Class: FHIR::DSTU2::Definitions

Inherits:
Object
  • Object
show all
Extended by:
Deprecate
Defined in:
lib/fhir_dstu2_models/bootstrap/definitions.rb

Constant Summary collapse

@@defns = 
File.expand_path '../definitions', File.dirname(File.absolute_path(__FILE__))
@@types = 
nil
@@resources = 
nil
@@profiles = 
nil
@@extensions = 
nil
@@valuesets = 
nil
@@search_params = 
nil
@@cache = 
{}

Class Method Summary collapse

Methods included from Deprecate

deprecate

Class Method Details

.basetype(uri) ⇒ Object

Get the basetype (String) for a given profile or extension.



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 117

def self.basetype(uri)
  return nil if uri.nil?

  defn = profiles.detect { |x| x['url'] == uri } || extensions.detect { |x| x['url'] == uri }
  return nil if defn.nil?

  defn['baseType']
end

.complex_types ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 37

def self.complex_types
  # complex data types start with an uppercase letter
  # and we'll filter out profiles on types (for example, Age is a profile on Quantity)
  @complex_types ||= types.select { |t| t['id'].start_with?(*('A'..'Z').to_a) && (t['id'] == t['snapshot']['element'].first['path']) }
end

.extension_definition(extension_name) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 106

def self.extension_definition(extension_name)
  return nil if extension_name.nil?

  extension = extensions.find { |x| x['xmlId'] == extension_name || x['name'] == extension_name || x['url'] == extension_name }
  return nil if extension.nil?

  FHIR::DSTU2::StructureDefinition.new(extension)
end

.get_codes(uri, parent_code = nil) ⇒ Object

Get codes (Array of Strings) for a given expansion.



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 207

def self.get_codes(uri, parent_code = nil)
  return nil if uri.nil?
  return @@cache[uri] if @@cache[uri]

  FHIR::DSTU2.logger.debug "Looking up codes for #{uri}"
  valueset = valuesets.select { |x| x['url'] == uri }.first
  if valueset.nil?
    # if we can't identify the valueset by id/uri, see if we can match the codeSystem
    FHIR::DSTU2.logger.debug "Could not find valueset, looking for codeSystem #{uri}"
    valueset = valuesets.select { |v| !v['codeSystem'].nil? && v['codeSystem']['system'] == uri }.first
  end
  if valueset.nil?
    FHIR::DSTU2.logger.debug 'Could not find valueset or code system.'
  else
    FHIR::DSTU2.logger.debug "Found valueset #{valueset['url']}"
    @@cache[uri] = {}
    if !valueset['codeSystem'].nil? && !valueset['codeSystem']['system'].nil?
      FHIR::DSTU2.logger.debug 'Looking at codeSystem...'
      @@cache[uri][valueset['codeSystem']['system']] = []
      valueset['codeSystem']['concept'].each do |concept|
        @@cache[uri][valueset['codeSystem']['system']] += get_codes_from_concept(concept, parent_code)
      end
    end
    if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil?
      FHIR::DSTU2.logger.debug 'Looking at expansion...'
      keys = valueset['expansion']['contains'].map { |x| x['system'] }.uniq
      keys.each { |x| @@cache[uri][x] = [] }
      valueset['expansion']['contains'].each { |x| @@cache[uri][x['system']] << x['code'] }
    end
    if !valueset['compose'].nil? && !valueset['compose']['include'].nil?
      FHIR::DSTU2.logger.debug 'Looking at compose.include...'
      valueset['compose']['include'].each do |x|
        system = x['system']
        unless @@cache[uri].keys.include?(system)
          included_codes = get_codes(system)
          @@cache[uri][system] = if included_codes
                                   included_codes[system]
                                 else
                                   []
                                 end
        end
        x['concept']&.each { |y| @@cache[uri][system] += get_codes_from_concept(y, parent_code) }
        next unless x['filter']

        x['filter'].each do |filter|
          if filter['property'] == 'concept' && filter['op'] == 'is-a'
            codes = get_codes(system, filter['value'])
            @@cache[uri][system] += codes[system] if codes && codes[system]
          end
        end
      end
      unless valueset['compose']['exclude'].nil?
        FHIR::DSTU2.logger.debug 'Looking at compose.exclude...'
        valueset['compose']['exclude'].each do |x|
          system = x['system']
          unless @@cache[uri].keys.include?(system)
            included_codes = get_codes(system)[system]
            @@cache[uri][system] = if included_codes
                                     included_codes[system]
                                   else
                                     []
                                   end
          end
          x['concept']&.each { |y| @@cache[uri][system].delete(y['code']) }
        end
      end
    end
    if !valueset['compose'].nil? && !valueset['compose']['import'].nil?
      FHIR::DSTU2.logger.debug 'Looking at compose.import...'
      imported_systems = valueset['compose']['import']
      FHIR::DSTU2.logger.debug "Searching #{imported_systems}..."
      imported_systems.each do |importsys|
        # @@cache[uri][system] = [] unless @@cache[uri].keys.include?(system)
        FHIR::DSTU2.logger.debug "Looking at compose.import #{importsys}..."
        results = get_codes(importsys)
        results.each do |sys, codes|
          if codes.empty?
            lookup = get_codes(sys)
            codes = lookup[sys] if lookup
          end
          next unless codes

          codes.each do |code|
            @@cache[uri][sys] = [] unless @@cache[uri].keys.include?(sys)
            @@cache[uri][sys] << code
          end
        end
      end
    end
    @@cache[uri].each { |_system, codes| codes.uniq! }
  end
  FHIR::DSTU2.logger.debug "Done caching codes for #{uri}"
  @@cache[uri]
end

.get_codes_from_concept(concept, filter_code = nil) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 302

def self.get_codes_from_concept(concept, filter_code = nil)
  codes = []
  codes << concept['code'] if concept['code'] == filter_code || filter_code.nil?
  if concept['concept']
    filter_code = nil if concept['code'] == filter_code
    concept['concept'].each do |item|
      codes += get_codes_from_concept(item, filter_code)
    end
  end
  codes
rescue StandardError => e
  FHIR::DSTU2.logger.debug "Unable to extract codes from concept #{concept}: #{e.message}"
end

.get_profile_class(uri) ⇒ Object

Get a dynamically generated class for a given profile.



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 146

def self.get_profile_class(uri)
  return nil if uri.nil?

  load_profiles
  load_extensions

  defn = @@profiles.select { |x| x['url'] == uri }.first
  defn = @@extensions.select { |x| x['url'] == uri }.first if defn.nil?

  klass = nil
  unless defn.nil?
    generator = FHIR::DSTU2::Boot::Generator.new(false)
    type = defn['baseType']
    id = defn['id'].gsub(/-|_/, '').capitalize
    defn['id'] = type # override profile id with baseType name for generator
    template = generator.generate_class([type], defn)
    f = Tempfile.new(["profile-#{id}", '.rb'])
    f.write("module FHIR::DSTU2\n")
    f.write("module Profile\n")
    f.write("module #{id}\n")
    f.write(template.to_s)
    3.times { f.write("\nend") }
    f.close
    begin
      # load the profiled class
      load f
      # set the return class type
      klass = Object.const_get("FHIR::DSTU2::Profile::#{id}::#{type}")
    rescue StandardError
      FHIR::DSTU2.logger.error "Failed to generate class for profile #{uri}"
    end
    # unlink the file so it can be garbage collected
    f.unlink
  end
  klass
end

.primitive_types ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 31

def self.primitive_types
  # primitive data types start with a lowercase letter
  @primitive_types ||= types.select { |t| t['id'].start_with?(*('a'..'z').to_a) }
end

.profile(uri) ⇒ Object

Get the StructureDefinition for a given profile.



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 128

def self.profile(uri)
  return nil if uri.nil?

  defn = profiles.detect { |x| x['url'] == uri } || extensions.detect { |x| x['url'] == uri }
  return nil if defn.nil?

  FHIR::DSTU2::StructureDefinition.new(defn)
end

.profiles_for_resource(resource_name) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 138

def self.profiles_for_resource(resource_name)
  return nil if resource_name.nil?

  profiles.select { |x| x['baseType'] == resource_name }.map { |x| FHIR::DSTU2::StructureDefinition.new(x) }
end

.resource_definition(resource_name) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 74

def self.resource_definition(resource_name)
  return nil if resource_name.nil?
  return @@cache[resource_name] if @@cache[resource_name]

  definition = resources.find { |x| x['xmlId'] == resource_name || x['name'] == resource_name || x['url'] == resource_name }
  @@cache[resource_name] = FHIR::DSTU2::StructureDefinition.new(definition) if definition
  @@cache[resource_name]
end

.resource_definitions ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 69

def self.resource_definitions
  resources.select { |r| r['kind'] == 'resource' }
end

.search_parameters(type_name) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 356

def self.search_parameters(type_name)
  return nil if type_name.nil?

  search_params.select { |p| p['base'].include?(type_name) && p['xpath'] && !p['xpath'].include?('extension') }.map { |p| p['code'] }
end

.type_definition(type_name) ⇒ Object 



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 44

def self.type_definition(type_name)
  return nil if type_name.nil?
  return @@cache[type_name] if @@cache[type_name]

  definition = types.find { |x| x['xmlId'] == type_name || x['name'] == type_name || x['url'] == type_name }
  @@cache[type_name] = FHIR::DSTU2::StructureDefinition.new(definition) if definition
  @@cache[type_name]
end

.valuesets ⇒ Object 

ValueSet Code Expansions



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# File 'lib/fhir_dstu2_models/bootstrap/definitions.rb', line 187

def self.valuesets
  @@valuesets ||= begin
    # load the valuesets
    filename = File.join(@@defns, 'valuesets', 'valuesets.json')
    raw = File.open(filename, 'r:UTF-8', &:read)
    vs = JSON.parse(raw)['entry'].map { |e| e['resource'] }

    filename = File.join(@@defns, 'valuesets', 'v3-codesystems.json')
    raw = File.open(filename, 'r:UTF-8', &:read)
    v3 = JSON.parse(raw)['entry'].map { |e| e['resource'] }

    filename = File.join(@@defns, 'valuesets', 'v2-tables.json')
    raw = File.open(filename, 'r:UTF-8', &:read)
    v2 = JSON.parse(raw)['entry'].map { |e| e['resource'] }

    vs + v3 + v2
  end
end