Fix doc embeddings invocation (#672)

* Fix doc embeddings invocation

* Tidy query embeddings invocation

trustgraph-base/trustgraph/api/flow.py

@@ -599,6 +599,7 @@ class FlowInstance:
                 collection="scientists",
                 limit=5
             )
+            # results contains {"entities": [{"entity": {...}, "score": 0.95}, ...]}
             ```
         """
 
@@ -633,7 +634,7 @@ class FlowInstance:
             limit: Maximum number of results (default: 10)
 
         Returns:
-            dict: Query results with chunk_ids of matching document chunks
+            dict: Query results with chunks containing chunk_id and score
 
         Example:
             ```python
@@ -644,7 +645,7 @@ class FlowInstance:
                 collection="research-papers",
                 limit=5
             )
-            # results contains {"chunk_ids": ["doc1/p0/c0", "doc2/p1/c3", ...]}
+            # results contains {"chunks": [{"chunk_id": "doc1/p0/c0", "score": 0.95}, ...]}
             ```
         """
 

trustgraph-base/trustgraph/api/socket_client.py

@@ -695,7 +695,7 @@ class SocketFlowInstance:
                 collection="research-papers",
                 limit=5
             )
-            # results contains {"chunk_ids": ["doc1/p0/c0", ...]}
+            # results contains {"chunks": [{"chunk_id": "...", "score": 0.95}, ...]}
             ```
         """
         # First convert text to embedding vector

trustgraph-cli/trustgraph/cli/invoke_document_embeddings.py

@@ -26,12 +26,14 @@ def query(url, flow_id, query_text, user, collection, limit, token=None):
             limit=limit
         )
 
-        chunk_ids = result.get("chunk_ids", [])
+        chunks = result.get("chunks", [])
-        if not chunk_ids:
+        if not chunks:
             print("No matching chunks found.")
         else:
-            for i, chunk_id in enumerate(chunk_ids, 1):
+            for i, chunk in enumerate(chunks, 1):
-                print(f"{i}. {chunk_id}")
+                chunk_id = chunk.get("chunk_id", "")
+                score = chunk.get("score", 0.0)
+                print(f"{i}. {chunk_id} (score: {score:.4f})")
 
     finally:
         # Clean up socket connection

trustgraph-cli/trustgraph/cli/invoke_graph_embeddings.py

@@ -27,8 +27,23 @@ def query(url, flow_id, query_text, user, collection, limit, token=None):
         )
 
         entities = result.get("entities", [])
-        for entity in entities:
+        if not entities:
-            print(entity)
+            print("No matching entities found.")
+        else:
+            for i, match in enumerate(entities, 1):
+                entity = match.get("entity", {})
+                score = match.get("score", 0.0)
+                # Format entity based on type (wire format uses compact keys)
+                term_type = entity.get("t", "")
+                if term_type == "i":  # IRI
+                    entity_str = entity.get("i", "")
+                elif term_type == "l":  # Literal
+                    entity_str = f'"{entity.get("v", "")}"'
+                elif term_type == "b":  # Blank node
+                    entity_str = f'_:{entity.get("d", "")}'
+                else:
+                    entity_str = str(entity)
+                print(f"{i}. {entity_str} (score: {score:.4f})")
 
     finally:
         # Clean up socket connection