[Question]: Set id property of EntityNode in PropertyGraphIndex

[bldev2473]

Question Validation

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Question

Hi, I'm using PropertyGraphIndex and SchemaLLMPathExtractor to build a kg with Neo4j using an LLM.
After constructing the index and knowledge graph, I noticed that the 'id' and 'name' properties of the generated EntityNodes are identical. I'd like to set the 'id' of each EntityNode to a UUID or another unique key.

My requirement is that one or more entities should be generated with the same name but different values for other properties.

I tried to set the metadata of the document with "id" key, but following error occurred.

neo4j.exceptions.ConstraintError: {code: Neo.ClientError.Schema.ConstraintValidationFailed} {message: Node(34) already exists with label Nodeand propertyid= '142033'}
Is there a solution for this?
Thank you.

[dosubot]

Hey @bldev2473! I'm here to help you with your Neo4j issue. Let's work together to solve this!

To set the 'id' property of each EntityNode to a UUID or another unique key in PropertyGraphIndex when using Neo4j, you can modify the upsert_triplet method to generate a UUID for each node if it doesn't already have a unique 'id'. Here's a code snippet to help you achieve this:

import uuid

def upsert_triplet(self, subj: str, rel: str, obj: str) -> None:
    """Add triplet with unique UUIDs for nodes."""
    # Generate UUIDs if 'subj' or 'obj' are not provided
    subj_id = subj if subj else str(uuid.uuid4())
    obj_id = obj if obj else str(uuid.uuid4())

    query = """
        MERGE (n1:`%s` {id:$subj_id})
        MERGE (n2:`%s` {id:$obj_id})
        MERGE (n1)-[:`%s`]->(n2)
    """

    prepared_statement = query % (
        self.node_label,
        self.node_label,
        rel.replace(" ", "_").upper(),
    )

    with self._driver.session(database=self._database) as session:
        session.run(prepared_statement, {"subj_id": subj_id, "obj_id": obj_id})

This modification ensures that each node has a unique identifier by using UUIDs, which should help you avoid the ConstraintError due to duplicate 'id' values ^[1].

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[bldev2473]

@dosu, Neo4jPropertyGraphStore has no upsert_triplet method. Should i modify upsert_nodes?

[dosubot]

Yes, you should modify the upsert_nodes method in the Neo4jPropertyGraphStore class to set the 'id' property of each EntityNode to a UUID or another unique key. You can generate a UUID for each node if it doesn't already have a unique 'id'. Here's an example of how you might modify the method:

import uuid

def upsert_nodes(self, nodes: List[LabelledNode]) -> None:
    entity_dicts: List[dict] = []
    chunk_dicts: List[dict] = []

    for item in nodes:
        if isinstance(item, EntityNode):
            # Generate a UUID if the id is not provided
            item_id = item.id if item.id else str(uuid.uuid4())
            entity_dicts.append({**item.dict(), "id": item_id})
        elif isinstance(item, ChunkNode):
            chunk_dicts.append({**item.dict(), "id": item.id})
        else:
            pass

    if chunk_dicts:
        for d in chunk_dicts:
            self.structured_query(
                """
                WITH $data AS row
                MERGE (c:Chunk {id: row.id})
                SET c.text = row.text
                SET c += removeKeyFromMap(row.properties, '')
                RETURN count(*)
                """,
                param_map={"data": d},
            )
    if entity_dicts:
        for d in entity_dicts:
            self.structured_query(
                f"""
                WITH $data AS row
                MERGE (e:`{BASE_NODE_LABEL}` {{id: row.id}})
                SET e += removeKeyFromMap(row.properties, '')
                SET e.name = row.name, e:`{BASE_ENTITY_LABEL}`
                SET e:`{d['label']}`
                WITH e, row
                WHERE removeKeyFromMap(row.properties, '').triplet_source_id IS NOT NULL
                MERGE (c:Chunk {{id: removeKeyFromMap(row.properties, '').triplet_source_id}})
                MERGE (e)<-[:MENTIONS]-(c)
                RETURN count(*) as count
                """,
                param_map={"data": d},
            )

This modification ensures that each EntityNode has a unique identifier by using UUIDs, which should help you avoid the ConstraintError due to duplicate 'id' values.

To continue talking to Dosu, mention @dosu.

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[bldev2473]

@dosu, modification you suggested can change id of EntityNode. However, this could cause issues with establishing the relationships between EntityNodes.

Therefore, the 'id' change should be processed within the _insert_nodes method of the PropertyGraphIndex class.

[dosubot]

To address the issue of setting unique IDs for EntityNode objects while maintaining their relationships, you can modify the _insert_nodes method in the PropertyGraphIndex class. This approach ensures that the unique ID assignment happens before the nodes are inserted into the graph, preserving the relationships. Here's how you can adjust the method:

1. Generate a UUID for each node if it doesn't already have a unique 'id'.
2. Ensure that the relationships are established using these unique IDs.

Here's a code snippet to illustrate this:

import uuid

def _insert_nodes(self, nodes: Sequence[BaseNode]) -> Sequence[BaseNode]:
    """Insert nodes to the index struct with unique IDs."""
    if len(nodes) == 0:
        return nodes

    # Run transformations on nodes to extract triplets
    if self._use_async:
        nodes = asyncio.run(
            arun_transformations(
                nodes, self._kg_extractors, show_progress=self._show_progress
            )
        )
    else:
        nodes = run_transformations(
            nodes, self._kg_extractors, show_progress=self._show_progress
        )

    # Ensure all nodes have nodes and/or relations in metadata
    assert all(
        node.metadata.get(KG_NODES_KEY) is not None
        or node.metadata.get(KG_RELATIONS_KEY) is not None
        for node in nodes
    )

    kg_nodes_to_insert: List[LabelledNode] = []
    kg_rels_to_insert: List[Relation] = []
    for node in nodes:
        # Generate a UUID if the id is not provided
        node.id_ = node.id_ if node.id_ else str(uuid.uuid4())

        # Remove nodes and relations from metadata
        kg_nodes = node.metadata.pop(KG_NODES_KEY, [])
        kg_rels = node.metadata.pop(KG_RELATIONS_KEY, [])

        # Add source id to properties
        for kg_node in kg_nodes:
            kg_node.properties[TRIPLET_SOURCE_KEY] = node.id_
        for kg_rel in kg_rels:
            kg_rel.properties[TRIPLET_SOURCE_KEY] = node.id_

        # Add nodes and relations to insert lists
        kg_nodes_to_insert.extend(kg_nodes)
        kg_rels_to_insert.extend(kg_rels)

    # Filter out duplicate kg nodes
    kg_node_ids = {node.id for node in kg_nodes_to_insert}
    existing_kg_nodes = self.property_graph_store.get(ids=list(kg_node_ids))
    existing_kg_node_ids = {node.id for node in existing_kg_nodes}
    kg_nodes_to_insert = [
        node for node in kg_nodes_to_insert if node.id not in existing_kg_node_ids
    ]

    # Upsert nodes and relations
    if len(kg_nodes_to_insert) > 0:
        self.property_graph_store.upsert_nodes(kg_nodes_to_insert)

    if len(kg_rels_to_insert) > 0:
        self.property_graph_store.upsert_relations(kg_rels_to_insert)

    return nodes

This modification ensures that each EntityNode has a unique identifier by using UUIDs, which should help maintain the integrity of relationships between nodes ^[1].

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[bldev2473]

@dosu, That approach is insufficient because the source_id and target_id of the Relation also need to be updated. Where are Relations initially created within the PropertyGraphIndex?

[dosubot]

Relations are initially created within the PropertyGraphIndex by using the add_relation method of the LabelledPropertyGraph class. This method ensures that both source_id and target_id of the Relation are updated by checking if they exist in the nodes dictionary and adding them if they do not. It then adds the relation by calling the add_triplet method, which updates the triplets, nodes, and relations data structures ^[1].

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