Load your code knowledge graph into Neo4j

Graphify stores its graph as graph.json, but you can load it into Neo4j to query it in Cypher, join it with other data, or view it in Neo4j Browser and Bloom. You can write a Cypher script and import it, or push the graph straight to a running database.

What you’ll build

A cypher.txt import script for your graph.
The graph loaded into Neo4j, with indexes on node ids.
Cypher queries for callers, hubs and dependencies.

Setup

uv tool install "graphifyy[neo4j]"
cd your-repo
graphify extract . --code-only

The neo4j extra adds the Python driver used by --push. The script export doesn’t need it. You need a Neo4j 5 database, local or hosted.

Step 1: Write a Cypher script

graphify export neo4j

This writes graphify-out/cypher.txt. Nodes come first, labeled by type, then relationships:

// Neo4j Cypher import - generated by /graphify
MERGE (n:Code {id: 'tests_fixtures_typescript_advanced_userservice', label: 'UserService'});
MATCH (a {id: '...'}), (b {id: 'injectable'}) MERGE (a)-[:REFERENCES {confidence: 'EXTRACTED'}]->(b);

For the open-source Graphify-Labs/graphify repository the script has about 64,000 statements. Node labels include Code, Rationale and Concept. Relationship types are the graph’s relations in upper case, such as CALLS, CONTAINS, IMPORTS and REFERENCES, and each carries its confidence.

Step 2: Import the script

cypher-shell -u neo4j -p "$NEO4J_PASSWORD" < graphify-out/cypher.txt

Relationship statements match nodes by id. On a large graph, create an index for each node label first so the import doesn’t scan every node:

CREATE INDEX IF NOT EXISTS FOR (n:Code) ON (n.id);
CREATE INDEX IF NOT EXISTS FOR (n:Rationale) ON (n.id);
CREATE INDEX IF NOT EXISTS FOR (n:Concept) ON (n.id);

Step 3: Or push directly

export NEO4J_PASSWORD="$(your-secret-tool get neo4j)"
graphify export neo4j --push bolt://localhost:7687 --user neo4j

--push creates an index on id for each node label, then upserts nodes and relationships with MERGE, so you can push again after a rebuild without duplicates. Pushed nodes carry every scalar property from the graph, including source_file, source_location and community. The script from Step 1 only sets id and label, so use --push when you want file and line in your query results. Set the password in NEO4J_PASSWORD rather than --password, so it stays out of your shell history and process list.

Step 4: Query in Cypher

The most connected functions:

MATCH (n:Code)-[r]-()
RETURN n.label AS node, count(r) AS degree
ORDER BY degree DESC LIMIT 10;

Everything that calls a function:

MATCH (caller)-[:CALLS]->(f:Code {label: '_rebuild_code()'})
RETURN caller.label, caller.source_file, caller.source_location;

Callers up to three hops away:

MATCH p = (caller)-[:CALLS*1..3]->(f:Code {label: '_rebuild_code()'})
RETURN DISTINCT caller.label LIMIT 50;

When it goes wrong

neo4j driver not installed. Install the extra: uv tool install "graphifyy[neo4j]". The import is very slow. Create the indexes in Step 2 before running the script, or use --push, which creates them for you. Labels have odd names. Graphify strips characters Neo4j can’t use in a label, falling back to Entity. Relationship names are upper-cased, with spaces and dashes turned into underscores.

Production patterns

Rebuild and push from CI on the default branch, so the database matches what shipped.
Use FalkorDB the same way with graphify export falkordb and --push.
For other tools, graphify export graphml writes GraphML for Gephi and similar.
In Graphify, the hosted product, you query the graph from your agent over MCP with no database to run.

Complete example

uv tool install "graphifyy[neo4j]"
cd your-repo
graphify extract . --code-only
export NEO4J_PASSWORD="$(your-secret-tool get neo4j)"
graphify export neo4j --push bolt://localhost:7687 --user neo4j
cypher-shell -u neo4j -p "$NEO4J_PASSWORD" \
  "MATCH (n:Code)-[r]-() RETURN n.label, count(r) AS d ORDER BY d DESC LIMIT 10;"

What you built

Your code graph lives in Neo4j, indexed and queryable in Cypher, and you can refresh it after every rebuild.

Next steps

Exports

Every export format: wiki, HTML, GraphML, Neo4j and more.

Postgres schema graph

Add your database schema before you export.

Try it in Graphify

We build and host the graph for you. Start with a 14-day Pro trial, then keep up to 3 repositories on Free. No card required.

Essentials

Team

Agents

Data

CI and Ops

Load your code knowledge graph into Neo4j

What you’ll build

Setup

Step 1: Write a Cypher script

Step 2: Import the script

Step 3: Or push directly

Step 4: Query in Cypher

When it goes wrong

Production patterns

Complete example

What you built

Next steps

Exports

Postgres schema graph

Try it in Graphify

​What you’ll build

​Setup

​Step 1: Write a Cypher script

​Step 2: Import the script

​Step 3: Or push directly

​Step 4: Query in Cypher

​When it goes wrong

​Production patterns

​Complete example

​What you built

​Next steps

Exports

Postgres schema graph

Try it in Graphify

What you’ll build

Setup

Step 1: Write a Cypher script

Step 2: Import the script

Step 3: Or push directly

Step 4: Query in Cypher

When it goes wrong

Production patterns

Complete example

What you built

Next steps