abstractor 1.0.8

data/lib/setup/data/icdo3_sites_with_laterality.txt

@@ -0,0 +1,11 @@
+icdo3_code
+C70.0
+C71.0
+C71.1
+C71.2
+C71.3
+C71.4
+C72.2
+C72.3
+C72.4
+C72.5

data/lib/setup/data/site_site_categories.txt

@@ -0,0 +1,28 @@
+site_category	icdo3_code
+central nervous system	C70.0
+central nervous system	C70.1
+central nervous system	C70.9
+central nervous system	C71.0
+central nervous system	C71.1
+central nervous system	C71.2
+central nervous system	C71.3
+central nervous system	C71.4
+central nervous system	C71.5
+central nervous system	C71.6
+central nervous system	C71.7
+central nervous system	C71.8
+central nervous system	C71.9
+central nervous system	C72.0
+central nervous system	C72.1
+central nervous system	C72.2
+central nervous system	C72.3
+central nervous system	C72.4
+central nervous system	C72.5
+central nervous system	C72.8
+central nervous system	C72.9
+central nervous system	C75.1
+central nervous system	C75.2
+central nervous system	C75.3
+central nervous system	C41.0
+central nervous system	C41.1
+central nervous system	C44.4

data/lib/tasks/abstractor_tasks.rake

@@ -0,0 +1,22 @@
+# desc "Explaining what the task does"
+# task :abstractor do
+#   # Task goes here
+# end
+
+namespace :abstractor do
+  namespace :setup do
+    desc 'Load abstraction schemas (specify file to parse with FILE=myfile.yml) '
+    task :abstraction_schemas => :environment do
+      file = ENV["FILE"]
+      raise "File name has to be provided" if file.blank?
+      raise "File does not exist: #{file}" unless FileTest.exists?(file)
+      puts 'Little my says not done yet!  Get to work!'
+    end
+
+    desc 'Load '
+    task :system => :environment do
+      # raise "File does not exist: #{file}" unless FileTest.exists?(file)
+      Abstractor::Setup.system
+    end
+  end
+end

data/lib/tasks/cucumber.rake

@@ -0,0 +1,65 @@
+# IMPORTANT: This file is generated by cucumber-rails - edit at your own peril.
+# It is recommended to regenerate this file in the future when you upgrade to a 
+# newer version of cucumber-rails. Consider adding your own code to a new file 
+# instead of editing this one. Cucumber will automatically load all features/**/*.rb
+# files.
+
+
+unless ARGV.any? {|a| a =~ /^gems/} # Don't load anything when running the gems:* tasks
+
+vendored_cucumber_bin = Dir["#{Rails.root}/vendor/{gems,plugins}/cucumber*/bin/cucumber"].first
+$LOAD_PATH.unshift(File.dirname(vendored_cucumber_bin) + '/../lib') unless vendored_cucumber_bin.nil?
+
+begin
+  require 'cucumber/rake/task'
+
+  namespace :cucumber do
+    Cucumber::Rake::Task.new({:ok => 'db:test:prepare'}, 'Run features that should pass') do |t|
+      t.binary = vendored_cucumber_bin # If nil, the gem's binary is used.
+      t.fork = true # You may get faster startup if you set this to false
+      t.profile = 'default'
+    end
+
+    Cucumber::Rake::Task.new({:wip => 'db:test:prepare'}, 'Run features that are being worked on') do |t|
+      t.binary = vendored_cucumber_bin
+      t.fork = true # You may get faster startup if you set this to false
+      t.profile = 'wip'
+    end
+
+    Cucumber::Rake::Task.new({:rerun => 'db:test:prepare'}, 'Record failing features and run only them if any exist') do |t|
+      t.binary = vendored_cucumber_bin
+      t.fork = true # You may get faster startup if you set this to false
+      t.profile = 'rerun'
+    end
+
+    desc 'Run all features'
+    task :all => [:ok, :wip]
+
+    task :statsetup do
+      require 'rails/code_statistics'
+      ::STATS_DIRECTORIES << %w(Cucumber\ features features) if File.exist?('features')
+      ::CodeStatistics::TEST_TYPES << "Cucumber features" if File.exist?('features')
+    end
+  end
+  desc 'Alias for cucumber:ok'
+  task :cucumber => 'cucumber:ok'
+
+  task :default => :cucumber
+
+  task :features => :cucumber do
+    STDERR.puts "*** The 'features' task is deprecated. See rake -T cucumber ***"
+  end
+
+  # In case we don't have ActiveRecord, append a no-op task that we can depend upon.
+  task 'db:test:prepare' do
+  end
+
+  task :stats => 'cucumber:statsetup'
+rescue LoadError
+  desc 'cucumber rake task not available (cucumber not installed)'
+  task :cucumber do
+    abort 'Cucumber rake task is not available. Be sure to install cucumber as a gem or plugin'
+  end
+end
+
+end

metadata

@@ -0,0 +1,754 @@
+--- !ruby/object:Gem::Specification
+name: abstractor
+version: !ruby/object:Gem::Version
+  version: 1.0.8
+platform: ruby
+authors:
+- Michael Gurley, Yulia Bushmanova
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-05-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: jquery-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.1'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+- !ruby/object:Gem::Dependency
+  name: jquery-ui-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.2'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.2'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.2.0
+- !ruby/object:Gem::Dependency
+  name: haml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.5
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.5
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.0.5
+- !ruby/object:Gem::Dependency
+  name: sass-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.6
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.2.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.2.6
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.2.6
+- !ruby/object:Gem::Dependency
+  name: paper_trail
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+- !ruby/object:Gem::Dependency
+  name: stanford-core-nlp
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.8
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.3.8
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.8
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.3.8
+- !ruby/object:Gem::Dependency
+  name: rspec-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.14.1
+- !ruby/object:Gem::Dependency
+  name: factory_girl_rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.4.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.4.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.4.0
+- !ruby/object:Gem::Dependency
+  name: cucumber-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+- !ruby/object:Gem::Dependency
+  name: capybara
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+- !ruby/object:Gem::Dependency
+  name: selenium-webdriver
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.40.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.40.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.40.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.40.0
+- !ruby/object:Gem::Dependency
+  name: database_cleaner
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+- !ruby/object:Gem::Dependency
+  name: ansi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.3
+- !ruby/object:Gem::Dependency
+  name: sprockets
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.2.1
+- !ruby/object:Gem::Dependency
+  name: nubic-gem-tasks
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: redcarpet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Rails engine that provides functionality for the defintion of discrete
+  data points to be derived from narrative text via natural language processing (NLP)
+  and the presentation of NLP-derived abstracted data points for confirmation/revision.
+email:
+- m-gurley@northwestern.edu, y.bushmanova@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- MIT-LICENSE
+- README.md
+- Rakefile
+- app/assets/images/abstractor/add.png
+- app/assets/images/abstractor/ajax-loader.gif
+- app/assets/images/abstractor/bar.gif
+- app/assets/images/abstractor/bti_logo.jpg
+- app/assets/images/abstractor/bullet_arrow_down.png
+- app/assets/images/abstractor/bullet_arrow_up.png
+- app/assets/images/abstractor/cog.png
+- app/assets/images/abstractor/delete.png
+- app/assets/images/abstractor/edit.png
+- app/assets/images/abstractor/excel.png
+- app/assets/images/abstractor/favicon.ico
+- app/assets/images/abstractor/greencheck.gif
+- app/assets/images/abstractor/loading.gif
+- app/assets/images/abstractor/nu_logo.jpg
+- app/assets/images/abstractor/nubic_logo.png
+- app/assets/images/abstractor/page.png
+- app/assets/images/abstractor/rails.png
+- app/assets/images/abstractor/robert_h_lurie.jpg
+- app/assets/images/abstractor/show.png
+- app/assets/images/abstractor/switch_minus.gif
+- app/assets/images/abstractor/switch_plus.gif
+- app/assets/javascripts/abstractor/abstractor.js
+- app/assets/javascripts/abstractor/application.js
+- app/assets/javascripts/abstractor/combobox.js
+- app/assets/javascripts/abstractor/jquery/jquery.form.js
+- app/assets/javascripts/abstractor/nested_attributes.js
+- app/assets/stylesheets/abstractor/abstractor_abstractions.css
+- app/assets/stylesheets/abstractor/application.css
+- app/assets/stylesheets/abstractor/jquery.ui.override.css.scss
+- app/controllers/abstractor/abstractor_abstraction_groups_controller.rb
+- app/controllers/abstractor/abstractor_abstractions_controller.rb
+- app/controllers/abstractor/abstractor_suggestions_controller.rb
+- app/controllers/abstractor/application_controller.rb
+- app/helpers/abstractor/application_helper.rb
+- app/models/abstractor/abstractor_abstraction.rb
+- app/models/abstractor/abstractor_abstraction_group.rb
+- app/models/abstractor/abstractor_abstraction_group_member.rb
+- app/models/abstractor/abstractor_abstraction_schema.rb
+- app/models/abstractor/abstractor_abstraction_schema_object_value.rb
+- app/models/abstractor/abstractor_abstraction_schema_predicate_variant.rb
+- app/models/abstractor/abstractor_abstraction_schema_relation.rb
+- app/models/abstractor/abstractor_abstraction_source.rb
+- app/models/abstractor/abstractor_object_type.rb
+- app/models/abstractor/abstractor_object_value.rb
+- app/models/abstractor/abstractor_object_value_variant.rb
+- app/models/abstractor/abstractor_relation_type.rb
+- app/models/abstractor/abstractor_rule_type.rb
+- app/models/abstractor/abstractor_subject.rb
+- app/models/abstractor/abstractor_subject_group.rb
+- app/models/abstractor/abstractor_subject_group_member.rb
+- app/models/abstractor/abstractor_subject_relation.rb
+- app/models/abstractor/abstractor_suggestion.rb
+- app/models/abstractor/abstractor_suggestion_object_value.rb
+- app/models/abstractor/abstractor_suggestion_source.rb
+- app/models/abstractor/abstractor_suggestion_status.rb
+- app/views/abstractor/abstractor_abstraction_groups/_form.html.haml
+- app/views/abstractor/abstractor_abstraction_groups/edit.html.haml
+- app/views/abstractor/abstractor_abstractions/_fields.html.haml
+- app/views/abstractor/abstractor_abstractions/_list.html.haml
+- app/views/abstractor/abstractor_abstractions/edit.html.haml
+- app/views/abstractor/abstractor_abstractions/show.html.haml
+- app/views/abstractor/shared/_error_messages.html.haml
+- config/cucumber.yml
+- config/routes.rb
+- db/migrate/20131227205140_create_abstractor_object_types.rb
+- db/migrate/20131227205219_create_abstractor_object_values.rb
+- db/migrate/20131227205256_create_abstractor_object_value_variants.rb
+- db/migrate/20131227205320_create_abstractor_relation_types.rb
+- db/migrate/20131227205354_create_abstractor_rule_types.rb
+- db/migrate/20131227205432_create_abstractor_abstraction_schemas.rb
+- db/migrate/20131227205456_create_abstractor_abstraction_schema_object_values.rb
+- db/migrate/20131227205529_create_abstractor_abstraction_schema_predicate_variants.rb
+- db/migrate/20131227205610_create_abstractor_abstraction_schema_relations.rb
+- db/migrate/20131227205652_create_abstractor_subjects.rb
+- db/migrate/20131227205732_create_abstractor_subject_relations.rb
+- db/migrate/20131227205831_create_abstractor_abstraction_sources.rb
+- db/migrate/20131227210211_create_abstractor_subject_groups.rb
+- db/migrate/20131227210244_create_abstractor_subject_group_members.rb
+- db/migrate/20131227210350_create_abstractor_abstraction_groups.rb
+- db/migrate/20131227210353_create_abstractor_abstraction_group_members.rb
+- db/migrate/20131227211050_create_abstractor_suggestion_statuses.rb
+- db/migrate/20131227211303_create_abstractor_abstractions.rb
+- db/migrate/20131227213427_create_abstractor_suggestions.rb
+- db/migrate/20131228041944_create_abstractor_suggestion_object_values.rb
+- db/migrate/20131228041945_create_abstractor_suggestion_sources.rb
+- db/seeds.rb
+- lib/abstractor.rb
+- lib/abstractor/abstractable.rb
+- lib/abstractor/core_ext/string.rb
+- lib/abstractor/engine.rb
+- lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb
+- lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb
+- lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb
+- lib/abstractor/methods/models/abstractor_abstraction.rb
+- lib/abstractor/methods/models/abstractor_abstraction_group.rb
+- lib/abstractor/methods/models/abstractor_abstraction_group_member.rb
+- lib/abstractor/methods/models/abstractor_abstraction_schema.rb
+- lib/abstractor/methods/models/abstractor_abstraction_schema_object_value.rb
+- lib/abstractor/methods/models/abstractor_abstraction_schema_predicate_variant.rb
+- lib/abstractor/methods/models/abstractor_abstraction_schema_relation.rb
+- lib/abstractor/methods/models/abstractor_abstraction_source.rb
+- lib/abstractor/methods/models/abstractor_object_type.rb
+- lib/abstractor/methods/models/abstractor_object_value.rb
+- lib/abstractor/methods/models/abstractor_object_value_variant.rb
+- lib/abstractor/methods/models/abstractor_relation_type.rb
+- lib/abstractor/methods/models/abstractor_rule_type.rb
+- lib/abstractor/methods/models/abstractor_subject.rb
+- lib/abstractor/methods/models/abstractor_subject_group.rb
+- lib/abstractor/methods/models/abstractor_subject_group_member.rb
+- lib/abstractor/methods/models/abstractor_subject_relation.rb
+- lib/abstractor/methods/models/abstractor_suggestion.rb
+- lib/abstractor/methods/models/abstractor_suggestion_object_value.rb
+- lib/abstractor/methods/models/abstractor_suggestion_source.rb
+- lib/abstractor/methods/models/abstractor_suggestion_status.rb
+- lib/abstractor/methods/models/soft_delete.rb
+- lib/abstractor/negation_detection.rb
+- lib/abstractor/parser.rb
+- lib/abstractor/setup.rb
+- lib/abstractor/user_interface.rb
+- lib/abstractor/utility.rb
+- lib/abstractor/version.rb
+- lib/generators/abstractor/install/install_generator.rb
+- lib/generators/abstractor/install/templates/controllers/abstractor_abstraction_groups_controller.rb
+- lib/generators/abstractor/install/templates/controllers/abstractor_abstractions_controller.rb
+- lib/generators/abstractor/install/templates/controllers/abstractor_suggestions_controller.rb
+- lib/generators/abstractor/install/templates/dictionaries.yml
+- lib/generators/abstractor/install/templates/helpers/abstractions_helper.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_group.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_group_member.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_object_value.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_predicate_variant.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_relation.rb
+- lib/generators/abstractor/install/templates/models/abstractor_abstraction_source.rb
+- lib/generators/abstractor/install/templates/models/abstractor_object_type.rb
+- lib/generators/abstractor/install/templates/models/abstractor_object_value.rb
+- lib/generators/abstractor/install/templates/models/abstractor_object_value_variant.rb
+- lib/generators/abstractor/install/templates/models/abstractor_relation_type.rb
+- lib/generators/abstractor/install/templates/models/abstractor_rule_type.rb
+- lib/generators/abstractor/install/templates/models/abstractor_subject.rb
+- lib/generators/abstractor/install/templates/models/abstractor_subject_group.rb
+- lib/generators/abstractor/install/templates/models/abstractor_subject_group_member.rb
+- lib/generators/abstractor/install/templates/models/abstractor_subject_relation.rb
+- lib/generators/abstractor/install/templates/models/abstractor_suggestion.rb
+- lib/generators/abstractor/install/templates/models/abstractor_suggestion_object_value.rb
+- lib/generators/abstractor/install/templates/models/abstractor_suggestion_source.rb
+- lib/generators/abstractor/install/templates/models/abstractor_suggestion_status.rb
+- lib/lingscope/build.xml
+- lib/lingscope/build/built-jar.properties
+- lib/lingscope/build/classes/lingscope/algorithms/AbnerTokenizer.class
+- lib/lingscope/build/classes/lingscope/algorithms/AnnotationComparer.class
+- lib/lingscope/build/classes/lingscope/algorithms/Annotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/BaselineAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/BaselineCueAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/BaselineScopeAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/CrfAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/NegexAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/NegexCueAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/NegexScopeAnnotator.class
+- lib/lingscope/build/classes/lingscope/algorithms/PosTagger.class
+- lib/lingscope/build/classes/lingscope/algorithms/negex/GenNegEx.class
+- lib/lingscope/build/classes/lingscope/algorithms/negex/Sorter.class
+- lib/lingscope/build/classes/lingscope/drivers/AnnotatedFilesMerger.class
+- lib/lingscope/build/classes/lingscope/drivers/AnnotationComparerDriver.class
+- lib/lingscope/build/classes/lingscope/drivers/BaselineDriver.class
+- lib/lingscope/build/classes/lingscope/drivers/CrfDriver.class
+- lib/lingscope/build/classes/lingscope/drivers/CueAndPosFilesMerger.class
+- lib/lingscope/build/classes/lingscope/drivers/ModelTrainer.class
+- lib/lingscope/build/classes/lingscope/drivers/NegexDriver.class
+- lib/lingscope/build/classes/lingscope/drivers/PosTaggerDriver.class
+- lib/lingscope/build/classes/lingscope/drivers/SentencePosTagger.class
+- lib/lingscope/build/classes/lingscope/drivers/SentenceTagger.class
+- lib/lingscope/build/classes/lingscope/io/AnnotatedSentencesIO.class
+- lib/lingscope/build/classes/lingscope/structures/AnnotatedSentence.class
+- lib/lingscope/dist/README.TXT
+- lib/lingscope/dist/javadoc/allclasses-frame.html
+- lib/lingscope/dist/javadoc/allclasses-noframe.html
+- lib/lingscope/dist/javadoc/constant-values.html
+- lib/lingscope/dist/javadoc/deprecated-list.html
+- lib/lingscope/dist/javadoc/help-doc.html
+- lib/lingscope/dist/javadoc/index-files/index-1.html
+- lib/lingscope/dist/javadoc/index-files/index-10.html
+- lib/lingscope/dist/javadoc/index-files/index-11.html
+- lib/lingscope/dist/javadoc/index-files/index-12.html
+- lib/lingscope/dist/javadoc/index-files/index-13.html
+- lib/lingscope/dist/javadoc/index-files/index-14.html
+- lib/lingscope/dist/javadoc/index-files/index-15.html
+- lib/lingscope/dist/javadoc/index-files/index-16.html
+- lib/lingscope/dist/javadoc/index-files/index-2.html
+- lib/lingscope/dist/javadoc/index-files/index-3.html
+- lib/lingscope/dist/javadoc/index-files/index-4.html
+- lib/lingscope/dist/javadoc/index-files/index-5.html
+- lib/lingscope/dist/javadoc/index-files/index-6.html
+- lib/lingscope/dist/javadoc/index-files/index-7.html
+- lib/lingscope/dist/javadoc/index-files/index-8.html
+- lib/lingscope/dist/javadoc/index-files/index-9.html
+- lib/lingscope/dist/javadoc/index.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/AbnerTokenizer.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/AnnotationComparer.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/Annotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineCueAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineScopeAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/CrfAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/NegexAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/NegexCueAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/NegexScopeAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/PosTagger.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AbnerTokenizer.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AnnotationComparer.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/Annotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineCueAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineScopeAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/CrfAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexCueAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexScopeAnnotator.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/PosTagger.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/GenNegEx.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/Sorter.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/GenNegEx.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/Sorter.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-frame.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-summary.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-tree.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-use.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/package-frame.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/package-summary.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/package-tree.html
+- lib/lingscope/dist/javadoc/lingscope/algorithms/package-use.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/AnnotatedFilesMerger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/AnnotationComparerDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/BaselineDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/CrfDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/CueAndPosFilesMerger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/ModelTrainer.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/NegexDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/PosTaggerDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/SentencePosTagger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/SentenceTagger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotatedFilesMerger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotationComparerDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/BaselineDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CrfDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CueAndPosFilesMerger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/ModelTrainer.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/NegexDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/PosTaggerDriver.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentencePosTagger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentenceTagger.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/package-frame.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/package-summary.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/package-tree.html
+- lib/lingscope/dist/javadoc/lingscope/drivers/package-use.html
+- lib/lingscope/dist/javadoc/lingscope/io/AnnotatedSentencesIO.html
+- lib/lingscope/dist/javadoc/lingscope/io/class-use/AnnotatedSentencesIO.html
+- lib/lingscope/dist/javadoc/lingscope/io/package-frame.html
+- lib/lingscope/dist/javadoc/lingscope/io/package-summary.html
+- lib/lingscope/dist/javadoc/lingscope/io/package-tree.html
+- lib/lingscope/dist/javadoc/lingscope/io/package-use.html
+- lib/lingscope/dist/javadoc/lingscope/structures/AnnotatedSentence.html
+- lib/lingscope/dist/javadoc/lingscope/structures/class-use/AnnotatedSentence.html
+- lib/lingscope/dist/javadoc/lingscope/structures/package-frame.html
+- lib/lingscope/dist/javadoc/lingscope/structures/package-summary.html
+- lib/lingscope/dist/javadoc/lingscope/structures/package-tree.html
+- lib/lingscope/dist/javadoc/lingscope/structures/package-use.html
+- lib/lingscope/dist/javadoc/overview-frame.html
+- lib/lingscope/dist/javadoc/overview-summary.html
+- lib/lingscope/dist/javadoc/overview-tree.html
+- lib/lingscope/dist/javadoc/package-list
+- lib/lingscope/dist/javadoc/resources/inherit.gif
+- lib/lingscope/dist/javadoc/stylesheet.css
+- lib/lingscope/dist/lib/abner.jar
+- lib/lingscope/dist/lib/commons-lang-2.4.jar
+- lib/lingscope/dist/lib/java_utils.jar
+- lib/lingscope/dist/lib/sptoolkit.jar
+- lib/lingscope/dist/lib/stanford-postagger.jar
+- lib/lingscope/dist/lingscope.jar
+- lib/lingscope/lingscope.zip
+- lib/lingscope/manifest.mf
+- lib/lingscope/nbproject/build-impl.xml
+- lib/lingscope/nbproject/genfiles.properties
+- lib/lingscope/nbproject/private/config.properties
+- lib/lingscope/nbproject/private/private.properties
+- lib/lingscope/nbproject/private/private.xml
+- lib/lingscope/nbproject/project.properties
+- lib/lingscope/nbproject/project.xml
+- lib/lingscope/negation_models.zip
+- lib/lingscope/negation_models/baseline_cue_all_both.model
+- lib/lingscope/negation_models/baseline_cue_all_clinical.model
+- lib/lingscope/negation_models/crf_cue_all_both.model
+- lib/lingscope/negation_models/crf_cue_all_clinical.model
+- lib/lingscope/negation_models/crf_scope_cue_crf_all_both.model
+- lib/lingscope/negation_models/crf_scope_cue_crf_all_clinical.model
+- lib/lingscope/negation_models/crf_scope_cue_regex_all_both.model
+- lib/lingscope/negation_models/crf_scope_cue_regex_all_clinical.model
+- lib/lingscope/negation_models/crf_scope_words_all_both.model
+- lib/lingscope/negation_models/crf_scope_words_all_clinical.model
+- lib/lingscope/negation_models/crf_scope_words_crf_all_both.model
+- lib/lingscope/negation_models/crf_scope_words_crf_all_clinical.model
+- lib/lingscope/negation_models/crf_scope_words_regex_all_both.model
+- lib/lingscope/negation_models/crf_scope_words_regex_all_clinical.model
+- lib/lingscope/src/lingscope/algorithms/AbnerTokenizer.java
+- lib/lingscope/src/lingscope/algorithms/AnnotationComparer.java
+- lib/lingscope/src/lingscope/algorithms/Annotator.java
+- lib/lingscope/src/lingscope/algorithms/BaselineAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/BaselineCueAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/BaselineScopeAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/CrfAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/NegexAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/NegexCueAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/NegexScopeAnnotator.java
+- lib/lingscope/src/lingscope/algorithms/PosTagger.java
+- lib/lingscope/src/lingscope/algorithms/negex/GenNegEx.java
+- lib/lingscope/src/lingscope/algorithms/negex/Sorter.java
+- lib/lingscope/src/lingscope/drivers/AnnotatedFilesMerger.java
+- lib/lingscope/src/lingscope/drivers/AnnotationComparerDriver.java
+- lib/lingscope/src/lingscope/drivers/BaselineDriver.java
+- lib/lingscope/src/lingscope/drivers/CrfDriver.java
+- lib/lingscope/src/lingscope/drivers/CueAndPosFilesMerger.java
+- lib/lingscope/src/lingscope/drivers/ModelTrainer.java
+- lib/lingscope/src/lingscope/drivers/NegexDriver.java
+- lib/lingscope/src/lingscope/drivers/PosTaggerDriver.java
+- lib/lingscope/src/lingscope/drivers/SentencePosTagger.java
+- lib/lingscope/src/lingscope/drivers/SentenceTagger.java
+- lib/lingscope/src/lingscope/io/AnnotatedSentencesIO.java
+- lib/lingscope/src/lingscope/structures/AnnotatedSentence.java
+- lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.csv
+- lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.txt
+- lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.csv
+- lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.txt
+- lib/setup/data/ICD-O-3_CSV-metadata/icd-o3 readme.txt
+- lib/setup/data/custom_site_synonyms.csv
+- lib/setup/data/diagnosis_categorizations.csv
+- lib/setup/data/high_level_primary_cns_diagnosis_categorizations.yml
+- lib/setup/data/icdo3_sites_with_laterality.txt
+- lib/setup/data/site_site_categories.txt
+- lib/tasks/abstractor_tasks.rake
+- lib/tasks/cucumber.rake
+homepage: 
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Rails engine that provides functionality for the defintion of discrete data
+  points to be derived from narrative text via natural language processing (NLP) and
+  the presentation of NLP-derived abstracted data points for confirmation/revision.
+test_files: []