Proof of Concept: Implement Directed Acyclic Graph DB with Version Control using Elasticsearch

Sep. 28, 2017

Git and Elasticsearch are my two favorite technologies. In a technical sense, they don’t share anything in common but both are elegantly designed, and vastly useful in the area of my work. See my previous post (co-authored with Linda) for an example how we used Git server as a job scheduling orchestrator.

In this post I will walk you through, step by step, a proof of concept design on how Elasticsearch could be used to implement a directed acyclic graph (DAG) database with version control capability. With no surprise, the version control part was inspired by how Git works internally.

OK, let’s get started.

What is a version controlled DAG DB anyway?

As depicted in Figure 1, the graph schema defines that the DAG consists of four types of entities with derivative relationship as such: D derives from B and/or C, C derives from B, B derives from A.

Figure 1: DAG with Version Control

The graph as a whole is denoted as DAG appended with a revision number, eg, DAG.1. Nodes are labelled using its ID appended with a revision number. For example, a1.1 denotes entity a1 at revision 1. Relationships are represented as arrows pointing from child node to parent node.

At a very minimum, we would expect a DAG database to record every node and its relationships to other nodes and allow changes (update, create and delete) to be made to the nodes and relationships in conformity with the defined schema. For querying, a DAG DB should be able to lookup for any node by its ID and traverse the graph to retrieve related nodes.

A version controlled DAG DB will add additional capabilities to keep full history of changes made to the DAG, allowing access to any snapshot of the entire DAG and any revision of individual node. In a sense, much like what you can do in Git.

In Figure 1, changes in version 2 of the DAG include:

  • updated b1.1 to b1.2
  • updated c1.1 to c1.2
  • created c3.1
  • deleted c2.1
  • created d2.1

After all the changes have been applied to the database, a version controlled DAG DB would allow us travel back in time, access the DAG as if there were no change made at all. It’s also possible to retrieve all historic revisions of a particular node, and find out what exact change had made to it at each revision.

If all that sounds like magic to you, or you may think it’s going to be too hard to implement such a system. Please follow along, let’s make the magic happen together.

Model DAG using JSON documents

It’s fairly straightforward to represent node as a JSON document, edge as JSON field containing ID(s) of parent node(s). Two examples given below illustrate how a1 and d1 may be represented as JSON documents.

a1 = {
"type": "A", // entity type
"id": "a1", // identifier of the node
"p_id": [], // list of identifier of direct parent(s)
"data": {} // any arbitrary JSON object
}
d1 = {
"type": "D",
"id": "d1",
"p_id": ["b1", "c1"],
"data": {}
}

Add revision in JSON documents

In order to track individual revision of a particular node, we add its revision number to the identifier, for example, a1.1 and a1.2 represent a1 at revision 1 and 2 respectively. This new identifier becomes globally unique that can be used to unambiguously identify a unique JSON document in the database.

Here is how the JSON document for d1.1 looks like when revision information is incorporated.

d1.1 = {
"type": "D",
"id": "d1", // unique ID in a given revision of the DAG
"_id": "d1.1", // true unique ID for the node
"p_id": ["b1", "c1"],
"a_id": ["a1", "b1", "c1"], // add all ancestor IDs to facilitate query
"data": {}
}

Add revision to the DAG as a whole

For any given revision of the DAG, we need to know which particular JSON documents (each representing a node) were part of the DAG. This can be achieved by creating a list of unique IDs of every member node of the graph. For example, DAG.2 contains a1.1, b1.2, b2.1, c1.2, c3.1 d1.1 and d2.1. As nodes are defined in different types, we may alternatively keep revisions for each node type, and then combine all node types to the DAG level. This tiered approach is advantageous as it helps reduce the size of the list and tracks revision at node type level as well. Below is what it looks like. For example, B.2 denotes revision 2 of node type B and its participating member nodes include b1.2 and b2.1.

A.1 = ["a1.1"]
B.1 = ["b1.1", "b2.1"]
B.2 = ["b1.2", "b2.1"]
C.1 = ["c1.1", "c2.1"]
C.2 = ["c1.2", "c3.1"]
D.1 = ["d1.1"]
D.2 = ["d1.1", "d2.1"]
DAG.1 = ["A.1", "B.1", "C.1", "D.1"]
DAG.2 = ["A.1", "B.2", "C.2", "D.2"]

Up to this point, it should be clear how all revisions of the DAG are accessible at any given time. To access DAG.1 we simply look up JSON documents included in A.1, B.1, C.1 and D.1, which works out to be a1.1, b1.1, b2.1,c1.1, c2.1 and d1.1.

All three types of possible change to the DAG are handled as follows:

  • create new node: create a JSON doc with new ID and assign revision 1
  • update existing node: create a JSON doc with the same ID as existing one and increment revision by 1
  • delete existing node: simply exclude it in the graph member list

As you may have noticed all JSON documents in the DAG are completely immutable, they will never be deleted or changed once written. This is essentially how Git version control system works under the hood. The node JSON docs are like Git blob objects; the graph member lists for each node type are similar to Git tree objects.

Implement it in Elasticsearch

Now we are ready to put everything into Elasticsearch, you should be able to simply copy and paste the curl commands to run on your computer if you have Elasticsearch installed and accessible at http://localhost:9200.

Create version 1 of the DAG

We will have two different kinds of Elasticsearch indexes, one for data, the other to keep list of graph member nodes’ ID for each revision.

First create JSON docs for each node in DAG.1. Here shows example curl commands to create a1.1 and b1.1:

# create a1.1, note that we do not need to have _id (a1.1) in the JSON document, the _id is specified in the HTTP request URL as document ID
# we use '.d.' as namespace prefix to separate out from other indexes unrelated to our work
curl -XPUT 'localhost:9200/.d.dag.data.a/A/a1.1' -d'
{
"type": "A",
"id": "a1",
"p_id": [ ],
"a_id": [ ],
"data": { }
}
'

curl -XPUT 'localhost:9200/.d.dag.data.b/B/b1.1' -d'
{
"type": "B",
"id": "b1",
"p_id": [ "a1" ],
"a_id": [ "a1" ],
"data": { }
}
'

The full list of the curl commands to create all nodes is here.

Now, let’s create JSON docs for graph member lists. Here is an example for A.1:

curl -XPUT 'localhost:9200/.d.dag.rev.a/A/A.1' -d'
{ "m_ids": ["a1.1"] }
'

Again, the full list of commands is here.

Finally, we need to link DAG.1 to the collection of versioned node types: ["A.1", "B.1", "C.1", "D.1"]. An elegant way to do this in Elasticsearch is to create an index alias with terms lookup filter to provide a virtual view to the underlying JSON docs with desired filtering. This is the core of the whole design.

curl -XPOST 'localhost:9200/_aliases' -d '
{
"actions": [
{
"add": {
"index": ".d.dag.data.*",
"alias": ".d.dag.1",
"filter": {
"bool": { "minimum_should_match": 1,
"should": [
{ "terms": { "_id": { "index": ".d.dag.rev.a", "type": "A", "id": "A.1", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.b", "type": "B", "id": "B.1", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.c", "type": "C", "id": "C.1", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.d", "type": "D", "id": "D.1", "path": "m_ids" } } }
]
}
}
}
}
]
}
'

Version 1 of the DAG can always be accessible via the alias: .d.dag.1.

Create version 2 of the DAG

Let’s make changes to the DAG to make it version 2.

Update b1 from b1.1 to b1.2, just need to create b1.2. We leave b1.1 unchanged.

curl -XPUT 'localhost:9200/.d.dag.data.b/B/b1.2' -d'
{
"type": "B",
"id": "b1",
"p_id": [ "a1" ],
"a_id": [ "a1" ],
"data": { "something": "changed in revsion 2 of b1 node" }
}
'

To reflect the change of b1.1 to b1.2, we need to update graph member list to drop b1.1 and add b1.2 for revision 2 of node type B, ie, B.2.

curl -XPUT 'localhost:9200/.d.dag.rev.b/B/B.2' -d'
{ "m_ids": ["b1.2", "b2.1"] }
'

In a similar way we can perform other changes. Full list of the commands is here. Please download and run them on your computer.

The last step is to create another index alias: .d.dag.2:

curl -XPOST 'localhost:9200/_aliases' -d '
{
"actions": [
{
"add": {
"index": ".d.dag.data.*",
"alias": ".d.dag.2",
"filter": {
"bool": { "minimum_should_match": 1,
"should": [
{ "terms": { "_id": { "index": ".d.dag.rev.a", "type": "A", "id": "A.1", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.b", "type": "B", "id": "B.2", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.c", "type": "C", "id": "C.2", "path": "m_ids" } } },
{ "terms": { "_id": { "index": ".d.dag.rev.d", "type": "D", "id": "D.2", "path": "m_ids" } } }
]
}
}
}
}
]
}
'

We can also create aliases for .d.dag.latest to access latest version of the DAG and .d.dag.all to access all nodes including historic revisions. Here are the curl commands.

Cool things you can do with version controlled DAG DB

As all nodes are indexed in Elasticsearch, you get all powerful search and aggregation for free. Some graph specific queries should be very performant since there is no traversal needed. Below are just some quick examples.

  • get b1 from the latest revision of the DAG
curl -XGET 'localhost:9200/.d.dag.latest/_search' -d '
{ "query": { "term": { "id": { "value": "b1" } } } }
'
  • get b1 from the revision 1 of the DAG
curl -XGET 'localhost:9200/.d.dag.1/_search' -d '
{ "query": { "term": { "id": { "value": "b1" } } } }
'
  • get all revisions of b1 from the DAG (query across all revisions)
curl -XGET 'localhost:9200/.d.dag.all/_search' -d '
{ "query": { "term": { "id": { "value": "b1" } } } }
'
  • get all descendant nodes for b1 from the latest revision of the DAG
curl -XGET 'localhost:9200/.d.dag.latest/_search' -d '
{ "query": { "term": { "a_id": { "value": "b1" } } } }
'
  • get all ancestor nodes for d2 in DAG.2
# first, get d2 in DAG.2
curl -XGET 'localhost:9200/.d.dag.2/_search' -d '
{ "query": { "term": { "id": { "value": "d2" } } } }
'

# we get "a_id": [ "a1", "b1", "b2", "c3" ], now we lookup nodes with these IDs
curl -XGET 'localhost:9200/.d.dag.2/_search' -d '
{ "query": { "terms": { "id": ["a1", "b1", "b2", "c3"] } } }
'

Further thoughts

Benefited from the data immutability nature in the design, it’s reasonable to expect high reliability and ease of use for both end users and administrators. Any entity or a group of entities (via creation of arbitrary entity collection) can be exposed as resources with permanent URI.

One thing needs to keep in mind is that although Elasticsearch is highly scalable, the DAG DB may not be able to scale for very large graph, this is because the number of elements (node IDs) for terms lookup filter is not supposed to be very large, tens of thousands per node type may be the upper limit. This is not necessarily a show-stopper, proper modeling of the graph schema to partition the data and avoid single large node type can effectively address this potential limitation.

Although most resiliency issues have been addressed in Elassticsearch, it is still not officially recommended to use it as the primary datastore. However, as the proposed DAG DB is append only, frequent Elasticsearch incremental backup should be quick to perform and will help minimizing the risk of data loss.

Some prototype work should be helpful in order to understand better the characteristics of this proposed version controlled DAG DB design. To find out how it turns out, stay tuned for my next blog post on this. Until then!

Junjun Zhang, Bioinformatics Team Lead
True hybrid expertise in both biology world and information technology world. Enjoy working with biologists and software developers, serving as a bridge bringing best software solutions to complex biological data management challenges. Fascinated and inspired by ingenious open source software solutions, such as Elasticsearch, wishing to come up with his own one day.