Class: QRDA::Cat1::PatientImporter

Inherits:
Object
  • Object
show all
Includes:
DemographicsImporter, Singleton
Defined in:
lib/qrda-import/patient_importer.rb

Overview

This class is the central location for taking a QRDA Cat 1 XML document and converting it into the processed form we store in MongoDB. The class does this by running each measure independently on the XML document

This class is a Singleton. It should be accessed by calling PatientImporter.instance

Instance Method Summary collapse

Methods included from DemographicsImporter

#code_if_present, #get_demographics

Constructor Details

#initialize ⇒ PatientImporter

Returns a new instance of PatientImporter.



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# File 'lib/qrda-import/patient_importer.rb', line 12

def initialize
  # This differs from other HDS patient importers in that sections can have multiple importers
  @data_element_importers = []
  @data_element_importers << AdverseEventImporter.new
  @data_element_importers << AllergyIntoleranceImporter.new
  @data_element_importers << AssessmentOrderImporter.new
  @data_element_importers << AssessmentPerformedImporter.new
  @data_element_importers << AssessmentRecommendedImporter.new
  @data_element_importers << CommunicationPerformedImporter.new
  @data_element_importers << DeviceOrderImporter.new
  @data_element_importers << DeviceRecommendedImporter.new
  @data_element_importers << DiagnosisImporter.new
  @data_element_importers << DiagnosticStudyOrderImporter.new
  @data_element_importers << DiagnosticStudyPerformedImporter.new
  @data_element_importers << DiagnosticStudyRecommendedImporter.new
  @data_element_importers << EncounterOrderImporter.new
  @data_element_importers << EncounterPerformedImporter.new
  @data_element_importers << EncounterRecommendedImporter.new
  @data_element_importers << FamilyHistoryImporter.new
  @data_element_importers << ImmunizationAdministeredImporter.new
  @data_element_importers << ImmunizationOrderImporter.new
  @data_element_importers << InterventionOrderImporter.new
  @data_element_importers << InterventionPerformedImporter.new
  @data_element_importers << InterventionRecommendedImporter.new
  @data_element_importers << LaboratoryTestOrderImporter.new
  @data_element_importers << LaboratoryTestPerformedImporter.new
  @data_element_importers << LaboratoryTestRecommendedImporter.new
  @data_element_importers << MedicationActiveImporter.new
  @data_element_importers << MedicationAdministeredImporter.new
  @data_element_importers << MedicationDischargeImporter.new
  @data_element_importers << MedicationDispensedImporter.new
  @data_element_importers << MedicationOrderImporter.new
  @data_element_importers << PatientCareExperienceImporter.new
  @data_element_importers << PatientCharacteristicClinicalTrialParticipantImporter.new
  @data_element_importers << PatientCharacteristicExpiredImporter.new
  @data_element_importers << PatientCharacteristicPayerImporter.new
  @data_element_importers << PhysicalExamOrderImporter.new
  @data_element_importers << PhysicalExamPerformedImporter.new
  @data_element_importers << PhysicalExamRecommendedImporter.new
  @data_element_importers << ProcedureOrderImporter.new
  @data_element_importers << ProcedurePerformedImporter.new
  @data_element_importers << ProcedureRecommendedImporter.new
  @data_element_importers << ProgramParticipationImporter.new
  @data_element_importers << ProviderCareExperienceImporter.new
  @data_element_importers << RelatedPersonImporter.new
  @data_element_importers << SubstanceAdministeredImporter.new
  @data_element_importers << SubstanceOrderImporter.new
  @data_element_importers << SubstanceRecommendedImporter.new
  @data_element_importers << SymptomImporter.new
end

Instance Method Details

#get_patient_expired(record, doc) ⇒ Object 



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# File 'lib/qrda-import/patient_importer.rb', line 139

def get_patient_expired(record, doc)
  entry_elements = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']/cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
  return unless entry_elements.empty?

  record.expired = true
  record.deathdate = DateTime.parse(entry_elements.at_xpath("./cda:effectiveTime/cda:low")['value']).to_i
end

#import_data_elements(patient, doc, entry_id_map, codes = Set.new, codes_modifiers = {}, warnings = []) ⇒ Object 



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# File 'lib/qrda-import/patient_importer.rb', line 75

def import_data_elements(patient, doc, entry_id_map, codes = Set.new, codes_modifiers = {}, warnings = [])
  context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
  nrh = NarrativeReferenceHandler.new
  nrh.build_id_map(doc)
  @data_element_importers.each do |importer|
    data_elements, id_map = importer.create_entries(context, nrh)
    new_data_elements = []

    id_map.each_pair do |key, elem_ids|
      split_id = key.split('***')
      id_string = "#{split_id[1]}(root), #{split_id[0]}(extension)"
      warnings << ValidationError.new(message: "Two or more entries share the Id: #{id_string}.") if elem_ids.length > 1
      elem_id = elem_ids.last
      data_element = data_elements.find { |de| de.id == elem_id }

      # If a data_element isn't returned, there was an issue parsing the template, provide a warning
      if data_element.nil?
        warnings << ValidationError.new(message: "Error parsing template with Id: #{id_string}.")
        next
      end

      # Keep the first element with a shared ID
      new_data_elements << data_element

      # Encounters require elements beyond id for uniqueness
      next unless data_element._type == 'QDM::EncounterPerformed'
      unique_element_keys = []
      # Add key_elements_for_determining_encounter_uniqueness to array, this is used to determine if other
      # elements with the same ID should be considered as unique
      unique_element_keys << key_elements_for_determining_encounter_uniqueness(data_element)

      # Loop through all other data elements with the same id
      elem_ids[0,elem_ids.length - 1].each do |dup_id|
        dup_element = data_elements.find { |de| de.id == dup_id }
        dup_element_keys = key_elements_for_determining_encounter_uniqueness(dup_element)
        # See if a previously selected data element shared all of the keys files
        # If all key fields match, move on.
        next if unique_element_keys.include?(dup_element_keys)
        # If all key fields don't match, keep element
        new_data_elements << dup_element
        # Add to list of unique element keys
        unique_element_keys << dup_element_keys
      end
    end

    patient.qdmPatient.dataElements << new_data_elements
    entry_id_map.merge!(id_map)
    warnings.concat(importer.warnings)
    codes.merge(importer.codes)
    codes_modifiers.merge!(importer.codes_modifiers)
    # reset warnings and codes after they're captured so that the importer can be re-used
    importer.warnings = []
    importer.codes_modifiers = {}
    importer.codes = Set.new
  end
end

#key_elements_for_determining_encounter_uniqueness(encounter) ⇒ Object 



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# File 'lib/qrda-import/patient_importer.rb', line 132

def key_elements_for_determining_encounter_uniqueness(encounter)
  codes = encounter.codes.collect { |dec| "#{dec.code}_#{dec.system}" }.sort.to_s
  admission_date_time = encounter&.relevantPeriod&.low.to_s
  discharge_date_time = encounter&.relevantPeriod&.high.to_s
  "#{codes}#{admission_date_time}#{discharge_date_time}"
end

#normalize_references(patient, entry_id_map, warnings) ⇒ Object 



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# File 'lib/qrda-import/patient_importer.rb', line 147

def normalize_references(patient, entry_id_map, warnings)
  patient.qdmPatient.dataElements.each do |data_element|
    next unless data_element.respond_to?(:relatedTo) && data_element.relatedTo

    relations_to_add = []
    data_element.relatedTo.each do |related_to|
      relation_to_add = entry_id_map["#{related_to['value']}***#{related_to['namingSystem']}"]
      # Add the relation if it can be found, otherwise return a warning
      relations_to_add += relation_to_add unless relation_to_add.nil?
      if relation_to_add.nil?
        id_warning_str = "Related To Id: #{related_to['namingSystem']}(root), #{related_to['value']}(extension) cannot be found in QRDA file."
        warnings << ValidationError.new(message: id_warning_str)
      end
    end
    data_element.relatedTo = relations_to_add.map(&:to_s)
  end
end

#parse_cat1(doc) ⇒ Object 



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# File 'lib/qrda-import/patient_importer.rb', line 63

def parse_cat1(doc)
  patient = CQM::Patient.new
  warnings = []
  codes = Set.new
  codes_modifiers = {}
  entry_id_map = {}
  import_data_elements(patient, doc, entry_id_map, codes, codes_modifiers, warnings)
  normalize_references(patient, entry_id_map, warnings)
  get_demographics(patient, doc, codes)
  [patient, warnings, codes, codes_modifiers]
end