dagnabit 2.2.6 → 3.0.0

data/.autotest

@@ -1,5 +0,0 @@
-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

@@ -1,5 +0,0 @@
-README.rdoc
-lib/**/*.rb
-bin/*
-features/**/*.feature
-LICENSE

data/.gitignore

@@ -1,7 +0,0 @@
-*.sw?
-.DS_Store
-coverage
-rdoc
-pkg
-*.log
-.bundle

data/Gemfile

@@ -1,15 +0,0 @@
-# A sample Gemfile
-source :gemcutter
-
-gem 'activerecord', '~> 2.3.5'
-
-group :development do
-  gem 'jeweler'
-  gem 'mocha', '0.9.8'
-  gem 'pg'
-  gem 'shoulda', '2.10.2'
-  gem 'sqlite3-ruby'
-  gem 'redgreen'
-  gem 'rcov'
-  gem 'ZenTest'
-end

data/Gemfile.lock

@@ -1,38 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    ZenTest (4.4.0)
-    activerecord (2.3.9)
-      activesupport (= 2.3.9)
-    activesupport (2.3.9)
-    gemcutter (0.6.1)
-    git (1.2.5)
-    jeweler (1.4.0)
-      gemcutter (>= 0.1.0)
-      git (>= 1.2.5)
-      rubyforge (>= 2.0.0)
-    json_pure (1.4.6)
-    mocha (0.9.8)
-      rake
-    pg (0.9.0)
-    rake (0.8.7)
-    rcov (0.9.9)
-    redgreen (1.2.2)
-    rubyforge (2.0.4)
-      json_pure (>= 1.1.7)
-    shoulda (2.10.2)
-    sqlite3-ruby (1.3.1)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  ZenTest
-  activerecord (~> 2.3.5)
-  jeweler
-  mocha (= 0.9.8)
-  pg
-  rcov
-  redgreen
-  shoulda (= 2.10.2)
-  sqlite3-ruby

data/History.txt

@@ -1,81 +0,0 @@
-== 2.2.6 2010-01-01
-
-=== Bugfixes
-
-* Fixed version requirements.
-
-== 2.2.5 2010-10-01
-
-=== Minor changes
-
-* Ported development code to Bundler 1.0.
-* Removed usage of Object#returning, which was deprecated in ActiveSupport
-  2.3.9.
-
-== 2.2.4 2010-03-15
-
-=== Bugfixes
-
-* Ensure that ActiveRecord is loaded before dagnabit's extensions are loaded.
-  This fixes a problem that would occasionally occur when using dagnabit in
-  Bundler.
-
-== 2.2.3 2010-02-17
-
-=== Bugfixes
-
-* It was not possible to delete links having custom data attributes in dagnabit
-  versions <= 2.3.2.  This has been fixed.
-
-== 2.2.2 2010-02-04
-
-=== Minor enhancements
-
-* Slightly smarter transitive closure maintenance: if a link was saved but
-  neither its ancestor nor descendant changed, the transitive closure will not
-  be recalculated.
-* Removed usage of deprecated "require 'activesupport'".
-
-== 2.2.1 2009-12-07
-
-=== Minor enhancements
-
-* Added NUBIC provenance.
-  More information on NUBIC: http://www.nucats.northwestern.edu/centers/nubic/index.html
-
-== 2.2.0 2009-09-14
-
-=== Minor enhancements
-
-* Commonized models used in dagnabit's tests.
-* Switched to named scopes to implement Link#linking and TransitiveClosureLink#linking.
-
-== 2.1.0 2009-09-04
-
-=== Bugfixes
-
-* Fixed overzealous on-destroy transitive closure maintenance in situations like these:
-
-    n1 -> n2 -> n3
-     |__________|
-
-  Previously, deleting the edges (n1, n2) and (n2, n3) would also delete the
-  edge (n1, n3).
-
-== 2.0.0 2009-08-17
-
-=== Major changes
-
-* Link models now validate their ancestor and descendant.  This means that
-  Link#connect will fail if a link cannot be made due to node validation
-  failures.
-
-  Unfortunately, this also means you can no longer write code like this:
-
-    node1.links_as_parent.build(:descendant => node2)
-
-  or
-
-    node2.links_as_child.build(:ancestor => node1)
-
-  See commit 61d6e3841b63fdcaad7fcecd05b24f4b9f217ba2 for more details.

data/README.rdoc

@@ -1,202 +0,0 @@
-= Read this first
-
-dagnabit is shutting down.  Errors will be fixed, but no new features will be
-added.
-
-If you need fast reachability queries in a Ruby application that uses an SQL
-database, consider using a database that supports recursive common table
-expressions (e.g. PostgreSQL) and Sequel, which has a Ruby interface for
-constructing recursive CTEs.
-
-= 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>.
-
-dagnabit is hosted at Gitorious and Github:
-
-http://gitorious.org/dagnabit/dagnabit
-http://github.com/yipdw/dagnabit
-
-The Gitorious repository is always updated before the Github repository, and
-should be considered canonical.
-
-== 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.
-
-For a code example of a complete setup, see the <tt>dagnabit-test</tt> script
-in +bin+.
-
-=== 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>.
-* +transitive_closure_class_name+: The transitive closure is represented with
-  an ActiveRecord class whose name defaults to +TransitiveClosureLink+.  Set this
-  option to change that name.
-* +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:
- 
-* +children+: All children of the node.  Read-only.
-* +parents+: All parents of the node.  Read-only.
-* +ancestors+: All ancestors of the node.  Read-only.
-* +descendants+: All descendants of the node.  Read-only.
-
-=== Link interface
-
-The following class methods are available on links:
-
-* +paths+: Retrieves all paths from one node to another.
-* <tt>path?</tt>: Returns whether a node is reachable from another node.
-* +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>.
-
-== 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

@@ -1,52 +0,0 @@
-require 'rake'
-require 'yaml'
-require 'bundler'
-Bundler.setup
-
-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_bundler_dependencies
-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
-
-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/*,.bundle/environment.rb'
-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

@@ -1,5 +0,0 @@
---- 
-:major: 2
-:minor: 2
-:build: 
-:patch: 6

data/dagnabit.gemspec

@@ -1,142 +0,0 @@
-# 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 = "2.2.6"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["David Yip"]
-  s.date = %q{2010-10-01}
-  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",
-     "Gemfile",
-     "Gemfile.lock",
-     "History.txt",
-     "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{1.3.7}
-  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::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<activerecord>, ["~> 2.3.5"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<mocha>, ["= 0.9.8"])
-      s.add_development_dependency(%q<pg>, [">= 0"])
-      s.add_development_dependency(%q<shoulda>, ["= 2.10.2"])
-      s.add_development_dependency(%q<sqlite3-ruby>, [">= 0"])
-      s.add_development_dependency(%q<redgreen>, [">= 0"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<ZenTest>, [">= 0"])
-    else
-      s.add_dependency(%q<activerecord>, ["~> 2.3.5"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<mocha>, ["= 0.9.8"])
-      s.add_dependency(%q<pg>, [">= 0"])
-      s.add_dependency(%q<shoulda>, ["= 2.10.2"])
-      s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
-      s.add_dependency(%q<redgreen>, [">= 0"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<ZenTest>, [">= 0"])
-    end
-  else
-    s.add_dependency(%q<activerecord>, ["~> 2.3.5"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<mocha>, ["= 0.9.8"])
-    s.add_dependency(%q<pg>, [">= 0"])
-    s.add_dependency(%q<shoulda>, ["= 2.10.2"])
-    s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
-    s.add_dependency(%q<redgreen>, [">= 0"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<ZenTest>, [">= 0"])
-  end
-end
-