@@ -541,15 +539,13 @@ class EntityCentricKnowledgeGraph:
 
     def __init__(
             self, hosts=None,
-            keyspace="trustgraph", username=None, password=None,
-            replication_factor=1,
+            keyspace="trustgraph", username=None, password=None
     ):
 
         if hosts is None:
             hosts = ["localhost"]
 
         self.keyspace = keyspace
-        self.replication_factor = replication_factor
         self.username = username
 
         # 2-table entity-centric schema
@@ -560,7 +556,7 @@ class EntityCentricKnowledgeGraph:
         self.collection_metadata_table = "collection_metadata"
 
         if username and password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(username=username, password=password)
             self.cluster = Cluster(hosts, auth_provider=auth_provider, ssl_context=ssl_context)
         else:
@@ -584,7 +580,7 @@ class EntityCentricKnowledgeGraph:
             create keyspace if not exists {self.keyspace}
                 with replication = {{
                    'class' : 'SimpleStrategy',
-                   'replication_factor' : {self.replication_factor}
+                   'replication_factor' : 1
                 }};
         """)
 

trustgraph-flow/trustgraph/iam/service/service.py

@@ -101,7 +101,6 @@ class Processor(AsyncProcessor):
             username=cassandra_username,
             password=cassandra_password,
             default_keyspace="iam",
-            replication_factor=params.get("cassandra_replication_factor"),
         )
 
         self.cassandra_host = hosts

trustgraph-flow/trustgraph/librarian/service.py

@@ -146,8 +146,7 @@ class Processor(WorkspaceProcessor):
             host=cassandra_host,
             username=cassandra_username,
             password=cassandra_password,
-            default_keyspace="librarian",
-            replication_factor=params.get("cassandra_replication_factor"),
+            default_keyspace="librarian"
         )
 
         # Store resolved configuration

trustgraph-flow/trustgraph/query/doc_embeddings/qdrant/service.py

@@ -12,33 +12,31 @@ from qdrant_client import QdrantClient
 from .... schema import DocumentEmbeddingsResponse, ChunkMatch
 from .... schema import Error
 from .... base import DocumentEmbeddingsQueryService
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 
 # Module logger
 logger = logging.getLogger(__name__)
 
 default_ident = "doc-embeddings-query"
 
+default_store_uri = 'http://localhost:6333'
+
 class Processor(DocumentEmbeddingsQueryService):
 
     def __init__(self, **params):
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
+        store_uri = params.get("store_uri", default_store_uri)
 
-        url, api_key, _, _ = resolve_qdrant_config(
-            url=store_uri,
-            api_key=api_key,
-        )
+        #optional api key
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
 
     async def query_document_embeddings(self, workspace, msg):
 
@@ -87,7 +85,18 @@ class Processor(DocumentEmbeddingsQueryService):
     def add_args(parser):
 
         DocumentEmbeddingsQueryService.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant store URI (default: {default_store_uri})'
+        )
+        
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help=f'API key for qdrant (default: None)'
+        )
 
 def run():
 

trustgraph-flow/trustgraph/query/graph_embeddings/qdrant/service.py

@@ -12,32 +12,31 @@ from qdrant_client import QdrantClient
 from .... schema import GraphEmbeddingsResponse, EntityMatch
 from .... schema import Error, Term, IRI, LITERAL
 from .... base import GraphEmbeddingsQueryService
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 
 # Module logger
 logger = logging.getLogger(__name__)
 
 default_ident = "graph-embeddings-query"
 
+default_store_uri = 'http://localhost:6333'
+
 class Processor(GraphEmbeddingsQueryService):
 
     def __init__(self, **params):
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
+        store_uri = params.get("store_uri", default_store_uri)
 
-        url, api_key, _, _ = resolve_qdrant_config(
-            url=store_uri, api_key=api_key,
-        )
+        #optional api key
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
 
     def create_value(self, ent):
         if ent.startswith("http://") or ent.startswith("https://"):
@@ -105,7 +104,18 @@ class Processor(GraphEmbeddingsQueryService):
     def add_args(parser):
 
         GraphEmbeddingsQueryService.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant store URI (default: {default_store_uri})'
+        )
+        
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help=f'API key for qdrant (default: None)'
+        )
 
 def run():
 

trustgraph-flow/trustgraph/query/ontology/sparql_cassandra.py

@@ -116,7 +116,7 @@ class CassandraTripleStore(Store if RDFLIB_AVAILABLE else object):
         # Create keyspace
         self.session.execute(f"""
             CREATE KEYSPACE IF NOT EXISTS {self.keyspace}
-            WITH replication = {{'class': 'SimpleStrategy', 'replication_factor': {self.cassandra_config.get('replication_factor', 1)}}}
+            WITH replication = {{'class': 'SimpleStrategy', 'replication_factor': 1}}
         """)
 
         # Create triples table optimized for SPARQL queries

trustgraph-flow/trustgraph/query/row_embeddings/qdrant/service.py

@@ -19,12 +19,12 @@ from .... schema import (
     RowIndexMatch, Error
 )
 from .... base import FlowProcessor, ConsumerSpec, ProducerSpec
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 
 # Module logger
 logger = logging.getLogger(__name__)
 
 default_ident = "row-embeddings-query"
+default_store_uri = 'http://localhost:6333'
 default_concurrency = 10
 
 
@@ -35,17 +35,13 @@ class Processor(FlowProcessor):
         id = params.get("id", default_ident)
         concurrency = params.get("concurrency", default_concurrency)
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
-
-        url, api_key, _, _ = resolve_qdrant_config(
-            url=store_uri, api_key=api_key,
-        )
+        store_uri = params.get("store_uri", default_store_uri)
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
                 "id": id,
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
@@ -66,7 +62,7 @@ class Processor(FlowProcessor):
             )
         )
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
 
     def sanitize_name(self, name: str) -> str:
         """Sanitize names for Qdrant collection naming"""
@@ -196,9 +192,21 @@ class Processor(FlowProcessor):
 
     @staticmethod
     def add_args(parser):
+        """Add command-line arguments"""
 
         FlowProcessor.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant store URI (default: {default_store_uri})'
+        )
+
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help='API key for Qdrant (default: None)'
+        )
 
         parser.add_argument(
             '-c', '--concurrency',

trustgraph-flow/trustgraph/query/rows/cassandra/service.py

@@ -24,7 +24,7 @@ from .... schema import RowsQueryRequest, RowsQueryResponse, GraphQLError
 from .... schema import Error, RowSchema, Field as SchemaField
 from .... base import FlowProcessor, ConsumerSpec, ProducerSpec
 from .... base.cassandra_config import add_cassandra_args, resolve_cassandra_config
-from .... tables.cassandra_async import async_execute, async_execute_paged, async_scan
+from .... tables.cassandra_async import async_execute
 
 from ... graphql import GraphQLSchemaBuilder, SortDirection
 
@@ -180,7 +180,7 @@ class Processor(FlowProcessor):
                         description=field_def.get("description", ""),
                         required=field_def.get("required", False),
                         enum_values=field_def.get("enum", []),
-                        indexed=field_def.get("indexed", False),
+                        indexed=field_def.get("indexed", False)
                     )
                     fields.append(field)
 
@@ -232,8 +232,6 @@ class Processor(FlowProcessor):
         for index_name in index_names:
             if index_name in filters:
                 value = filters[index_name]
-                if value == "" or value is None:
-                    continue
                 # Single field index -> single element list
                 index_value = [str(value)]
                 return (index_name, index_value)
@@ -284,13 +282,11 @@ class Processor(FlowProcessor):
                 query += f" LIMIT {limit}"
 
             try:
-                pages = await async_execute_paged(
-                    self.session, query, params
-                )
-                for page in pages:
-                    for row in page:
-                        row_dict = dict(row.data) if row.data else {}
-                        results.append(row_dict)
+                rows = await async_execute(self.session, query, params)
+                for row in rows:
+                    # Convert data map to dict with proper field names
+                    row_dict = dict(row.data) if row.data else {}
+                    results.append(row_dict)
             except Exception as e:
                 logger.error(f"Failed to query rows: {e}", exc_info=True)
                 raise
@@ -312,6 +308,8 @@ class Processor(FlowProcessor):
             # Query using the first index (arbitrary choice for scan)
             primary_index = index_names[0]
 
+            # We need to scan all values for this index
+            # This requires ALLOW FILTERING or a different approach
             query = f"""
             SELECT data, source FROM {safe_keyspace}.rows
             WHERE collection = %s
@@ -322,18 +320,17 @@ class Processor(FlowProcessor):
             params = [collection, schema_name, primary_index]
 
             try:
-                def row_filter(row):
-                    row_dict = dict(row.data) if row.data else {}
-                    return self._matches_filters(row_dict, filters, row_schema)
+                rows = await async_execute(self.session, query, params)
 
-                matched_rows = await async_scan(
-                    self.session, query, params,
-                    row_filter=row_filter,
-                    limit=limit,
-                )
-                for row in matched_rows:
+                for row in rows:
                     row_dict = dict(row.data) if row.data else {}
-                    results.append(row_dict)
+
+                    # Apply post-filters
+                    if self._matches_filters(row_dict, filters, row_schema):
+                        results.append(row_dict)
+
+                        if limit and len(results) >= limit:
+                            break
 
             except Exception as e:
                 logger.error(f"Failed to scan rows: {e}", exc_info=True)
@@ -366,7 +363,7 @@ class Processor(FlowProcessor):
             # Parse filter key for operator
             if '_' in filter_key:
                 parts = filter_key.rsplit('_', 1)
-                if parts[1] in ['gt', 'gte', 'lt', 'lte', 'contains', 'in', 'not', 'startsWith', 'endsWith', 'not_in']:
+                if parts[1] in ['gt', 'gte', 'lt', 'lte', 'contains', 'in']:
                     field_name = parts[0]
                     operator = parts[1]
                 else:
@@ -403,18 +400,6 @@ class Processor(FlowProcessor):
                 elif operator == 'in':
                     if str(row_value) not in [str(v) for v in filter_value]:
                         return False
-                elif operator == 'not':
-                    if str(row_value) == str(filter_value):
-                        return False
-                elif operator == 'startsWith':
-                    if not str(row_value).startswith(str(filter_value)):
-                        return False
-                elif operator == 'endsWith':
-                    if not str(row_value).endswith(str(filter_value)):
-                        return False
-                elif operator == 'not_in':
-                    if str(row_value) in [str(v) for v in filter_value]:
-                        return False
             except (ValueError, TypeError):
                 return False
 

trustgraph-flow/trustgraph/storage/doc_embeddings/qdrant/write.py

@@ -14,36 +14,29 @@ from qdrant_client.models import Distance, VectorParams
 from .... base import DocumentEmbeddingsStoreService, CollectionConfigHandler
 from .... base import AsyncProcessor, Consumer, Producer
 from .... base import ConsumerMetrics, ProducerMetrics
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 
 # Module logger
 logger = logging.getLogger(__name__)
 
 default_ident = "doc-embeddings-write"
 
+default_store_uri = 'http://localhost:6333'
+
 class Processor(CollectionConfigHandler, DocumentEmbeddingsStoreService):
 
     def __init__(self, **params):
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
-
-        url, api_key, replication_factor, shard_number = resolve_qdrant_config(
-            url=store_uri, api_key=api_key,
-            replication_factor=params.get("qdrant_replication_factor"),
-            shard_number=params.get("qdrant_shard_number"),
-        )
+        store_uri = params.get("store_uri", default_store_uri)
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
-        self.replication_factor = replication_factor
-        self.shard_number = shard_number
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
         self._cache_lock = asyncio.Lock()
         self._known_collections: set[str] = set()
 
@@ -68,8 +61,6 @@ class Processor(CollectionConfigHandler, DocumentEmbeddingsStoreService):
                     vectors_config=VectorParams(
                         size=dim, distance=Distance.COSINE
                     ),
-                    replication_factor=self.replication_factor,
-                    shard_number=self.shard_number,
                 )
             self._known_collections.add(collection_name)
 
@@ -118,7 +109,18 @@ class Processor(CollectionConfigHandler, DocumentEmbeddingsStoreService):
     def add_args(parser):
 
         DocumentEmbeddingsStoreService.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant URI (default: {default_store_uri})'
+        )
+        
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help=f'Qdrant API key (default: None)'
+        )
 
     async def create_collection(self, workspace: str, collection: str, metadata: dict):
         """

trustgraph-flow/trustgraph/storage/graph_embeddings/qdrant/write.py

@@ -14,7 +14,6 @@ from qdrant_client.models import Distance, VectorParams
 from .... base import GraphEmbeddingsStoreService, CollectionConfigHandler
 from .... base import AsyncProcessor, Consumer, Producer
 from .... base import ConsumerMetrics, ProducerMetrics
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 from .... schema import IRI, LITERAL
 
 # Module logger
@@ -30,34 +29,29 @@ def get_term_value(term):
     elif term.type == LITERAL:
         return term.value
     else:
+        # For blank nodes or other types, use id or value
         return term.id or term.value
 
 
 default_ident = "graph-embeddings-write"
 
+default_store_uri = 'http://localhost:6333'
+
 class Processor(CollectionConfigHandler, GraphEmbeddingsStoreService):
 
     def __init__(self, **params):
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
-
-        url, api_key, replication_factor, shard_number = resolve_qdrant_config(
-            url=store_uri, api_key=api_key,
-            replication_factor=params.get("qdrant_replication_factor"),
-            shard_number=params.get("qdrant_shard_number"),
-        )
+        store_uri = params.get("store_uri", default_store_uri)
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
-        self.replication_factor = replication_factor
-        self.shard_number = shard_number
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
         self._cache_lock = asyncio.Lock()
         self._known_collections: set[str] = set()
 
@@ -82,8 +76,6 @@ class Processor(CollectionConfigHandler, GraphEmbeddingsStoreService):
                     vectors_config=VectorParams(
                         size=dim, distance=Distance.COSINE
                     ),
-                    replication_factor=self.replication_factor,
-                    shard_number=self.shard_number,
                 )
             self._known_collections.add(collection_name)
 
@@ -136,7 +128,18 @@ class Processor(CollectionConfigHandler, GraphEmbeddingsStoreService):
     def add_args(parser):
 
         GraphEmbeddingsStoreService.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant store URI (default: {default_store_uri})'
+        )
+        
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help=f'Qdrant API key'
+        )
 
     async def create_collection(self, workspace: str, collection: str, metadata: dict):
         """

trustgraph-flow/trustgraph/storage/knowledge/store.py

@@ -27,8 +27,7 @@ class Processor(FlowProcessor):
             host=params.get("cassandra_host"),
             username=params.get("cassandra_username"),
             password=params.get("cassandra_password"),
-            default_keyspace='knowledge',
-            replication_factor=params.get("cassandra_replication_factor"),
+            default_keyspace='knowledge'
         )
 
         super(Processor, self).__init__(

trustgraph-flow/trustgraph/storage/row_embeddings/qdrant/write.py

@@ -27,12 +27,12 @@ from qdrant_client.models import PointStruct, Distance, VectorParams
 from .... schema import RowEmbeddings
 from .... base import FlowProcessor, ConsumerSpec
 from .... base import CollectionConfigHandler
-from .... base.qdrant_config import add_qdrant_args, resolve_qdrant_config
 
 # Module logger
 logger = logging.getLogger(__name__)
 
 default_ident = "row-embeddings-write"
+default_store_uri = 'http://localhost:6333'
 
 
 class Processor(CollectionConfigHandler, FlowProcessor):
@@ -41,19 +41,13 @@ class Processor(CollectionConfigHandler, FlowProcessor):
 
         id = params.get("id", default_ident)
 
-        store_uri = params.get("store_uri")
-        api_key = params.get("api_key")
-
-        url, api_key, replication_factor, shard_number = resolve_qdrant_config(
-            url=store_uri, api_key=api_key,
-            replication_factor=params.get("qdrant_replication_factor"),
-            shard_number=params.get("qdrant_shard_number"),
-        )
+        store_uri = params.get("store_uri", default_store_uri)
+        api_key = params.get("api_key", None)
 
         super(Processor, self).__init__(
             **params | {
                 "id": id,
-                "store_uri": url,
+                "store_uri": store_uri,
                 "api_key": api_key,
             }
         )
@@ -69,9 +63,7 @@ class Processor(CollectionConfigHandler, FlowProcessor):
         # Register config handler for collection management
         self.register_config_handler(self.on_collection_config, types=["collection"])
 
-        self.qdrant = QdrantClient(url=url, api_key=api_key)
-        self.replication_factor = replication_factor
-        self.shard_number = shard_number
+        self.qdrant = QdrantClient(url=store_uri, api_key=api_key)
         self._cache_lock = asyncio.Lock()
         self._known_collections: set[str] = set()
 
@@ -111,8 +103,6 @@ class Processor(CollectionConfigHandler, FlowProcessor):
                         size=dimension,
                         distance=Distance.COSINE
                     ),
-                    replication_factor=self.replication_factor,
-                    shard_number=self.shard_number,
                 )
             self._known_collections.add(collection_name)
 
@@ -259,9 +249,21 @@ class Processor(CollectionConfigHandler, FlowProcessor):
 
     @staticmethod
     def add_args(parser):
+        """Add command-line arguments"""
 
         FlowProcessor.add_args(parser)
-        add_qdrant_args(parser)
+
+        parser.add_argument(
+            '-t', '--store-uri',
+            default=default_store_uri,
+            help=f'Qdrant URI (default: {default_store_uri})'
+        )
+
+        parser.add_argument(
+            '-k', '--api-key',
+            default=None,
+            help='Qdrant API key (default: None)'
+        )
 
 
 def run():

trustgraph-flow/trustgraph/storage/rows/cassandra/write.py

@@ -47,18 +47,16 @@ class Processor(CollectionConfigHandler, FlowProcessor):
         cassandra_password = params.get("cassandra_password")
 
         # Resolve configuration with environment variable fallback
-        hosts, username, password, keyspace, replication_factor = resolve_cassandra_config(
+        hosts, username, password, keyspace, _ = resolve_cassandra_config(
             host=cassandra_host,
             username=cassandra_username,
-            password=cassandra_password,
-            replication_factor=params.get("cassandra_replication_factor"),
+            password=cassandra_password
         )
 
         # Store resolved configuration with proper names
         self.cassandra_host = hosts  # Store as list
         self.cassandra_username = username
         self.cassandra_password = password
-        self.replication_factor = replication_factor
 
         # Config key for schemas
         self.config_key = params.get("config_type", "schema")
@@ -172,7 +170,7 @@ class Processor(CollectionConfigHandler, FlowProcessor):
                         description=field_def.get("description", ""),
                         required=field_def.get("required", False),
                         enum_values=field_def.get("enum", []),
-                        indexed=field_def.get("indexed", False),
+                        indexed=field_def.get("indexed", False)
                     )
                     fields.append(field)
 
@@ -234,7 +232,7 @@ class Processor(CollectionConfigHandler, FlowProcessor):
         CREATE KEYSPACE IF NOT EXISTS {safe_keyspace}
         WITH REPLICATION = {{
             'class': 'SimpleStrategy',
-            'replication_factor': {self.replication_factor}
+            'replication_factor': 1
         }}
         """
 

trustgraph-flow/trustgraph/tables/cassandra_async.py

@@ -80,14 +80,14 @@ def _set_exception_if_pending(fut, exc):
         fut.set_exception(exc)
 
 
-async def async_execute_paged(session, query, parameters=None, fetch_size=5000):
+async def async_execute_paged(session, query, parameters=None, fetch_size=100):
     """Execute a CQL query with page-by-page iteration.
 
     Uses synchronous session.execute() inside run_in_executor so that
     the driver's ResultSet paging works correctly without materialising
     the entire result set in memory.
 
-    Returns all pages as a list of lists.
+    Yields one page of rows at a time (as a list).
     """
     loop = asyncio.get_running_loop()
 
@@ -111,50 +111,3 @@ async def async_execute_paged(session, query, parameters=None, fetch_size=5000):
     return await loop.run_in_executor(
         None, _fetch_all_pages
     )
-
-
-async def async_scan(
-    session, query, parameters=None, row_filter=None,
-    limit=None, fetch_size=5000,
-):
-    """Scan a CQL query page-by-page, applying a filter and limit.
-
-    Only matching rows accumulate in memory.  Each page is discarded
-    after processing, so peak memory is bounded by fetch_size plus
-    the number of matching rows (capped by limit).
-
-    Args:
-        session: cassandra.cluster.Session
-        query: CQL statement string
-        parameters: bind params
-        row_filter: callable(row) -> bool, or None to accept all
-        limit: max results to return, or None for unlimited
-        fetch_size: rows per Cassandra page fetch
-
-    Returns:
-        List of matching rows.
-    """
-    loop = asyncio.get_running_loop()
-
-    if isinstance(query, str):
-        stmt = SimpleStatement(query, fetch_size=fetch_size)
-    else:
-        stmt = query
-        stmt.fetch_size = fetch_size
-
-    def _scan():
-        results = []
-        result_set = session.execute(stmt, parameters)
-        while True:
-            for row in result_set.current_rows:
-                if row_filter is None or row_filter(row):
-                    results.append(row)
-                    if limit and len(results) >= limit:
-                        return results
-            if result_set.has_more_pages:
-                result_set.fetch_next_page()
-            else:
-                break
-        return results
-
-    return await loop.run_in_executor(None, _scan)

trustgraph-flow/trustgraph/tables/config.py

@@ -4,7 +4,7 @@ from .. schema import Metadata, GraphEmbeddings
 
 from cassandra.cluster import Cluster
 from cassandra.auth import PlainTextAuthProvider
-import ssl
+from ssl import SSLContext, PROTOCOL_TLSv1_2
 
 import uuid
 import time
@@ -33,7 +33,7 @@ class ConfigTableStore:
             cassandra_host = [h.strip() for h in cassandra_host.split(',')]
 
         if cassandra_username and cassandra_password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(
                 username=cassandra_username, password=cassandra_password
             )

trustgraph-flow/trustgraph/tables/iam.py

@@ -15,7 +15,7 @@ import logging
 
 from cassandra.cluster import Cluster
 from cassandra.auth import PlainTextAuthProvider
-import ssl
+from ssl import SSLContext, PROTOCOL_TLSv1_2
 
 from . cassandra_async import async_execute
 
@@ -39,7 +39,7 @@ class IamTableStore:
             cassandra_host = [h.strip() for h in cassandra_host.split(",")]
 
         if cassandra_username and cassandra_password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(
                 username=cassandra_username, password=cassandra_password,
             )

trustgraph-flow/trustgraph/tables/knowledge.py

@@ -23,7 +23,7 @@ def tuple_to_term(value, is_uri):
     else:
         return Term(type=LITERAL, value=value)
 from cassandra.auth import PlainTextAuthProvider
-import ssl
+from ssl import SSLContext, PROTOCOL_TLSv1_2
 
 import uuid
 import time
@@ -50,7 +50,7 @@ class KnowledgeTableStore:
             cassandra_host = [h.strip() for h in cassandra_host.split(',')]
 
         if cassandra_username and cassandra_password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(
                 username=cassandra_username, password=cassandra_password
             )

trustgraph-flow/trustgraph/tables/library.py

@@ -24,7 +24,7 @@ from .. exceptions import RequestError
 from cassandra.cluster import Cluster
 from cassandra.auth import PlainTextAuthProvider
 from cassandra.query import BatchStatement
-import ssl
+from ssl import SSLContext, PROTOCOL_TLSv1_2
 
 import uuid
 import time
@@ -53,7 +53,7 @@ class LibraryTableStore:
             cassandra_host = [h.strip() for h in cassandra_host.split(',')]
 
         if cassandra_username and cassandra_password:
-            ssl_context = ssl.create_default_context()
+            ssl_context = SSLContext(PROTOCOL_TLSv1_2)
             auth_provider = PlainTextAuthProvider(
                 username=cassandra_username, password=cassandra_password
             )

trustgraph-mcp/trustgraph/mcp_server/tg_socket.py

@@ -1,110 +1,49 @@
 
+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 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]
-
+import time
 
 class WebSocketManager:
-    """Manages an authenticated WebSocket connection to the TrustGraph
-    gateway on behalf of a single caller.
 
-    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):
+    def __init__(self, url, token=None):
         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
-        self.last_used = None
+
+    # FIXME: authentication is broken. The /api/v1/socket endpoint uses
+    # 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):
-        """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.socket = await connect(self._build_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
-        if hasattr(self, "reader_task"):
-            await self.reader_task
+        await self.reader_task
 
     async def reader(self):
-        """Background task: read WebSocket frames and route them to the
-        correct pending-request queue by ``id``."""
+        """
+        Background task to read websocket responses and route to correct
+        request
+        """
 
         while self.running:
             try:
@@ -120,21 +59,23 @@ 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:
-                    logger.warning(
-                        "Response for unknown request ID: %s", request_id
+                    logging.warning(
+                        f"Response for unknown request ID: {request_id}"
                     )
 
             except Exception as e:
 
-                logger.error("Error in websocket reader: %s", e)
+                logging.error(f"Error in websocket reader: {e}")
 
+                # Put error in all pending queues
                 for queue in self.pending_requests.values():
                     try:
                         await queue.put({"error": str(e)})
-                    except Exception:
+                    except:
                         pass
 
                 self.pending_requests.clear()
@@ -145,29 +86,25 @@ class WebSocketManager:
 
     async def request(
             self, service, request_data, flow_id="default",
-            workspace=None,
     ):
-        """Send a request via WebSocket and yield 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.
+        """
+        Send a request via websocket and handle single or streaming responses
         """
 
-        import time
-        self.last_used = time.monotonic()
-
+        # Generate unique request ID
         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,
@@ -177,16 +114,7 @@ class WebSocketManager:
             if flow_id is not None:
                 message["flow"] = flow_id
 
-            # ── 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
-
+            # Send request
             await self.socket.send(json.dumps(message))
 
             while self.running:
@@ -199,17 +127,19 @@ class WebSocketManager:
                     continue
 
                 if "error" in response:
-                    if isinstance(response["error"], dict):
-                        raise RuntimeError(
-                            response["error"].get("message", str(response["error"]))
-                        )
+                    if "message" in response["error"]:
+                        raise RuntimeError(response["error"]["text"])
                     else:
                         raise RuntimeError(str(response["error"]))
 
                 yield response["response"]
 
-                if response.get("complete"):
-                    break
+                if "complete" in response:
+                    if response["complete"]:
+                        break
 
-        finally:
+        except Exception as e:
+            # Clean up on error
             self.pending_requests.pop(request_id, None)
+            raise e
+