lib/health-data-standards/import/cat1/patient_importer.rb
module HealthDataStandards
module Import
module Cat1
# 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
class PatientImporter
include Singleton
def initialize
# This differs from other HDS patient importers in that sections can have multiple importers
@section_importers = {}
@section_importers[:care_goals] = [generate_importer(CDA::SectionImporter, "./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.1']", '2.16.840.1.113883.3.560.1.9')] #care goal
@section_importers[:conditions] = [generate_importer(GestationalAgeImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
generate_importer(EcogStatusImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
generate_importer(SymptomActiveImporter, nil, '2.16.840.1.113883.3.560.1.69', 'active'),
generate_importer(DiagnosisActiveImporter, nil, '2.16.840.1.113883.3.560.1.2', 'active'),
generate_importer(DiagnosisImporter, nil, '2.16.840.1.113883.10.20.28.3.110'),
generate_importer(CDA::ConditionImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']", '2.16.840.1.113883.3.560.1.404'), # patient characteristic age
generate_importer(CDA::ConditionImporter, "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.14']", '2.16.840.1.113883.3.560.1.24', 'resolved'), #diagnosis resolved
generate_importer(DiagnosisInactiveImporter, nil, '2.16.840.1.113883.3.560.1.23', 'inactive'), #diagnosis inactive
generate_importer(ClinicalTrialParticipantImporter, nil, '2.16.840.1.113883.3.560.1.401')]
@section_importers[:medications] = [generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.105']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16']", '2.16.840.1.113883.3.560.1.199', 'discharge'), #discharge medication activity
generate_importer(MedicationActiveImporter, nil, '2.16.840.1.113883.3.560.1.13', 'active'), #medication active
generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16']", '2.16.840.1.113883.3.560.1.14', 'administered'), #medication administered
generate_importer(CDA::MedicationImporter, "./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']", '2.16.840.1.113883.3.560.1.17', 'ordered'), #medication order TODO: ADD NEGATON REASON HANDLING SOMEHOW
generate_importer(MedicationDispensedImporter, nil, '2.16.840.1.113883.3.560.1.8', 'dispensed'),
generate_importer(MedicationDispensedActImporter, nil, '2.16.840.1.113883.3.560.1.8', 'dispensed'),
generate_importer(ImmunizationAdministeredImporter, nil, '2.16.840.1.113883.10.20.28.3.112', 'administered')] #immunization
@section_importers[:communications] = [generate_importer(CDA::CommunicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.31'), #comm from provider to patient
generate_importer(CDA::CommunicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']", '2.16.840.1.113883.3.560.1.30'), #comm from patient to provider
generate_importer(CDA::CommunicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']", '2.16.840.1.113883.3.560.1.129')] #comm from provider to provider, not done
@section_importers[:procedures] = [generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']", '2.16.840.1.113883.3.560.1.57', 'performed'), #physical exam performed
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']", '2.16.840.1.113883.3.560.1.45', 'ordered'), #intervention ordered
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']", '2.16.840.1.113883.3.560.1.46', 'performed'), #intervention performed
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
generate_importer(ProcedureOrderImporter, nil, '2.16.840.1.113883.3.560.1.62', 'ordered'),
generate_importer(ProcedurePerformedImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'), #risk category assessment
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.20']", '2.16.840.1.113883.3.560.1.11'), #diagnostic study result
generate_importer(DiagnosticStudyOrderImporter, nil, '2.16.840.1.113883.3.560.1.40', 'ordered')]
@section_importers[:allergies] = [generate_importer(ProcedureIntoleranceImporter, nil, '2.16.840.1.113883.3.560.1.61'),
generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.46']", '2.16.840.1.113883.3.560.1.67'), #medication intolerance
generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.43']", '2.16.840.1.113883.3.560.1.7'), #medication adverse effect
generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.44']", '2.16.840.1.113883.3.560.1.1')] #medication allergy
@section_importers[:medical_equipment] = [generate_importer(CDA::MedicalEquipmentImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']", '2.16.840.1.113883.3.560.1.110', 'applied'),
generate_importer(CDA::MedicalEquipmentImporter, "./cda:entry/cda:act[cda:code/@code = 'SPLY']", '2.16.840.1.113883.3.560.1.137'),
generate_importer(DeviceOrderImporter, nil, '2.16.840.1.113883.3.560.1.37')]
@section_importers[:results] = [generate_importer(LabOrderImporter, nil, '2.16.840.1.113883.3.560.1.50', 'ordered'), #lab ordered
generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']", '2.16.840.1.113883.3.560.1.5', 'performed'), #lab performed
generate_importer(CDA::ResultImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.57']", '2.16.840.1.113883.3.560.1.18'), #physical exam finding
generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result
generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.26']", '2.16.840.1.113883.3.560.1.85'), #functional status, performed
generate_importer(LabResultImporter, nil, '2.16.840.1.113883.3.560.1.12')] #lab result
@section_importers[:encounters] = [generate_importer(EncounterPerformedImporter, "./cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']", '2.16.840.1.113883.3.560.1.79', 'performed'), #encounter performed
generate_importer(EncounterPerformedActImporter, nil, '2.16.840.1.113883.3.560.1.79'),
generate_importer(EncounterOrderActImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered'),
generate_importer(EncounterOrderImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered'),
generate_importer(TransferToImporter, nil, '2.16.840.1.113883.3.560.1.72'),
generate_importer(TransferFromImporter, nil, '2.16.840.1.113883.3.560.1.71'),
generate_importer(TransferToActImporter, nil, '2.16.840.1.113883.3.560.1.72'),
generate_importer(TransferFromActImporter, nil, '2.16.840.1.113883.3.560.1.71')
]
@section_importers[:social_history] = [generate_importer(TobaccoUseImporter, nil, '2.16.840.1.113883.3.560.1.1001', 'completed')]
@section_importers[:insurance_providers] = [generate_importer(InsuranceProviderImporter, nil, '2.16.840.1.113883.3.560.1.405')]
end
def parse_cat1(doc)
record = Record.new
HealthDataStandards::Import::C32::PatientImporter.instance.get_demographics(record, doc)
import_sections(record, doc)
get_patient_expired(record, doc)
record.dedup_record!
normalize_references(record)
record
end
def import_sections(record, doc)
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 = CDA::NarrativeReferenceHandler.new
nrh.build_id_map(doc)
@section_importers.each do |section, entry_packages|
entry_packages.each do |entry_package|
record.send(section) << entry_package.package_entries(context, nrh)
end
end
end
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']")
if !entry_elements.empty?
record.expired = true
record.deathdate = HealthDataStandards::Util::HL7Helper.timestamp_to_integer(entry_elements.at_xpath("./cda:effectiveTime/cda:low")['value'])
end
end
def normalize_references(record)
ref_ids = {}
record.procedures.each do |procedure|
if procedure.cda_identifier
ref_ids[procedure.cda_identifier.extension] = procedure._id
end
end
if ref_ids
record.communications.each do |communication|
communication.references.each do |reference|
reference.referenced_id = ref_ids[reference.referenced_id].to_s if ref_ids.has_key?(reference.referenced_id)
end
end
end
end
private
def generate_importer(importer_class, xpath, hqmf_oid, status=nil)
if importer_class.parent_name == "HealthDataStandards::Import::CDA"
importer = EntryPackage.new(importer_class.new(CDA::EntryFinder.new(xpath)), hqmf_oid, status)
else
importer = EntryPackage.new(importer_class.new, hqmf_oid, status)
end
importer
end
end
end
end
end