Class: CQM::Converter::HDSRecord

Inherits:
Object
  • Object
show all
Defined in:
lib/cqm/converter/hds_record.rb

Overview

CQM Converter class for HDS based records.

Instance Method Summary collapse

Constructor Details

#initialize ⇒ HDSRecord

Initialize a new HDSRecord converter. NOTE: This should be done once, and then used for every HDS Record you want to convert, since it takes a few seconds to initialize the conversion environment using Sprockets.



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# File 'lib/cqm/converter/hds_record.rb', line 11

def initialize
  # Create a new sprockets environment.
  environment = Sprockets::Environment.new

  # Populate the JavaScript environment with the cql_qdm_patientapi mappings and
  # its dependencies.
  cql_qdm_patientapi_spec = Gem::Specification.find_by_name('cql_qdm_patientapi')
  momentjs_rails_spec = Gem::Specification.find_by_name('momentjs-rails')
  environment.append_path(cql_qdm_patientapi_spec.gem_dir + '/app/assets/javascripts')
  environment.append_path(cql_qdm_patientapi_spec.gem_dir + '/vendor/assets/javascripts')
  environment.append_path(momentjs_rails_spec.gem_dir + '/vendor/assets/javascripts')
  @js_dependencies = environment['moment'].to_s
  @js_dependencies += environment['cql4browsers'].to_s
  @js_dependencies += environment['cql_qdm_patientapi'].to_s
  @qdm_model_attrs = Utils.gather_qdm_model_attrs
end

Instance Method Details

#generate_qdm_data_element(dc_fixed_keys, dc_type) ⇒ Object 



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# File 'lib/cqm/converter/hds_record.rb', line 134

def generate_qdm_data_element(dc_fixed_keys, dc_type)
  data_element = QDM.const_get(dc_type).new(dc_fixed_keys)

  # Any nested QDM types that need initialization should be handled here
  # when converting from the QDM models to the HDS models.
  # For now, that should just be FacilityLocation objects and Id
  if data_element.is_a?(QDM::EncounterPerformed)
    data_element.facilityLocations = data_element.facilityLocations.map do |facility|
      QDM::FacilityLocation.new.from_json(facility.to_json)
    end
  end

  data_element
end

#to_qdm(record) ⇒ Object

Given an HDS record, return a corresponding QDM patient.



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# File 'lib/cqm/converter/hds_record.rb', line 29

def to_qdm(record)
  # Start with a new QDM patient.
  patient = QDM::Patient.new

  # Build and execute JavaScript that will create a 'CQL_QDM.Patient'
  # JavaScript version of the HDS record. Specifically, we will use
  # this to build our patient's 'dataElements'.
  cql_qdm_patient = ExecJS.exec Utils.hds_to_qdm_js(@js_dependencies, record, @qdm_model_attrs)

  # Make sure all date times are in the correct form.
  Utils.date_time_adjuster(cql_qdm_patient) if cql_qdm_patient

  # Grab the results from the CQL_QDM.Patient and add a new 'data_element'
  # for each datatype found on the CQL_QDM.Patient to the new QDM Patient.
  cql_qdm_patient.keys.each do |dc_type|
    cql_qdm_patient[dc_type].each do |dc|
      # Convert snake_case to camelCase
      dc_fixed_keys = dc.deep_transform_keys { |key| key.to_s.gsub(/^_/, '').camelize(:lower) }

      # Our Code model uses 'codeSystem' to describe the code system (since system is
      # a reserved keyword). The cql.Code calls this 'system', so make sure the proper
      # conversion is made. Also do this for 'display', where we call this descriptor.
      dc_fixed_keys = dc_fixed_keys.deep_transform_keys { |key| key.to_s == 'system' ? :codeSystem : key }
      dc_fixed_keys = dc_fixed_keys.deep_transform_keys { |key| key.to_s == 'display' ? :descriptor : key }

      patient.dataElements << generate_qdm_data_element(dc_fixed_keys, dc_type)
    end
  end

  # Convert patient characteristic birthdate.
  birthdate = record.birthdate
  if birthdate
    birth_datetime = DateTime.strptime(birthdate.to_s, '%s')
    code = QDM::Code.new('21112-8', 'LOINC')
    patient.dataElements << QDM::PatientCharacteristicBirthdate.new(birthDatetime: birth_datetime, dataElementCodes: [code])
  end

  # Convert patient characteristic clinical trial participant.
  # TODO, Adam 4/1: The Bonnie team is working on implementing this in HDS. When that work
  # is complete, this should be updated to reflect how that looks in HDS.
  # patient.dataElements << QDM::PatientCharacteristicClinicalTrialParticipant.new

  # Convert patient characteristic ethnicity.
  ethnicity = record.ethnicity
  if ethnicity
    # See: https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238
    # Bonnie currently uses 'CDC Race' instead of the correct 'cdcrec'.  This incorrect code is here as a temporary
    # workaround until the larger change of making bonnie use 'cdcrec' can be implemented.
    # Same change is present in `race` below.
    code = QDM::Code.new(ethnicity['code'], 'CDC Race', ethnicity['name'], '2.16.840.1.113883.6.238')
    # code = QDM::Code.new(ethnicity['code'], 'cdcrec', ethnicity['name'], '2.16.840.1.113883.6.238')
    patient.dataElements << QDM::PatientCharacteristicEthnicity.new(dataElementCodes: [code])
  end

  # Convert patient characteristic expired.
  expired = record.deathdate
  if expired
    expired_datetime = DateTime.strptime(expired.to_s, '%s')
    code = QDM::Code.new('419099009', 'SNOMED-CT')
    patient.dataElements << QDM::PatientCharacteristicExpired.new(expiredDatetime: expired_datetime, dataElementCodes: [code])
  end

  # Convert patient characteristic race.
  race = record.race
  if race
    # See: https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.6.238
    code = QDM::Code.new(race['code'], 'CDC Race', race['name'], '2.16.840.1.113883.6.238')
    # code = QDM::Code.new(race['code'], 'cdcrec', race['name'], '2.16.840.1.113883.6.238')
    patient.dataElements << QDM::PatientCharacteristicRace.new(dataElementCodes: [code])
  end

  # Convert patient characteristic sex.
  sex = record.gender
  if sex
    # See: https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.5.1
    code = QDM::Code.new(sex, 'AdministrativeGender', sex, '2.16.840.1.113883.5.1')
    patient.dataElements << QDM::PatientCharacteristicSex.new(dataElementCodes: [code])
  end

  # Convert remaining metadata.
  patient.birthDatetime = DateTime.strptime(record.birthdate.to_s, '%s') if record.birthdate
  patient.givenNames = record.first ? [record.first] : []
  patient.familyName = record.last if record.last
  patient.bundleId = record.bundle_id if record.bundle_id

  # Convert extended_data.
  patient.extendedData = {}
  patient.extendedData['type'] = record.type if record.respond_to?('type')
  patient.extendedData['measure_ids'] = record.measure_ids if record.respond_to?('measure_ids')
  patient.extendedData['source_data_criteria'] = record.source_data_criteria if record.respond_to?('source_data_criteria')
  patient.extendedData['expected_values'] = record.expected_values if record.respond_to?('expected_values')
  patient.extendedData['notes'] = record.notes if record.respond_to?('notes')
  patient.extendedData['is_shared'] = record.is_shared if record.respond_to?('is_shared')
  patient.extendedData['origin_data'] = record.origin_data if record.respond_to?('origin_data')
  patient.extendedData['test_id'] = record.test_id if record.respond_to?('test_id')
  patient.extendedData['medical_record_number'] = record.medical_record_number if record.respond_to?('medical_record_number')
  patient.extendedData['medical_record_assigner'] = record.medical_record_assigner if record.respond_to?('medical_record_assigner')
  patient.extendedData['description'] = record.description if record.respond_to?('description')
  patient.extendedData['description_category'] = record.description_category if record.respond_to?('description_category')
  patient.extendedData['insurance_providers'] = record.insurance_providers.to_json(except: '_id') if record.respond_to?('insurance_providers')
  patient.extendedData['provider_performances'] = record.provider_performances.to_json(except: '_id') unless record.provider_performances.empty?

  patient
end