Module: QDM::PatientGeneration

Defined in:
lib/generate_patients.rb

Overview

PatientGeneration module can be used to generate patients with dataElements that are populated with every possible attribute that said type supports

Class Method Summary collapse

Class Method Details

.generate_exhaustive_data_element_patients(new_patient_for_each_type = true, model_info_file = 'qdm-modelinfo-5.6.xml') ⇒ Object

Generates patient(s) with fully-loaded dataElements if new_patient_for_each_type is false then a single patient will be returned that has every data element on it



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# File 'lib/generate_patients.rb', line 12

def self.generate_exhaustive_data_element_patients(new_patient_for_each_type = true, model_info_file = 'qdm-modelinfo-5.6.xml')
  datatypes = get_datatypes(File.join(File.dirname(__FILE__), "../modelinfo/#{model_info_file}"))
  patients = []
  cqm_patient = nil
  qdm_patient = nil
  datatypes.each do |type|
    next if type.include? 'PatientCharacteristic'

    # 1 Patient Per data element type containing negated and non-negated type (if negatable)
    if cqm_patient.nil? || qdm_patient.nil? || new_patient_for_each_type
      cqm_patient = QDM::BaseTypeGeneration.generate_cqm_patient(type)
      qdm_patient = QDM::BaseTypeGeneration.generate_qdm_patient
      # Add patient characteristics
      sex = generate_loaded_datatype('QDM::PatientCharacteristicSex')
      race = generate_loaded_datatype('QDM::PatientCharacteristicRace')
      ethnicity = generate_loaded_datatype('QDM::PatientCharacteristicEthnicity')
      birthdate = generate_loaded_datatype('QDM::PatientCharacteristicBirthdate')
      qdm_patient.dataElements.push(sex)
      qdm_patient.dataElements.push(race)
      qdm_patient.dataElements.push(ethnicity)
      qdm_patient.dataElements.push(birthdate)
      cqm_patient.qdmPatient = qdm_patient
    end
    data_element = generate_loaded_datatype(type)
    qdm_patient.dataElements.push(data_element)
    # if type is negatable, add a negated version to the patient
    if data_element.fields.key?('negationRationale')
      negated_data_element = generate_loaded_datatype(type, true)
      qdm_patient.dataElements.push(negated_data_element)
    end
    patients.push(cqm_patient)
  end
  patients
end

.generate_loaded_datatype(data_element_type, negate_data_element = false) ⇒ Object 



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# File 'lib/generate_patients.rb', line 64

def self.generate_loaded_datatype(data_element_type, negate_data_element = false)
  data_element = QDM.const_get(data_element_type).new
  fields = data_element.typed_attributes.keys
  fields.each do |field_name|
    # Ignore these fields, they are used by mongo
    next if %w[_id _type].include? field_name

    populate_fields(field_name, data_element, negate_data_element) if !data_element[field_name] || data_element[field_name] == []
  end
  QDM::EntityGeneration.generate_entities(data_element)
  data_element.identifier = QDM::BaseTypeGeneration.generate_qdm_id if data_element.respond_to? 'identifier'
  data_element
end

.get_datatypes(modelinfo_file) ⇒ Object 



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# File 'lib/generate_patients.rb', line 47

def self.get_datatypes(modelinfo_file)
  modelinfo = File.open(modelinfo_file) { |f| Nokogiri::XML(f) }
  datatypes = []
  # Loop through each typeInfo node (each of these is a QDM datatype)
  modelinfo.xpath('//ns4:typeInfo').each do |type|
    # Grab the name of this QDM datatype
    datatype_name = type.attributes['name'].value.split('.').last
    exclusion_array = %w[Component Identifier Patient ResultComponent FacilityLocation]
    # Store datatype and its attributes (reject irrelevant datatypes)
    next if datatype_name.include?('Negative') || datatype_name.include?('Positive') ||
            datatype_name.include?('QDMBaseType') || (exclusion_array.include? datatype_name)

    datatypes.push(datatype_name)
  end
  datatypes
end

.populate_field_by_type(field_name, data_element) ⇒ Object 



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# File 'lib/generate_patients.rb', line 111

def self.populate_field_by_type(field_name, data_element)
  field_type = data_element.fields[field_name].type
  if field_type == QDM::Code
    data_element[field_name] = QDM::BaseTypeGeneration.generate_code_field
  elsif field_type == DateTime
    data_element[field_name] = QDM::BaseTypeGeneration.generate_datetime
  elsif field_type == QDM::Interval
    data_element[field_name] = QDM::BaseTypeGeneration.generate_date_interval_field
  elsif field_type == QDM::Quantity
    data_element[field_name] = QDM::BaseTypeGeneration.generate_quantity
  elsif field_type == QDM::Identifier
    data_element[field_name] = QDM::BaseTypeGeneration.generate_qdm_id
  elsif field_type == Integer
    # TODO: randomize value
    data_element[field_name] = 3
  else
    puts("Unknown Type in patient generator for field #{field_name}, type #{field_type} in #{data_element._type}")
  end
end

.populate_fields(field_name, data_element, negate_data_element) ⇒ Object 



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# File 'lib/generate_patients.rb', line 78

def self.populate_fields(field_name, data_element, negate_data_element)
  # There are certain fields that we want to populate manually
  if field_name == 'description'
    # Skip the setting of patient description for now
  elsif field_name == 'codeListId'
    # Skip the setting code list id. It is not used in a patient's data_element, only in the measure's
  elsif field_name == 'negationRationale'
    data_element[field_name] = QDM::BaseTypeGeneration.generate_code_field if negate_data_element
  elsif field_name == 'components'
    data_element[field_name] = [QDM::BaseTypeGeneration.generate_component]
  elsif field_name == 'dataElementCodes'
    # TODO: Populate dataElementCodes with codes specifically for data element type
    # might need to build a large map of data element type to relevent codes
    # should also be done for <data element type>.attribute -> relevant code for the coded attributes
    data_element[field_name] = [QDM::BaseTypeGeneration.generate_code_field]
  elsif field_name == 'diagnoses'
    data_element[field_name] = [QDM::BaseTypeGeneration.generate_diagnosis]
  elsif field_name == 'result'
    data_element[field_name] = QDM::BaseTypeGeneration.generate_result
  elsif field_name == 'facilityLocations'
    # create up to 5 facility locations
    data_element[field_name] = (0..rand(5)).map { QDM::BaseTypeGeneration.generate_facility_location }
  elsif field_name == 'facilityLocation'
    data_element[field_name] = QDM::BaseTypeGeneration.generate_facility_location
  elsif field_name == 'targetOutcome'
    # TODO: Randomize type of targetOutcome, use code for now
    data_element[field_name] = QDM::BaseTypeGeneration.generate_code_field
  else
    # Fallback to populating fields by expected type
    populate_field_by_type(field_name, data_element)
  end
end