coupler 0.0.1-java

data/.document

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

data/.gitmodules

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+[submodule "pages"]
+	path = pages
+	url = git@github.com:coupler/coupler.github.com.git

data/.rvmrc

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+rvm jruby

data/.vimrc

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+function! s:AlternateFile()
+  let fn = substitute(expand('%'), "^".getcwd()."/", "", "")
+  let head = fnamemodify(fn, ':h')
+  let tail = fnamemodify(fn, ':t')
+
+  if match(head, '^lib/coupler/extensions') >= 0
+    return substitute(head, '^lib/coupler', 'test/integration', '').'/test_'.tail
+  elseif match(head, '^lib') >= 0
+    return substitute(head, '^lib/coupler', 'test/unit', '').'/test_'.tail
+  elseif match(head, '^test/integration/extensions') >= 0
+    return substitute(head, '^test/integration', 'lib/coupler', '').'/'.substitute(tail, '^test_', '', '')
+  elseif match(head, '^test') >= 0
+    return substitute(head, '^test/unit', 'lib/coupler', '').'/'.substitute(tail, '^test_', '', '')
+  endif
+  return ''
+endfunction
+
+function! s:Alternate(cmd)
+  let file = s:AlternateFile()
+  "if file != '' && filereadable(file)
+    if a:cmd == 'T'
+      let cmd = 'tabe'
+    elseif a:cmd == 'S'
+      let cmd = 'sp'
+    else
+      let cmd = 'e'
+    endif
+    exe ':'.cmd.' '.file
+  "else
+    "echomsg 'No alternate file is defined: '.file
+  "endif
+endfunction
+
+command! A  :call s:Alternate('')
+command! AE :call s:Alternate('E')
+command! AS :call s:Alternate('S')
+command! AV :call s:Alternate('V')
+command! AT :call s:Alternate('T')
+
+let @a='OHv/def

data/Gemfile

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+source "http://rubygems.org"
+gem 'sinatra'
+gem 'sequel'
+gem 'rack-flash'
+gem 'json'
+gem 'fastercsv'
+gem 'carrierwave'
+gem 'mongrel'
+gem 'jdbc-mysql'
+#gem 'mvn:com.h2database:h2'
+
+group :development do
+  gem 'rake'
+  gem 'jeweler'
+  gem 'forgery', :require => false
+  gem 'test-unit', '2.2.0', :require => 'test/unit'
+  gem 'mocha'
+  gem 'rack-test', :require => 'rack/test'
+  gem 'nokogiri'
+  gem 'timecop'
+  gem 'factory_girl'
+  gem 'git'
+  gem 'thor'
+  gem 'rake'
+  gem 'table_maker'
+  gem 'ruby-debug'
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.0.7)
+    carrierwave (0.5.3)
+      activesupport (~> 3.0)
+    columnize (0.3.2)
+    factory_girl (1.3.3)
+    fastercsv (1.5.4)
+    forgery (0.3.8)
+      nokogiri (~> 1.4)
+    gem_plugin (0.2.3)
+    git (1.2.5)
+    jdbc-mysql (5.1.13)
+    jeweler (1.6.0)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    json (1.5.1-java)
+    mocha (0.9.12)
+    mongrel (1.1.5-java)
+      gem_plugin (>= 0.2.3)
+    nokogiri (1.4.4.2-java)
+      weakling (>= 0.0.3)
+    rack (1.2.2)
+    rack-flash (0.1.1)
+      rack
+    rack-test (0.6.0)
+      rack (>= 1.0)
+    rake (0.8.7)
+    ruby-debug (0.10.4)
+      columnize (>= 0.1)
+      ruby-debug-base (~> 0.10.4.0)
+    ruby-debug-base (0.10.4-java)
+    sequel (3.23.0)
+    sinatra (1.2.6)
+      rack (~> 1.1)
+      tilt (>= 1.2.2, < 2.0)
+    table_maker (0.0.2)
+      sequel
+    test-unit (2.2.0)
+    thor (0.14.6)
+    tilt (1.3)
+    timecop (0.3.5)
+    weakling (0.0.4-java)
+
+PLATFORMS
+  java
+
+DEPENDENCIES
+  carrierwave
+  factory_girl
+  fastercsv
+  forgery
+  git
+  jdbc-mysql
+  jeweler
+  json
+  mocha
+  mongrel
+  nokogiri
+  rack-flash
+  rack-test
+  rake
+  ruby-debug
+  sequel
+  sinatra
+  table_maker
+  test-unit (= 2.2.0)
+  thor
+  timecop

data/LICENSE

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+Copyright (c) 2009, 2010, 2011 Vanderbilt University
+
+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/NOTES

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+How to run IRB with JDBC/MySQL
+------------------------------
+
+GEM_HOME=/opt/jruby/lib/ruby/gems/1.8 java -cp \
+  vendor/java/mysql-connector-java-5.1.13/mysql-connector-java-5.1.13-bin.jar:vendor/java/jruby-complete.jar \
+  org.jruby.Main -S irb

data/README.rdoc

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+= coupler
+
+Coupler is a Sinatra application for linking databases together.
+
+== Note on Patches/Pull Requests
+
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but
+  bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2009-2011 Vanderbilt University. See LICENSE for details.

data/Rakefile

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+if RUBY_PLATFORM != 'java'
+  puts "ERROR: JRuby is required to run Coupler."
+  exit
+end
+
+require 'open-uri'
+require 'tempfile'
+require 'fileutils'
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+def confirm(prompt)
+  answer = nil
+  while answer != "y" && answer != "n"
+    print "#{prompt} Are you sure? [yn] "
+    $stdout.flush
+    answer = $stdin.gets.chomp.downcase
+  end
+  exit if answer == "n"
+end
+
+alias :original_ruby :ruby
+def ruby(*args, &block)
+  # turn on objectspace (for nokogiri)
+  unless String === args[0]
+    args = [""] + args
+  end
+  args[0] = "-X+O #{args[0]}"
+  original_ruby(args, &block)
+end
+
+Dir['tasks/*.rake'].sort.each { |f| import f }
+
+task :default => :test

data/TODO

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+Major features/bugs:
+- Job management: canceling, etc.
+- Chain matchers
+- package:dist changes bundler config; fix this!
+
+Other ideas:
+- Do authorization on projects
+- Allow user to enter resource password whenever needed; don't store it
+- Better migrations based on commit hashes
+  - Use classes in a previous state
+  - Run migrations before upgrading code, or vice versa

data/VERSION

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+0.0.1

data/bin/coupler

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+#!/usr/bin/env jruby
+require 'rubygems'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), "..", "lib"))
+require 'coupler'
+
+Coupler::Runner.new

data/db/.gitignore

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+test
+production
+development
+bin
+data
+share

data/db/migrate/001_initial_schema.rb

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+class InitialSchema < Sequel::Migration
+  def up
+    create_table(:connections) do
+      primary_key :id
+      String :name
+      String :slug
+      String :adapter
+      String :host
+      Integer :port
+      String :username
+      String :password
+      String :database_name
+      Time :created_at
+      Time :updated_at
+    end
+
+    [:projects, :projects_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :name
+        String :slug
+        String :description
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:resources, :resources_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :name
+        String :slug
+        String :table_name
+        String :primary_key_name, :default => "id"
+        Integer :connection_id
+        Integer :project_id
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :transformed_at
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:fields, :fields_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :name
+        String :type
+        String :db_type
+        String :local_type
+        String :local_db_type
+        Boolean :is_primary_key, :default => false
+        Boolean :is_selected, :default => true
+        Integer :resource_id
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:transformers, :transformers_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :name
+        Text :code
+        String :allowed_types
+        String :result_type
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:transformations, :transformations_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        Integer :transformer_id
+        Integer :field_id
+        Integer :resource_id
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:scenarios, :scenarios_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :name
+        String :slug
+        String :description
+        Integer :project_id
+        Integer :resource_1_id
+        Integer :resource_2_id
+        String :linkage_type
+        Integer :score_set_id
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :last_run_at
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    [:matchers, :matchers_versions].each do |name|
+      create_table(name) do
+        primary_key :id
+        String :comparator_name
+        Text :comparator_options
+        Integer :scenario_id
+        Integer :version, :default => 0
+        Integer :current_id   if name.to_s =~ /_versions$/
+        Time :created_at
+        Time :updated_at
+      end
+    end
+
+    create_table :jobs do
+      primary_key :id
+      String :name
+      String :status
+      Integer :resource_id
+      Integer :scenario_id
+      Integer :total, :default => 0
+      Integer :completed, :default => 0
+      Time :created_at
+      Time :updated_at
+      Time :started_at
+      Time :completed_at
+    end
+
+    create_table :results do
+      primary_key :id
+      Integer :scenario_id
+      Integer :scenario_version
+      Integer :score_set_id
+      Time :created_at
+      Time :updated_at
+    end
+  end
+
+  def down
+    drop_table(
+      :projects,
+      :projects_versions,
+      :resources,
+      :resources_versions,
+      :transformers,
+      :transformers_versions,
+      :transformations,
+      :transformations_versions,
+      :scenarios,
+      :scenarios_versions,
+      :matchers,
+      :matchers_versions,
+      :jobs,
+      :results
+    )
+  end
+end

data/db/migrate/002_stub.rb

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+Sequel.migration do
+  up { }
+  down { }
+end

data/db/migrate/003_stub.rb

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+Sequel.migration do
+  up { }
+  down { }
+end

data/db/migrate/004_create_comparisons.rb

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+class CreateComparisons < Sequel::Migration
+  def up
+    create_table :comparisons do
+      primary_key :id
+      Integer :matcher_id
+      Integer :matcher_version
+      Integer :field_1_id
+      Integer :field_2_id
+      Time :created_at
+      Time :updated_at
+    end
+
+    [:matchers, :matchers_versions].each do |name|
+      alter_table(name) do
+        drop_column :comparator_options
+      end
+    end
+  end
+
+  def down
+    [:matchers, :matchers_versions].each do |name|
+      alter_table(name) do
+        add_column :comparator_options, :text
+      end
+    end
+    drop_table :comparisons
+  end
+end

data/db/migrate/005_move_database_name.rb

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+class MoveDatabaseName < Sequel::Migration
+  def up
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { add_column(:database_name, String) }
+    end
+
+    self[:connections].each do |connection|
+      [:resources, :resources_versions].each do |name|
+        self[name].filter(:connection_id => connection[:id]).update(:database_name => connection[:database_name])
+      end
+    end
+
+    alter_table(:connections) { drop_column(:database_name) }
+  end
+
+  def down
+    raise "This migration is not reversible."
+  end
+end

data/db/migrate/006_upgrade_comparisons.rb

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+class UpgradeComparisons < Sequel::Migration
+  def marshal(v)
+    [Marshal.dump(v)].pack('m')
+  end
+
+  def up
+    alter_table(:comparisons) do
+      add_column :lhs_type, String
+      add_column :lhs_value, String
+      add_column :operator, String
+      add_column :rhs_type, String
+      add_column :rhs_value, String
+    end
+    dataset = self[:comparisons]
+    dataset.each do |comparison|
+      dataset.filter(:id => comparison[:id]).update({
+        :lhs_type => "field", :lhs_value => marshal(comparison[:field_1_id]),
+        :rhs_type => "field", :rhs_value => marshal(comparison[:field_2_id]),
+        :operator => "equals"
+      })
+    end
+    alter_table(:comparisons) do
+      drop_column :field_1_id
+      drop_column :field_2_id
+    end
+
+    alter_table(:matchers) { drop_column(:comparator_name) }
+    alter_table(:matchers_versions) { drop_column(:comparator_name) }
+  end
+
+  def down
+    raise "This migration is not reversible."
+  end
+end

data/db/migrate/007_add_which_to_comparisons.rb

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+Sequel.migration do
+  up do
+    alter_table :comparisons do
+      add_column :lhs_which, Integer
+      add_column :rhs_which, Integer
+    end
+    ds = self[:comparisons].
+      select(:comparisons__id).
+      join(:matchers, :matchers__id => :comparisons__matcher_id).
+      join(:scenarios, :scenarios__id => :matchers__scenario_id).
+      filter(:scenarios__resource_2_id => nil)
+    ids = ds.all.collect { |x| x[:id] }
+    self[:comparisons].filter(:id => ids, :lhs_type => 'field').update(:lhs_which => 1)
+    self[:comparisons].filter(:id => ids, :rhs_type => 'field').update(:rhs_which => 2)
+  end
+
+  down do
+    alter_table :comparisons do
+      drop_column :lhs_which
+      drop_column :rhs_which
+    end
+  end
+end

data/db/migrate/008_add_result_field_to_transformations.rb

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+Sequel.migration do
+  up do
+    [:transformations, :transformations_versions].each do |name|
+      alter_table(name) do
+        rename_column(:field_id, :source_field_id)
+        add_column(:result_field_id, Integer)
+        add_column(:position, Integer)
+      end
+      self[name].update(:result_field_id => :source_field_id)
+
+      position = nil
+      last_resource_id = nil
+      self[name].order(:id).each do |record|
+        if record[:resource_id] != last_resource_id
+          position = 0
+          last_resource_id = record[:resource_id]
+        end
+        position += 1
+        self[name].filter(:id => record[:id]).update(:position => position)
+      end
+    end
+  end
+
+  down do
+    [:transformations, :transformations_versions].each do |name|
+      alter_table(name) do
+        rename_column(:source_field_id, :field_id)
+        drop_column(:result_field_id)
+        drop_column(:position)
+      end
+    end
+  end
+end

data/db/migrate/009_add_generated_flag_to_fields.rb

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+Sequel.migration do
+  up do
+    [:fields, :fields_versions].each do |name|
+      alter_table(name) { add_column(:is_generated, :boolean, :default => false) }
+      self[name].update(:is_generated => false)
+    end
+  end
+
+  down do
+    alter_table(:fields) { drop_column(:is_generated) }
+    alter_table(:fields_versions) { drop_column(:is_generated) }
+  end
+end

data/db/migrate/010_create_imports.rb

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+Sequel.migration do
+  up do
+    create_table :imports do
+      primary_key :id
+      String :name
+      String :data
+      String :type, :default => "csv"
+      Text :fields
+      Integer :project_id
+      Time :created_at
+      Time :updated_at
+    end
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { add_column :import_id, Integer }
+    end
+  end
+
+  down do
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { drop_column :import_id }
+    end
+    drop_table :imports
+  end
+end

data/db/migrate/011_add_primary_key_type.rb

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+Sequel.migration do
+  up do
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { add_column(:primary_key_type, String) }
+      self[name].update(:primary_key_type => 'integer')
+    end
+  end
+
+  down do
+    alter_table(:resources) { drop_column(:primary_key_type) }
+    alter_table(:resources_versions) { drop_column(:primary_key_type) }
+  end
+end

data/db/migrate/012_add_transformed_with_to_resources.rb

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+Sequel.migration do
+  up do
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { add_column(:transformed_with, String) }
+    end
+  end
+
+  down do
+    [:resources, :resources_versions].each do |name|
+      alter_table(name) { drop_column(:transformed_with) }
+    end
+  end
+end

data/db/migrate/013_add_run_count_to_scenarios.rb

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+Sequel.migration do
+  up do
+    [:scenarios, :scenarios_versions].each do |name|
+      alter_table(name) { add_column(:run_count, Integer, :default => 0) }
+    end
+  end
+
+  down do
+    [:scenarios, :scenarios_versions].each do |name|
+      alter_table(name) { drop_column(:run_count) }
+    end
+  end
+end