So I lied

dagnabit is actually still alive. I still think you should be using something like Sequel if you really want to do graphs in a SQL database, but if you're using ActiveRecord for whatever reason, dagnabit might still be useful.

Version 3 is a rework of dagnabit as a PostgreSQL-specific ActiveRecord plugin. It's blatantly incompatible with the 2.x series of dagnabit. There are some migration notes in MIGRATION.md.

dagnabit

dagnabit is (yet another) ActiveRecord plugin for directed acyclic graphs. It stores directed acyclic graphs as an adjacency list, using recursive common table expressions to perform fast reachability queries.

dagnabit was developed at the Northwestern University Biomedical Informatics Center for a Ruby on Rails application designed for management and querying of large-and-rapidly-growing biospecimen banks (i.e. for cancer research). The application uses directed acyclic graphs for knowledge representation (storage and application of workflows) and representing biospecimen heritage.

dagnabit is hosted at Gitorious and Github:

Installation

gem install dagnabit

Related work

This plugin was inspired by Matthew Leventi's acts-as-dag plugin. Indeed, Leventi's acts-as-dag plugin was originally used in the application from which this plugin was extracted.

The primary differences between dagnabit and acts-as-dag are:

  • dagnabit does not maintain a separate transitive closure table, which speeds up insertion.

  • acts-as-dag does not permit linking of unpersisted nodes, i.e.

    n1 = Vertex.new n2 = Vertex.new e1 = Edge.new(:parent => n1, :child => n2) ... other code ...

    [n1, n2, e1].map { |o| o.save }

    With acts-as-dag, one must save the nodes before creating the edge. The above code segment works in dagnabit.

Database compatibility

PostgreSQL 8.4. That's all I know that'll work with dagnabit, anyway. Versions of PostgreSQL less than 8.4 will not work because they do not implement WITH RECURSIVE.

It's possible other SQL databases will work, but I have no tests to demonstrate that situation.

Using dagnabit

Database schema

You'll need at least one table for storing your graph's vertices. Additionally, for every vertex table you create, you will need one edge table.

Polymorphic vertices are supported via single table inheritance.

Here's an example schema written as an ActiveRecord schema definition:

create_table :vertices do |t|
  t.integer :ordinal
  t.string  :type     # only if you're using STI
end

create_table :edges do |t|
  t.references :parent, :null => false
  t.references :child,  :null => false
end

add_index :edges, [:parent_id, :child_id], :unique => true

Maintaining a directed acyclic simple graph and some words on validation

dagnabit is designed to operate on directed, acyclic, simple graphs. That means:

  1. each edge has a direction (_directed_),
  2. there cannot exist any edges that create a cycle (_acyclic_),
  3. any edge must connect two and only two vertices (no hyperedges), and
  4. there may be only zero or one edges connecting any two vertices (_simple_).

dagnabit is set up to make the database enforce these invariants:

  1. The directionality of each edge is implicit in the edge table structure from parent to child.
  2. dagnabit provides a PL/pgSQL trigger that you can use to abort saving edges that, when inserted, causes a cycle. More on this below.
  3. As each edge may only address one parent and one child, the maximum of two vertices is guaranteed. NOT NULL constraints on the parent_id and child_id columns guarantee the minimum of two. (It is recommended that you also set up foreign key constraints from edges to vertices, though that addresses a different issue.)
  4. The (parent_id, child_id) index prevents multiple edges connecting the same vertices.

You may, of course, relax invariants 2-4 by omitting indices or constraints; however, if you do that, you risk problems such as Dagnabit::Vertex::Connectivity methods generating infinite loops.

Note that dagnabit currently does not provide a way to catch data that would violate these invariants via ActiveRecord's validation subsystem. Violations, therefore, will result in quite nasty (from the ActiveRecord perspective of things) PGErrors.

If you design your application code such that these invariants cannot be violated via typical user actions, then this is probably fine, because in that case the PGError exception (which, in this case, you probably don't want to handle) indicates either the existence of an error in the code and/or malicious activity that was prevented.

On the other hand, if users of your application will be building dags as part of their interactions with your application, then it is a very real possibility that violation of the above invarints may occur in the course of normal user activity. In this case, you must trap these errors and provide adequate feedback to your users so that they can correct the problem. This, like many UI problems, is not a trivial problem to solve, and I do not have any general solution for it.

dagnabit's cycle-checking trigger

dagnabit ships with a PL/pgSQL trigger that can be installed on edge tables. The trigger algorithm is run per inserted or updated row, and is implemented with a depth-first search:

trigger check_cycle(seen = [], edge = (a, b)):
  if b is not in seen
    if b has no children
      ok
    else
      for each child c of b
        check_cycle(seen + [b], (b, c))
    end
  else
    abort
  end

The implementation uses a WITH RECURSIVE query.

The Dagnabit::Migration module provides methods for creating and dropping triggers on edge tables:

class CreateEdges < ActiveRecord::Migration
  extend Dagnabit::Migration

  def self.up
    create_table :edges do |t|
      ...
    end

    create_cycle_check_trigger :edges
  end

  def self.down
    drop_cycle_check_trigger :edges

    drop_table :edges
  end
end

Using dagnabit in your application

dagnabit is activated on vertex and edge models by extending vertex and edge classes with Dagnabit::Vertex::Activation and Dagnabit::Edge::Activation, respectively:

class Vertex < ActiveRecord::Base
  extend Dagnabit::Vertex::Activation

  acts_as_vertex
  connected_by 'Edge'
end

class Edge < ActiveRecord::Base
  extend Dagnabit::Edge::Activation

  acts_as_edge
  connects 'Vertex'
end

By default, the vertex connectivity queries expect the edge table to be called "edges", but that is by no means required. Just associate the vertex with a different edge model:

class OtherVertex < ActiveRecord::Base
  extend Dagnabit::Vertex::Activation

  acts_as_vertex
  connected_by 'OtherEdge'
end

For further information, see the library API documentation. Also see the listing of the dagnabit-test program.

Copyright

Copyright (c) 2009, 2010, 2011 David Yip. Released under the MIT License; see LICENSE for details.