5 Tips & Tricks for Fast Batched Updates of Graph Structures with Neo4j and Cypher

Posted by Michael Hunger on Mar 2, 2017 in Uncategorized, cypher, import, neo4j |

Michael Hunger, @mesirii

When you’re writing a lot of data to the graph from your application or library, you want to be efficent.

Inefficient Solutions

These approaches are not very efficient:

  • hard coding values instead of using parameters

  • sending a single query / tx per individual update

  • sending many single queries within a single tx with individual updates

  • generating large, complex statements (hundreds of lines) and sending one of them per tx and update

  • sending in HUGE (millions) of updates in a single tx, will cause out-of-memory issues

Better Approach

You want small enough queries, that are constant in their shape (for caching) and are using parameters.

Each query can update from a single property to a whole subgraph (100 nodes) but has to be the same in overall structure for caching.

UNWIND to the Rescue

To achieve that you just prefix your regular “single-update-query” with an UNWIND that turns a batch of data (up to 10k or 50k entries)
into individual rows, which contain the information for each of the (more or less complex) updates.

You send in a {batch} parameter (up to 10k-50k) of data (hopefully a delta) as a list of maps, which are then applied in a compact query, which is also properly compiled and cached, as it has a fixed structure.

Overall Syntax Structure

{batch: [{row1},{row2},{row3},...10k]}
UNWIND {batch} as row

// now perform updates with the data in each "row" map

Examples

Here are some examples:

Create node with properties

{batch: [{name:"Alice",age:32},{name:"Bob",age:42}]}
UNWIND {batch} as row
CREATE (n:Label)
SET n += row

MERGE node with properties

{batch: [{id:"alice@example.com",properties:{name:"Alice",age:32}},{id:"bob@example.com",properties:{name:"Bob",age:42}}]}
UNWIND {batch} as row
MERGE (n:Label {row.id})
(ON CREATE) SET n += row.properties

Node lookup and MERGE/CREATE relationship between with properties

{batch: [{from:"alice@example.com",to:"bob@example.com",properties:{since:2012}},{from:"alice@example.com",to:"charlie@example.com",properties:{since:2016}}]}
UNWIND {batch} as row
MATCH (from:Label {row.from})
MATCH (to:Label {row.to})
CREATE/MERGE (from)-[rel:KNOWS]->(to)
(ON CREATE) SET rel += row.properties

Lookup by id, or even list of ids

good for parent-child trees

Here we’re passing a single property created.
Alternatively you could pass in no properties or a map of properties to be set/updated.

{batch: [{from:123,to:[44,12,128],created:"2016-01-13"}, {from:34,to:[23,35,2983],created:"2016-01-15"},...]
UNWIND {batch} as row
MATCH (from) WHERE id(from) = row.from
MATCH (to) WHERE id(from) IN row.to // list of ids
CREATE/MERGE (from)-[rel:FOO]->(to)
SET rel.created = row.created

Faster, Better, Further: All the tricks

There are some more tricks.

You can also send in a map where the keys are node- or relationship-ids (converted to as strings) that’s more compact and faster too for the id lookup.

Update of existing nodes by id

{ batch : [{"1":334,"2":222,3:3840, ... 100k}]}
WITH {batch} as data, [k in keys({batch}) | toInt(k)] as ids
MATCH (n) WHERE id(n) IN ids

// single property value
SET n.count = data[toString(id(n))]

// or override all properties
SET n = data[toString(id(n))]

// or add all properties
SET n += data[toString(id(n))]

Update of existing relationships by id

{ batch : [{"1":334,"2":222,3:3840, ... 100k}]}
WITH {batch} as data, [k in keys({batch}) | toInt(k)] as ids
MATCH ()-[rel]->() WHERE id(rel) IN ids
SET rel.foo = data[toString(id(rel))] // single property
SET rel= data[toString(id(rel))] // all properties

Conditional Data Creation

Sometimes you want to create data dynamically based on inputs, e.g. a node with a certain label.

As cypher currently has no conditional WHEN or IF clause, and case when is just an expression, you have to use a trick I came up with many years ago.

Fortunately there is FOREACH which is meant to iterate over a list of items and execute update operations for each of them.

Fortunately a list of 0 or 1 elements can serve as a conditional of false and true, i.e. no iteration or one iteration.

General idea:

...
FOREACH (_ IN CASE WHEN predicate THEN [true] ELSE [] END |
... update operations ....
)

Note that the true value in that list could be anything, 42, "", null etc. as long as it is any single value so that we have a non-empty list.

You can achieve something similar with a RANGE(1, CASE WHEN predicate THEN 1 ELSE 0 END) which will yield an empty list when the predicate is false.
Or if you fancy filter then you can use: filter(_ IN [1] WHERE predicate).

Here is a concrete example:

LOAD CSV FROM {url} AS row
MATCH (o:Organization {name:row.org})
FOREACH (_ IN case when row.type = 'Person' then [1] else [] end|
   MERGE (p:Person {name:row.name})
   CREATE (p)-[:WORKS_FOR]->(o)
)
FOREACH (_ IN case when row.type = 'Agency' then [1] else [] end|
   MERGE (a:Agency {name:row.name})
   CREATE (a)-[:WORKS_FOR]->(o)
)

Note that identifiers created within FOREACH are not accessible from the outside, you would have to re-match the value later on, or you have to move all your update operations into the foreach.

Utilizing APOC Procedures

The APOC procedure library comes with a lot of useful procedures that can help you here, I want to highlight 3 of them:

  • create nodes / relationships with dynamic labels and propeties

  • batched transactions / iteration of updates

  • functions for creating and manipulating maps to be set as properties

Creating Nodes and Relationships dynamically

With apoc.create.node and apoc.create.relationship you can have dynamically computed node-labels and relationship-types as well as any map of properties.

  • labels is a string array

  • properties is just a map

UWNIND {batch} as row
CALL apoc.create.node(row.labels, row.properties) yield node
RETURN count(*)

There are also procedures in apoc.create.* for setting/updating/removing properties and labels with dynamic string keys.

UWNIND {batch} as row
MATCH (from) WHERE id(n) = row.from
MATCH (to:Label) where to.key = row.to
CALL apoc.create.relationship(from, row.type, row.properties, to) yield rel
RETURN count(*)

Batched Transactions

As mentioned at the beginning huge transactions are a problem, you can update a million records with around 2G – 4G of heap but it gets difficult with larger volumes.
My biggest volume per single transaction was about 10M nodes / relationships with 32G heap.

That’s where apoc.periodic.iterate comes in.

The idea is simple, you have two Cypher statements, the first statement provides the data to operate on and can produce a huge (many millions) stream of data (nodes, rels, scalar values).

The second statement does the actual update work, it is called for each item, but a new transaction is created only for each batch of items.

(There is a new variant of this which will go into the next version of APOC that actually does an UNWIND variant of the second statement, so it executes only one inner statement per tx).

So for example your first statement returns 5 million nodes to update, with a computed value.
The inner statement is executed once for each of those 5 M nodes.
If your batch size is 10k then that happens in batches of 10k statements per transaction.

If your updates are independent of each other (think creation of nodes or updates of properties, or updates of independent subgraphs), then you can run this procedure with a parallel:true option which will use all your CPUs.

For example if you want to compute a score of many rated items and update this property in a batched fashion, this is what you would do:

call apoc.periodic.iterate('
MATCH (n:User)-[r1:LIKES]->(thing)<-[r2:RATED]-(m:User) WHERE id(n)<id(m) RETURN thing, avg( r1.rating + r2.rating ) as score
','
WITH {thing} as t SET t.score = {score}
', {batchSize:10000, parallel:true})

Creating / Updating Maps dynamically

While lists can be created and processed quite easily in Cypher with range, collect, unwind, reduce, extract, filter, size etc, maps have more limited means esp. for creation and modification.

The apoc.map.* package comes with a number of functions that make your life easier:

Creating Maps from other data:

RETURN apoc.map.fromPairs([["alice",38],["bob",42],...])
// {alice:38, bob: 42, ...}

RETURN apoc.map.fromLists(["alice","bob",...],[38,42])
// {alice:38, bob: 42, ...}

// groups nodes, relationships, maps by key, good for quick lookups by that key
RETURN apoc.map.groupBy([{name:"alice",gender:"female"},{name:"bob",gender:"male"}],"gender")
// {female:{name:"alice",gender:"female"}, male:{name:"bob",gender:"male"}}

RETURN apoc.map.groupByMulti([{name:"alice",gender:"female"},{name:"bob",gender:"male"},{name:"Jane",gender:"female"}],"gender")
// {female:[{name:"alice",gender:"female"},{name:"jane",gender:"female"}], male:[{name:"bob",gender:"male"}]}

Updating Maps

RETURN apoc.map.merge({alice: 38},{bob:42})
// {alice:38, bob: 42}

RETURN apoc.map.setKey({alice:38},"bob",42)
// {alice:38, bob: 42}

RETURN apoc.map.removeKey({alice:38, bob: 42},"alice")
// {bob: 42}

RETURN apoc.map.removeKey({alice:38, bob: 42},["alice","bob","charlie"])
// {}

// remove the given keys and values, good for data from load-csv/json/jdbc/xml
RETURN apoc.map.clean({name: "Alice", ssn:2324434, age:"n/a", location:""},["ssn"],["n/a",""])
// {name:"Alice"}

Conclusion

I used these approaches successfully for high volume update operations, and also in implementation of object graph mappers for bulk updates.

Of course you can combine these variants for more complex operations.

If you try them out and are successful, please let me know.

If you have any other tricks that helped you to achieve more write throughput with Cypher, please let me know too and I’ll update this post.

Follow me on Twitter for more tips like this.

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