aker-confident 0.1.1

data/.gitignore

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+pkg/*
+*.gem
+.bundle
+.rvmrc
+spec/assets/*.db
+
+
+testbed/log/*.log
+testbed/db/*
+testbed/.bundle
+testbed/*

data/.rbenv-version

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+ree-1.8.7-2011.03

data/Gemfile

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+source "http://rubygems.org"
+source "http://download.bioinformatics.northwestern.edu/gems/"
+
+# Specify your gem's dependencies in confident.gemspec
+gemspec
+
+gem 'ruby-debug'

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    aker-confident (0.1.0)
+      aker
+      aker-rails
+      haml
+      schema_qualified_tables
+      sinatra
+
+GEM
+  remote: http://rubygems.org/
+  remote: http://download.bioinformatics.northwestern.edu/gems/
+  specs:
+    abstract (1.0.0)
+    actionmailer (3.0.11)
+      actionpack (= 3.0.11)
+      mail (~> 2.2.19)
+    actionpack (3.0.11)
+      activemodel (= 3.0.11)
+      activesupport (= 3.0.11)
+      builder (~> 2.1.2)
+      erubis (~> 2.6.6)
+      i18n (~> 0.5.0)
+      rack (~> 1.2.1)
+      rack-mount (~> 0.6.14)
+      rack-test (~> 0.5.7)
+      tzinfo (~> 0.3.23)
+    activemodel (3.0.11)
+      activesupport (= 3.0.11)
+      builder (~> 2.1.2)
+      i18n (~> 0.5.0)
+    activerecord (3.0.11)
+      activemodel (= 3.0.11)
+      activesupport (= 3.0.11)
+      arel (~> 2.0.10)
+      tzinfo (~> 0.3.23)
+    activeresource (3.0.11)
+      activemodel (= 3.0.11)
+      activesupport (= 3.0.11)
+    activesupport (3.0.11)
+    aker (3.0.3)
+      activesupport (>= 2.3.0)
+      castanet (~> 1.0.0)
+      i18n (~> 0.4)
+      net-ldap (~> 0.1.1)
+      rubytree (~> 0.7.0)
+      warden (~> 1.0)
+    aker-rails (3.0.2)
+      aker (~> 3.0)
+      rails (~> 3.0, >= 3.0.4)
+    arel (2.0.10)
+    builder (2.1.2)
+    capybara (0.3.7)
+      culerity (>= 0.2.4)
+      mime-types (>= 1.16)
+      nokogiri (>= 1.3.3)
+      rack (>= 1.0.0)
+      rack-test (>= 0.5.2)
+      selenium-webdriver (>= 0.0.3)
+    castanet (1.0.1)
+    childprocess (0.3.1)
+      ffi (~> 1.0.6)
+    columnize (0.3.6)
+    culerity (0.2.15)
+    diff-lcs (1.1.3)
+    erubis (2.6.6)
+      abstract (>= 1.0.0)
+    ffi (1.0.11)
+    haml (3.1.4)
+    i18n (0.5.0)
+    json (1.6.5)
+    linecache (0.46)
+      rbx-require-relative (> 0.0.4)
+    mail (2.2.19)
+      activesupport (>= 2.3.6)
+      i18n (>= 0.4.0)
+      mime-types (~> 1.16)
+      treetop (~> 1.4.8)
+    mime-types (1.17.2)
+    multi_json (1.0.4)
+    net-ldap (0.1.1)
+    nokogiri (1.5.0)
+    polyglot (0.3.3)
+    rack (1.2.5)
+    rack-mount (0.6.14)
+      rack (>= 1.0.0)
+    rack-test (0.5.7)
+      rack (>= 1.0)
+    rails (3.0.11)
+      actionmailer (= 3.0.11)
+      actionpack (= 3.0.11)
+      activerecord (= 3.0.11)
+      activeresource (= 3.0.11)
+      activesupport (= 3.0.11)
+      bundler (~> 1.0)
+      railties (= 3.0.11)
+    railties (3.0.11)
+      actionpack (= 3.0.11)
+      activesupport (= 3.0.11)
+      rake (>= 0.8.7)
+      rdoc (~> 3.4)
+      thor (~> 0.14.4)
+    rake (0.9.2.2)
+    rbx-require-relative (0.0.5)
+    rdoc (3.12)
+      json (~> 1.4)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
+    rspec-rails (2.8.1)
+      actionpack (>= 3.0)
+      activesupport (>= 3.0)
+      railties (>= 3.0)
+      rspec (~> 2.8.0)
+    ruby-debug (0.10.4)
+      columnize (>= 0.1)
+      ruby-debug-base (~> 0.10.4.0)
+    ruby-debug-base (0.10.4)
+      linecache (>= 0.3)
+    rubytree (0.7.0)
+    rubyzip (0.9.6.1)
+    schema_qualified_tables (1.0.1)
+      activerecord (>= 2.3)
+    selenium-webdriver (2.19.0)
+      childprocess (>= 0.2.5)
+      ffi (~> 1.0.9)
+      multi_json (~> 1.0.4)
+      rubyzip
+    sinatra (1.2.8)
+      rack (~> 1.1)
+      tilt (>= 1.2.2, < 2.0)
+    sqlite3 (1.3.5)
+    thor (0.14.6)
+    tilt (1.3.3)
+    treetop (1.4.10)
+      polyglot
+      polyglot (>= 0.3.1)
+    tzinfo (0.3.31)
+    warden (1.1.0)
+      rack (>= 1.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  aker-confident!
+  capybara (= 0.3.7)
+  rack-test
+  rails (= 3.0.11)
+  rspec
+  rspec-rails
+  ruby-debug
+  sqlite3

data/LICENSE

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+Copyright (C) 2011 by William Dix, Peter Nyberg
+ 
+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

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+Confident
+=========
+
+Confident is a Rails gem-plugin which handles user 
+confidentiality agreements.  It prevents access to resources
+without a signed confidentiality agreement and provides an interface
+to sign said agreement.
+
+### Configuration
+
+To configure Confident create an initializer in initializers/confident.rb. 
+
+    Confident.configure{ :conf_model => Signature, 
+	                 :conf_file => "../../agreement.txt",
+                         :conf_host_hook => {|env| env['aker.check']}
+ 
+The class passed as conf\_model must be respond to signed? and sign methods which take
+a Aker::User as arguments.  The conf\_file option is a path to the file
+containing the desired text for the confidentiality agreement. The conf\_host\_hook
+option is an object which responds to call and receives the rack env. The hook 
+determines whether confident will be active or not on a request. 
+
+
+### Running Tests
+
+The tests which do not require a full Rails application are in the top level
+of the spec/ directory.  Within integration are specs requiring a Rails application.
+
+In order to set up the testbed application and run Rails integration tests:
+
+    rake -f init_testbed.rakefile 
+    cd testbed
+    rake spec

data/Rakefile

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+require 'bundler'
+Bundler::GemHelper.install_tasks

data/aker-confident.gemspec

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+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "aker/confident/version"
+
+Gem::Specification.new do |s|
+  s.name        = "aker-confident"
+  s.version     = Aker::Confident::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["William Dix", "Peter Nyberg"]
+  s.email       = ["wjdix@northwestern.edu"]
+  s.homepage    = ""
+  s.summary     = %q{Confidentiality gem for Aker }
+  s.description = %q{ialdskj}
+
+  s.rubyforge_project = "aker-confident"
+  
+  s.add_dependency('aker')
+  s.add_dependency('aker-rails')
+  s.add_dependency('sinatra')
+  s.add_dependency('haml')
+  s.add_dependency('schema_qualified_tables')
+  
+  s.add_development_dependency('rails', "3.0.11")
+  s.add_development_dependency('rspec')
+  s.add_development_dependency('rspec-rails')
+  s.add_development_dependency('capybara', '0.3.7')
+  s.add_development_dependency('rack-test')
+  s.add_development_dependency('sqlite3')
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+end

data/assets/templates/agreement.haml

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+:css
+  div#agreement {
+    width: 500px;
+    margin-left: 200px;
+    margin-top: 20px;
+    font-family: Arial,Sans-serif;
+    font-size: small;
+  }
+  input#agree_button {
+    margin-left:200px;
+    margin-top: 20px;
+  }
+  #image{
+    margin-left: 200px;
+  }
+
+#agreement
+  =@conf_agreement
+%form{:action => "#{@root_url}/sign_agreement", :method => "post"}
+  %input{:type => "hidden", :value => @original_target, :name => "original"}
+  %br
+  %input#agree_button{:type => "submit", :value => "I agree and accept the terms"}
+          
+          

data/init_testbed.rakefile

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+desc "Set up a rails app for testing in the spec dir"
+task :default => [:"testbed:generate", :"testbed:generate_resource", :"testbed:generate_sig_model", :"testbed:migrate", 
+                  :"testbed:config_confident", :"testbed:conf_agreement", :"testbed:bcsec"]
+
+namespace "testbed" do
+  # "testbed" is also hardcoded in the spec/spec_helper.rb features/support/env.rb and gitignore file. Change it there too...
+  
+  desc "Generate rails, rspec, cucumber"
+  task :generate do
+    chdir("testbed") do
+      sh "bundle install"
+      sh "bundle exec rails new . --skip-gemfile"
+      sh "bundle exec rails generate rspec:install"
+      sh "rm -rf features"
+      spec_helper = <<-HELPER
+      ENV["RAILS_ENV"] ||= 'test'
+      require File.expand_path(File.join(File.dirname(__FILE__),'..','config','environment'))
+      require 'spec/autorun'
+      require 'spec/rails'
+      require 'capybara/dsl'
+      require 'capybara/rails'
+      Dir[File.expand_path(File.join(File.dirname(__FILE__),'support','**','*.rb'))].each {|f| require f}
+
+      Spec::Runner.configure do |config|
+        # If you're not using ActiveRecord you should remove these
+        # lines, delete config/database.yml and disable :active_record
+        # in your config/boot.rb
+        config.use_transactional_fixtures = false
+        config.use_instantiated_fixtures  = false
+        config.fixture_path = RAILS_ROOT + '/spec/fixtures/'
+        config.include(Capybara, :type => :integration)
+        Capybara.current_driver = :selenium
+      end
+      HELPER
+    end
+  end
+ 
+  desc "create sample resource"
+  task :generate_resource do
+    chdir("testbed") do
+      sh "bundle exec rails generate scaffold lab name:string result:integer"
+    end
+  end
+  
+  desc "create model for conf signature"
+  task :generate_sig_model do
+    chdir("testbed") do
+      sh "bundle exec rails generate model Signature username:string created_at:date"
+      sig_model = <<-MODEL
+      class Signature < ActiveRecord::Base
+        def self.signed?(user)
+          find_by_username(user.username)
+        end
+        def self.sign(user)
+          create(:username => user.username)
+        end
+      end
+      MODEL
+      File.open('app/models/signature.rb', 'w') do |f|
+        f.write sig_model
+      end
+    end
+  end
+
+  desc "Generate, migrate testbed"
+  task :migrate do
+    chdir("testbed") do
+      sh "bundle exec rake db:migrate db:test:prepare"
+    end
+  end
+  
+  desc "add initializer file for confident"
+  task :config_confident do
+    chdir("testbed") do
+      conf_config = "Aker::Confident.configure({:conf_model => Signature, :conf_file => File.join(File.dirname(__FILE__), \"..\", \"..\", \"conf_agreement.txt\")})\n"
+      File.open("config/initializers/confident.rb", 'w'){ |f| f.write conf_config }
+    end
+  end
+  
+  desc "add initializer file for bcsec"
+  task :bcsec do
+    chdir("testbed") do
+      bcsec_conf = <<-CONF
+      Aker.configure {
+        ui_mode :form
+        portal :test
+        authority Aker::Authorities::Static.from_file \"\#{RAILS_ROOT}/../spec/assets/test-users.yml\"
+      }
+      CONF
+      File.open("config/initializers/aker.rb", 'w'){ |f| f.write bcsec_conf }
+      con_file = File.read "app/controllers/application_controller.rb"
+      File.open("app/controllers/application_controller.rb", 'w') do |f|
+        f.write con_file.sub!("class ApplicationController < ActionController::Base", "class ApplicationController < ActionController::Base\n  include Aker::Rails::SecuredController")
+      end
+    end
+  end
+  
+  desc "add conf_agreement file"
+  task :conf_agreement do
+    chdir("testbed") do
+      conf_agreement = "Don't share this, dirtbag!"
+      File.open("conf_agreement.txt", 'w'){|f| f.write conf_agreement}
+    end
+  end
+
+  desc "Remove testbed app"
+  task :remove do
+    puts "Removing the test_app in the spec folder"
+    chdir("testbed") do
+      sh 'rm -rf Gemfile.lock README Rakefile app config db doc features lib log public script spec surveys test tmp vendor conf_agreement.txt'
+    end
+  end
+end

data/lib/aker-confident.rb

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+require 'aker/confident'

data/lib/aker/confident.rb

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+require 'active_support'
+require 'aker'
+module Aker
+  module Confident
+    autoload :Configuration,  'aker/confident/configuration'
+    autoload :Signer, 'aker/confident/signer'
+    autoload :Sinatra, 'aker/confident/sinatra'
+    autoload :Rack, 'aker/confident/rack'
+    autoload :DefaultConfiguration, 'aker/confident/configuration'
+    autoload :AkerUserExt, 'aker/confident/aker_user_ext'
+    autoload :AkerSlice, 'aker/confident/aker_slice'
+
+    class << self
+      include Signer
+      attr_accessor :configuration
+
+      def configuration
+        @configuration
+      end
+
+      def configure(hash_options={}, &config_block)
+        if config_block
+          @configuration = Confident::Configuration.new(hash_options).define &config_block
+        else
+          @configuration = Confident::Configuration.new(hash_options)
+        end
+        @configuration.verify!
+      end
+
+      def conf_model
+        @configuration.model
+      end
+      def root_url
+        @configuration.root_url
+      end
+      def host_hook
+        @configuration.host_hook
+      end
+
+      def pass_through?(env)
+        hooks.any?{|hook| hook.call(env) }
+      end
+
+      # if true Confident should intercept requests
+      def default_pass_through_hooks
+        [
+          lambda {|env| !env['aker.interactive'] },
+          lambda {|env| (env['aker.check'] && env['aker.check'].user == nil) },
+          lambda {|env| env['PATH_INFO'] == '/logout' },
+          lambda {|env| env['REQUEST_METHOD'] == 'POST' && env['PATH_INFO'] != '/sign_agreement' },
+          lambda {|env| env['aker.check'].user.signed? }
+        ]
+      end
+
+      def hooks
+        default_pass_through_hooks + configuration.pass_through_hooks
+      end
+    end
+    Aker::Configuration.add_default_slice Confident::AkerSlice.new
+    Aker::User.send(:include, Confident::AkerUserExt)
+  end
+end