discerner 1.1.18

data/lib/generators/discerner/install/install_generator.rb

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+# encoding: UTF-8
+require "rails/generators"
+
+module Discerner
+  class InstallGenerator < Rails::Generators::Base
+    class_option "no-migrate", :type => :boolean
+    class_option "customize-all", :type => :boolean
+    class_option "customize-controllers", :type => :boolean
+    class_option "customize-models", :type => :boolean
+    class_option "customize-helpers", :type => :boolean
+    class_option "customize-layout", :type => :boolean
+    class_option "current-user-helper", :type => :string
+
+    def self.source_paths
+      paths = self.superclass.source_paths
+      paths << File.expand_path("../templates", __FILE__)
+      paths.flatten
+    end
+
+    desc "Used to install Discerner"
+
+    def install_migrations
+      puts "Copying over Discerner migrations..."
+      Dir.chdir(Rails.root) do
+        `rake discerner:install:migrations`
+      end
+    end
+
+    ## shameless steal from forem git://github.com/radar/forem.git
+    def add_discerner_user_method
+      current_user_helper = options["current-user-helper"].presence ||
+                            ask("What is the current_user helper called in your app? [current_user]").presence ||
+                            'current_user if defined?(current_user)'
+      puts "Defining discerner_user method inside ApplicationController..."
+
+      discerner_user_method = %Q{
+  def discerner_user
+    #{current_user_helper}
+  end
+  helper_method :discerner_user
+}
+      inject_into_file("#{Rails.root}/app/controllers/application_controller.rb",
+                       discerner_user_method,
+                       :after => "ActionController::Base\n", :force => false)
+    end
+
+    def add_discerner_view_helpers
+      puts "Defining discerner view helpers inside ApplicationHelper..."
+
+      discerner_helper_methods = %Q{
+  def export_discerner_results?
+    true
+  end
+
+  def show_discerner_results?
+    true
+  end
+
+  def enable_combined_searches?
+    true
+  end
+}
+      inject_into_file("#{Rails.root}/app/helpers/application_helper.rb",
+                       discerner_helper_methods,
+                       :after => "ApplicationHelper\n")
+    end
+
+    def run_migrations
+      unless options["no-migrate"]
+        puts "Running rake db:migrate"
+        `rake db:migrate`
+      end
+    end
+
+    def seed_database_with_operators
+      unless options["no-migrate"]
+        puts "Running rake discerner:setup:operators"
+        `rake discerner:setup:operators`
+      end
+    end
+
+    def mount_engine
+      puts "Mounting Discerner::Engine at \"/\" in config/routes.rb..."
+      insert_into_file("#{Rails.root}/config/routes.rb", :after => /routes.draw.do\n/) do
+        %Q{  mount Discerner::Engine, :at => "/"\n}
+      end
+    end
+
+    def sample_dictionary
+      path = "#{Rails.root}/lib/setup"
+      empty_directory "#{path}"
+      copy_file "dictionaries.yml", "#{path}/dictionaries.yml"
+    end
+
+    def make_customizable
+      if options["customize-all"] || options["customize-controllers"]
+        path = "#{Rails.root}/app/controllers/discerner"
+        empty_directory path
+        copy_file "controllers/searches_controller.rb", "#{path}/searches_controller.rb"
+        copy_file "controllers/parameters_controller.rb", "#{path}/parameters_controller.rb"
+        copy_file "controllers/export_parameters_controller.rb", "#{path}/export_parameters_controller.rb"
+      end
+
+      if options["customize-all"] || options["customize-helpers"]
+        path = "#{Rails.root}/app/helpers/discerner"
+        empty_directory "#{path}"
+        copy_file "helpers/searches_helper.rb", "#{path}/searches_helper.rb"
+      end
+
+      if options["customize-all"] || options["customize-models"]
+        path = "#{Rails.root}/app/models/discerner"
+        empty_directory "#{path}"
+        copy_file "models/dictionary.rb", "#{path}/dictionary.rb"
+        copy_file "models/export_parameter.rb", "#{path}/export_parameter.rb"
+        copy_file "models/operator.rb", "#{path}/operator.rb"
+        copy_file "models/parameter_category.rb", "#{path}/parameter_category.rb"
+        copy_file "models/parameter_type.rb", "#{path}/parameter_type.rb"
+        copy_file "models/parameter_value.rb", "#{path}/parameter_value.rb"
+        copy_file "models/parameter.rb", "#{path}/parameter.rb"
+        copy_file "models/search_combination.rb", "#{path}/search_combination.rb"
+        copy_file "models/search_parameter_value.rb", "#{path}/search_parameter_value.rb"
+        copy_file "models/search_parameter.rb", "#{path}/search_parameter.rb"
+        copy_file "models/search.rb", "#{path}/search.rb"
+      end
+
+      if options["customize-all"] || options["customize-layout"]
+        path = "#{Rails.root}/app/views/layouts/discerner"
+        empty_directory "#{path}"
+        copy_file "views/layouts/searches.html.erb", "#{path}/searches.html.erb"
+      end
+    end
+
+    def finished
+      output = "\n\n" + ("*" * 53)
+      output += "\nDone! Discerner has been successfully installed. Here's what happened:\n\n"
+      output += "-- Discerner's migrations were copied over into db/migrate.\n"
+      output += "-- A new method called `discerner_user` was inserted into your ApplicationController. This lets Discerner know what the current user of your application is.\n"
+
+      unless options["no-migrate"]
+        output += "-- `rake db:migrate` was run, running all the migrations against your database.\n"
+        output += "-- Seed operators were loaded into your database.\n"
+      end
+      output += "-- The engine was mounted in your config/routes.rb file using this line:
+        mount Discerner::Engine, :at => \"/\""
+      output += "\nIf you want to change where the searches are located, just change the \"/searches\" path at the end of this line to whatever you want."
+      output += "\n--  Sample search dictionary was copied into lib/setup. If you want to try it out, run `rails generate discerner:dictionary lib/setup/dictionaries.yml`. This will:\n"
+      output += "\n-- parse dictionary definitions from lib/setup/dictionaries.yml into the database."
+      output += "\n-- create corresponsing classes"
+      output += "\n-- create corresponsing views for results display"
+      puts output
+    end
+  end
+end

data/lib/generators/discerner/install/templates/controllers/export_parameters_controller.rb

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+module Discerner
+  module ExportParametersControllerCustomMethods
+    def self.included(base)
+      base.send :layout, "search"
+    end
+
+    def index
+      super
+    end
+
+    def assign
+      super
+    end
+  end
+
+  class ExportParametersController < ApplicationController
+    include Discerner::Methods::Controllers::ExportParametersController
+    include Discerner::ExportParametersControllerCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/controllers/parameters_controller.rb

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+module Discerner
+  module ParametersControllerCustomMethods
+    def self.included(base)
+    end
+
+    def show
+      super
+    end
+  end
+
+  class ParametersController < ApplicationController
+    include Discerner::Methods::Controllers::ParametersController
+    include Discerner::ParametersControllerCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/controllers/searches_controller.rb

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+module Discerner
+  module SearchesControllerCustomMethods
+    def self.included(base)
+    end
+
+    def new
+      super
+    end
+
+    def create
+      super
+    end
+
+    def edit
+      super
+    end
+
+    def update
+      super
+    end
+
+    def index
+      super
+    end
+
+    def destroy
+      super
+    end
+
+    def show
+      super
+    end
+  end
+
+  class SearchesController < ApplicationController
+    include Discerner::Methods::Controllers::SearchesController
+    include Discerner::SearchesControllerCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/dictionaries.yml

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+# ---- General structure:
+#   :dictionaries:
+#    - :name: string                                                            # has to be unique within not-deleted dictionaries
+#      :parameter_categories:
+#       - :name: string                                                         # has to be unique within the dictionary
+#         :parameters:
+#           - :name: string                                                     # used for display
+#             :unique_identifier:                                               # has to be unique within the dictionary
+#             :export:
+#               :model                                                          # name of the model to be used for exporting
+#               :method                                                         # name of the model method to be used for exporting
+#             :search:                                                          # parameter search model and method combination has to be unique within the category
+#               :model: string                                                  # name of the model to be used for searching
+#               :method: string                                                 # name of the model method to be used for searching
+#               :parameter_type: numeric/date/list/combobox/text/string         # used to define applicable operators/display options. does not have to be restricted to the given list, but additional parameters will require adding operators to match
+#               :parameter_value_categories_source:                             # used to define parameter value categories
+#                 :model: string                                                # source model to be used to load parameter value categiories
+#                 :method: string                                               # method in the source model that returns parameter_value_categories in a form of [{:name => 'string, :unique_identifier => 'adventure', :display_order => 1, :collapse => true}]
+#               :parameter_value_categories:                                    # used to define parameter value categories
+#                 - :name: string
+#                   :unique_identifier: string                                  # has to be unique within parameter
+#                   :collapse: boolean                                          # used to define if parameter category should be collapsed in the list and its values hidden from the view
+#                   :display_order: integer
+#               :allow_empty_values: boolean                                    # default: true. If set to true, "none" value will be added to the list ov values
+#               :parameter_values:                                              # needs to be defined for list/combobox parameters unless parameter values come from the model, see ':source'
+#                 - :name: string                                               # used for display, if not provided, 'search_value' will be used instead
+#                   :search_value: string                                       # has to be unique within parameter, intendend to be used as a database value while searching
+#                   :parameter_value_category: string                           # used to define category for parameter value, should match one of parameter_value_categories unique_identifiers listed above
+#               :source:
+#                 :model: string                                                # source model to be used to load parameter values
+#                 :method: string                                               # method/method in the source model to be used to load parameter values
+
+---
+:dictionaries:
+  - :name: Sample dictionary
+    :parameter_categories:
+      - :name: Demographic criteria
+        :parameters:
+          - :name: Age at case collection date
+            :unique_identifier: age_at_case_collect
+            :search:
+              :model: Patient
+              :method: age_at_case_collect
+              :parameter_type: numeric
+
+          - :name: Age based on current date
+            :unique_identifier: age_based_on_current_date
+            :export:
+              :model: Patient
+              :method: age_based_on_current_date
+
+          - :name: Date of birth
+            :unique_identifier: birth_dt_tm
+            :search:
+              :model: Patient
+              :method: birth_dt_tm
+              :parameter_type: date
+            :export:
+              :model: Patient
+              :method: age_based_on_current_date
+
+          - :name: Ethnic group
+            :unique_identifier: ethnic_grp
+            :search:
+              :model: Patient
+              :method: ethnic_grp
+              :parameter_type: combobox
+              :parameter_values:
+                - :name: Hispanic or Latino
+                  :search_value: hisp_or_latino
+                - :name: NOT Hispanic or Latino
+                  :search_value: not_hisp_or_latino
+                - :name: Unable to answer
+                  :search_value: unknown
+                - :name: Declined to answer
+                  :search_value: declined
+
+          - :name: Consented
+            :unique_identifier: surg_inpatient_mortality
+            :search:
+              :model: Surgery
+              :method: consented
+              :parameter_type: list
+              :parameter_values:
+                - :search_value: yes
+                - :search_value: no
+
+          - :name: Gender
+            :unique_identifier: sex
+            :search:
+              :model: Patient
+              :method: sex
+              :parameter_type: list
+              :parameter_values:
+                - :name: Male
+                  :search_value: male
+                - :name: Female
+                  :search_value: female
+                - :name: Indeterminent
+                  :search_value: indeterminent
+                - :name: Unknown
+                  :search_value: unknown
+                - :name: Unspecified
+                  :search_value: uncpecified
+            :export:
+              :model: Patient
+              :method: gender
+
+          - :name: Race
+            :exclusive: false
+            :unique_identifier: race
+            :search:
+              :model: Patient
+              :method: race
+              :parameter_type: list
+              :parameter_values:
+                - :search_value: American Indian or Alaska Native
+                - :search_value: Asian
+                - :search_value: Black or African American
+                - :search_value: Hispanic or Latino
+                - :search_value: Native Hawaiian or Other Pacific Islander
+                - :search_value: White or Caucasian
+                - :search_value: Other
+                - :search_value: Declined to answer
+                - :search_value: Unable to answer
+            :export:
+              :model: Patient
+              :method: race
+
+      - :name: Case criteria
+        :parameters:
+          - :name: Accession date
+            :unique_identifier: accessioned_dt_tm
+            :search:
+              :model: Case
+              :method: accessioned_dt_tm
+              :parameter_type: date
+
+          - :name: Text search diagnosis
+            :exclusive: false
+            :unique_identifier: case_specimen_diagnosis
+            :search:
+              :model: Case
+              :method: case_specimen_diagnosis
+              :parameter_type: text
+
+  - :name: Librarian dictionary
+    :parameter_categories:
+      - :name: By author
+        :parameters:
+          - :name: "Last name"
+            :unique_identifier: autor_last_name
+            :search:
+              :model: Author
+              :method: autor_last_name
+              :parameter_type: string
+
+          - :name: "First name"
+            :unique_identifier: autor_first_name
+            :search:
+              :model: Author
+              :method: autor_first_name
+              :parameter_type: text
+
+          - :name: "Country"
+            :unique_identifier: country
+            :search:
+              :model: Author
+              :method: country
+              :parameter_type: text
+
+          - :name: "Type"
+            :unique_identifier: author_type
+            :search:
+              :model: Book
+              :method: type
+              :parameter_type: list
+              :parameter_values:
+                - :search_value: author
+                - :search_value: co-author
+                - :search_value: reviewer
+      - :name: Book criteria
+        :parameters:
+          - :name: "Type"
+            :unique_identifier: book_type
+            :search:
+              :model: Book
+              :method: type
+              :parameter_type: combobox
+              :parameter_values:
+                - :search_value: book
+                - :search_value: journal
+                - :search_value: article
+                - :search_value: electronic journal
+
+          - :name: "Genre"
+            :unique_identifier: book_genre
+            :search:
+              :model: Book
+              :method: Genre
+              :parameter_type: combobox
+              :parameter_value_categories:
+                - :name: Adventure
+                  :unique_identifier: adventure
+                  :collapse: true
+                  :display_order: 1
+                - :name: Comic novel
+                  :unique_identifier: comic
+                - :name: Historical
+                  :unique_identifier: historical
+              :parameter_values:
+                - :search_value: "Robinsonade"
+                  :parameter_value_category: adventure
+                - :search_value: "Black comedy"
+                  :parameter_value_category: comic
+                - :search_value: "Parody"
+                  :parameter_value_category: comic
+                - :search_value: "Lost World"
+                  :parameter_value_category: adventure
+                - :search_value: "Brit lit"
+                - :search_value: "Pulp fiction"
+
+          - :name: "Title"
+            :unique_identifier: title
+            :search:
+              :model: Book
+              :method: title
+              :parameter_type: text
+
+          - :name: "Keyword"
+            :unique_identifier: text
+            :search:
+              :model: Book
+              :method: text
+              :parameter_type: text
+

data/lib/generators/discerner/install/templates/helpers/searches_helper.rb

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+module Discerner
+  module SearchesHelperCustomMethods
+  end
+
+  module SearchesHelper
+    include Discerner::Methods::Helpers::SearchesHelper
+    include Discerner::SearchesHelperCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/book.rb

@@ -0,0 +1,15 @@
+class Book
+  def self.genres
+    [
+      {:name => 'Adventure', :unique_identifier => 'adventure', :display_order => 1, :collapse => true},
+      {:name => 'Drama', :unique_identifier => 'drama', :display_order => 2, :collapse => false},
+    ]
+  end
+
+  def self.generes
+    [
+      {:name => 'Adventure', :display_order => 1, :collapse => true},
+      {:name => 'Drama', :unique_identifier => 'drama', :display_order => 2, :collapse => false},
+    ]
+  end
+end

data/lib/generators/discerner/install/templates/models/dictionary.rb

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+module Discerner
+  module DictionaryCustomMethods
+  end
+
+  class Dictionary < ActiveRecord::Base
+    include Discerner::Methods::Models::Dictionary
+    include Discerner::DictionaryCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/export_parameter.rb

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+module Discerner
+  module ExportParameterCustomMethods
+  end
+
+  class ExportParameter < ActiveRecord::Base
+    include Discerner::Methods::Models::ExportParameter
+    include Discerner::ExportParameterCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/operator.rb

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+module Discerner
+  module OperatorCustomMethods
+  end
+
+  class Operator < ActiveRecord::Base
+    include Discerner::Methods::Models::Operator
+    include Discerner::OperatorCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/parameter.rb

@@ -0,0 +1,10 @@
+module Discerner
+  module ParameterCustomMethods
+  end
+
+  class Parameter < ActiveRecord::Base
+    include Discerner::Methods::Models::Parameter
+    include Discerner::ParameterCustomMethods
+  end
+end
+

data/lib/generators/discerner/install/templates/models/parameter_category.rb

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+module Discerner
+  module ParameterCategoryCustomMethods
+  end
+
+  class ParameterCategory < ActiveRecord::Base
+    include Discerner::Methods::Models::ParameterCategory
+    include Discerner::ParameterCategoryCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/parameter_type.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module ParameterTypeCustomMethods
+  end
+
+  class ParameterType < ActiveRecord::Base
+    include Discerner::Methods::Models::ParameterType
+    include Discerner::ParameterTypeCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/parameter_value.rb

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+module Discerner
+  module ParameterValueCustomMethods
+  end
+
+  class ParameterValue < ActiveRecord::Base
+    include Discerner::Methods::Models::ParameterValue
+    include Discerner::ParameterValueCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/parameter_value_categorization.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module ParameterValueCategorizationCustomMethods
+  end
+
+  class ParameterValueCategorization < ActiveRecord::Base
+    include Discerner::Methods::Models::ParameterValueCategorization
+    include Discerner::ParameterValueCategorizationCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/parameter_value_category.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module ParameterValueCategoryCustomMethods
+  end
+
+  class ParameterValueCategory < ActiveRecord::Base
+    include Discerner::Methods::Models::ParameterValueCategory
+    include Discerner::ParameterValueCategoryCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/search.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module SearchCustomMethods
+  end
+
+  class Search < ActiveRecord::Base
+    include Discerner::Methods::Models::Search
+    include Discerner::SearchCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/search_combination.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module SearchCombinationCustomMethods
+  end
+
+  class SearchCombination < ActiveRecord::Base
+    include Discerner::Methods::Models::SearchCombination
+    include Discerner::SearchCombinationCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/search_parameter.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module SearchParameterCustomMethods
+  end
+
+  class SearchParameter < ActiveRecord::Base
+    include Discerner::Methods::Models::SearchParameter
+    include Discerner::SearchParameterCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/models/search_parameter_value.rb

@@ -0,0 +1,9 @@
+module Discerner
+  module SearchParameterValueCustomMethods
+  end
+
+  class SearchParameterValue < ActiveRecord::Base
+    include Discerner::Methods::Models::SearchParameterValue
+    include Discerner::SearchParameterValueCustomMethods
+  end
+end

data/lib/generators/discerner/install/templates/views/layouts/searches.html.erb

@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <%= yield :title %>
+  <%= stylesheet_link_tag    "discerner/application", :media => "all" %>
+  <%= javascript_include_tag "discerner/application" %>
+  <%= csrf_meta_tags %>
+</head>
+<body class="discerner">
+   <% flash.each do |message_type, message| %>
+      <div class="message" id="<%= message_type %>">
+         <%= message %>
+      </div>
+   <% end %>
+   <%= yield %>
+</body>
+</html>