Feature/prompts jsonl (#619)

* Tech spec

* JSONL implementation complete

* Updated prompt client users

* Fix tests

docs/tech-specs/jsonl-prompt-output.md

@@ -0,0 +1,455 @@
+# JSONL Prompt Output Technical Specification
+
+## Overview
+
+This specification describes the implementation of JSONL (JSON Lines) output
+format for prompt responses in TrustGraph. JSONL enables truncation-resilient
+extraction of structured data from LLM responses, addressing critical issues
+with JSON array outputs being corrupted when LLM responses hit output token
+limits.
+
+This implementation supports the following use cases:
+
+1. **Truncation-Resilient Extraction**: Extract valid partial results even when
+   LLM output is truncated mid-response
+2. **Large-Scale Extraction**: Handle extraction of many items without risk of
+   complete failure due to token limits
+3. **Mixed-Type Extraction**: Support extraction of multiple entity types
+   (definitions, relationships, entities, attributes) in a single prompt
+4. **Streaming-Compatible Output**: Enable future streaming/incremental
+   processing of extraction results
+
+## Goals
+
+- **Backward Compatibility**: Existing prompts using `response-type: "text"` and
+  `response-type: "json"` continue to work without modification
+- **Truncation Resilience**: Partial LLM outputs yield partial valid results
+  rather than complete failure
+- **Schema Validation**: Support JSON Schema validation for individual objects
+- **Discriminated Unions**: Support mixed-type outputs using a `type` field
+  discriminator
+- **Minimal API Changes**: Extend existing prompt configuration with new
+  response type and schema key
+
+## Background
+
+### Current Architecture
+
+The prompt service supports two response types:
+
+1. `response-type: "text"` - Raw text response returned as-is
+2. `response-type: "json"` - JSON parsed from response, validated against
+   optional `schema`
+
+Current implementation in `trustgraph-flow/trustgraph/template/prompt_manager.py`:
+
+```python
+class Prompt:
+    def __init__(self, template, response_type = "text", terms=None, schema=None):
+        self.template = template
+        self.response_type = response_type
+        self.terms = terms
+        self.schema = schema
+```
+
+### Current Limitations
+
+When extraction prompts request output as JSON arrays (`[{...}, {...}, ...]`):
+
+- **Truncation corruption**: If the LLM hits output token limits mid-array, the
+  entire response becomes invalid JSON and cannot be parsed
+- **All-or-nothing parsing**: Must receive complete output before parsing
+- **No partial results**: A truncated response yields zero usable data
+- **Unreliable for large extractions**: More extracted items = higher failure risk
+
+This specification addresses these limitations by introducing JSONL format for
+extraction prompts, where each extracted item is a complete JSON object on its
+own line.
+
+## Technical Design
+
+### Response Type Extension
+
+Add a new response type `"jsonl"` alongside existing `"text"` and `"json"` types.
+
+#### Configuration Changes
+
+**New response type value:**
+
+```
+"response-type": "jsonl"
+```
+
+**Schema interpretation:**
+
+The existing `"schema"` key is used for both `"json"` and `"jsonl"` response
+types. The interpretation depends on the response type:
+
+- `"json"`: Schema describes the entire response (typically an array or object)
+- `"jsonl"`: Schema describes each individual line/object
+
+```json
+{
+  "response-type": "jsonl",
+  "schema": {
+    "type": "object",
+    "properties": {
+      "entity": { "type": "string" },
+      "definition": { "type": "string" }
+    },
+    "required": ["entity", "definition"]
+  }
+}
+```
+
+This avoids changes to prompt configuration tooling and editors.
+
+### JSONL Format Specification
+
+#### Simple Extraction
+
+For prompts extracting a single type of object (definitions, relationships,
+topics, rows), the output is one JSON object per line with no wrapper:
+
+**Prompt output format:**
+```
+{"entity": "photosynthesis", "definition": "Process by which plants convert sunlight"}
+{"entity": "chlorophyll", "definition": "Green pigment in plants"}
+{"entity": "mitochondria", "definition": "Powerhouse of the cell"}
+```
+
+**Contrast with previous JSON array format:**
+```json
+[
+  {"entity": "photosynthesis", "definition": "Process by which plants convert sunlight"},
+  {"entity": "chlorophyll", "definition": "Green pigment in plants"},
+  {"entity": "mitochondria", "definition": "Powerhouse of the cell"}
+]
+```
+
+If the LLM truncates after line 2, the JSON array format yields invalid JSON,
+while JSONL yields two valid objects.
+
+#### Mixed-Type Extraction (Discriminated Unions)
+
+For prompts extracting multiple types of objects (e.g., both definitions and
+relationships, or entities, relationships, and attributes), use a `"type"`
+field as discriminator:
+
+**Prompt output format:**
+```
+{"type": "definition", "entity": "DNA", "definition": "Molecule carrying genetic instructions"}
+{"type": "relationship", "subject": "DNA", "predicate": "located_in", "object": "cell nucleus", "object-entity": true}
+{"type": "definition", "entity": "RNA", "definition": "Molecule that carries genetic information"}
+{"type": "relationship", "subject": "RNA", "predicate": "transcribed_from", "object": "DNA", "object-entity": true}
+```
+
+**Schema for discriminated unions uses `oneOf`:**
+```json
+{
+  "response-type": "jsonl",
+  "schema": {
+    "oneOf": [
+      {
+        "type": "object",
+        "properties": {
+          "type": { "const": "definition" },
+          "entity": { "type": "string" },
+          "definition": { "type": "string" }
+        },
+        "required": ["type", "entity", "definition"]
+      },
+      {
+        "type": "object",
+        "properties": {
+          "type": { "const": "relationship" },
+          "subject": { "type": "string" },
+          "predicate": { "type": "string" },
+          "object": { "type": "string" },
+          "object-entity": { "type": "boolean" }
+        },
+        "required": ["type", "subject", "predicate", "object", "object-entity"]
+      }
+    ]
+  }
+}
+```
+
+#### Ontology Extraction
+
+For ontology-based extraction with entities, relationships, and attributes:
+
+**Prompt output format:**
+```
+{"type": "entity", "entity": "Cornish pasty", "entity_type": "fo/Recipe"}
+{"type": "entity", "entity": "beef", "entity_type": "fo/Food"}
+{"type": "relationship", "subject": "Cornish pasty", "subject_type": "fo/Recipe", "relation": "fo/has_ingredient", "object": "beef", "object_type": "fo/Food"}
+{"type": "attribute", "entity": "Cornish pasty", "entity_type": "fo/Recipe", "attribute": "fo/serves", "value": "4 people"}
+```
+
+### Implementation Details
+
+#### Prompt Class
+
+The existing `Prompt` class requires no changes. The `schema` field is reused
+for JSONL, with its interpretation determined by `response_type`:
+
+```python
+class Prompt:
+    def __init__(self, template, response_type="text", terms=None, schema=None):
+        self.template = template
+        self.response_type = response_type
+        self.terms = terms
+        self.schema = schema  # Interpretation depends on response_type
+```
+
+#### PromptManager.load_config
+
+No changes required - existing configuration loading already handles the
+`schema` key.
+
+#### JSONL Parsing
+
+Add a new parsing method for JSONL responses:
+
+```python
+def parse_jsonl(self, text):
+    """
+    Parse JSONL response, returning list of valid objects.
+
+    Invalid lines (malformed JSON, empty lines) are skipped with warnings.
+    This provides truncation resilience - partial output yields partial results.
+    """
+    results = []
+
+    for line_num, line in enumerate(text.strip().split('\n'), 1):
+        line = line.strip()
+
+        # Skip empty lines
+        if not line:
+            continue
+
+        # Skip markdown code fence markers if present
+        if line.startswith('```'):
+            continue
+
+        try:
+            obj = json.loads(line)
+            results.append(obj)
+        except json.JSONDecodeError as e:
+            # Log warning but continue - this provides truncation resilience
+            logger.warning(f"JSONL parse error on line {line_num}: {e}")
+
+    return results
+```
+
+#### PromptManager.invoke Changes
+
+Extend the invoke method to handle the new response type:
+
+```python
+async def invoke(self, id, input, llm):
+    logger.debug("Invoking prompt template...")
+
+    terms = self.terms | self.prompts[id].terms | input
+    resp_type = self.prompts[id].response_type
+
+    prompt = {
+        "system": self.system_template.render(terms),
+        "prompt": self.render(id, input)
+    }
+
+    resp = await llm(**prompt)
+
+    if resp_type == "text":
+        return resp
+
+    if resp_type == "json":
+        try:
+            obj = self.parse_json(resp)
+        except:
+            logger.error(f"JSON parse failed: {resp}")
+            raise RuntimeError("JSON parse fail")
+
+        if self.prompts[id].schema:
+            try:
+                validate(instance=obj, schema=self.prompts[id].schema)
+                logger.debug("Schema validation successful")
+            except Exception as e:
+                raise RuntimeError(f"Schema validation fail: {e}")
+
+        return obj
+
+    if resp_type == "jsonl":
+        objects = self.parse_jsonl(resp)
+
+        if not objects:
+            logger.warning("JSONL parse returned no valid objects")
+            return []
+
+        # Validate each object against schema if provided
+        if self.prompts[id].schema:
+            validated = []
+            for i, obj in enumerate(objects):
+                try:
+                    validate(instance=obj, schema=self.prompts[id].schema)
+                    validated.append(obj)
+                except Exception as e:
+                    logger.warning(f"Object {i} failed schema validation: {e}")
+            return validated
+
+        return objects
+
+    raise RuntimeError(f"Response type {resp_type} not known")
+```
+
+### Affected Prompts
+
+The following prompts should be migrated to JSONL format:
+
+| Prompt ID | Description | Type Field |
+|-----------|-------------|------------|
+| `extract-definitions` | Entity/definition extraction | No (single type) |
+| `extract-relationships` | Relationship extraction | No (single type) |
+| `extract-topics` | Topic/definition extraction | No (single type) |
+| `extract-rows` | Structured row extraction | No (single type) |
+| `agent-kg-extract` | Combined definition + relationship extraction | Yes: `"definition"`, `"relationship"` |
+| `extract-with-ontologies` / `ontology-extract` | Ontology-based extraction | Yes: `"entity"`, `"relationship"`, `"attribute"` |
+
+### API Changes
+
+#### Client Perspective
+
+JSONL parsing is transparent to prompt service API callers. The parsing occurs
+server-side in the prompt service, and the response is returned via the standard
+`PromptResponse.object` field as a serialized JSON array.
+
+When clients call the prompt service (via `PromptClient.prompt()` or similar):
+
+- **`response-type: "json"`** with array schema → client receives Python `list`
+- **`response-type: "jsonl"`** → client receives Python `list`
+
+From the client's perspective, both return identical data structures. The
+difference is entirely in how the LLM output is parsed server-side:
+
+- JSON array format: Single `json.loads()` call; fails completely if truncated
+- JSONL format: Line-by-line parsing; yields partial results if truncated
+
+This means existing client code expecting a list from extraction prompts
+requires no changes when migrating prompts from JSON to JSONL format.
+
+#### Server Return Value
+
+For `response-type: "jsonl"`, the `PromptManager.invoke()` method returns a
+`list[dict]` containing all successfully parsed and validated objects. This
+list is then serialized to JSON for the `PromptResponse.object` field.
+
+#### Error Handling
+
+- Empty results: Returns empty list `[]` with warning log
+- Partial parse failure: Returns list of successfully parsed objects with
+  warning logs for failures
+- Complete parse failure: Returns empty list `[]` with warning logs
+
+This differs from `response-type: "json"` which raises `RuntimeError` on
+parse failure. The lenient behavior for JSONL is intentional to provide
+truncation resilience.
+
+### Configuration Example
+
+Complete prompt configuration example:
+
+```json
+{
+  "prompt": "Extract all entities and their definitions from the following text. Output one JSON object per line.\n\nText:\n{{text}}\n\nOutput format per line:\n{\"entity\": \"<name>\", \"definition\": \"<definition>\"}",
+  "response-type": "jsonl",
+  "schema": {
+    "type": "object",
+    "properties": {
+      "entity": {
+        "type": "string",
+        "description": "The entity name"
+      },
+      "definition": {
+        "type": "string",
+        "description": "A clear definition of the entity"
+      }
+    },
+    "required": ["entity", "definition"]
+  }
+}
+```
+
+## Security Considerations
+
+- **Input Validation**: JSON parsing uses standard `json.loads()` which is safe
+  against injection attacks
+- **Schema Validation**: Uses `jsonschema.validate()` for schema enforcement
+- **No New Attack Surface**: JSONL parsing is strictly safer than JSON array
+  parsing due to line-by-line processing
+
+## Performance Considerations
+
+- **Memory**: Line-by-line parsing uses less peak memory than loading full JSON
+  arrays
+- **Latency**: Parsing performance is comparable to JSON array parsing
+- **Validation**: Schema validation runs per-object, which adds overhead but
+  enables partial results on validation failure
+
+## Testing Strategy
+
+### Unit Tests
+
+- JSONL parsing with valid input
+- JSONL parsing with empty lines
+- JSONL parsing with markdown code fences
+- JSONL parsing with truncated final line
+- JSONL parsing with invalid JSON lines interspersed
+- Schema validation with `oneOf` discriminated unions
+- Backward compatibility: existing `"text"` and `"json"` prompts unchanged
+
+### Integration Tests
+
+- End-to-end extraction with JSONL prompts
+- Extraction with simulated truncation (artificially limited response)
+- Mixed-type extraction with type discriminator
+- Ontology extraction with all three types
+
+### Extraction Quality Tests
+
+- Compare extraction results: JSONL vs JSON array format
+- Verify truncation resilience: JSONL yields partial results where JSON fails
+
+## Migration Plan
+
+### Phase 1: Implementation
+
+1. Implement `parse_jsonl()` method in `PromptManager`
+2. Extend `invoke()` to handle `response-type: "jsonl"`
+3. Add unit tests
+
+### Phase 2: Prompt Migration
+
+1. Update `extract-definitions` prompt and configuration
+2. Update `extract-relationships` prompt and configuration
+3. Update `extract-topics` prompt and configuration
+4. Update `extract-rows` prompt and configuration
+5. Update `agent-kg-extract` prompt and configuration
+6. Update `extract-with-ontologies` prompt and configuration
+
+### Phase 3: Downstream Updates
+
+1. Update any code consuming extraction results to handle list return type
+2. Update code that categorizes mixed-type extractions by `type` field
+3. Update tests that assert on extraction output format
+
+## Open Questions
+
+None at this time.
+
+## References
+
+- Current implementation: `trustgraph-flow/trustgraph/template/prompt_manager.py`
+- JSON Lines specification: https://jsonlines.org/
+- JSON Schema `oneOf`: https://json-schema.org/understanding-json-schema/reference/combining.html#oneof
+- Related specification: Streaming LLM Responses (`docs/tech-specs/streaming-llm-responses.md`)

tests/integration/test_agent_kg_extraction_integration.py

@@ -30,38 +30,16 @@ class TestAgentKgExtractionIntegration:
         # Mock agent client
         agent_client = AsyncMock()
         
-        # Mock successful agent response
+        # Mock successful agent response in JSONL format
         def mock_agent_response(recipient, question):
-            # Simulate agent processing and return structured response
+            # Simulate agent processing and return structured JSONL response
             mock_response = MagicMock()
             mock_response.error = None
             mock_response.answer = '''```json
-{
+{"type": "definition", "entity": "Machine Learning", "definition": "A subset of artificial intelligence that enables computers to learn from data without explicit programming."}
-    "definitions": [
+{"type": "definition", "entity": "Neural Networks", "definition": "Computing systems inspired by biological neural networks that process information."}
-        {
+{"type": "relationship", "subject": "Machine Learning", "predicate": "is_subset_of", "object": "Artificial Intelligence", "object-entity": true}
-            "entity": "Machine Learning",
+{"type": "relationship", "subject": "Neural Networks", "predicate": "used_in", "object": "Machine Learning", "object-entity": true}
-            "definition": "A subset of artificial intelligence that enables computers to learn from data without explicit programming."
-        },
-        {
-            "entity": "Neural Networks", 
-            "definition": "Computing systems inspired by biological neural networks that process information."
-        }
-    ],
-    "relationships": [
-        {
-            "subject": "Machine Learning",
-            "predicate": "is_subset_of", 
-            "object": "Artificial Intelligence",
-            "object-entity": true
-        },
-        {
-            "subject": "Neural Networks",
-            "predicate": "used_in",
-            "object": "Machine Learning", 
-            "object-entity": true
-        }
-    ]
-}
 ```'''
             return mock_response.answer
         
@@ -120,7 +98,7 @@ class TestAgentKgExtractionIntegration:
         
         # Copy the methods we want to test
         extractor.to_uri = real_extractor.to_uri
-        extractor.parse_json = real_extractor.parse_json
+        extractor.parse_jsonl = real_extractor.parse_jsonl
         extractor.process_extraction_data = real_extractor.process_extraction_data
         extractor.emit_triples = real_extractor.emit_triples
         extractor.emit_entity_contexts = real_extractor.emit_entity_contexts
@@ -156,7 +134,7 @@ class TestAgentKgExtractionIntegration:
             agent_response = agent_client.invoke(recipient=lambda x: True, question=prompt)
             
             # Parse and process
-            extraction_data = extractor.parse_json(agent_response)
+            extraction_data = extractor.parse_jsonl(agent_response)
             triples, entity_contexts = extractor.process_extraction_data(extraction_data, v.metadata)
             
             # Add metadata triples
@@ -248,7 +226,7 @@ class TestAgentKgExtractionIntegration:
 
     @pytest.mark.asyncio
     async def test_invalid_json_response_handling(self, configured_agent_extractor, sample_chunk, mock_flow_context):
-        """Test handling of invalid JSON responses from agent"""
+        """Test handling of invalid JSON responses from agent - JSONL is lenient and skips invalid lines"""
         # Arrange - mock invalid JSON response
         agent_client = mock_flow_context("agent-request")
 
@@ -261,9 +239,15 @@ class TestAgentKgExtractionIntegration:
         mock_message.value.return_value = sample_chunk
         mock_consumer = MagicMock()
 
-        # Act & Assert
+        # Act - JSONL parsing is lenient, invalid lines are skipped
-        with pytest.raises((ValueError, json.JSONDecodeError)):
+        await configured_agent_extractor.on_message(mock_message, mock_consumer, mock_flow_context)
-            await configured_agent_extractor.on_message(mock_message, mock_consumer, mock_flow_context)
+
+        # Assert - should emit triples (with just metadata) but no entity contexts
+        triples_publisher = mock_flow_context("triples")
+        triples_publisher.send.assert_called_once()
+
+        entity_contexts_publisher = mock_flow_context("entity-contexts")
+        entity_contexts_publisher.send.assert_not_called()
 
     @pytest.mark.asyncio
     async def test_empty_extraction_results(self, configured_agent_extractor, sample_chunk, mock_flow_context):
@@ -272,7 +256,8 @@ class TestAgentKgExtractionIntegration:
         agent_client = mock_flow_context("agent-request")
         
         def mock_empty_response(recipient, question):
-            return '{"definitions": [], "relationships": []}'
+            # Return empty JSONL (just empty/whitespace)
+            return ''
         
         agent_client.invoke = mock_empty_response
         
@@ -303,7 +288,8 @@ class TestAgentKgExtractionIntegration:
         agent_client = mock_flow_context("agent-request")
         
         def mock_malformed_response(recipient, question):
-            return '''{"definitions": [{"entity": "Missing Definition"}], "relationships": [{"subject": "Missing Object"}]}'''
+            # JSONL with definition missing required field
+            return '{"type": "definition", "entity": "Missing Definition"}'
         
         agent_client.invoke = mock_malformed_response
         
@@ -330,7 +316,7 @@ class TestAgentKgExtractionIntegration:
         def capture_prompt(recipient, question):
             # Verify the prompt contains the test text
             assert test_text in question
-            return '{"definitions": [], "relationships": []}'
+            return ''  # Empty JSONL response
         
         agent_client.invoke = capture_prompt
         
@@ -361,7 +347,7 @@ class TestAgentKgExtractionIntegration:
         responses = []
         
         def mock_response(recipient, question):
-            response = f'{{"definitions": [{{"entity": "Entity {len(responses)}", "definition": "Definition {len(responses)}"}}], "relationships": []}}'
+            response = f'{{"type": "definition", "entity": "Entity {len(responses)}", "definition": "Definition {len(responses)}"}}'
             responses.append(response)
             return response
         
@@ -398,7 +384,7 @@ class TestAgentKgExtractionIntegration:
             # Verify unicode text was properly decoded and included
             assert "学习机器" in question
             assert "人工知能" in question
-            return '''{"definitions": [{"entity": "機械学習", "definition": "人工知能の一分野"}], "relationships": []}'''
+            return '{"type": "definition", "entity": "機械学習", "definition": "人工知能の一分野"}'
         
         agent_client.invoke = mock_unicode_response
         
@@ -433,7 +419,7 @@ class TestAgentKgExtractionIntegration:
         def mock_large_text_response(recipient, question):
             # Verify large text was included
             assert len(question) > 10000
-            return '''{"definitions": [{"entity": "Machine Learning", "definition": "Important AI technique"}], "relationships": []}'''
+            return '{"type": "definition", "entity": "Machine Learning", "definition": "Important AI technique"}'
         
         agent_client.invoke = mock_large_text_response
         

tests/unit/test_knowledge_graph/test_agent_extraction.py

@@ -33,7 +33,7 @@ class TestAgentKgExtractor:
         
         # Set up the methods we want to test
         extractor.to_uri = real_extractor.to_uri
-        extractor.parse_json = real_extractor.parse_json
+        extractor.parse_jsonl = real_extractor.parse_jsonl
         extractor.process_extraction_data = real_extractor.process_extraction_data
         extractor.emit_triples = real_extractor.emit_triples
         extractor.emit_entity_contexts = real_extractor.emit_entity_contexts
@@ -62,39 +62,40 @@ class TestAgentKgExtractor:
 
     @pytest.fixture
     def sample_extraction_data(self):
-        """Sample extraction data in expected format"""
+        """Sample extraction data in JSONL format (list with type discriminators)"""
-        return {
+        return [
-            "definitions": [
+            {
-                {
+                "type": "definition",
-                    "entity": "Machine Learning",
+                "entity": "Machine Learning",
-                    "definition": "A subset of artificial intelligence that enables computers to learn from data without explicit programming."
+                "definition": "A subset of artificial intelligence that enables computers to learn from data without explicit programming."
-                },
+            },
-                {
+            {
-                    "entity": "Neural Networks",
+                "type": "definition",
-                    "definition": "Computing systems inspired by biological neural networks that process information."
+                "entity": "Neural Networks",
-                }
+                "definition": "Computing systems inspired by biological neural networks that process information."
-            ],
+            },
-            "relationships": [
+            {
-                {
+                "type": "relationship",
-                    "subject": "Machine Learning",
+                "subject": "Machine Learning",
-                    "predicate": "is_subset_of",
+                "predicate": "is_subset_of",
-                    "object": "Artificial Intelligence",
+                "object": "Artificial Intelligence",
-                    "object-entity": True
+                "object-entity": True
-                },
+            },
-                {
+            {
-                    "subject": "Neural Networks",
+                "type": "relationship",
-                    "predicate": "used_in",
+                "subject": "Neural Networks",
-                    "object": "Machine Learning",
+                "predicate": "used_in",
-                    "object-entity": True
+                "object": "Machine Learning",
-                },
+                "object-entity": True
-                {
+            },
-                    "subject": "Deep Learning",
+            {
-                    "predicate": "accuracy",
+                "type": "relationship",
-                    "object": "95%",
+                "subject": "Deep Learning",
-                    "object-entity": False
+                "predicate": "accuracy",
-                }
+                "object": "95%",
-            ]
+                "object-entity": False
-        }
+            }
+        ]
 
     def test_to_uri_conversion(self, agent_extractor):
         """Test URI conversion for entities"""
@@ -113,60 +114,66 @@ class TestAgentKgExtractor:
         expected = f"{TRUSTGRAPH_ENTITIES}"
         assert uri == expected
 
-    def test_parse_json_with_code_blocks(self, agent_extractor):
+    def test_parse_jsonl_with_code_blocks(self, agent_extractor):
-        """Test JSON parsing from code blocks"""
+        """Test JSONL parsing from code blocks"""
-        # Test JSON in code blocks
+        # Test JSONL in code blocks - note: JSON uses lowercase true/false
         response = '''```json
-        {
+{"type": "definition", "entity": "AI", "definition": "Artificial Intelligence"}
-            "definitions": [{"entity": "AI", "definition": "Artificial Intelligence"}],
+{"type": "relationship", "subject": "AI", "predicate": "is", "object": "technology", "object-entity": false}
-            "relationships": []
+```'''
-        }
-        ```'''
 
-        result = agent_extractor.parse_json(response)
+        result = agent_extractor.parse_jsonl(response)
 
-        assert result["definitions"][0]["entity"] == "AI"
+        assert len(result) == 2
-        assert result["definitions"][0]["definition"] == "Artificial Intelligence"
+        assert result[0]["entity"] == "AI"
-        assert result["relationships"] == []
+        assert result[0]["definition"] == "Artificial Intelligence"
+        assert result[1]["type"] == "relationship"
 
-    def test_parse_json_without_code_blocks(self, agent_extractor):
+    def test_parse_jsonl_without_code_blocks(self, agent_extractor):
-        """Test JSON parsing without code blocks"""
+        """Test JSONL parsing without code blocks"""
-        response = '''{"definitions": [{"entity": "ML", "definition": "Machine Learning"}], "relationships": []}'''
+        response = '''{"type": "definition", "entity": "ML", "definition": "Machine Learning"}
+{"type": "definition", "entity": "AI", "definition": "Artificial Intelligence"}'''
 
-        result = agent_extractor.parse_json(response)
+        result = agent_extractor.parse_jsonl(response)
 
-        assert result["definitions"][0]["entity"] == "ML"
+        assert len(result) == 2
-        assert result["definitions"][0]["definition"] == "Machine Learning"
+        assert result[0]["entity"] == "ML"
+        assert result[1]["entity"] == "AI"
 
-    def test_parse_json_invalid_format(self, agent_extractor):
+    def test_parse_jsonl_invalid_lines_skipped(self, agent_extractor):
-        """Test JSON parsing with invalid format"""
+        """Test JSONL parsing skips invalid lines gracefully"""
-        invalid_response = "This is not JSON at all"
+        response = '''{"type": "definition", "entity": "Valid", "definition": "Valid def"}
+This is not JSON at all
+{"type": "definition", "entity": "Also Valid", "definition": "Another def"}'''
 
-        with pytest.raises(json.JSONDecodeError):
+        result = agent_extractor.parse_jsonl(response)
-            agent_extractor.parse_json(invalid_response)
 
-    def test_parse_json_malformed_code_blocks(self, agent_extractor):
+        # Should get 2 valid objects, skipping the invalid line
-        """Test JSON parsing with malformed code blocks"""
+        assert len(result) == 2
-        # Missing closing backticks
+        assert result[0]["entity"] == "Valid"
-        response = '''```json
+        assert result[1]["entity"] == "Also Valid"
-        {"definitions": [], "relationships": []}
-        '''
 
-        # Should still parse the JSON content
+    def test_parse_jsonl_truncation_resilience(self, agent_extractor):
-        with pytest.raises(json.JSONDecodeError):
+        """Test JSONL parsing handles truncated responses"""
-            agent_extractor.parse_json(response)
+        # Simulates output cut off mid-line
+        response = '''{"type": "definition", "entity": "Complete", "definition": "Full def"}
+{"type": "definition", "entity": "Trunca'''
+
+        result = agent_extractor.parse_jsonl(response)
+
+        # Should get 1 valid object, the truncated line is skipped
+        assert len(result) == 1
+        assert result[0]["entity"] == "Complete"
 
     def test_process_extraction_data_definitions(self, agent_extractor, sample_metadata):
         """Test processing of definition data"""
-        data = {
+        data = [
-            "definitions": [
+            {
-                {
+                "type": "definition",
-                    "entity": "Machine Learning",
+                "entity": "Machine Learning",
-                    "definition": "A subset of AI that enables learning from data."
+                "definition": "A subset of AI that enables learning from data."
-                }
+            }
-            ],
+        ]
-            "relationships": []
-        }
 
         triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
         
@@ -196,17 +203,15 @@ class TestAgentKgExtractor:
 
     def test_process_extraction_data_relationships(self, agent_extractor, sample_metadata):
         """Test processing of relationship data"""
-        data = {
+        data = [
-            "definitions": [],
+            {
-            "relationships": [
+                "type": "relationship",
-                {
+                "subject": "Machine Learning",
-                    "subject": "Machine Learning",
+                "predicate": "is_subset_of",
-                    "predicate": "is_subset_of",
+                "object": "Artificial Intelligence",
-                    "object": "Artificial Intelligence",
+                "object-entity": True
-                    "object-entity": True
+            }
-                }
+        ]
-            ]
-        }
 
         triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
         
@@ -224,14 +229,11 @@ class TestAgentKgExtractor:
         assert predicate_label.o.value == "is_subset_of"
         
         # Check main relationship triple
-        # NOTE: Current implementation has bugs:
+        object_uri = f"{TRUSTGRAPH_ENTITIES}Artificial%20Intelligence"
-        # 1. Uses data.get("object-entity") instead of rel.get("object-entity")
-        # 2. Sets object_value to predicate_uri instead of actual object URI
-        # This test documents the current buggy behavior
         rel_triple = next((t for t in triples if t.s.value == subject_uri and t.p.value == predicate_uri), None)
         assert rel_triple is not None
-        # Due to bug, object value is set to predicate_uri
+        assert rel_triple.o.value == object_uri
-        assert rel_triple.o.value == predicate_uri
+        assert rel_triple.o.is_uri == True
         
         # Check subject-of relationships
         subject_of_triples = [t for t in triples if t.p.value == SUBJECT_OF and t.o.value == "doc123"]
@@ -239,17 +241,15 @@ class TestAgentKgExtractor:
 
     def test_process_extraction_data_literal_object(self, agent_extractor, sample_metadata):
         """Test processing of relationships with literal objects"""
-        data = {
+        data = [
-            "definitions": [],
+            {
-            "relationships": [
+                "type": "relationship",
-                {
+                "subject": "Deep Learning",
-                    "subject": "Deep Learning",
+                "predicate": "accuracy",
-                    "predicate": "accuracy",
+                "object": "95%",
-                    "object": "95%",
+                "object-entity": False
-                    "object-entity": False
+            }
-                }
+        ]
-            ]
-        }
 
         triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
 
@@ -275,12 +275,9 @@ class TestAgentKgExtractor:
     def test_process_extraction_data_no_metadata_id(self, agent_extractor):
         """Test processing when metadata has no ID"""
         metadata = Metadata(id=None, metadata=[])
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": "Test Entity", "definition": "Test definition"}
-                {"entity": "Test Entity", "definition": "Test definition"}
+        ]
-            ],
-            "relationships": []
-        }
 
         triples, entity_contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -293,44 +290,34 @@ class TestAgentKgExtractor:
 
     def test_process_extraction_data_empty_data(self, agent_extractor, sample_metadata):
         """Test processing of empty extraction data"""
-        data = {"definitions": [], "relationships": []}
+        data = []
 
         triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
 
-        # Should only have metadata triples
+        # Should have no entity contexts
         assert len(entity_contexts) == 0
-        # Triples should only contain metadata triples if any
+        # Triples should be empty
+        assert len(triples) == 0
 
-    def test_process_extraction_data_missing_keys(self, agent_extractor, sample_metadata):
+    def test_process_extraction_data_unknown_types_ignored(self, agent_extractor, sample_metadata):
-        """Test processing data with missing keys"""
+        """Test processing data with unknown type values"""
-        # Test missing definitions key
+        data = [
-        data = {"relationships": []}
+            {"type": "definition", "entity": "Valid", "definition": "Valid def"},
-        triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
+            {"type": "unknown_type", "foo": "bar"},  # Unknown type - should be ignored
-        assert len(entity_contexts) == 0
+            {"type": "relationship", "subject": "A", "predicate": "rel", "object": "B", "object-entity": True}
+        ]
 
-        # Test missing relationships key
-        data = {"definitions": []}
         triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
-        assert len(entity_contexts) == 0
 
-        # Test completely missing keys
+        # Should process valid items and ignore unknown types
-        data = {}
+        assert len(entity_contexts) == 1  # Only the definition creates entity context
-        triples, entity_contexts = agent_extractor.process_extraction_data(data, sample_metadata)
-        assert len(entity_contexts) == 0
 
     def test_process_extraction_data_malformed_entries(self, agent_extractor, sample_metadata):
         """Test processing data with malformed entries"""
-        # Test definition missing required fields
+        # Test items missing required fields - should raise KeyError
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": "Test"},  # Missing definition
-                {"entity": "Test"},  # Missing definition
+        ]
-                {"definition": "Test def"}  # Missing entity
-            ],
-            "relationships": [
-                {"subject": "A", "predicate": "rel"},  # Missing object
-                {"subject": "B", "object": "C"}  # Missing predicate
-            ]
-        }
 
         # Should handle gracefully or raise appropriate errors
         with pytest.raises(KeyError):

tests/unit/test_knowledge_graph/test_agent_extraction_edge_cases.py

@@ -32,7 +32,7 @@ class TestAgentKgExtractionEdgeCases:
         
         # Set up the methods we want to test
         extractor.to_uri = real_extractor.to_uri
-        extractor.parse_json = real_extractor.parse_json
+        extractor.parse_jsonl = real_extractor.parse_jsonl
         extractor.process_extraction_data = real_extractor.process_extraction_data
         extractor.emit_triples = real_extractor.emit_triples
         extractor.emit_entity_contexts = real_extractor.emit_entity_contexts
@@ -85,114 +85,90 @@ class TestAgentKgExtractionEdgeCases:
             # Verify the URI is properly encoded
             assert unicode_text not in uri  # Original unicode should be encoded
 
-    def test_parse_json_whitespace_variations(self, agent_extractor):
+    def test_parse_jsonl_whitespace_variations(self, agent_extractor):
-        """Test JSON parsing with various whitespace patterns"""
+        """Test JSONL parsing with various whitespace patterns"""
-        # Test JSON with different whitespace patterns
+        # Test JSONL with different whitespace patterns
         test_cases = [
             # Extra whitespace around code blocks
-            "   ```json\n{\"test\": true}\n```   ",
+            '   ```json\n{"type": "definition", "entity": "test", "definition": "def"}\n```   ',
-            # Tabs and mixed whitespace
+            # Multiple newlines between lines
-            "\t\t```json\n\t{\"test\": true}\n\t```\t",
+            '{"type": "definition", "entity": "A", "definition": "def A"}\n\n\n{"type": "definition", "entity": "B", "definition": "def B"}',
-            # Multiple newlines
+            # JSONL without code blocks but with whitespace
-            "\n\n\n```json\n\n{\"test\": true}\n\n```\n\n",
+            '   {"type": "definition", "entity": "test", "definition": "def"}   ',
-            # JSON without code blocks but with whitespace
-            "   {\"test\": true}   ",
-            # Mixed line endings
-            "```json\r\n{\"test\": true}\r\n```",
         ]
 
         for response in test_cases:
-            result = agent_extractor.parse_json(response)
+            result = agent_extractor.parse_jsonl(response)
-            assert result == {"test": True}
+            assert len(result) >= 1
+            assert result[0].get("type") == "definition"
 
-    def test_parse_json_code_block_variations(self, agent_extractor):
+    def test_parse_jsonl_code_block_variations(self, agent_extractor):
-        """Test JSON parsing with different code block formats"""
+        """Test JSONL parsing with different code block formats"""
         test_cases = [
             # Standard json code block
-            "```json\n{\"valid\": true}\n```",
+            '```json\n{"type": "definition", "entity": "A", "definition": "def"}\n```',
+            # jsonl code block
+            '```jsonl\n{"type": "definition", "entity": "A", "definition": "def"}\n```',
             # Code block without language
-            "```\n{\"valid\": true}\n```",
+            '```\n{"type": "definition", "entity": "A", "definition": "def"}\n```',
-            # Uppercase JSON
+            # Code block with extra content before/after
-            "```JSON\n{\"valid\": true}\n```",
+            'Here\'s the result:\n```json\n{"type": "definition", "entity": "A", "definition": "def"}\n```\nDone!',
-            # Mixed case
-            "```Json\n{\"valid\": true}\n```",
-            # Multiple code blocks (should take first one)
-            "```json\n{\"first\": true}\n```\n```json\n{\"second\": true}\n```",
-            # Code block with extra content
-            "Here's the result:\n```json\n{\"valid\": true}\n```\nDone!",
         ]
 
         for i, response in enumerate(test_cases):
-            try:
+            result = agent_extractor.parse_jsonl(response)
-                result = agent_extractor.parse_json(response)
+            assert len(result) >= 1, f"Case {i} failed"
-                assert result.get("valid") == True or result.get("first") == True
+            assert result[0].get("entity") == "A"
-            except json.JSONDecodeError:
-                # Some cases may fail due to regex extraction issues
-                # This documents current behavior - the regex may not match all cases
-                print(f"Case {i} failed JSON parsing: {response[:50]}...")
-                pass
 
-    def test_parse_json_malformed_code_blocks(self, agent_extractor):
+    def test_parse_jsonl_truncation_resilience(self, agent_extractor):
-        """Test JSON parsing with malformed code block formats"""
+        """Test JSONL parsing with truncated responses"""
-        # These should still work by falling back to treating entire text as JSON
+        # Simulates LLM output being cut off mid-line
-        test_cases = [
+        response = '''{"type": "definition", "entity": "Complete1", "definition": "Full definition"}
-            # Unclosed code block
+{"type": "definition", "entity": "Complete2", "definition": "Another full def"}
-            "```json\n{\"test\": true}",
+{"type": "definition", "entity": "Trunca'''
-            # No opening backticks
-            "{\"test\": true}\n```",
-            # Wrong number of backticks
-            "`json\n{\"test\": true}\n`",
-            # Nested backticks (should handle gracefully)
-            "```json\n{\"code\": \"```\", \"test\": true}\n```",
-        ]
 
-        for response in test_cases:
+        result = agent_extractor.parse_jsonl(response)
-            try:
-                result = agent_extractor.parse_json(response)
-                assert "test" in result  # Should successfully parse
-            except json.JSONDecodeError:
-                # This is also acceptable for malformed cases
-                pass
 
-    def test_parse_json_large_responses(self, agent_extractor):
+        # Should get 2 valid objects, the truncated line is skipped
-        """Test JSON parsing with very large responses"""
+        assert len(result) == 2
-        # Create a large JSON structure
+        assert result[0]["entity"] == "Complete1"
-        large_data = {
+        assert result[1]["entity"] == "Complete2"
-            "definitions": [
-                {
-                    "entity": f"Entity {i}",
-                    "definition": f"Definition {i} " + "with more content " * 100
-                }
-                for i in range(100)
-            ],
-            "relationships": [
-                {
-                    "subject": f"Subject {i}",
-                    "predicate": f"predicate_{i}",
-                    "object": f"Object {i}",
-                    "object-entity": i % 2 == 0
-                }
-                for i in range(50)
-            ]
-        }
 
-        large_json_str = json.dumps(large_data)
+    def test_parse_jsonl_large_responses(self, agent_extractor):
-        response = f"```json\n{large_json_str}\n```"
+        """Test JSONL parsing with very large responses"""
+        # Create a large JSONL response
+        lines = []
+        for i in range(100):
+            lines.append(json.dumps({
+                "type": "definition",
+                "entity": f"Entity {i}",
+                "definition": f"Definition {i} " + "with more content " * 100
+            }))
+        for i in range(50):
+            lines.append(json.dumps({
+                "type": "relationship",
+                "subject": f"Subject {i}",
+                "predicate": f"predicate_{i}",
+                "object": f"Object {i}",
+                "object-entity": i % 2 == 0
+            }))
 
-        result = agent_extractor.parse_json(response)
+        response = f"```json\n{chr(10).join(lines)}\n```"
 
-        assert len(result["definitions"]) == 100
+        result = agent_extractor.parse_jsonl(response)
-        assert len(result["relationships"]) == 50
+
-        assert result["definitions"][0]["entity"] == "Entity 0"
+        definitions = [r for r in result if r.get("type") == "definition"]
+        relationships = [r for r in result if r.get("type") == "relationship"]
+
+        assert len(definitions) == 100
+        assert len(relationships) == 50
+        assert definitions[0]["entity"] == "Entity 0"
 
     def test_process_extraction_data_empty_metadata(self, agent_extractor):
         """Test processing with empty or minimal metadata"""
         # Test with None metadata - may not raise AttributeError depending on implementation
         try:
-            triples, contexts = agent_extractor.process_extraction_data(
+            triples, contexts = agent_extractor.process_extraction_data([], None)
-                {"definitions": [], "relationships": []}, 
-                None
-            )
             # If it doesn't raise, check the results
             assert len(triples) == 0
             assert len(contexts) == 0
@@ -202,19 +178,13 @@ class TestAgentKgExtractionEdgeCases:
 
         # Test with metadata without ID
         metadata = Metadata(id=None, metadata=[])
-        triples, contexts = agent_extractor.process_extraction_data(
+        triples, contexts = agent_extractor.process_extraction_data([], metadata)
-            {"definitions": [], "relationships": []},
-            metadata
-        )
         assert len(triples) == 0
         assert len(contexts) == 0
 
         # Test with metadata with empty string ID
         metadata = Metadata(id="", metadata=[])
-        data = {
+        data = [{"type": "definition", "entity": "Test", "definition": "Test def"}]
-            "definitions": [{"entity": "Test", "definition": "Test def"}],
-            "relationships": []
-        }
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
         # Should not create subject-of triples when ID is empty string
@@ -238,13 +208,10 @@ class TestAgentKgExtractionEdgeCases:
             "Parentheses: (test)",
         ]
 
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": entity, "definition": f"Definition for {entity}"}
-                {"entity": entity, "definition": f"Definition for {entity}"}
+            for entity in special_entities
-                for entity in special_entities
+        ]
-            ],
-            "relationships": []
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -263,12 +230,9 @@ class TestAgentKgExtractionEdgeCases:
         # Create very long definition
         long_definition = "This is a very long definition. " * 1000
 
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": "Test Entity", "definition": long_definition}
-                {"entity": "Test Entity", "definition": long_definition}
+        ]
-            ],
-            "relationships": []
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -285,15 +249,12 @@ class TestAgentKgExtractionEdgeCases:
         """Test processing with duplicate entity names"""
         metadata = Metadata(id="doc123", metadata=[])
 
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": "Machine Learning", "definition": "First definition"},
-                {"entity": "Machine Learning", "definition": "First definition"},
+            {"type": "definition", "entity": "Machine Learning", "definition": "Second definition"},  # Duplicate
-                {"entity": "Machine Learning", "definition": "Second definition"},  # Duplicate
+            {"type": "definition", "entity": "AI", "definition": "AI definition"},
-                {"entity": "AI", "definition": "AI definition"},
+            {"type": "definition", "entity": "AI", "definition": "Another AI definition"},  # Duplicate
-                {"entity": "AI", "definition": "Another AI definition"},  # Duplicate
+        ]
-            ],
-            "relationships": []
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -310,18 +271,14 @@ class TestAgentKgExtractionEdgeCases:
         """Test processing with empty strings in data"""
         metadata = Metadata(id="doc123", metadata=[])
 
-        data = {
+        data = [
-            "definitions": [
+            {"type": "definition", "entity": "", "definition": "Definition for empty entity"},
-                {"entity": "", "definition": "Definition for empty entity"},
+            {"type": "definition", "entity": "Valid Entity", "definition": ""},
-                {"entity": "Valid Entity", "definition": ""},
+            {"type": "definition", "entity": "  ", "definition": "   "},  # Whitespace only
-                {"entity": "  ", "definition": "   "},  # Whitespace only
+            {"type": "relationship", "subject": "", "predicate": "test", "object": "test", "object-entity": True},
-            ],
+            {"type": "relationship", "subject": "test", "predicate": "", "object": "test", "object-entity": True},
-            "relationships": [
+            {"type": "relationship", "subject": "test", "predicate": "test", "object": "", "object-entity": True},
-                {"subject": "", "predicate": "test", "object": "test", "object-entity": True},
+        ]
-                {"subject": "test", "predicate": "", "object": "test", "object-entity": True},
-                {"subject": "test", "predicate": "test", "object": "", "object-entity": True},
-            ]
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -336,19 +293,18 @@ class TestAgentKgExtractionEdgeCases:
         """Test processing when definitions contain JSON-like strings"""
         metadata = Metadata(id="doc123", metadata=[])
 
-        data = {
+        data = [
-            "definitions": [
+            {
-                {
+                "type": "definition",
-                    "entity": "JSON Entity",
+                "entity": "JSON Entity",
-                    "definition": 'Definition with JSON: {"key": "value", "nested": {"inner": true}}'
+                "definition": 'Definition with JSON: {"key": "value", "nested": {"inner": true}}'
-                },
+            },
-                {
+            {
-                    "entity": "Array Entity", 
+                "type": "definition",
-                    "definition": 'Contains array: [1, 2, 3, "string"]'
+                "entity": "Array Entity",
-                }
+                "definition": 'Contains array: [1, 2, 3, "string"]'
-            ],
+            }
-            "relationships": []
+        ]
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -361,25 +317,22 @@ class TestAgentKgExtractionEdgeCases:
         """Test processing with various boolean values for object-entity"""
         metadata = Metadata(id="doc123", metadata=[])
 
-        data = {
+        data = [
-            "definitions": [],
+            # Explicit True
-            "relationships": [
+            {"type": "relationship", "subject": "A", "predicate": "rel1", "object": "B", "object-entity": True},
-                # Explicit True
+            # Explicit False
-                {"subject": "A", "predicate": "rel1", "object": "B", "object-entity": True},
+            {"type": "relationship", "subject": "A", "predicate": "rel2", "object": "literal", "object-entity": False},
-                # Explicit False  
+            # Missing object-entity (should default to True based on code)
-                {"subject": "A", "predicate": "rel2", "object": "literal", "object-entity": False},
+            {"type": "relationship", "subject": "A", "predicate": "rel3", "object": "C"},
-                # Missing object-entity (should default to True based on code)
+            # String "true" (should be treated as truthy)
-                {"subject": "A", "predicate": "rel3", "object": "C"},
+            {"type": "relationship", "subject": "A", "predicate": "rel4", "object": "D", "object-entity": "true"},
-                # String "true" (should be treated as truthy)
+            # String "false" (should be treated as truthy in Python)
-                {"subject": "A", "predicate": "rel4", "object": "D", "object-entity": "true"},
+            {"type": "relationship", "subject": "A", "predicate": "rel5", "object": "E", "object-entity": "false"},
-                # String "false" (should be treated as truthy in Python)
+            # Number 0 (falsy)
-                {"subject": "A", "predicate": "rel5", "object": "E", "object-entity": "false"},
+            {"type": "relationship", "subject": "A", "predicate": "rel6", "object": "literal2", "object-entity": 0},
-                # Number 0 (falsy)
+            # Number 1 (truthy)
-                {"subject": "A", "predicate": "rel6", "object": "literal2", "object-entity": 0},
+            {"type": "relationship", "subject": "A", "predicate": "rel7", "object": "F", "object-entity": 1},
-                # Number 1 (truthy)
+        ]
-                {"subject": "A", "predicate": "rel7", "object": "F", "object-entity": 1},
-            ]
-        }
 
         triples, contexts = agent_extractor.process_extraction_data(data, metadata)
 
@@ -438,28 +391,27 @@ class TestAgentKgExtractionEdgeCases:
         """Test performance with large extraction datasets"""
         metadata = Metadata(id="large-doc", metadata=[])
 
-        # Create large dataset
+        # Create large dataset in JSONL format
         num_definitions = 1000
         num_relationships = 2000
 
-        large_data = {
+        large_data = [
-            "definitions": [
+            {
-                {
+                "type": "definition",
-                    "entity": f"Entity_{i:04d}",
+                "entity": f"Entity_{i:04d}",
-                    "definition": f"Definition for entity {i} with some detailed explanation."
+                "definition": f"Definition for entity {i} with some detailed explanation."
-                }
+            }
-                for i in range(num_definitions)
+            for i in range(num_definitions)
-            ],
+        ] + [
-            "relationships": [
+            {
-                {
+                "type": "relationship",
-                    "subject": f"Entity_{i % num_definitions:04d}",
+                "subject": f"Entity_{i % num_definitions:04d}",
-                    "predicate": f"predicate_{i % 10}",
+                "predicate": f"predicate_{i % 10}",
-                    "object": f"Entity_{(i + 1) % num_definitions:04d}",
+                "object": f"Entity_{(i + 1) % num_definitions:04d}",
-                    "object-entity": True
+                "object-entity": True
-                }
+            }
-                for i in range(num_relationships)
+            for i in range(num_relationships)
-            ]
+        ]
-        }
 
         import time
         start_time = time.time()

tests/unit/test_prompt_manager.py

@@ -343,3 +343,246 @@ class TestPromptManager:
         assert pm.config.system_template == "Be helpful."  # Default system
         assert pm.terms == {}  # Default empty terms
         assert len(pm.prompts) == 0
+
+
+@pytest.mark.unit
+class TestPromptManagerJsonl:
+    """Unit tests for PromptManager JSONL functionality"""
+
+    @pytest.fixture
+    def jsonl_config(self):
+        """Configuration with JSONL response type prompts"""
+        return {
+            "system": json.dumps("You are an extraction assistant."),
+            "template-index": json.dumps(["extract_simple", "extract_with_schema", "extract_mixed"]),
+            "template.extract_simple": json.dumps({
+                "prompt": "Extract entities from: {{ text }}",
+                "response-type": "jsonl"
+            }),
+            "template.extract_with_schema": json.dumps({
+                "prompt": "Extract definitions from: {{ text }}",
+                "response-type": "jsonl",
+                "schema": {
+                    "type": "object",
+                    "properties": {
+                        "entity": {"type": "string"},
+                        "definition": {"type": "string"}
+                    },
+                    "required": ["entity", "definition"]
+                }
+            }),
+            "template.extract_mixed": json.dumps({
+                "prompt": "Extract knowledge from: {{ text }}",
+                "response-type": "jsonl",
+                "schema": {
+                    "oneOf": [
+                        {
+                            "type": "object",
+                            "properties": {
+                                "type": {"const": "definition"},
+                                "entity": {"type": "string"},
+                                "definition": {"type": "string"}
+                            },
+                            "required": ["type", "entity", "definition"]
+                        },
+                        {
+                            "type": "object",
+                            "properties": {
+                                "type": {"const": "relationship"},
+                                "subject": {"type": "string"},
+                                "predicate": {"type": "string"},
+                                "object": {"type": "string"}
+                            },
+                            "required": ["type", "subject", "predicate", "object"]
+                        }
+                    ]
+                }
+            })
+        }
+
+    @pytest.fixture
+    def prompt_manager(self, jsonl_config):
+        """Create a PromptManager with JSONL configuration"""
+        pm = PromptManager()
+        pm.load_config(jsonl_config)
+        return pm
+
+    def test_parse_jsonl_basic(self, prompt_manager):
+        """Test basic JSONL parsing"""
+        text = '{"entity": "cat", "definition": "A small furry animal"}\n{"entity": "dog", "definition": "A loyal pet"}'
+
+        result = prompt_manager.parse_jsonl(text)
+
+        assert len(result) == 2
+        assert result[0]["entity"] == "cat"
+        assert result[1]["entity"] == "dog"
+
+    def test_parse_jsonl_with_empty_lines(self, prompt_manager):
+        """Test JSONL parsing skips empty lines"""
+        text = '{"entity": "cat"}\n\n\n{"entity": "dog"}\n'
+
+        result = prompt_manager.parse_jsonl(text)
+
+        assert len(result) == 2
+
+    def test_parse_jsonl_with_markdown_fences(self, prompt_manager):
+        """Test JSONL parsing strips markdown code fences"""
+        text = '''```json
+{"entity": "cat", "definition": "A furry animal"}
+{"entity": "dog", "definition": "A loyal pet"}
+```'''
+
+        result = prompt_manager.parse_jsonl(text)
+
+        assert len(result) == 2
+        assert result[0]["entity"] == "cat"
+        assert result[1]["entity"] == "dog"
+
+    def test_parse_jsonl_with_jsonl_fence(self, prompt_manager):
+        """Test JSONL parsing strips jsonl-marked code fences"""
+        text = '''```jsonl
+{"entity": "cat"}
+{"entity": "dog"}
+```'''
+
+        result = prompt_manager.parse_jsonl(text)
+
+        assert len(result) == 2
+
+    def test_parse_jsonl_truncation_resilience(self, prompt_manager):
+        """Test JSONL parsing handles truncated final line"""
+        text = '{"entity": "cat", "definition": "Complete"}\n{"entity": "dog", "defi'
+
+        result = prompt_manager.parse_jsonl(text)
+
+        # Should get the first valid object, skip the truncated one
+        assert len(result) == 1
+        assert result[0]["entity"] == "cat"
+
+    def test_parse_jsonl_invalid_lines_skipped(self, prompt_manager):
+        """Test JSONL parsing skips invalid JSON lines"""
+        text = '''{"entity": "valid1"}
+not json at all
+{"entity": "valid2"}
+{broken json
+{"entity": "valid3"}'''
+
+        result = prompt_manager.parse_jsonl(text)
+
+        assert len(result) == 3
+        assert result[0]["entity"] == "valid1"
+        assert result[1]["entity"] == "valid2"
+        assert result[2]["entity"] == "valid3"
+
+    def test_parse_jsonl_empty_input(self, prompt_manager):
+        """Test JSONL parsing with empty input"""
+        result = prompt_manager.parse_jsonl("")
+        assert result == []
+
+        result = prompt_manager.parse_jsonl("\n\n\n")
+        assert result == []
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_response(self, prompt_manager):
+        """Test invoking a prompt with JSONL response"""
+        mock_llm = AsyncMock()
+        mock_llm.return_value = '{"entity": "photosynthesis", "definition": "Plant process"}\n{"entity": "mitosis", "definition": "Cell division"}'
+
+        result = await prompt_manager.invoke(
+            "extract_simple",
+            {"text": "Biology text"},
+            mock_llm
+        )
+
+        assert isinstance(result, list)
+        assert len(result) == 2
+        assert result[0]["entity"] == "photosynthesis"
+        assert result[1]["entity"] == "mitosis"
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_with_schema_validation(self, prompt_manager):
+        """Test JSONL response with schema validation"""
+        mock_llm = AsyncMock()
+        mock_llm.return_value = '{"entity": "cat", "definition": "A pet"}\n{"entity": "dog", "definition": "Another pet"}'
+
+        result = await prompt_manager.invoke(
+            "extract_with_schema",
+            {"text": "Animal text"},
+            mock_llm
+        )
+
+        assert len(result) == 2
+        assert all("entity" in obj and "definition" in obj for obj in result)
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_schema_filters_invalid(self, prompt_manager):
+        """Test JSONL schema validation filters out invalid objects"""
+        mock_llm = AsyncMock()
+        # Second object is missing required 'definition' field
+        mock_llm.return_value = '{"entity": "valid", "definition": "Has both fields"}\n{"entity": "invalid_missing_definition"}\n{"entity": "also_valid", "definition": "Complete"}'
+
+        result = await prompt_manager.invoke(
+            "extract_with_schema",
+            {"text": "Test text"},
+            mock_llm
+        )
+
+        # Only the two valid objects should be returned
+        assert len(result) == 2
+        assert result[0]["entity"] == "valid"
+        assert result[1]["entity"] == "also_valid"
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_mixed_types(self, prompt_manager):
+        """Test JSONL with discriminated union schema (oneOf)"""
+        mock_llm = AsyncMock()
+        mock_llm.return_value = '''{"type": "definition", "entity": "DNA", "definition": "Genetic material"}
+{"type": "relationship", "subject": "DNA", "predicate": "found_in", "object": "nucleus"}
+{"type": "definition", "entity": "RNA", "definition": "Messenger molecule"}'''
+
+        result = await prompt_manager.invoke(
+            "extract_mixed",
+            {"text": "Biology text"},
+            mock_llm
+        )
+
+        assert len(result) == 3
+
+        # Check definitions
+        definitions = [r for r in result if r.get("type") == "definition"]
+        assert len(definitions) == 2
+
+        # Check relationships
+        relationships = [r for r in result if r.get("type") == "relationship"]
+        assert len(relationships) == 1
+        assert relationships[0]["subject"] == "DNA"
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_empty_result(self, prompt_manager):
+        """Test JSONL response that yields no valid objects"""
+        mock_llm = AsyncMock()
+        mock_llm.return_value = "No JSON here at all"
+
+        result = await prompt_manager.invoke(
+            "extract_simple",
+            {"text": "Test"},
+            mock_llm
+        )
+
+        assert result == []
+
+    @pytest.mark.asyncio
+    async def test_invoke_jsonl_without_schema(self, prompt_manager):
+        """Test JSONL response without schema validation"""
+        mock_llm = AsyncMock()
+        mock_llm.return_value = '{"any": "structure"}\n{"completely": "different"}'
+
+        result = await prompt_manager.invoke(
+            "extract_simple",
+            {"text": "Test"},
+            mock_llm
+        )
+
+        assert len(result) == 2
+        assert result[0] == {"any": "structure"}
+        assert result[1] == {"completely": "different"}

trustgraph-flow/trustgraph/extract/kg/agent/extract.py

@@ -126,16 +126,42 @@ class Processor(FlowProcessor):
 
         await pub.send(ecs)
 
-    def parse_json(self, text):
+    def parse_jsonl(self, text):
-        json_match = re.search(r'```(?:json)?(.*?)```', text, re.DOTALL)
+        """
+        Parse JSONL response, returning list of valid objects.
 
-        if json_match:
+        Invalid lines (malformed JSON, empty lines) are skipped with warnings.
-            json_str = json_match.group(1).strip()
+        This provides truncation resilience - partial output yields partial results.
-        else:
+        """
-            # If no delimiters, assume the entire output is JSON
+        results = []
-            json_str = text.strip()
 
-        return json.loads(json_str)
+        # Strip markdown code fences if present
+        text = text.strip()
+        if text.startswith('```'):
+            # Remove opening fence (possibly with language hint)
+            text = re.sub(r'^```(?:json|jsonl)?\s*\n?', '', text)
+        if text.endswith('```'):
+            text = text[:-3]
+
+        for line_num, line in enumerate(text.strip().split('\n'), 1):
+            line = line.strip()
+
+            # Skip empty lines
+            if not line:
+                continue
+
+            # Skip any remaining fence markers
+            if line.startswith('```'):
+                continue
+
+            try:
+                obj = json.loads(line)
+                results.append(obj)
+            except json.JSONDecodeError as e:
+                # Log warning but continue - this provides truncation resilience
+                logger.warning(f"JSONL parse error on line {line_num}: {e}")
+
+        return results
 
     async def on_message(self, msg, consumer, flow):
 
@@ -178,11 +204,12 @@ class Processor(FlowProcessor):
                 question = prompt
             )
             
-            # Parse JSON response
+            # Parse JSONL response
-            try:
+            extraction_data = self.parse_jsonl(agent_response)
-                extraction_data = self.parse_json(agent_response)
+
-            except json.JSONDecodeError as e:
+            if not extraction_data:
-                raise ValueError(f"Invalid JSON response from agent: {e}")
+                logger.warning("JSONL parse returned no valid objects")
+                return
             
             # Process extraction data
             triples, entity_contexts = self.process_extraction_data(
@@ -209,12 +236,21 @@ class Processor(FlowProcessor):
             raise
 
     def process_extraction_data(self, data, metadata):
-        """Process combined extraction data to generate triples and entity contexts"""
+        """Process JSONL extraction data to generate triples and entity contexts.
+
+        Data is a flat list of objects with 'type' discriminator field:
+        - {"type": "definition", "entity": "...", "definition": "..."}
+        - {"type": "relationship", "subject": "...", "predicate": "...", "object": "...", "object-entity": bool}
+        """
         triples = []
         entity_contexts = []
 
+        # Categorize items by type
+        definitions = [item for item in data if item.get("type") == "definition"]
+        relationships = [item for item in data if item.get("type") == "relationship"]
+
         # Process definitions
-        for defn in data.get("definitions", []):
+        for defn in definitions:
 
             entity_uri = self.to_uri(defn["entity"])
             
@@ -247,17 +283,18 @@ class Processor(FlowProcessor):
             ))
         
         # Process relationships
-        for rel in data.get("relationships", []):
+        for rel in relationships:
 
             subject_uri = self.to_uri(rel["subject"])
             predicate_uri = self.to_uri(rel["predicate"])
 
             subject_value = Value(value=subject_uri, is_uri=True)
             predicate_value = Value(value=predicate_uri, is_uri=True)
-            if data.get("object-entity", False):
+            if rel.get("object-entity", True):
-                object_value = Value(value=predicate_uri, is_uri=True)
+                object_uri = self.to_uri(rel["object"])
+                object_value = Value(value=object_uri, is_uri=True)
             else:
-                object_value = Value(value=predicate_uri, is_uri=False)
+                object_value = Value(value=rel["object"], is_uri=False)
             
             # Add subject and predicate labels
             triples.append(Triple(

trustgraph-flow/trustgraph/extract/kg/ontology/simplified_parser.py

@@ -49,8 +49,17 @@ class ExtractionResult:
 def parse_extraction_response(response: Any) -> Optional[ExtractionResult]:
     """Parse LLM extraction response into structured format.
 
+    Supports two formats:
+    1. JSONL format (list): Flat list of objects with 'type' discriminator field
+       [{"type": "entity", ...}, {"type": "relationship", ...}, {"type": "attribute", ...}]
+    2. Legacy format (dict): Nested structure with separate arrays
+       {"entities": [...], "relationships": [...], "attributes": [...]}
+
     Args:
-        response: LLM response (string JSON or already parsed dict)
+        response: LLM response - can be:
+            - string (JSON to parse)
+            - dict (legacy nested format)
+            - list (JSONL format - flat list with type discriminators)
 
     Returns:
         ExtractionResult with parsed entities/relationships/attributes,
@@ -64,17 +73,89 @@ def parse_extraction_response(response: Any) -> Optional[ExtractionResult]:
             logger.error(f"Failed to parse JSON response: {e}")
             logger.debug(f"Response was: {response[:500]}")
             return None
-    elif isinstance(response, dict):
+    elif isinstance(response, (dict, list)):
         data = response
     else:
         logger.error(f"Unexpected response type: {type(response)}")
         return None
 
-    # Validate structure
+    # Handle JSONL format (flat list with type discriminators)
-    if not isinstance(data, dict):
+    if isinstance(data, list):
-        logger.error(f"Expected dict, got {type(data)}")
+        return parse_jsonl_format(data)
-        return None
 
+    # Handle legacy format (nested dict)
+    if isinstance(data, dict):
+        return parse_legacy_format(data)
+
+    logger.error(f"Expected dict or list, got {type(data)}")
+    return None
+
+
+def parse_jsonl_format(data: List[Dict[str, Any]]) -> ExtractionResult:
+    """Parse JSONL format response (flat list with type discriminators).
+
+    Each item has a 'type' field: 'entity', 'relationship', or 'attribute'.
+
+    Args:
+        data: List of dicts with type discriminator
+
+    Returns:
+        ExtractionResult with categorized items
+    """
+    entities = []
+    relationships = []
+    attributes = []
+
+    for item in data:
+        if not isinstance(item, dict):
+            logger.warning(f"Skipping non-dict item: {type(item)}")
+            continue
+
+        item_type = item.get('type')
+
+        if item_type == 'entity':
+            try:
+                entity = parse_entity_jsonl(item)
+                if entity:
+                    entities.append(entity)
+            except Exception as e:
+                logger.warning(f"Failed to parse entity {item}: {e}")
+
+        elif item_type == 'relationship':
+            try:
+                relationship = parse_relationship(item)
+                if relationship:
+                    relationships.append(relationship)
+            except Exception as e:
+                logger.warning(f"Failed to parse relationship {item}: {e}")
+
+        elif item_type == 'attribute':
+            try:
+                attribute = parse_attribute(item)
+                if attribute:
+                    attributes.append(attribute)
+            except Exception as e:
+                logger.warning(f"Failed to parse attribute {item}: {e}")
+
+        else:
+            logger.warning(f"Unknown item type '{item_type}': {item}")
+
+    return ExtractionResult(
+        entities=entities,
+        relationships=relationships,
+        attributes=attributes
+    )
+
+
+def parse_legacy_format(data: Dict[str, Any]) -> ExtractionResult:
+    """Parse legacy format response (nested dict with arrays).
+
+    Args:
+        data: Dict with 'entities', 'relationships', 'attributes' arrays
+
+    Returns:
+        ExtractionResult with parsed items
+    """
     # Parse entities
     entities = []
     entities_data = data.get('entities', [])
@@ -127,6 +208,37 @@ def parse_extraction_response(response: Any) -> Optional[ExtractionResult]:
     )
 
 
+def parse_entity_jsonl(data: Dict[str, Any]) -> Optional[Entity]:
+    """Parse entity from JSONL format dict.
+
+    JSONL format uses 'entity_type' instead of 'type' for the entity's type
+    (since 'type' is the discriminator field).
+
+    Args:
+        data: Entity dict with 'entity' and 'entity_type' fields
+
+    Returns:
+        Entity object or None if invalid
+    """
+    if not isinstance(data, dict):
+        logger.warning(f"Entity data is not a dict: {type(data)}")
+        return None
+
+    entity = data.get('entity')
+    # JSONL format uses 'entity_type' since 'type' is the discriminator
+    entity_type = data.get('entity_type')
+
+    if not entity or not entity_type:
+        logger.warning(f"Missing required fields in entity: {data}")
+        return None
+
+    if not isinstance(entity, str) or not isinstance(entity_type, str):
+        logger.warning(f"Entity fields must be strings: {data}")
+        return None
+
+    return Entity(entity=entity, type=entity_type)
+
+
 def parse_entity(data: Dict[str, Any]) -> Optional[Entity]:
     """Parse entity from dict.
 

trustgraph-flow/trustgraph/template/prompt_manager.py

@@ -92,6 +92,43 @@ class PromptManager:
 
         return json.loads(json_str)
 
+    def parse_jsonl(self, text):
+        """
+        Parse JSONL response, returning list of valid objects.
+
+        Invalid lines (malformed JSON, empty lines) are skipped with warnings.
+        This provides truncation resilience - partial output yields partial results.
+        """
+        results = []
+
+        # Strip markdown code fences if present
+        text = text.strip()
+        if text.startswith('```'):
+            # Remove opening fence (possibly with language hint)
+            text = re.sub(r'^```(?:json|jsonl)?\s*\n?', '', text)
+        if text.endswith('```'):
+            text = text[:-3]
+
+        for line_num, line in enumerate(text.strip().split('\n'), 1):
+            line = line.strip()
+
+            # Skip empty lines
+            if not line:
+                continue
+
+            # Skip any remaining fence markers
+            if line.startswith('```'):
+                continue
+
+            try:
+                obj = json.loads(line)
+                results.append(obj)
+            except json.JSONDecodeError as e:
+                # Log warning but continue - this provides truncation resilience
+                logger.warning(f"JSONL parse error on line {line_num}: {e}")
+
+        return results
+
     def render(self, id, input):
 
         if id not in self.prompts:
@@ -121,21 +158,41 @@ class PromptManager:
         if resp_type == "text":
             return resp
 
-        if resp_type != "json":
+        if resp_type == "json":
-            raise RuntimeError(f"Response type {resp_type} not known")
-
-        try:
-            obj = self.parse_json(resp)
-        except:
-            logger.error(f"JSON parse failed: {resp}")
-            raise RuntimeError("JSON parse fail")
-
-        if self.prompts[id].schema:
             try:
-                validate(instance=obj, schema=self.prompts[id].schema)
+                obj = self.parse_json(resp)
-                logger.debug("Schema validation successful")
+            except:
-            except Exception as e:
+                logger.error(f"JSON parse failed: {resp}")
-                raise RuntimeError(f"Schema validation fail: {e}")
+                raise RuntimeError("JSON parse fail")
 
-        return obj
+            if self.prompts[id].schema:
+                try:
+                    validate(instance=obj, schema=self.prompts[id].schema)
+                    logger.debug("Schema validation successful")
+                except Exception as e:
+                    raise RuntimeError(f"Schema validation fail: {e}")
+
+            return obj
+
+        if resp_type == "jsonl":
+            objects = self.parse_jsonl(resp)
+
+            if not objects:
+                logger.warning("JSONL parse returned no valid objects")
+                return []
+
+            # Validate each object against schema if provided
+            if self.prompts[id].schema:
+                validated = []
+                for i, obj in enumerate(objects):
+                    try:
+                        validate(instance=obj, schema=self.prompts[id].schema)
+                        validated.append(obj)
+                    except Exception as e:
+                        logger.warning(f"Object {i} failed schema validation: {e}")
+                return validated
+
+            return objects
+
+        raise RuntimeError(f"Response type {resp_type} not known")