Class: HealthDataStandards::Import::C32::PatientImporter

Inherits:
Object
  • Object
show all
Includes:
Util, Singleton
Defined in:
lib/health-data-standards/import/c32/patient_importer.rb

Overview

This class is the central location for taking a HITSP C32 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

Constructor Details

#initialize(check_usable = true) ⇒ PatientImporter

Creates a new PatientImporter with the following XPath expressions used to find content in a HITSP C32:

Encounter entries

//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.127']/cda:entry/cda:encounter

Procedure entries

//cda:procedure[cda:templateId/@root='2.16.840.1.113883.10.20.1.29']

Result entries - There seems to be some confusion around the correct templateId, so the code checks for both

//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15.1'] | //cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15']

Vital sign entries

//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.14']

Medication entries

//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.112']/cda:entry/cda:substanceAdministration

Codes for medications are found in the substanceAdministration with the following relative XPath

./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code

Condition entries

//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.103']/cda:entry/cda:act/cda:entryRelationship/cda:observation

Codes for conditions are determined by examining the value child element as opposed to the code child element

Social History entries (non-C32 section, specified in the HL7 CCD)

//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.19']

Care Goal entries(non-C32 section, specified in the HL7 CCD)

//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.25']

Allergy entries

//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.18']

Immunization entries

//cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.1.24']

Codes for immunizations are found in the substanceAdministration with the following relative XPath

./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 55

def initialize(check_usable = true)
  @section_importers = {}
  @section_importers[:encounters] = EncounterImporter.new
  @section_importers[:procedures] = ProcedureImporter.new
  @section_importers[:results] = ResultImporter.new
  @section_importers[:vital_signs] = VitalSignImporter.new
  @section_importers[:medications] = MedicationImporter.new
  @section_importers[:conditions] = ConditionImporter.new
  @section_importers[:social_history] = SectionImporter.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.19']")
  @section_importers[:care_goals] = CareGoalImporter.new
  @section_importers[:medical_equipment] = MedicalEquipmentImporter.new
  @section_importers[:allergies] = AllergyImporter.new
  @section_importers[:immunizations] = ImmunizationImporter.new
  @section_importers[:insurance_providers] = InsuranceProviderImporter.new
end

Instance Method Details

#build_id_map(doc) ⇒ Object 



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 71

def build_id_map(doc)
  id_map = {}
  path = "//*[@ID]"
  ids = doc.xpath(path)
  ids.each do |id|
    tag = id['ID']
    value = id.content
    id_map[tag] = value
  end

  id_map
end

#check_for_cause_of_death(c32_patient) ⇒ Object

Checks the conditions to see if any of them have a cause of death set. If they do, it will set the expired field on the Record. This is done here rather than replacing the expried method on Record because other formats may actully tell you whether a patient is dead or not.

Parameters:

  • c32_patient (Record) —

    to check the conditions on and set the expired property if applicable



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 111

def check_for_cause_of_death(c32_patient)
  if c32_patient.conditions.any? {|condition| condition.cause_of_death }
    c32_patient.expired = true
  end
end

#check_usable(check_usable_entries) ⇒ Object

Parameters:

  • value (boolean) —

    for check_usable_entries…importer uses true, stats uses false



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 85

def check_usable(check_usable_entries)
  @section_importers.each_pair do |section, importer|
    importer.check_for_usable = check_usable_entries
  end
end

#create_c32_hash(record, doc) ⇒ Hash

Create a simple representation of the patient from a HITSP C32

Parameters:

  • record (Record) —

    Mongoid model to append the Entry objects to

  • doc (Nokogiri::XML::Document) —

    It is expected that the root node of this document will have the “cda” namespace registered to “urn:hl7-org:v3”

Returns:

  • (Hash) —

    a represnetation of the patient with symbols as keys for each section



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 122

def create_c32_hash(record, doc)
  id_map = build_id_map(doc)
  @section_importers.each_pair do |section, importer|
    record.send(section.to_setter, importer.create_entries(doc, id_map))
  end
end

#get_demographics(patient, doc) ⇒ Object

Inspects a C32 document and populates the patient Hash with first name, last name birth date, gender and the effectiveTime.

Parameters:

  • patient (Hash) —

    A hash that is used to represent the patient

  • doc (Nokogiri::XML::Node) —

    The C32 document parsed by Nokogiri



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 134

def get_demographics(patient, doc)
  effective_date = doc.at_xpath('/cda:ClinicalDocument/cda:effectiveTime')['value']
  patient.effective_time = HL7Helper.timestamp_to_integer(effective_date)
  patient_element = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:patient')
  patient.first = patient_element.at_xpath('cda:name/cda:given').text
  patient.last = patient_element.at_xpath('cda:name/cda:family').text
  birthdate_in_hl7ts_node = patient_element.at_xpath('cda:birthTime')
  birthdate_in_hl7ts = birthdate_in_hl7ts_node['value']
  patient.birthdate = HL7Helper.timestamp_to_integer(birthdate_in_hl7ts)
  gender_node = patient_element.at_xpath('cda:administrativeGenderCode')
  patient.gender = gender_node['code']
  id_node = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:id')
  patient.medical_record_number = id_node['extension']
  
  # parse race, ethnicity, and spoken language
  race_node = patient_element.at_xpath('cda:raceCode')
  patient.race = { code: race_node['code'], code_set: 'CDC-RE' } if race_node
  ethnicity_node = patient_element.at_xpath('cda:ethnicGroupCode')
  patient.ethnicity = {code: ethnicity_node['code'], code_set: 'CDC-RE'} if ethnicity_node

  languages = patient_element.search('languageCommunication').map {|lc| lc.at_xpath('cda:languageCode')['code'] }
  patient.languages = languages unless languages.empty?
  
end

#parse_c32(doc) ⇒ Record

Parses a HITSP C32 document and returns a Hash of of the patient.

Parameters:

  • doc (Nokogiri::XML::Document) —

    It is expected that the root node of this document will have the “cda” namespace registered to “urn:hl7-org:v3”

Returns:

  • (Record) —

    a Mongoid model representing the patient



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# File 'lib/health-data-standards/import/c32/patient_importer.rb', line 96

def parse_c32(doc)
  c32_patient = Record.new
  get_demographics(c32_patient, doc)
  create_c32_hash(c32_patient, doc)
  check_for_cause_of_death(c32_patient)
  
  c32_patient
end