forest 0.1.1

data/.document

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

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC
+
+
+tmp/*

data/Gemfile

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+source "http://rubygems.org"
+
+gem "rubytree"

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    rubytree (0.8.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  rubytree

data/LICENSE

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+Copyright (c) 2009 Makoto Inoue
+
+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.md

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+# Forest
+
+## Summary
+
+A simple collection class to aggregate tree objects.
+It takes [Adjacency List](http://sqlsummit.com/AdjacencyList.htm) as input, shows some stats and the top x biggest trees.
+
+## Why ?
+
+Most database tables have some hierarchy related data (eg: who's your boss, who invited you to join, etc) without evan realising it in adjacency list format. Aggregating info from these trees are [a bit difficult if the depth of each trees are not even](http://dev.mysql.com/tech-resources/articles/hierarchical-data.html). Also, most trees only have 0 or 1 node attached, which need to be filtered out before rendering. That's why I created a simple wrapper to extract only trees (top x giggest trees) which are interesting enough to render.
+
+## Usage
+
+forest [filename]
+
+## Input file format
+
+[parent key], [child key], [any content(optional)]
+
+- If last field is either nil, NULL, or "", then the row becomes a root tree
+- Any middle columns are optional. If you specify them, it will be showed at tree diagram as optional information.
+- Example sql to generate the input csv "select parent_id, id, name from foo"
+
+## Input file example
+
+### examples/input.csv
+
+    1,,foo,foo2,foo3
+    2,1
+    13,2
+    3,1,bar
+    4,3
+    5,3
+    6,3
+    10,9
+    9,8
+    8,7
+    7,
+    11,
+    14,12
+    12,
+    16,15
+    15,
+    17,15
+    18,15
+    19,15
+    20,15
+
+This will form the following tree hirarchy.
+
+    1 - 2 - 13
+      - 3 - 4
+          - 5
+          - 6
+    7 - 8 - 9 - 10
+    11
+    12 - 14
+    15 - 16
+       - 17
+       - 18
+       - 19
+       - 20
+
+And here is the output.
+    
+    forest examples/input.csv
+    
+    Total 20: Average :4.0 Max size :7 Max height :4 Max width :5, Sandard Deviation 2.28035085019828
+    Top 3 trees
+    #1, sum 7, height 2
+    * 1 foo,foo2,foo3
+    |---+ 2 
+    |    +---> 13 
+    +---+ 3 bar
+        |---> 4 
+        |---> 5 
+        +---> 6 
+    Node Name: 2 Content:  Parent: 1 Children: 1 Total Nodes: 2
+    Node Name: 3 Content: bar Parent: 1 Children: 3 Total Nodes: 4
+    #2, sum 6, height 1
+    * 15 
+    |---> 16 
+    |---> 17 
+    |---> 18 
+    |---> 19 
+    +---> 20 
+    Node Name: 16 Content:  Parent: 15 Children: 0 Total Nodes: 1
+    Node Name: 17 Content:  Parent: 15 Children: 0 Total Nodes: 1
+    Node Name: 18 Content:  Parent: 15 Children: 0 Total Nodes: 1
+    Node Name: 19 Content:  Parent: 15 Children: 0 Total Nodes: 1
+    Node Name: 20 Content:  Parent: 15 Children: 0 Total Nodes: 1
+    #3, sum 4, height 3
+    * 7 
+    +---+ 8 
+        +---+ 9 
+            +---> 10 
+    Node Name: 8 Content:  Parent: 7 Children: 1 Total Nodes: 3
+    #4, sum 2, height 1
+    * 12 
+    +---> 14 
+    Node Name: 14 Content:  Parent: 12 Children: 0 Total Nodes: 1
+    #5, sum 1, height 0
+    * 11 
+
+
+## Performance.
+
+I tried parsing about 80000 rows. It used to take about 20 min, but now it takes 40 sec with 200mb memory space. The result may very depending on how deep your each tree is.
+
+## TODO (or my wishlist)
+
+- Get rid of "Node Name" output (Annoying)
+- Add more aggregate functions
+- Add more filtering functions (eg: show trees which has depth of more than 3)
+- Create a conversion program to draw on graphiviz diagram
+- Create a conversion program to draw histogram on R
+- Create a conversion program to [nested set model](http://en.wikipedia.org/wiki/Nested_set_model) or [materialized path](http://stackoverflow.com/questions/2797720/sorting-tree-with-a-materialized-path)
+- Create an adapter to switch between rdbms, nosql, or file system to avoid storing everything in memory.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  require 'bundler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "forest"
+    gem.summary = %Q{A simple collection class to aggregate tree objects}
+    gem.description = %Q{A simple collection class to aggregate tree objects.
+    It takes [Adjacency List](http://sqlsummit.com/AdjacencyList.htm) as input, shows some stats and the top x biggest trees.}
+    gem.homepage = "http://github.com/makoto/forest"
+    gem.authors = ["Makoto Inoue"]
+    gem.add_bundler_dependencies
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  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 :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "forest #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/bin/forest

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', 'lib')
+require 'csv'
+require 'forest'
+
+data = []
+file_name = ARGV[0]
+CSV.open(file_name, 'r') do |row|
+  data << row
+end
+
+forest = Forest.new(data)
+forest.print_report(100)
+exit 0

data/examples/input.csv

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+1,,foo,foo2,foo3
+2,1
+13,2
+3,1,bar
+4,3
+5,3
+6,3
+10,9
+9,8
+8,7
+7,
+11,
+14,12
+12,
+16,15
+15,
+17,15
+18,15
+19,15
+20,15

data/forest.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{forest}
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Makoto Inoue"]
+  s.date = %q{2010-11-02}
+  s.default_executable = %q{forest}
+  s.description = %q{A simple collection class to aggregate tree objects.
+    It takes [Adjacency List](http://sqlsummit.com/AdjacencyList.htm) as input, shows some stats and the top x biggest trees.}
+  s.executables = ["forest"]
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.md"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "Gemfile",
+     "Gemfile.lock",
+     "LICENSE",
+     "README.md",
+     "Rakefile",
+     "VERSION",
+     "bin/forest",
+     "examples/input.csv",
+     "forest.gemspec",
+     "lib/forest.rb",
+     "test/test_forest.rb"
+  ]
+  s.homepage = %q{http://github.com/makoto/forest}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{A simple collection class to aggregate tree objects}
+  s.test_files = [
+    "test/test_forest.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<rubytree>, [">= 0"])
+    else
+      s.add_dependency(%q<rubytree>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<rubytree>, [">= 0"])
+  end
+end
+

data/lib/forest.rb

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+#! /usr/bin/ruby
+
+require 'rubygems'
+require "bundler/setup"
+require 'tree' 
+
+class Forest
+  attr_accessor :trees, :orphants
+  
+  def initialize(data)
+    grouped_tree = data.group_by{|d| [nil, "NULL", ""].include?(d[1])}
+    @root = grouped_tree[true]
+    @children = grouped_tree[false]
+    add_root
+    add_children
+  end
+  
+  def count
+    @trees.size
+  end
+  
+  def sum
+    @trees.values.inject(0){|sum, current| sum + current.size}
+  end
+  
+  def sd
+    standard_deviation(@trees.values.map{|v| v.size })
+  end
+  
+  def avg
+    sum.to_f / @trees.size
+  end
+  
+  def biggest_node
+    max_node(:size)
+  end
+  
+  def heighest_node
+    max_node(:node_height)
+  end
+  
+  def widest_node
+    max_node(:children_size)
+  end
+  
+  def max_sum
+    biggest_node.size
+  end
+
+  def max_height
+    heighest_node.node_height + 1
+  end
+  
+  def max_width
+    widest_node.children_size
+  end
+  
+  def top(n)
+    @trees.values.sort {|x,y| y.size <=> x.size }[0..(n - 1)]
+  end
+  
+  def print_report(num = 3)
+    puts "Total #{sum}: Average :#{avg} Max size :#{max_sum} Max height :#{max_height} Max width :#{max_width}, Sandard Deviation #{sd}"
+    puts "Top #{num} trees"
+    top(num).each_with_index {|value, index| 
+      puts "##{index + 1}, sum #{value.size}, height #{value.node_height}"
+      puts value.print_tree
+    }
+  end
+  
+  def add_root
+    @trees = @root.reduce({}) do |final, current|
+      key = current.first.to_s
+      final[key] = Tree::TreeNode.new(key, get_content(current))
+      final
+    end
+  end
+  
+  def add_children
+    add_recursive(@trees, @children)
+  end
+  
+private 
+  def max_node(obj)
+    @trees.values.max{|a, b| a.send(obj) <=> b.send(obj) }
+  end
+
+  def get_content(array)
+    array[2..-1].join(",")
+  end
+  
+  def variance(population)
+    n = 0
+    mean = 0.0
+    s = 0.0
+    population.each { |x|
+      n = n + 1
+      delta = x - mean
+      mean = mean + (delta / n)
+      s = s + delta * (x - mean)
+    }
+    # if you want to calculate std deviation
+    # of a sample change this to "s / (n-1)"
+    return s / n
+  end
+
+  # calculate the standard deviation of a population
+  # accepts: an array, the population
+  # returns: the standard deviation
+  def standard_deviation(population)
+    Math.sqrt(variance(population))
+  end
+
+  def add_recursive(ancestors, decendants, previous = 0)
+    remaining = []
+    current_generation = {}
+    counter = decendants.size
+    decendants.map do |c| 
+      # p "#{counter}: #{c.inspect}" if counter % 10 == 0
+      child  = c[0]
+      parent = c[1]
+      if parent_obj = ancestors[parent.to_s]
+        parent_obj << Tree::TreeNode.new(child.to_s, get_content(c))
+        current_generation[child.to_s] = parent_obj[child.to_s]
+      else
+        remaining << c
+      end
+      counter = counter - 1
+    end
+    # p "remaining.size: #{remaining.size} previous: #{previous}"
+    if remaining == [] || remaining.size == previous
+      @orphants = remaining 
+    else
+      # p remaining
+      add_recursive(current_generation , remaining, remaining.size)
+    end
+  end
+end
+
+#  Monkey patch
+class Tree::TreeNode
+  include Enumerable
+  
+  def children_size
+    children.size
+  end
+  
+  def print_tree(level = 0)
+    if is_root?
+      print "*"
+    else
+      print "|" unless parent.is_last_sibling?
+      print(' ' * (level - 1) * 4)
+      print(is_last_sibling? ? "+" : "|")
+      print "---"
+      print(has_children? ? "+" : ">")
+    end
+    
+    puts " #{name} #{content}"
+    
+    children { |child| child.print_tree(level + 1)}
+  end
+end

data/test/test_forest.rb

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+require "test/unit"
+
+require "forest"
+
+class TestForest < Test::Unit::TestCase
+  def setup
+    # 1 - 2 - 13
+    #   - 3 - 4
+    #       - 5
+    #       - 6
+    # 7 - 8 - 9 - 10
+    # 11
+    # 12 - 14
+    # 15 - 16
+    #    - 17
+    #    - 18
+    #    - 19
+    #    - 20
+    
+    @data = [
+      [1, nil, "foo", "foo2", "foo3"] ,
+      [2, 1]   ,
+      [13, 2]  ,
+      [3, 1, "bar"]   ,
+      [4, 3]   ,
+      [5, 3]   ,
+      [6, 3]   ,
+      [10, 9]  ,
+      [9, 8]   ,
+      [8, 7]   ,
+      [7, nil] ,
+      [11, nil],
+      [14, 12] ,
+      [12, nil],
+      [16, 15] ,
+      [15, nil],
+      [17, 15] ,
+      [18, 15] ,
+      [19, 15] ,
+      [20, 15]
+    ]
+    
+    @forest = Forest.new(@data)
+  end
+  
+  def test_count
+    assert_equal(5, @forest.count)
+  end
+  
+  def test_sum
+    assert_equal(20, @forest.sum)
+  end
+
+  def test_avg
+    assert_equal(4, @forest.avg)
+  end
+  
+  def test_max_sum
+    assert_equal(7, @forest.max_sum)
+  end
+
+  def test_max_height
+    assert_equal(4, @forest.max_height)
+  end
+
+  def test_max_width
+    assert_equal(5, @forest.max_width)
+  end
+  
+  def test_top
+    assert_equal(@forest.max_sum,  @forest.top(1).first.size)
+  end
+  
+  def test_non_matching_leaf
+    non_matching_leaf = [
+      [1, nil] ,
+      [3, 2] ,
+    ]
+    forest = Forest.new(non_matching_leaf)
+    assert_equal(1, forest.count)
+    assert_equal(1, forest.orphants.size)
+  end
+end
+

metadata

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+--- !ruby/object:Gem::Specification 
+name: forest
+version: !ruby/object:Gem::Version 
+  hash: 25
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 1
+  version: 0.1.1
+platform: ruby
+authors: 
+- Makoto Inoue
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-11-02 00:00:00 +00:00
+default_executable: forest
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  name: rubytree
+  prerelease: false
+  version_requirements: *id001
+description: |-
+  A simple collection class to aggregate tree objects.
+      It takes [Adjacency List](http://sqlsummit.com/AdjacencyList.htm) as input, shows some stats and the top x biggest trees.
+email: 
+executables: 
+- forest
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.md
+files: 
+- .document
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- Rakefile
+- VERSION
+- bin/forest
+- examples/input.csv
+- forest.gemspec
+- lib/forest.rb
+- test/test_forest.rb
+has_rdoc: true
+homepage: http://github.com/makoto/forest
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: A simple collection class to aggregate tree objects
+test_files: 
+- test/test_forest.rb