Testing & Cleanup¶

Between tests you can clean up data using the cleanup script or per-database commands.

cleanup.py — One-Step Cleanup¶

The cleanup.py script clears vector, graph, and search indexes in a single command. Run it from the flexible-graphrag directory:

cd flexible-graphrag
python cleanup.py

This will clear all configured databases (vector, property graph, search) in one step.

Vector Database Cleanup¶

When switching embedding models, you must delete existing vector indexes due to dimension incompatibility. See Vector Dimensions for per-database cleanup instructions.

Graph Database Cleanup¶

For graph-related cleanup commands, see Neo4j Setup.

ArcadeDB Cleanup¶

The cleanup.py script includes ArcadeDB-specific handling — it directly connects via arcadedb_python, queries schema types, and issues DELETE FROM <type> statements (avoiding index-already-exists errors from the LlamaIndex factory).

RDF Store Cleanup¶

Use scripts/rdf_cleanup.py to manage RDF store data:

# List ingested documents and triple counts
python scripts/rdf_cleanup.py list-docs

# Show total triple count in named graph
python scripts/rdf_cleanup.py count

# Delete all triples for a specific document
python scripts/rdf_cleanup.py clear-doc <ref_doc_id>

# Wipe entire named graph (with confirmation)
python scripts/rdf_cleanup.py clear-all --yes

# Target a specific store
python scripts/rdf_cleanup.py list-docs --fuseki
python scripts/rdf_cleanup.py list-docs --graphdb
python scripts/rdf_cleanup.py list-docs --oxigraph

BM25 Index Cleanup¶

The BM25 index is file-based. Delete the directory configured in SEARCH_DB_CONFIG:

# Default location
rm -rf ./bm25_index

Incremental State Cleanup¶

To reset incremental update state, you can clear the PostgreSQL document_state table:

-- Connect to flexible_graphrag_incremental database
TRUNCATE TABLE document_state;
TRUNCATE TABLE datasource_config;

Or use pgAdmin at http://localhost:5050 (master password: admin, server password: password).