Class: Inferno::Terminology::Loader

Inherits:
Object
  • Object
show all
Defined in:
lib/inferno/terminology/loader.rb

Constant Summary collapse

SKIP_SYS = 
[
  'http://hl7.org/fhir/ValueSet/message-events', # has 0 codes
  'http://hl7.org/fhir/ValueSet/care-team-category', # has 0 codes
  'http://hl7.org/fhir/ValueSet/action-participant-role', # has 0 codes
  'http://hl7.org/fhir/ValueSet/example-filter', # has fake property acme-plasma
  'http://hl7.org/fhir/ValueSet/all-distance-units', # UCUM filter "canonical"
  'http://hl7.org/fhir/ValueSet/all-time-units', # UCUM filter "canonical"
  'http://hl7.org/fhir/ValueSet/example-intensional', # Unhandled filter parent =
  'http://hl7.org/fhir/ValueSet/use-context', # ValueSet contains an unknown ValueSet
  'http://hl7.org/fhir/ValueSet/media-modality', # ValueSet contains an unknown ValueSet
  'http://hl7.org/fhir/ValueSet/example-hierarchical', # Example valueset with fake codes
  # We don't perform code system validation, this code system is no longer
  # in UMLS, and this bloom filter was not being correctly generated anyway
  'http://unitsofmeasure.org'
].freeze

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.validators_repo ⇒ Object (readonly)

Returns the value of attribute validators_repo.



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# File 'lib/inferno/terminology/loader.rb', line 43

def validators_repo
  @validators_repo
end

.value_sets_repo ⇒ Object (readonly)

Returns the value of attribute value_sets_repo.



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# File 'lib/inferno/terminology/loader.rb', line 43

def value_sets_repo
  @value_sets_repo
end

Class Method Details

.add_alternative_code_system_names(code_systems) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 55

def add_alternative_code_system_names(code_systems)
  code_systems << 'urn:oid:2.16.840.1.113883.6.285' if code_systems.include? 'http://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets'
  code_systems << 'urn:oid:2.16.840.1.113883.6.13' if code_systems.include? 'http://ada.org/cdt'
  if code_systems.include? 'http://www.ada.org/cdt'
    code_systems << 'http://ada.org/cdt'
    code_systems << 'urn:oid:2.16.840.1.113883.6.13'
  end
  code_systems << 'urn:oid:2.16.840.1.113883.6.101' if code_systems.include? 'http://nucc.org/provider-taxonomy'
  code_systems.uniq!
end

.add_value_set_from_file(vs_file) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 307

def add_value_set_from_file(vs_file)
  vs = ValueSet.new(@db)
  vs.read_value_set(vs_file)
  value_sets_repo.insert(vs)
  vs
end

.bloom_file_name(codesystem) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 326

def bloom_file_name(codesystem)
  system = codesystem.tr('|', '_')
  uri = URI(system)
  return (uri.host + uri.path).gsub(%r{[./]}, '_') if uri.host && uri.port

  system.gsub(/\W/, '_')
end

.create_code_system_metadata(system_urls, root_dir) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 161

def create_code_system_metadata(system_urls, root_dir)
  vs = ValueSet.new(@db)
  metadata_path = "#{root_dir}/metadata.yml"
  metadata =
    if File.file? metadata_path
      YAML.load_file(metadata_path)
    else
      {}
    end
  system_urls.each do |url|
    abbreviation = vs.umls_abbreviation(url)
    next if abbreviation.nil?

    versions = @db.execute("SELECT SVER FROM mrsab WHERE RSAB='#{abbreviation}' AND SABIN='Y'").flatten
    restriction_level = @db.execute(
      "SELECT SRL FROM mrsab WHERE RSAB='#{abbreviation}' AND SABIN='Y'"
    ).flatten.first
    system_metadata = metadata[url] || vs.code_system_metadata(url).dup || {}
    system_metadata[:versions] ||= []
    system_metadata[:versions].concat(versions).uniq!
    system_metadata[:restriction_level] = restriction_level

    metadata[url] = system_metadata
  end

  File.write(metadata_path, metadata.to_yaml)
end

.create_validators(type: :bloom, minimum_binding_strength: 'example', include_umls: true, delete_existing: true) ⇒ Object

Creates the valueset validators, based on the passed in parameters and the value_sets_repo

Parameters:

  • type (Symbol) (defaults to: :bloom) —

    the type of validators to create, either :bloom or :csv

  • minimum_binding_strength (String) (defaults to: 'example') —

    the lowest binding strength for which we should build validators

  • include_umls (Boolean) (defaults to: true) —

    a flag to determine if we should build validators that require UMLS

  • delete_existing (Boolean) (defaults to: true) —

    a flag to determine whether any existing validators of ‘type` should be deleted before the creation tasks run. Default to `true`. If `false`, the existing validators will be read in and combined with the validators created in this step.



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# File 'lib/inferno/terminology/loader.rb', line 79

def create_validators(
  type: :bloom,
  minimum_binding_strength: 'example',
  include_umls: true,
  delete_existing: true
)
  strengths = ['example', 'preferred', 'extensible', 'required'].drop_while do |s|
    s != minimum_binding_strength
  end
  umls_code_systems = Set.new(ValueSet::SAB.keys)
  root_dir = "resources/terminology/validators/#{type}"

  FileUtils.rm_r(root_dir, force: true) if delete_existing
  FileUtils.mkdir_p(root_dir)

  vs_validators = get_value_sets(strengths).map do |vs_url, vs|
    next if SKIP_SYS.include? vs_url
    next if !include_umls && !umls_code_systems.disjoint?(Set.new(vs.included_code_systems))

    Inferno.logger.debug "Processing #{vs_url}"
    filename = "#{root_dir}/#{(URI(vs.url).host + URI(vs.url).path).gsub(%r{[./]}, '_')}"
    begin
      # Save the validator to file, and get the "new" count of number of codes
      new_count = save_to_file(vs.value_set, filename, type)
      code_systems = vs.all_included_code_systems
      Inferno.logger.debug "  #{new_count} codes"
      next if new_count.zero?

      add_alternative_code_system_names(code_systems)
      {
        url: vs_url,
        file: name_by_type(File.basename(filename), type),
        count: new_count,
        type: type.to_s,
        code_systems:
      }
    rescue UnknownCodeSystemException,
           FilterOperationException,
           UnknownValueSetException,
           URI::InvalidURIError => e
      Inferno.logger.warn "#{e.message} for ValueSet: #{vs_url}"
      next
    end
  end
  vs_validators.compact!

  code_systems = vs_validators.flat_map { |validator| validator[:code_systems] }.uniq
  vs = ValueSet.new(@db)

  cs_validators = code_systems.map do |cs_name|
    next if SKIP_SYS.include? cs_name
    next if !include_umls && umls_code_systems.include?(cs_name)

    Inferno.logger.debug "Processing #{cs_name}"
    begin
      cs = vs.code_system_set(cs_name)
      filename = "#{root_dir}/#{bloom_file_name(cs_name)}"
      new_count = save_to_file(cs, filename, type)

      {
        url: cs_name,
        file: name_by_type(File.basename(filename), type),
        count: new_count,
        type: type.to_s,
        code_systems: cs_name
      }
    rescue UnknownCodeSystemException,
           FilterOperationException,
           UnknownValueSetException,
           URI::InvalidURIError => e
      Inferno.logger.warn "#{e.message} for CodeSystem #{cs_name}"
      next
    end
  end.compact
  validators = (vs_validators + cs_validators).compact

  # Write manifest for loading later
  File.write("#{root_dir}/manifest.yml", validators.to_yaml)

  create_code_system_metadata(cs_validators.map { |validator| validator[:url] }, root_dir)
end

.get_value_sets(strengths) ⇒ Object

NOTE: resources/value_sets.yml controls which value sets get loaded. It is currently manually generated from the US Core metadata.



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# File 'lib/inferno/terminology/loader.rb', line 216

def get_value_sets(strengths)
  expected_vs_urls =
    value_sets_to_load
      .select { |vs| strengths.include? vs[:strength] }
      .map! { |vs| vs[:system] }
      .compact
      .uniq

  available_value_sets = value_sets_repo.select_by_url(expected_vs_urls)

  # Throw an error message for each missing valueset
  # But don't halt the rake task
  (expected_vs_urls - available_value_sets.keys).each do |missing_vs_url|
    Inferno.logger.error "Inferno doesn't know about valueset #{missing_vs_url}"
  end
  available_value_sets
end

.load_validators(directory = 'resources/terminology/validators/bloom') ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 314

def load_validators(directory = 'resources/terminology/validators/bloom')
  manifest_file = "#{directory}/manifest.yml"
  return unless File.file? manifest_file

  validator_metadata = YAML.load_file(manifest_file)
  validator_metadata.each do |metadata|
    metadata[:bloom_filter] =
      Bloomer::Scalable.from_msgpack(File.read("#{directory}/#{metadata[:file]}"))
    validators_repo.insert(Validator.new(metadata))
  end
end

.load_value_sets_from_directory(directory, include_subdirectories = false) ⇒ Object

rubocop:disable Style/OptionalBooleanParameter



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# File 'lib/inferno/terminology/loader.rb', line 45

def load_value_sets_from_directory(directory, include_subdirectories = false) # rubocop:disable Style/OptionalBooleanParameter
  directory += '/**/' if include_subdirectories
  value_set_files = Dir["#{directory}/*.json"]
  value_set_files.each do |vs_file|
    next unless JSON.parse(File.read(vs_file))['resourceType'] == 'ValueSet'

    add_value_set_from_file(vs_file)
  end
end

.missing_validators ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 334

def missing_validators
  return @missing_validators if @missing_validators

  required_value_sets =
    value_sets_repo
      .select_by_binding_strength(['required', 'extensible', 'preferred'])
      .map(&:value_set_url)
  @missing_validators = required_value_sets.compact - validators_repo.all_urls
end

.name_by_type(filename, type) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 251

def name_by_type(filename, type)
  case type
  when :bloom
    "#{filename}.msgpack"
  when :csv
    "#{filename}.csv"
  else
    raise 'Unknown Validator Type!'
  end
end

.register_umls_db(database) ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 302

def register_umls_db(database)
  FileUtils.mkdir_p File.dirname(database)
  @db = SQLite3::Database.new database
end

.save_bloom_to_file(codings, filename) ⇒ Object

Saves the valueset bloomfilter to a msgpack file

Parameters:

  • filename (String) —

    the name of the file



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# File 'lib/inferno/terminology/loader.rb', line 265

def save_bloom_to_file(codings, filename)
  # If the file already exists, load it in
  bloom_filter =
    if File.file? filename
      Bloomer::Scalable.from_msgpack(File.read(filename))
    else
      Bloomer::Scalable.create_with_sufficient_size(codings.length)
    end
  codings.each do |coding|
    bloom_filter.add_without_duplication("#{coding[:system]}|#{coding[:code]}")
  end
  bloom_file = File.new(filename, 'wb')
  bloom_file.write(bloom_filter.to_msgpack) unless bloom_filter.nil?

  bloom_filter.count
end

.save_csv_to_file(codings, filename) ⇒ Object

Saves the valueset to a csv

Parameters:

  • filename (String) —

    the name of the file



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# File 'lib/inferno/terminology/loader.rb', line 284

def save_csv_to_file(codings, filename)
  # If the file already exists, add it to the Set
  csv_set = Set.new
  if File.file? filename
    CSV.read(filename).each do |code_array|
      csv_set.add({ code: code_array[1], system: code_array[0] })
    end
  end
  codings.merge csv_set

  CSV.open(filename, 'wb') do |csv|
    codings.each do |coding|
      csv << [coding[:system], coding[:code]]
    end
  end
  codings.length
end

.save_new_value_set_list ⇒ Object

Run this method in an inferno console to update the list of value set bindings. This is not done automatically during the build because Inferno isn’t loaded during the build process.



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# File 'lib/inferno/terminology/loader.rb', line 197

def save_new_value_set_list
  all_metadata =
    USCoreTestKit::USCoreV311::USCoreTestSuite.metadata +
    USCoreTestKit::USCoreV400::USCoreTestSuite.metadata +
    USCoreTestKit::USCoreV501::USCoreTestSuite.metadata +
    USCoreTestKit::USCoreV610::USCoreTestSuite.metadata +
    USCoreTestKit::USCoreV700::USCoreTestSuite.metadata

  all_metadata =
    all_metadata
      .flat_map { |metadata| metadata.bindings.map { |bind| bind.merge(profile_url: metadata.profile_url) } }
      .select { |metadata| metadata[:strength] == 'required' }
      .uniq

  File.write(File.join('resources', 'value_sets.yml'), all_metadata.to_yaml)
end

.save_to_file(codeset, filename, type) ⇒ Object

Chooses which filetype to save the validator as, based on the type variable passed in



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# File 'lib/inferno/terminology/loader.rb', line 235

def save_to_file(codeset, filename, type)
  if codeset.blank?
    Inferno.logger.debug "Unable to save #{filename} because it contains no codes"
    return 0
  end

  case type
  when :bloom
    save_bloom_to_file(codeset, name_by_type(filename, type))
  when :csv
    save_csv_to_file(codeset, name_by_type(filename, type))
  else
    raise 'Unknown Validator Type!'
  end
end

.value_sets_to_load ⇒ Object 



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# File 'lib/inferno/terminology/loader.rb', line 189

def value_sets_to_load
  @value_sets_to_load ||=
    YAML.load_file(File.join('resources', 'value_sets.yml'))
end