aqueduct-i2b2 0.1.0

data/test/dummy/config/environments/development.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # In the development environment your application's code is reloaded on
+  # every request. This slows down response time but is perfect for development
+  # since you don't have to restart the web server when you make code changes.
+  config.cache_classes = false
+
+  # Log error messages when you accidentally call methods on nil.
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Don't care if the mailer can't send
+  config.action_mailer.raise_delivery_errors = false
+
+  # Print deprecation notices to the Rails logger
+  config.active_support.deprecation = :log
+
+  # Only use best-standards-support built into browsers
+  config.action_dispatch.best_standards_support = :builtin
+
+  # Raise exception on mass assignment protection for Active Record models
+  config.active_record.mass_assignment_sanitizer = :strict
+
+  # Log the query plan for queries taking more than this (works
+  # with SQLite, MySQL, and PostgreSQL)
+  config.active_record.auto_explain_threshold_in_seconds = 0.5
+
+  # Do not compress assets
+  config.assets.compress = false
+
+  # Expands the lines which load the assets
+  config.assets.debug = true
+end

data/test/dummy/config/environments/production.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # Code is not reloaded between requests
+  config.cache_classes = true
+
+  # Full error reports are disabled and caching is turned on
+  config.consider_all_requests_local       = false
+  config.action_controller.perform_caching = true
+
+  # Disable Rails's static asset server (Apache or nginx will already do this)
+  config.serve_static_assets = false
+
+  # Compress JavaScripts and CSS
+  config.assets.compress = true
+
+  # Don't fallback to assets pipeline if a precompiled asset is missed
+  config.assets.compile = false
+
+  # Generate digests for assets URLs
+  config.assets.digest = true
+
+  # Defaults to Rails.root.join("public/assets")
+  # config.assets.manifest = YOUR_PATH
+
+  # Specifies the header that your server uses for sending files
+  # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+  # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+  # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+  # config.force_ssl = true
+
+  # See everything in the log (default is :info)
+  # config.log_level = :debug
+
+  # Prepend all log lines with the following tags
+  # config.log_tags = [ :subdomain, :uuid ]
+
+  # Use a different logger for distributed setups
+  # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+
+  # Use a different cache store in production
+  # config.cache_store = :mem_cache_store
+
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server
+  # config.action_controller.asset_host = "http://assets.example.com"
+
+  # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+  # config.assets.precompile += %w( search.js )
+
+  # Disable delivery errors, bad email addresses will be ignored
+  # config.action_mailer.raise_delivery_errors = false
+
+  # Enable threaded mode
+  # config.threadsafe!
+
+  # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+  # the I18n.default_locale when a translation can not be found)
+  config.i18n.fallbacks = true
+
+  # Send deprecation notices to registered listeners
+  config.active_support.deprecation = :notify
+
+  # Log the query plan for queries taking more than this (works
+  # with SQLite, MySQL, and PostgreSQL)
+  # config.active_record.auto_explain_threshold_in_seconds = 0.5
+end

data/test/dummy/config/environments/test.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # The test environment is used exclusively to run your application's
+  # test suite. You never need to work with it otherwise. Remember that
+  # your test database is "scratch space" for the test suite and is wiped
+  # and recreated between test runs. Don't rely on the data there!
+  config.cache_classes = true
+
+  # Configure static asset server for tests with Cache-Control for performance
+  config.serve_static_assets = true
+  config.static_cache_control = "public, max-age=3600"
+
+  # Log error messages when you accidentally call methods on nil
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Raise exceptions instead of rendering exception templates
+  config.action_dispatch.show_exceptions = false
+
+  # Disable request forgery protection in test environment
+  config.action_controller.allow_forgery_protection    = false
+
+  # Tell Action Mailer not to deliver emails to the real world.
+  # The :test delivery method accumulates sent emails in the
+  # ActionMailer::Base.deliveries array.
+  config.action_mailer.delivery_method = :test
+
+  # Raise exception on mass assignment protection for Active Record models
+  config.active_record.mass_assignment_sanitizer = :strict
+
+  # Print deprecation notices to the stderr
+  config.active_support.deprecation = :stderr
+end

data/test/dummy/config/initializers/backtrace_silencers.rb

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+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!

data/test/dummy/config/initializers/inflections.rb

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+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format
+# (all these examples are active by default):
+# ActiveSupport::Inflector.inflections do |inflect|
+#   inflect.plural /^(ox)$/i, '\1en'
+#   inflect.singular /^(ox)en/i, '\1'
+#   inflect.irregular 'person', 'people'
+#   inflect.uncountable %w( fish sheep )
+# end
+#
+# These inflection rules are supported but not enabled by default:
+# ActiveSupport::Inflector.inflections do |inflect|
+#   inflect.acronym 'RESTful'
+# end

data/test/dummy/config/initializers/mime_types.rb

@@ -0,0 +1,5 @@
+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf
+# Mime::Type.register_alias "text/html", :iphone

data/test/dummy/config/initializers/secret_token.rb

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+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+Dummy::Application.config.secret_token = '6232881d30c4dedb755c7639701379d2c5084a66e5e7c03be119c790693737ae9ebbb1eb3d5cb0415d4c93790c7461144adbc6b358ab0300d94ebfbcdf02122b'

data/test/dummy/config/initializers/session_store.rb

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+# Be sure to restart your server when you modify this file.
+
+Dummy::Application.config.session_store :cookie_store, key: '_dummy_session'
+
+# Use the database for sessions instead of the cookie-based default,
+# which shouldn't be used to store highly confidential information
+# (create the session table with "rails generate session_migration")
+# Dummy::Application.config.session_store :active_record_store

data/test/dummy/config/initializers/wrap_parameters.rb

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+# Be sure to restart your server when you modify this file.
+#
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+  wrap_parameters format: [:json]
+end
+
+# Disable root element in JSON by default.
+ActiveSupport.on_load(:active_record) do
+  self.include_root_in_json = false
+end

data/test/dummy/config/locales/en.yml

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+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+  hello: "Hello world"

data/test/dummy/config/routes.rb

@@ -0,0 +1,58 @@
+Dummy::Application.routes.draw do
+  # The priority is based upon order of creation:
+  # first created -> highest priority.
+
+  # Sample of regular route:
+  #   match 'products/:id' => 'catalog#view'
+  # Keep in mind you can assign values other than :controller and :action
+
+  # Sample of named route:
+  #   match 'products/:id/purchase' => 'catalog#purchase', :as => :purchase
+  # This route can be invoked with purchase_url(:id => product.id)
+
+  # Sample resource route (maps HTTP verbs to controller actions automatically):
+  #   resources :products
+
+  # Sample resource route with options:
+  #   resources :products do
+  #     member do
+  #       get 'short'
+  #       post 'toggle'
+  #     end
+  #
+  #     collection do
+  #       get 'sold'
+  #     end
+  #   end
+
+  # Sample resource route with sub-resources:
+  #   resources :products do
+  #     resources :comments, :sales
+  #     resource :seller
+  #   end
+
+  # Sample resource route with more complex sub-resources
+  #   resources :products do
+  #     resources :comments
+  #     resources :sales do
+  #       get 'recent', :on => :collection
+  #     end
+  #   end
+
+  # Sample resource route within a namespace:
+  #   namespace :admin do
+  #     # Directs /admin/products/* to Admin::ProductsController
+  #     # (app/controllers/admin/products_controller.rb)
+  #     resources :products
+  #   end
+
+  # You can have the root of your site routed with "root"
+  # just remember to delete public/index.html.
+  # root :to => 'welcome#index'
+
+  # See how all your routes lay out with "rake routes"
+
+  # This is a legacy wild controller route that's not recommended for RESTful applications.
+  # Note: This route will make all actions in every controller accessible via GET requests.
+  # match ':controller(/:action(/:id))(.:format)'
+end

data/test/dummy/db/schema.rb

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+# encoding: UTF-8
+# This file is auto-generated from the current state of the database. Instead
+# of editing this file, please use the migrations feature of Active Record to
+# incrementally modify your database, and then regenerate this schema definition.
+#
+# Note that this schema.rb definition is the authoritative source for your
+# database schema. If you need to create the application database on another
+# system, you should be using db:schema:load, not running all the migrations
+# from scratch. The latter is a flawed and unsustainable approach (the more migrations
+# you'll amass, the slower it'll run and the greater likelihood for issues).
+#
+# It's strongly recommended to check this file into your version control system.
+
+ActiveRecord::Schema.define(:version => 0) do
+
+end

data/test/dummy/log/test.log

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+   (0.1ms)  select sqlite_version(*)
+   (2.6ms)  CREATE TABLE "schema_migrations" ("version" varchar(255) NOT NULL) 
+   (0.0ms)  PRAGMA index_list("schema_migrations")
+   (1.5ms)  CREATE UNIQUE INDEX "unique_schema_migrations" ON "schema_migrations" ("version")
+   (0.2ms)  select sqlite_version(*)
+   (0.1ms)  SELECT "schema_migrations"."version" FROM "schema_migrations" 
+   (0.2ms)  begin transaction
+   (0.0ms)  rollback transaction

data/test/dummy/public/404.html

@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>The page you were looking for doesn't exist (404)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/404.html -->
+  <div class="dialog">
+    <h1>The page you were looking for doesn't exist.</h1>
+    <p>You may have mistyped the address or the page may have moved.</p>
+  </div>
+</body>
+</html>

data/test/dummy/public/422.html

@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>The change you wanted was rejected (422)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/422.html -->
+  <div class="dialog">
+    <h1>The change you wanted was rejected.</h1>
+    <p>Maybe you tried to change something you didn't have access to.</p>
+  </div>
+</body>
+</html>

data/test/dummy/public/500.html

@@ -0,0 +1,25 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>We're sorry, but something went wrong (500)</title>
+  <style type="text/css">
+    body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+    div.dialog {
+      width: 25em;
+      padding: 0 4em;
+      margin: 4em auto 0 auto;
+      border: 1px solid #ccc;
+      border-right-color: #999;
+      border-bottom-color: #999;
+    }
+    h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+  </style>
+</head>
+
+<body>
+  <!-- This file lives in public/500.html -->
+  <div class="dialog">
+    <h1>We're sorry, but something went wrong.</h1>
+  </div>
+</body>
+</html>

data/test/dummy/script/rails

@@ -0,0 +1,6 @@
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+APP_PATH = File.expand_path('../../config/application',  __FILE__)
+require File.expand_path('../../config/boot',  __FILE__)
+require 'rails/commands'

data/test/test_helper.rb

@@ -0,0 +1,10 @@
+# Configure Rails Environment
+ENV["RAILS_ENV"] = "test"
+
+require File.expand_path("../dummy/config/environment.rb",  __FILE__)
+require "rails/test_help"
+
+Rails.backtrace_cleaner.remove_silencers!
+
+# Load support files
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each { |f| require f }

metadata

@@ -0,0 +1,153 @@
+--- !ruby/object:Gem::Specification
+name: aqueduct-i2b2
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Remo Mueller
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-01-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: &70210129730760 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *70210129730760
+- !ruby/object:Gem::Dependency
+  name: aqueduct
+  requirement: &70210129729220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70210129729220
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: &70210129728740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70210129728740
+description: Connects to an instance of i2b2 through Aqueduct interface
+email:
+- remosm@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/aqueduct/wrappers/i2b2.rb
+- lib/aqueduct-i2b2/version.rb
+- lib/aqueduct-i2b2.rb
+- lib/tasks/aqueduct-i2b2_tasks.rake
+- aqueduct-i2b2.gemspec
+- CHANGELOG.rdoc
+- LICENSE
+- Rakefile
+- README.rdoc
+- test/aqueduct-i2b2_test.rb
+- test/dummy/app/assets/javascripts/application.js
+- test/dummy/app/assets/stylesheets/application.css
+- test/dummy/app/controllers/application_controller.rb
+- test/dummy/app/helpers/application_helper.rb
+- test/dummy/app/views/layouts/application.html.erb
+- test/dummy/config/application.rb
+- test/dummy/config/boot.rb
+- test/dummy/config/database.yml
+- test/dummy/config/environment.rb
+- test/dummy/config/environments/development.rb
+- test/dummy/config/environments/production.rb
+- test/dummy/config/environments/test.rb
+- test/dummy/config/initializers/backtrace_silencers.rb
+- test/dummy/config/initializers/inflections.rb
+- test/dummy/config/initializers/mime_types.rb
+- test/dummy/config/initializers/secret_token.rb
+- test/dummy/config/initializers/session_store.rb
+- test/dummy/config/initializers/wrap_parameters.rb
+- test/dummy/config/locales/en.yml
+- test/dummy/config/routes.rb
+- test/dummy/config.ru
+- test/dummy/db/schema.rb
+- test/dummy/db/test.sqlite3
+- test/dummy/log/test.log
+- test/dummy/public/404.html
+- test/dummy/public/422.html
+- test/dummy/public/500.html
+- test/dummy/public/favicon.ico
+- test/dummy/Rakefile
+- test/dummy/README.rdoc
+- test/dummy/script/rails
+- test/test_helper.rb
+homepage: https://github.com/remomueller
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Connect to an instance of i2b2 through Aqueduct
+test_files:
+- test/aqueduct-i2b2_test.rb
+- test/dummy/app/assets/javascripts/application.js
+- test/dummy/app/assets/stylesheets/application.css
+- test/dummy/app/controllers/application_controller.rb
+- test/dummy/app/helpers/application_helper.rb
+- test/dummy/app/views/layouts/application.html.erb
+- test/dummy/config/application.rb
+- test/dummy/config/boot.rb
+- test/dummy/config/database.yml
+- test/dummy/config/environment.rb
+- test/dummy/config/environments/development.rb
+- test/dummy/config/environments/production.rb
+- test/dummy/config/environments/test.rb
+- test/dummy/config/initializers/backtrace_silencers.rb
+- test/dummy/config/initializers/inflections.rb
+- test/dummy/config/initializers/mime_types.rb
+- test/dummy/config/initializers/secret_token.rb
+- test/dummy/config/initializers/session_store.rb
+- test/dummy/config/initializers/wrap_parameters.rb
+- test/dummy/config/locales/en.yml
+- test/dummy/config/routes.rb
+- test/dummy/config.ru
+- test/dummy/db/schema.rb
+- test/dummy/db/test.sqlite3
+- test/dummy/log/test.log
+- test/dummy/public/404.html
+- test/dummy/public/422.html
+- test/dummy/public/500.html
+- test/dummy/public/favicon.ico
+- test/dummy/Rakefile
+- test/dummy/README.rdoc
+- test/dummy/script/rails
+- test/test_helper.rb