dagnabit 2.2.1

data/.autotest

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+require 'redgreen/autotest'
+
+Autotest.add_hook(:initialize) do |autotest|
+  autotest.libs += File::PATH_SEPARATOR + File.join(File.dirname(__FILE__), 'test/connections/native_sqlite3')
+end

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+*.sw?
+.DS_Store
+coverage
+rdoc
+pkg
+*.log

data/LICENSE

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+Copyright (c) 2009 David Yip
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= This is the GitHub branch
+
+This branch is updated irregularly.  The canonical dagnabit repository is hosted on Gitorious:
+
+http://gitorious.org/dagnabit/dagnabit
+
+= dagnabit
+
+dagnabit is (yet another) ActiveRecord plugin for directed acyclic graphs.  It
+provides an underlying representation that facilitates fast reachability
+queries at the expense of edge insertion/deletion speed and execution time.
+
+The data structure used by dagnabit is the structure described in:
+
+DONG, G., LIBKIN, L., SU, J., and WONG, L.  "Maintaining the
+transitive closure of graphs in SQL."  In Int. J. Information Technology, vol.
+5, 1999.
+
+dagnabit was developed 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 was developed at the Northwestern University Biomedical Informatics
+Center <http://www.nucats.northwestern.edu/centers/nubic/index.html>.
+
+== Related work
+
+This plugin was inspired by Matthew Leventi's acts-as-dag plugin
+<http://github.com/mleventi/acts-as-dag/tree/master>.  Indeed, Leventi's
+acts-as-dag plugin was originally used in the application from which this
+plugin was extracted, and dagnabit's node and edge interfaces were modeled
+after the interfaces provided by acts-as-dag.
+
+The primary differences between dagnabit and acts-as-dag are:
+
+* acts-as-dag does not permit linking of unpersisted nodes, i.e.
+
+    n1 = Node.new
+    n2 = Node.new
+    e1 = Link.new(:ancestor => n1, :descendant => 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.
+
+* acts-as-dag issues O(x*y) queries on edge insert, update, and delete, where x
+  and y are the number of ancestors and descendants of a node.  In environments
+  where network latency between database and application server is considerable,
+  this can adversely affect application performance. 
+
+  dagnabit uses a constant number of queries for insert, update, and delete.
+  (The execution time and memory usage of queries are, of course, still
+  affected by the size of the transitive closure set being updated.)
+
+== Database compatibility
+
+dagnabit is only known to work with SQLite and PostgreSQL.  Other databases may
+work, but they have not been tested.
+
+dagnabit is known to _not_ work on Oracle XE 10g databases via the ActiveRecord
+oracle-enhanced adapter.
+
+== Setup
+
+dagnabit is distributed as a gem plugin; you can therefore install it as you
+would any other RubyGem.  Integration with your Rails application can be
+achieved by adding dagnabit to your application's gem dependencies list.
+
+Details for creating the link tables are discussed below.
+
+In your link model, put
+
+  acts_as_dag_link
+
+In your node models, put
+
+  acts_as_dag_node_linked_by (your link model name)
+
++acts_as_dag_link+ accepts some configuration options.  These configuration
+options are discussed below.
+
+=== Link table schemas
+
+Link storage is accomplished with two tables having identical schemas.  One
+table holds explicitly specified links between nodes.  The other table contains
+the _transitive closure_ of all graphs, i.e. one tuple per path in the graph.
+(The transitive closure table is therefore a superset of the direct link
+table.)
+
+The transitive closure table is automatically maintained by dagnabit and should
+not be manually modified.  The transitive closure table does not need to be
+mapped to a model in your application.
+
+The expected schema for both tables is:
+
+    t.integer :ancestor_id      # or configured foreign key ID
+    t.integer :descendant_id    # or configured foreign key ID
+    t.string :ancestor_type     # not configurable
+    t.string :descendant_type   # not configurable
+
+The behavior of the plugin with a deviant schema is unspecified.
+
+=== Configuration options for +acts_as_dag_link+
+
+* +transitive_closure_table_name+: The table where tuples in the transitive
+  closure of the graph should be stored.  Defaults to
+  <tt>#{link_table_name}_transitive_closure_tuples</tt>.
+* +descendant_id_column+: Column in the link tables for recording the ID of a
+  descendant.  Defaults to +descendant_id+.
+* +ancestor_id_column+: Column in the link tables for recording the ID of a
+  ancestor.  Defaults to +ancestor_id+.
+
+== Usage
+
+The recommended usage pattern is (in pseudocode)
+
+  nodes = make_nodes
+  links = connect_up(nodes)
+  save(nodes)
+  save(links)
+
+Node and edge creation is identical to creation of any ActiveRecord model.  For
+example, if your Node models were called +AlphaNode+ and +BetaNode+ and your
+edge model was called +Link+, these would be valid expressions:
+
+  n1 = AlphaNode.new
+  n2 = BetaNode.new
+
+  e1 = Link.new(:ancestor => n1, :descendant => n2)
+  n1.save
+  n2.save
+  e1.save
+
+=== Node interface
+
++acts_as_dag_node+ adds the following associations to nodes:
+
+* +links_as_child+: Links for which the node is a child.
+* +links_as_parent+: Links for which the node is a parent.
+* +links_as_ancestor+: Links for which the node is an ancestor.  Read-only.
+* +links_as_descendant+: Links for which the node is a descendant.  Read-only.
+
++acts_as_dag_node+ adds the following instance methods to nodes:
+ 
+* +descendants+: All descendants of the node.  Read-only.
+* +ancestors+: All ancestors of the node.  Read-only.
+
+=== Link interface
+
+The following class methods are available on links:
+
+* +paths+: Retrieves all paths from one node to another.
+* +path+: Returns whether a node is reachable from another node.
+* +find_edge+: Finds an edge from one node to another, or nil if none exists.
+* +build_edge+: Builds an edge from one node to another node.
+* +connect+: Builds and saves an edge from one node to another.  Identical to
+  <tt>build_edge(nodeA, nodeB).save</tt>.
+* <tt>connect!</tt>: Builds and saves an edge from one node to another, raising
+  an exception if save fails.  Identical to <tt>build_edge(nodeA,
+  nodeB).save!</tt>.
+
+== Introduction to the codebase
+
+Here are some starting points to become acquainted with the dagnabit codebase:
+
+[Dagnabit::Activation]
+  How to mix this functionality into your models.
+[Dagnabit::Link::Configuration]
+  Link configuration options.
+[Dagnabit::Link::Associations]
+  Associations exposed on links.
+[Dagnabit::Node::Associations]
+  Associations exposed on nodes.
+[Dagnabit::Node::Neighbors]
+  How to locate a node's neighbors.
+[Dagnabit::Link::TransitiveClosureRecalculation]
+  How the transitive closure is maintained.
+
+== Copyright
+
+Copyright (c) 2009 David Yip.  Released under the MIT License; see LICENSE for
+details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+gem 'net-ssh', '>= 1.99.1'
+require 'net/ssh'
+require 'net/scp'
+require 'yaml'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "dagnabit"
+    gem.summary = %Q{Directed acyclic graph plugin for ActiveRecord}
+    gem.email = "yipdw@northwestern.edu"
+    gem.homepage = "http://gitorious.org/dagnabit/dagnabit"
+    gem.authors = ["David Yip"]
+    gem.add_dependency 'activerecord', '>= 2.1.0'
+    gem.add_dependency 'activesupport', '>= 2.3.2'
+    gem.add_development_dependency 'mocha', '= 0.9.8'
+    gem.add_development_dependency 'shoulda', '= 2.10.2'
+
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+rescue LoadError
+  puts "Jeweler not available. Install it with: sudo gem install jeweler"
+end
+
+task :test => [:test_sqlite3, :test_postgresql]
+
+require 'rake/testtask'
+['sqlite3', 'postgresql'].map { |adapter| ["test_#{adapter}", "native_#{adapter}"] }.each do |task_name, adapter_name|
+  Rake::TestTask.new(task_name) do |test|
+    test.libs << 'lib' << 'test' << "test/connections/#{adapter_name}"
+    test.pattern = 'test/dagnabit/**/test_*.rb'
+    test.verbose = false
+  end
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test' << 'test/connections/native_sqlite3'
+    test.pattern = 'test/dagnabit/**/test_*.rb'
+    test.verbose = true
+    test.rcov_opts << '--exclude gems/*'
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  if File.exist?('VERSION.yml')
+    config = YAML.load(File.read('VERSION.yml'))
+    version = "#{config[:major]}.#{config[:minor]}.#{config[:patch]}"
+  else
+    version = ""
+  end
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "dagnabit #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION.yml

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+--- 
+:major: 2
+:minor: 2
+:patch: 1
+:build: 

data/bin/dagnabit-test

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+#!/usr/bin/env ruby
+
+#
+# Launches an irb session with an in-memory SQLite3 database and Node and Link
+# ActiveRecord models.
+#
+
+require 'rubygems'
+require 'activerecord'
+
+src = File.dirname(__FILE__) + '/../lib/dagnabit.rb'
+if File.exists?(src)
+  require src
+else
+  require 'dagnabit'
+end
+
+require 'irb'
+
+begin
+  require 'sqlite3'
+rescue LoadError
+  gem 'sqlite3-ruby'
+  require 'sqlite3'
+end
+
+ActiveRecord::Base.logger = Logger.new("#{File.basename(__FILE__)}.log")
+ActiveRecord::Base.establish_connection(:adapter => 'sqlite3', :database => ':memory:')
+
+ActiveRecord::Schema.define do
+  [:edges, :edges_transitive_closure_tuples].each do |table|
+    create_table table do |t|
+      t.integer :ancestor_id
+      t.integer :descendant_id
+      t.string :ancestor_type
+      t.string :descendant_type
+    end
+  end
+
+  create_table :nodes do |t|
+    t.string :data
+  end
+end
+
+class Edge < ActiveRecord::Base
+  acts_as_dag_link
+end
+
+class Node < ActiveRecord::Base
+  acts_as_dag_node_linked_by 'Edge'
+end
+
+IRB.start

data/dagnabit.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{dagnabit}
+  s.version = "2.2.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["David Yip"]
+  s.date = %q{2009-12-07}
+  s.default_executable = %q{dagnabit-test}
+  s.email = %q{yipdw@northwestern.edu}
+  s.executables = ["dagnabit-test"]
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".autotest",
+     ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION.yml",
+     "bin/dagnabit-test",
+     "dagnabit.gemspec",
+     "init.rb",
+     "lib/dagnabit.rb",
+     "lib/dagnabit/activation.rb",
+     "lib/dagnabit/link/associations.rb",
+     "lib/dagnabit/link/class_methods.rb",
+     "lib/dagnabit/link/configuration.rb",
+     "lib/dagnabit/link/cycle_prevention.rb",
+     "lib/dagnabit/link/named_scopes.rb",
+     "lib/dagnabit/link/transitive_closure_link_model.rb",
+     "lib/dagnabit/link/transitive_closure_recalculation.rb",
+     "lib/dagnabit/link/transitive_closure_recalculation/on_create.rb",
+     "lib/dagnabit/link/transitive_closure_recalculation/on_destroy.rb",
+     "lib/dagnabit/link/transitive_closure_recalculation/on_update.rb",
+     "lib/dagnabit/link/transitive_closure_recalculation/utilities.rb",
+     "lib/dagnabit/link/validations.rb",
+     "lib/dagnabit/node/associations.rb",
+     "lib/dagnabit/node/class_methods.rb",
+     "lib/dagnabit/node/configuration.rb",
+     "lib/dagnabit/node/neighbors.rb",
+     "test/connections/native_postgresql/connection.rb",
+     "test/connections/native_sqlite3/connection.rb",
+     "test/dagnabit/link/test_associations.rb",
+     "test/dagnabit/link/test_class_methods.rb",
+     "test/dagnabit/link/test_configuration.rb",
+     "test/dagnabit/link/test_cycle_prevention.rb",
+     "test/dagnabit/link/test_named_scopes.rb",
+     "test/dagnabit/link/test_transitive_closure_link_model.rb",
+     "test/dagnabit/link/test_transitive_closure_recalculation.rb",
+     "test/dagnabit/link/test_validations.rb",
+     "test/dagnabit/node/test_associations.rb",
+     "test/dagnabit/node/test_class_methods.rb",
+     "test/dagnabit/node/test_configuration.rb",
+     "test/dagnabit/node/test_neighbors.rb",
+     "test/helper.rb",
+     "test/models/beta_node.rb",
+     "test/models/custom_data_link.rb",
+     "test/models/customized_link.rb",
+     "test/models/customized_link_node.rb",
+     "test/models/link.rb",
+     "test/models/node.rb",
+     "test/schema/schema.rb"
+  ]
+  s.homepage = %q{http://gitorious.org/dagnabit/dagnabit}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.5}
+  s.summary = %q{Directed acyclic graph plugin for ActiveRecord}
+  s.test_files = [
+    "test/connections/native_postgresql/connection.rb",
+     "test/connections/native_sqlite3/connection.rb",
+     "test/dagnabit/link/test_associations.rb",
+     "test/dagnabit/link/test_class_methods.rb",
+     "test/dagnabit/link/test_configuration.rb",
+     "test/dagnabit/link/test_cycle_prevention.rb",
+     "test/dagnabit/link/test_named_scopes.rb",
+     "test/dagnabit/link/test_transitive_closure_link_model.rb",
+     "test/dagnabit/link/test_transitive_closure_recalculation.rb",
+     "test/dagnabit/link/test_validations.rb",
+     "test/dagnabit/node/test_associations.rb",
+     "test/dagnabit/node/test_class_methods.rb",
+     "test/dagnabit/node/test_configuration.rb",
+     "test/dagnabit/node/test_neighbors.rb",
+     "test/helper.rb",
+     "test/models/beta_node.rb",
+     "test/models/custom_data_link.rb",
+     "test/models/customized_link.rb",
+     "test/models/customized_link_node.rb",
+     "test/models/link.rb",
+     "test/models/node.rb",
+     "test/schema/schema.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<activerecord>, [">= 2.1.0"])
+      s.add_runtime_dependency(%q<activesupport>, [">= 2.3.2"])
+      s.add_development_dependency(%q<mocha>, ["= 0.9.8"])
+      s.add_development_dependency(%q<shoulda>, ["= 2.10.2"])
+    else
+      s.add_dependency(%q<activerecord>, [">= 2.1.0"])
+      s.add_dependency(%q<activesupport>, [">= 2.3.2"])
+      s.add_dependency(%q<mocha>, ["= 0.9.8"])
+      s.add_dependency(%q<shoulda>, ["= 2.10.2"])
+    end
+  else
+    s.add_dependency(%q<activerecord>, [">= 2.1.0"])
+    s.add_dependency(%q<activesupport>, [">= 2.3.2"])
+    s.add_dependency(%q<mocha>, ["= 0.9.8"])
+    s.add_dependency(%q<shoulda>, ["= 2.10.2"])
+  end
+end
+