fix: Improve edge extraction entity ID validation (#968)

* fix: Improve edge extraction entity ID validation

Fixes invalid entity ID references in edge extraction that caused warnings like:
"WARNING: source or target node not filled WILL_FIND. source_node_uuid: 23 and target_node_uuid: 3"

Changes:
- Format ENTITIES list as proper JSON in prompt for better LLM parsing
- Clarify field descriptions to reference entity id from ENTITIES list
- Add explicit entity ID validation as #1 extraction rule with examples
- Improve error logging (removed PII, added entity count and valid range)

These changes follow patterns from extract_nodes.py and dedupe_nodes.py where
entity referencing works reliably.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* wip

* fix: Align fact field naming and add description

- Change extraction rule to reference 'fact' instead of 'fact_text'
- Add descriptive text for fact field in Edge model

* fix: Remove ensure_ascii parameter from to_prompt_json call

Align with other to_prompt_json calls that don't use ensure_ascii

* fix: Use validated target_node_idx variable consistently

Line 190 was using raw edge_data.target_entity_id instead of the
validated target_node_idx variable, creating inconsistency with line 189

* fix: Improve edge extraction validation checks

- Add explicit check for empty nodes list
- Use more explicit 0 <= idx comparison instead of -1 < idx
- Prevents nonsensical error message when no entities provided

* chore: Restore uv.lock from main branch

Previously deleted in commit 7e4464b, now restored to match main branch state

* Update uv.lock

---------

Co-authored-by: Claude <noreply@anthropic.com>

graphiti_core/prompts/extract_edges.py

@@ -24,9 +24,16 @@ from .prompt_helpers import to_prompt_json
 
 class Edge(BaseModel):
     relation_type: str = Field(..., description='FACT_PREDICATE_IN_SCREAMING_SNAKE_CASE')
-    source_entity_id: int = Field(..., description='The id of the source entity of the fact.')
-    target_entity_id: int = Field(..., description='The id of the target entity of the fact.')
-    fact: str = Field(..., description='')
+    source_entity_id: int = Field(
+        ..., description='The id of the source entity from the ENTITIES list'
+    )
+    target_entity_id: int = Field(
+        ..., description='The id of the target entity from the ENTITIES list'
+    )
+    fact: str = Field(
+        ...,
+        description='A natural language description of the relationship between the entities, paraphrased from the source text',
+    )
     valid_at: str | None = Field(
         None,
         description='The date and time when the relationship described by the edge fact became true or was established. Use ISO 8601 format (YYYY-MM-DDTHH:MM:SS.SSSSSSZ)',
@@ -81,7 +88,7 @@ def edge(context: dict[str, Any]) -> list[Message]:
 </CURRENT_MESSAGE>
 
 <ENTITIES>
-{context['nodes']} 
+{to_prompt_json(context['nodes'], indent=2)}
 </ENTITIES>
 
 <REFERENCE_TIME>
@@ -107,11 +114,12 @@ You may use information from the PREVIOUS MESSAGES only to disambiguate referenc
 
 # EXTRACTION RULES
 
-1. Only emit facts where both the subject and object match IDs in ENTITIES.
+1. **Entity ID Validation**: `source_entity_id` and `target_entity_id` must use only the `id` values from the ENTITIES list provided above.
+   - **CRITICAL**: Using IDs not in the list will cause the edge to be rejected
 2. Each fact must involve two **distinct** entities.
 3. Use a SCREAMING_SNAKE_CASE string as the `relation_type` (e.g., FOUNDED, WORKS_AT).
 4. Do not emit duplicate or semantically redundant facts.
-5. The `fact_text` should closely paraphrase the original source sentence(s). Do not verbatim quote the original text.
+5. The `fact` should closely paraphrase the original source sentence(s). Do not verbatim quote the original text.
 6. Use `REFERENCE_TIME` to resolve vague or relative temporal expressions (e.g., "last week").
 7. Do **not** hallucinate or infer temporal bounds from unrelated events.
 

graphiti_core/utils/maintenance/edge_operations.py

@@ -179,13 +179,20 @@ async def extract_edges(
 
         source_node_idx = edge_data.source_entity_id
         target_node_idx = edge_data.target_entity_id
-        if not (-1 < source_node_idx < len(nodes) and -1 < target_node_idx < len(nodes)):
+
+        if len(nodes) == 0:
+            logger.warning('No entities provided for edge extraction')
+            continue
+
+        if not (0 <= source_node_idx < len(nodes) and 0 <= target_node_idx < len(nodes)):
             logger.warning(
-                f'WARNING: source or target node not filled {edge_data.relation_type}. source_node_uuid: {source_node_idx} and target_node_uuid: {target_node_idx} '
+                f'Invalid entity IDs in edge extraction for {edge_data.relation_type}. '
+                f'source_entity_id: {source_node_idx}, target_entity_id: {target_node_idx}, '
+                f'but only {len(nodes)} entities available (valid range: 0-{len(nodes) - 1})'
             )
             continue
         source_node_uuid = nodes[source_node_idx].uuid
-        target_node_uuid = nodes[edge_data.target_entity_id].uuid
+        target_node_uuid = nodes[target_node_idx].uuid
 
         if valid_at:
             try:

uv.lock

@@ -803,7 +803,6 @@ anthropic = [
 ]
 dev = [
     { name = "anthropic" },
-    { name = "boto3" },
     { name = "diskcache-stubs" },
     { name = "falkordb" },
     { name = "google-genai" },
@@ -812,11 +811,9 @@ dev = [
     { name = "jupyterlab" },
     { name = "kuzu" },
     { name = "langchain-anthropic" },
-    { name = "langchain-aws" },
     { name = "langchain-openai" },
     { name = "langgraph" },
     { name = "langsmith" },
-    { name = "opensearch-py" },
     { name = "pyright" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
@@ -858,7 +855,6 @@ voyageai = [
 requires-dist = [
     { name = "anthropic", marker = "extra == 'anthropic'", specifier = ">=0.49.0" },
     { name = "anthropic", marker = "extra == 'dev'", specifier = ">=0.49.0" },
-    { name = "boto3", marker = "extra == 'dev'", specifier = ">=1.39.16" },
     { name = "boto3", marker = "extra == 'neo4j-opensearch'", specifier = ">=1.39.16" },
     { name = "boto3", marker = "extra == 'neptune'", specifier = ">=1.39.16" },
     { name = "diskcache", specifier = ">=5.6.3" },
@@ -874,7 +870,6 @@ requires-dist = [
     { name = "kuzu", marker = "extra == 'dev'", specifier = ">=0.11.2" },
     { name = "kuzu", marker = "extra == 'kuzu'", specifier = ">=0.11.2" },
     { name = "langchain-anthropic", marker = "extra == 'dev'", specifier = ">=0.2.4" },
-    { name = "langchain-aws", marker = "extra == 'dev'", specifier = ">=0.2.29" },
     { name = "langchain-aws", marker = "extra == 'neptune'", specifier = ">=0.2.29" },
     { name = "langchain-openai", marker = "extra == 'dev'", specifier = ">=0.2.6" },
     { name = "langgraph", marker = "extra == 'dev'", specifier = ">=0.2.15" },
@@ -882,7 +877,6 @@ requires-dist = [
     { name = "neo4j", specifier = ">=5.26.0" },
     { name = "numpy", specifier = ">=1.0.0" },
     { name = "openai", specifier = ">=1.91.0" },
-    { name = "opensearch-py", marker = "extra == 'dev'", specifier = ">=3.0.0" },
     { name = "opensearch-py", marker = "extra == 'neo4j-opensearch'", specifier = ">=3.0.0" },
     { name = "opensearch-py", marker = "extra == 'neptune'", specifier = ">=3.0.0" },
     { name = "posthog", specifier = ">=3.0.0" },