patient_zipper_test.rb

# frozen_string_literal: true

require 'test_helper'
require 'fileutils'

class PatientZipperTest < ActiveSupport::TestCase
  setup do
    pt = FactoryBot.create(:multi_measure_test_static_result)
    pt.measure_ids = pt.bundle.measures.map(&:hqmf_id)
    pt.measure_ids << APP_CONSTANTS['result_measures'].first.hqmf_id
    pt.save
    @static_patient = FactoryBot.create(:static_test_patient, bundleId: pt.bundle.id, correlation_id: pt.id)
    @static_patient.save
    @patients = Patient.all.to_a.select { |p| p.gender == 'F' }

    prov = Provider.default_provider

    @patients.each do |p|
      p.providers << prov
      p.save!
    end
  end

  test 'Should create valid html file' do
    format = :html
    filename = "pTest-#{Time.now.to_i}.html.zip"
    file = Tempfile.new(filename)
    Cypress::PatientZipper.zip(file, @patients, format)
    file.close
    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.html') && !zip_entry.name.include?('__MACOSX')
        doc = Nokogiri::HTML(zip_entry.get_input_stream, &:strict)
        doc.at_css('head title').to_s
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal @patients.count, count, 'Zip file has wrong number of records'
  end

  test 'Should create valid qrda file with an encounter id' do
    format = :qrda
    filename = "pTest-#{Time.now.to_i}.qrda.zip"
    file = Tempfile.new(filename)
    patient = @static_patient
    # Include the inpatient encounter valueset in the bundle
    faked_inpatient_vs = patient.bundle.value_sets.first
    faked_inpatient_vs.oid = '2.16.840.1.113883.3.666.5.307'
    faked_inpatient_vs.save

    # Include the result measure in the bundle
    faked_result_measure = patient.bundle.measures.first
    faked_result_measure.hqmf_id = APP_CONSTANTS['result_measures'].first.hqmf_id
    faked_result_measure.save

    # Add Core Clinical Data Elements
    patient.qdmPatient.dataElements.push QDM::EncounterPerformed.new(relevantPeriod: QDM::Interval.new(DateTime.new(2011, 3, 24, 20, 53, 20).utc, DateTime.new(2011, 3, 25, 20, 53, 20).utc),
                                                                     dataElementCodes: [QDM::Code.new(faked_inpatient_vs.concepts.first.code, '2.16.840.1.113883.6.96')])
    patient.qdmPatient.dataElements.push QDM::LaboratoryTestPerformed.new(resultDatetime: DateTime.new(2011, 3, 24, 20, 53, 20).utc, relatedTo: [],
                                                                          dataElementCodes: [QDM::Code.new('6', '2.16.840.1.113883.6.96')])
    patient.qdmPatient.dataElements.push QDM::PhysicalExamPerformed.new(relevantDatetime: DateTime.new(2011, 3, 24, 20, 53, 20).utc, relatedTo: [],
                                                                        dataElementCodes: [QDM::Code.new('24', '2.16.840.1.113883.6.96')])
    patient.save

    Cypress::PatientZipper.zip(file, [patient], format)
    file.close

    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.xml') && !zip_entry.name.include?('__MACOSX')
        doc = Nokogiri::XML(zip_entry.get_input_stream, &:strict)
        doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
        doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
        assert_equal 2, doc.xpath('//sdtc:templateId[@root="2.16.840.1.113883.10.20.24.3.150"]').size, 'There should be 2 entry with encounter ids'
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal 1, count, 'Zip should contain 1 QRDA file for the patient with a negated valueset'
  end

  test 'Should create valid qrda file with a negated valueset' do
    format = :qrda
    filename = "pTest-#{Time.now.to_i}.qrda.zip"
    file = Tempfile.new(filename)

    patient = @static_patient
    modified_procedure = patient.qdmPatient.procedures.first
    modified_procedure.negationRationale = modified_procedure.codes.first

    # Add the negated code to a valueset
    measure = patient.bundle.measures.find_by(cms_id: 'CMS134v6')
    valueset_oids = measure.source_data_criteria.map { |sdc| sdc.codeListId if sdc._type == 'QDM::ProcedurePerformed' }.compact
    valueset_oids[0, 1].each do |valueset_oid|
      vs = patient.bundle.value_sets.find_by(oid: valueset_oid)
      modified_procedure.dataElementCodes.first[:code] = vs.concepts.first.code
      patient.save
    end

    Cypress::PatientZipper.zip(file, [patient], format)
    file.close

    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.xml') && !zip_entry.name.include?('__MACOSX')
        doc = Nokogiri::XML(zip_entry.get_input_stream, &:strict)
        doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
        doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
        assert_equal 1, doc.xpath('//cda:code[@nullFlavor="NA"]').size, 'There should be 1 negated code in the exported QRDA'
        assert_equal 1, doc.xpath("//cda:patientRole/cda:id[@extension='#{patient.id}']").size, 'The id should match the original patient id'
        confirm_imported_patient_can_be_saved_after_replaced_codes(doc, patient, modified_procedure.dataElementCodes.first[:code])
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal 1, count, 'Zip should contain 1 QRDA file for the patient with a negated valueset'
  end

  test 'Should create valid qrda file with two negated valuesets' do
    format = :qrda
    filename = "pTest-#{Time.now.to_i}.qrda.zip"
    file = Tempfile.new(filename)

    patient = @static_patient
    modified_procedure = patient.qdmPatient.procedures.first
    modified_procedure.negationRationale = modified_procedure.codes.first
    patient.save

    # Add the negated code to a second valueset
    measure = patient.bundle.measures.find_by(cms_id: 'CMS134v6')
    valueset_oids = measure.source_data_criteria.map { |sdc| sdc.codeListId if sdc._type == 'QDM::ProcedurePerformed' }.compact
    valueset_oids[0, 2].each do |valueset_oid|
      vs = patient.bundle.value_sets.find_by(oid: valueset_oid)
      vs.concepts.create(code: modified_procedure.codes.first.code, code_system_oid: modified_procedure.codes.first.system)
      vs.save
    end

    Cypress::PatientZipper.zip(file, [patient], format)
    file.close

    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.xml') && !zip_entry.name.include?('__MACOSX')
        doc = Nokogiri::XML(zip_entry.get_input_stream, &:strict)
        doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
        doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
        assert_equal 2, doc.xpath('//cda:code[@nullFlavor="NA"]').size, 'There should be 2 negated valusets in the exported QRDA'
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal 1, count, 'Zip should contain 1 QRDA file for the patient with negated valuesets'
  end

  def confirm_imported_patient_can_be_saved_after_replaced_codes(doc, patient, original_code)
    negated_oid = ValueSet.where('concepts.code': original_code).first.oid
    imported_patient, _warnings = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
    imported_patient.update(_type: CQM::VendorPatient)
    cloned_import = imported_patient.clone
    cloned_import2 = imported_patient.clone
    codefound = imported_patient.qdmPatient.procedures.first.dataElementCodes.any? { |dec| dec[:code] == original_code }
    assert_equal false, codefound, 'code should not be found prior to replace_negated_codes'
    # Should replace with a code from the valueset
    Cypress::QrdaPostProcessor.replace_negated_codes(imported_patient, patient.bundle)
    codefound = imported_patient.qdmPatient.procedures.first.dataElementCodes.any? { |dec| dec[:code] == original_code }
    assert codefound, 'replaced code should equal original code'
    assert imported_patient.save
    # Should not replace a code when valuesets do not exist
    ValueSet.destroy_all
    Cypress::QrdaPostProcessor.replace_negated_codes(cloned_import, patient.bundle)
    codefound = cloned_import.qdmPatient.procedures.first.dataElementCodes.any? { |dec| dec[:code] == original_code }
    assert_not codefound, 'Without valusets the code should not be replaced'
    assert cloned_import.save
    # Should replace with the default code
    APP_CONSTANTS['version_config']['~>2022.0']['default_negation_codes'][negated_oid] = { 'code' => '123', 'codeSystem' => 'SNOMEDCT' }
    Cypress::QrdaPostProcessor.replace_negated_codes(cloned_import2, patient.bundle)
    codefound = cloned_import2.qdmPatient.procedures.first.dataElementCodes.any? { |dec| dec[:code] == '123' }
    assert codefound, 'replaced code should equal default code'
    assert cloned_import2.save
  end

  test 'Should create valid qrda file' do
    format = :qrda
    filename = "pTest-#{Time.now.to_i}.qrda.zip"
    file = Tempfile.new(filename)

    Cypress::PatientZipper.zip(file, @patients, format)
    file.close

    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.xml') && !zip_entry.name.include?('__MACOSX')
        Nokogiri::XML(zip_entry.get_input_stream, &:strict)
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal @patients.count, count, 'Zip file has wrong number of records'
  end

  test 'Should create valid qrda file when not associated to test' do
    @patients = Patient.where(correlation_id: nil)

    format = :qrda
    filename = "pTest-#{Time.now.to_i}.qrda.zip"
    file = Tempfile.new(filename)

    Cypress::PatientZipper.zip(file, @patients, format)
    file.close

    count = 0
    Zip::ZipFile.foreach(file.path) do |zip_entry|
      if zip_entry.name.include?('.xml') && !zip_entry.name.include?('__MACOSX')
        Nokogiri::XML(zip_entry.get_input_stream, &:strict)
        count += 1
      end
    end
    File.delete(file.path)
    assert_equal @patients.count, count, 'Zip file has wrong number of records'
  end
end