Class: FHIR::Boot::Generator

Inherits:
Object
  • Object
show all
Defined in:
lib/fhir_models/bootstrap/generator.rb

Constant Summary collapse

KNOWN_MISSING_EXPANSIONS = 
%w[bcp47 bcp13.txt mimetypes LL379-9].freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(auto_setup: true) ⇒ Generator

Returns a new instance of Generator.



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# File 'lib/fhir_models/bootstrap/generator.rb', line 12

def initialize(auto_setup: true)
  # load the valueset expansions
  @defn = FHIR::Definitions
  # templates is an array
  @templates = []
  setup if auto_setup
end

Instance Attribute Details

#defn ⇒ Object

Returns the value of attribute defn.



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# File 'lib/fhir_models/bootstrap/generator.rb', line 7

def defn
  @defn
end

#lib ⇒ Object

Returns the value of attribute lib.



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# File 'lib/fhir_models/bootstrap/generator.rb', line 6

def lib
  @lib
end

#missing_expansions ⇒ Object

Returns the value of attribute missing_expansions.



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# File 'lib/fhir_models/bootstrap/generator.rb', line 10

def missing_expansions
  @missing_expansions
end

#missing_required_expansion ⇒ Object

Returns the value of attribute missing_required_expansion.



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# File 'lib/fhir_models/bootstrap/generator.rb', line 10

def missing_required_expansion
  @missing_required_expansion
end

#templates ⇒ Object

templates keeps track of all the templates in context within a given StructureDefinition



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# File 'lib/fhir_models/bootstrap/generator.rb', line 9

def templates
  @templates
end

Instance Method Details

#cap_first(string) ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 95

def cap_first(string)
  t = String.new(string)
  t[0] = t[0].upcase
  t
end

#generate_class(hierarchy, structure_def, top_level = false) ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 101

def generate_class(hierarchy, structure_def, top_level = false)
  type_name = structure_def['id']
  constrained_type = structure_def['type']
  path_type = type_name
  path_type = constrained_type if constrained_type

  template = FHIR::Boot::Template.new([type_name], top_level)
  template.hierarchy = hierarchy
  template.kind = structure_def['kind']
  return template if structure_def['snapshot'].nil? || structure_def['snapshot']['element'].nil?

  multiple_data_types = {}

  # examine the snapshot.elements... move the Element and BackboneElements,
  # and their children, into separate StructureDefiniton hashes and process as
  # child templates.
  child_templates = []
  structure_def['snapshot']['element'].each do |element|
    # skip the first element
    next if element['path'] == path_type
    next unless element['type']
    unique_types = element['type'].map { |t| t['code'] }.uniq
    if unique_types.include?('Element') || unique_types.include?('BackboneElement')
      child_templates << element['path']
    end
  end
  # now build the child templates...
  child_templates.each do |child_name|
    child_fixed_name = cap_first(child_name.gsub("#{type_name}.", ''))
    next if child_fixed_name.include?('.')
    child_def = { 'id' => child_fixed_name, 'snapshot' => { 'element' => [] } }
    # Copy the element definitions for the child structure
    structure_def['snapshot']['element'].each do |element|
      child_def['snapshot']['element'] << element.clone if element['path'].start_with?("#{child_name}.")
    end
    # Remove the child elements
    child_paths = child_def['snapshot']['element'].map { |e| e['path'] }
    # child_paths = child_paths.drop(1)
    structure_def['snapshot']['element'].keep_if do |element|
      !child_paths.include?(element['path'])
    end
    # Rename the child paths
    child_def['snapshot']['element'].each do |element|
      element['path'] = element['path'].gsub(child_name, child_fixed_name)
    end
    # add the child
    child_hierarchy = hierarchy + [child_fixed_name]
    child_klass = generate_class(child_hierarchy, child_def)
    template.templates << child_klass
    @templates << child_klass
  end

  # Process the remaining attributes (none of which are Elements or BackboneElements)
  structure_def['snapshot']['element'].each do |element|
    # skip the first element
    next if element['path'] == path_type

    field_base_name = element['path'].gsub("#{path_type}.", '')
    # If the element has a type, treat it as a datatype or resource
    # If not, treat it as a reference to an already declared internal class
    if !element['type'].nil?
      # profiles contains a list of profiles if the datatype is Reference or Extension
      profiles = []
      element['type'].select { |t| t['code'] == 'Reference' || t['code'] == 'Extension' }.each do |data_type|
        profiles << data_type['targetProfile']
      end
      profiles.reject!(&:nil?)
      profiles.flatten!

      # Calculate fields that have multiple data types
      if element['type'].length > 1
        fieldname = field_base_name.gsub('[x]', '')
        unique_types = element['type'].map { |t| t['code'] }.uniq
        multiple_data_types[fieldname] = unique_types if unique_types.length > 1
      end

      # generate a field for each valid datatype... this is for things like Resource.attribute[x]
      element['type'].each do |type|
        extension = type['extension']
        data_type = type['code'] || 'string'
        if element['path'].end_with?('.id')
          data_type = element['base']['path'] == 'Resource.id' ? 'id' : 'string'
        elsif data_type == 'http://hl7.org/fhirpath/System.String' && extension
          data_type = extension.first['valueUrl']
        end
        capitalized = cap_first(data_type)
        fieldname = field_base_name.gsub('[x]', capitalized)
        field = FHIR::Field.new(fieldname)
        field.path = element['path'].gsub(path_type, type_name)
        field.type = data_type
        field.type = 'Extension' if field.path.end_with?('extension')
        field.type_profiles = profiles if data_type == 'Reference' || data_type == 'Extension'
        field.min = element['min']
        field.max = element['max']
        field.max = field.max.to_i
        field.max = '*' if element['max'] == '*'

        if %w[code Coding CodeableConcept].include?(data_type) && element['binding']
          field.binding = element['binding']
          field.binding['uri'] = field.binding['valueSet']
          field.binding.delete('valueSet')
          field.binding.delete('description')
          field.binding.delete('extension')
          # set the actual code list
          binding_uri = field.binding['uri']
          # Strip off the |4.0.0 or |4.0.1 or |2014-03-26 or similar from the ends of URLs
          binding_uri&.gsub!(/\|[A-Za-z0-9\.\-]*/, '')
          codes = @defn.get_codes(binding_uri)
          field.valid_codes = codes unless codes.nil?
          if field.valid_codes.empty? && binding_uri && !binding_uri.end_with?(*KNOWN_MISSING_EXPANSIONS)
            FHIR.logger.warn "  MISSING EXPANSION -- #{field.path} #{field.min}..#{field.max}: #{binding_uri} (#{field.binding['strength']})"
            @missing_expansions = true
            @missing_required_expansion = (field.binding['strength'] == 'required') unless @missing_required_expansion
          end
        elsif %w[Element BackboneElement].include?(data_type)
          # This is a nested structure or class
          field.type = "#{hierarchy.join('::')}::#{cap_first(field.name)}"
        end

        template.fields << field
      end
    else # If there is no data type, treat the type as a reference to an already declared internal class
      field = FHIR::Field.new(field_base_name)
      field.path = element['path'].gsub(path_type, type_name)
      field.type = element['contentReference']
      field.type = field.type[1..-1] if field.type[0] == '#'
      if hierarchy.last == field.type
        # reference to self
        field.type = hierarchy.join('::').to_s
      else
        # reference to contained template
        klass = @templates.select { |x| x.hierarchy.last == field.type }.first
        field.type = if !klass.nil?
                       # the template/child class was declared somewhere else in this class hierarchy
                       klass.hierarchy.join('::')
                     else
                       # the template/child is a direct ancester (it isn't in @templates yet because it is being defined now)
                       field.type.split('.').map { |x| cap_first(x) }.join('::')
                     end
      end
      field.min = element['min']
      field.max = element['max']
      field.max = field.max.to_i
      field.max = '*' if element['max'] == '*'
      template.fields << field
    end
  end

  template.constants['MULTIPLE_TYPES'] = multiple_data_types unless multiple_data_types.empty?
  template
end

#generate_class_files(folder = @lib, structure_defs = []) ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 81

def generate_class_files(folder = @lib, structure_defs = [])
  structure_defs.each do |structure_def|
    @templates.clear
    type_name = structure_def['id']
    template = generate_class([type_name], structure_def, true)
    params = @defn.search_parameters(type_name)
    template.constants['SEARCH_PARAMS'] = params unless params.nil?
    filename = File.join(folder, "#{type_name}.rb")
    file = File.open(filename, 'w:UTF-8')
    file.write(template.to_s)
    file.close
  end
end

#generate_metadata ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 32

def generate_metadata
  template = FHIR::Boot::Template.new([], true)

  primitives = @defn.primitive_types
  hash = {}
  primitives.each do |p|
    field = FHIR::Field.new
    field.name = nil

    # try to find the element that describes the value
    type = p['snapshot']['element'].select { |e| e['path'].end_with?('.value') }.first['type'].first

    # try to find the JSON data type
    field.type = type['code'].gsub('http://hl7.org/fhirpath/System.', '').downcase

    # try to find a regex
    if type['extension']
      ext = type['extension'].find { |e| e['url'] == 'http://hl7.org/fhir/StructureDefinition/regex' }
      field.regex = ext['valueString'] if ext
    end

    hash[p['id']] = field.serialize
  end
  template.constants['PRIMITIVES'] = hash

  template.constants['TYPES'] = @defn.complex_types.map { |t| t['id'] }

  # resources
  template.constants['RESOURCES'] = @defn.resource_definitions.map { |r| r['id'] }

  filename = File.join(@lib, 'fhir', 'metadata.rb')
  file = File.open(filename, 'w:UTF-8')
  file.write(template.to_s)
  file.close
end

#generate_resources ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 76

def generate_resources
  folder = File.join @lib, 'fhir', 'resources'
  generate_class_files(folder, @defn.resource_definitions)
end

#generate_types ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 68

def generate_types
  folder = File.join @lib, 'fhir', '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 = @defn.complex_types
  generate_class_files(folder, complex_types)
end

#setup ⇒ Object 



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# File 'lib/fhir_models/bootstrap/generator.rb', line 20

def setup
  # make folders for generated content if they do not exist
  @lib = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
  Dir.mkdir(File.join(@lib, 'fhir')) unless Dir.exist?(File.join(@lib, 'fhir'))
  Dir.mkdir(File.join(@lib, 'fhir', 'types')) unless Dir.exist?(File.join(@lib, 'fhir', 'types'))
  Dir.mkdir(File.join(@lib, 'fhir', 'resources')) unless Dir.exist?(File.join(@lib, 'fhir', 'resources'))

  # delete previously generated folder contents
  Dir.glob(File.join(@lib, 'fhir', '*')).each { |f| File.delete(f) unless File.directory?(f) }
  Dir.glob(File.join(@lib, 'fhir', '**', '*')).each { |f| File.delete(f) unless File.directory?(f) }
end