onc_certification_g10_test_kit 2.0.0.rc1

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data/LICENSE

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data/lib/inferno/exceptions.rb

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+module Inferno
+  class UnknownValueSetException < StandardError
+    def initialize(value_set)
+      super("Unknown ValueSet: #{value_set}")
+    end
+  end
+
+  class FilterOperationException < StandardError
+    def initialize(filter_op)
+      super("Cannot Handle Filter Operation: #{filter_op}")
+    end
+  end
+
+  class UnknownCodeSystemException < StandardError
+    def initialize(code_system)
+      super("Unknown Code System: #{code_system}")
+    end
+  end
+
+  class FileExistsException < StandardError
+    def initialize(value_set)
+      super(value_set.to_s)
+    end
+  end
+
+  class ProhibitedSystemException < StandardError
+    def initialize(url)
+      super("Inferno is unable to validate codes from #{url} due to license restrictions")
+    end
+  end
+end

data/lib/inferno/ext/bloomer.rb

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+class Bloomer
+  class Scalable
+    # Scalable bloom filters report very inaccurate sizes because they contain
+    # multiple filters and don't check them all before adding something. This
+    # makes them check all of the filters before adding an element so that the
+    # size is more accurate.
+    def add_without_duplication(string)
+      return false if include? string
+
+      add string
+    end
+
+    def self.create_with_sufficient_size(length = 256)
+      size = initial_size(length)
+      new(size, 0.00001)
+    end
+
+    def self.initial_size(length)
+      size = 2**Math.log2(length).ceil
+
+      size < 256 ? 256 : size
+    end
+  end
+end

data/lib/inferno/repositiories/validators.rb

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+require 'inferno/repositories/in_memory_repository'
+
+module Inferno
+  module Repositories
+    class Validators < InMemoryRepository
+      def self.index_by_id
+        @all_by_id = {}
+        all.each { |vs| @all_by_id[vs.url] = vs }
+        @all_by_id
+      end
+
+      def all_urls
+        all_by_id.keys
+      end
+    end
+  end
+end

data/lib/inferno/repositiories/value_sets.rb

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+require 'inferno/repositories/in_memory_repository'
+
+module Inferno
+  module Repositories
+    class ValueSets < InMemoryRepository
+      def self.index_by_id
+        @all_by_id = {}
+        all.each { |vs| @all_by_id[vs.url] = vs }
+        @all_by_id
+      end
+
+      # @return [Hash] a Hash where the keys are vs urls and the values are vs
+      def select_by_url(urls)
+        self.class.all_by_id.slice(*urls)
+      end
+
+      def select_by_binding_strength(strengths)
+        all.select { |vs| strengths.include?(vs.strength) }
+      end
+
+      def find(url)
+        super || raise(UnknownValueSetException, url)
+      end
+    end
+  end
+end

data/lib/inferno/terminology/bcp47.rb

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+require_relative '../exceptions'
+
+module Inferno
+  module Terminology
+    module BCP47
+      # https://tools.ietf.org/html/bcp47
+      # https://tools.ietf.org/html/rfc5646
+      # https://www.iana.org/assignments/language-subtag-registry/language-subtag-registry
+      #
+      class << self
+        SEPARATOR = '%%'.freeze
+        REGISTRY_URL = 'https://www.iana.org/assignments/language-subtag-registry/language-subtag-registry'.freeze
+
+        def code_set(filter = nil)
+          filter_codes(filter)
+        end
+
+        def load_bcp47
+          response = RestClient.get REGISTRY_URL
+          response.body.split(SEPARATOR).drop(1)
+        end
+
+        def filter_codes(filter = nil)
+          bcp47 = bcp
+          cs_set = Set.new
+          bcp47.each do |raw_language|
+            language = parse_language(raw_language)
+            next if language['Subtag'].nil?
+            next if language['Type'] == 'region'
+
+            cs_set.add(system: 'urn:ietf:bcp:47', code: language['Subtag']) if meets_filter_criteria?(language, filter)
+          end
+          cs_set
+        end
+
+        private
+
+        @bcp = nil
+        def bcp
+          @bcp ||= load_bcp47
+        end
+
+        # Parse the language attributes chunk from the text file
+        #
+        # @param [String] language A single language and its attributes from the file
+        # @return [Hash] the language attributes as key value pairs
+        def parse_language(language)
+          # Need to use scan because match only returns the first match group
+          language.scan(regex).to_h
+        end
+
+        def regex
+          /^(?<key>\S+): (?<value>.*)$/
+        end
+
+        def string_to_boolean(boolean_string)
+          case boolean_string
+          when 'true'
+            true
+          when 'false'
+            false
+          end
+        end
+
+        def meets_filter_criteria?(language, filter)
+          return true unless filter
+
+          meets_criteria = true
+
+          raise FilterOperationException, filter.op unless filter.op == 'exists'
+
+          filter_value = string_to_boolean(filter.value)
+          raise FilterOperationException, filter.to_s if filter_value.nil?
+
+          case filter.property
+          when 'ext-lang'
+            meets_criteria = (language['Type'] == 'extlang') == filter_value
+          when 'script'
+            meets_criteria = (language['Type'] == 'script') == filter_value
+          when 'variant'
+            meets_criteria = (language['Type'] == 'variant') == filter_value
+          when 'extension'
+            meets_criteria = language['Subtag'].match?(/-\w-/) == filter_value
+          when 'private-use'
+            meets_criteria = (language['Scope'] == 'private-use') == filter_value
+          else
+            raise FilterOperationException, filter.to_s
+          end
+
+          meets_criteria
+        end
+      end
+    end
+  end
+end

data/lib/inferno/terminology/bcp_13.rb

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+module Inferno
+  module Terminology
+    module BCP13
+      @code_set = nil
+
+      def self.code_set
+        @code_set ||= parse_code_set
+      end
+
+      def self.parse_code_set
+        require 'mime/types'
+        cs_set = Set.new
+        MIME::Types.each do |type|
+          cs_set.add(system: 'urn:ietf:bcp:13', code: preprocess_code(type.simplified))
+        end
+        cs_set
+      end
+
+      # "preprocess" step for BCP13 codes, to remove any of the optional parameters
+      # and downcase them
+      def self.preprocess_code(code)
+        code&.split(';')&.first&.downcase
+      end
+    end
+  end
+end

data/lib/inferno/terminology/codesystem.rb

@@ -0,0 +1,49 @@
+require_relative '../exceptions'
+require_relative 'bcp_13'
+require_relative 'bcp47'
+
+module Inferno
+  module Terminology
+    class Codesystem
+      attr_accessor :codesystem_model
+
+      def initialize(cs_model)
+        @codesystem_model = cs_model
+      end
+
+      def all_codes_in_concept(concepts)
+        Set.new.tap { |cs_set| load_codes(concepts.flatten, cs_set) }
+      end
+
+      def load_codes(concepts, cs_set)
+        concepts.each do |concept|
+          cs_set.add(system: codesystem_model.url, code: concept.code)
+          load_codes(concept.concept, cs_set) unless concept.concept.blank?
+        end
+      end
+
+      def find_concept(code, concepts = codesystem_model.concept)
+        return if concepts.nil?
+
+        concepts.find do |concept|
+          concept.code == code || find_concept(code, concept.concept)
+        end
+      end
+
+      def is_a_concept_filter?(filter) # rubocop:disable Naming/PredicateName
+        (filter.op == 'is-a') && (codesystem_model.hierarchyMeaning == 'is-a') && (filter.property == 'concept')
+      end
+
+      def filter_codes(filter = nil)
+        if filter.nil?
+          all_codes_in_concept(codesystem_model.concept)
+        elsif is_a_concept_filter? filter
+          parent_concept = find_concept(filter.value)
+          all_codes_in_concept([parent_concept])
+        else
+          raise FilterOperationException, filter.to_s
+        end
+      end
+    end
+  end
+end