cqm-parsers 0.2.4 → 2.0.0

data/lib/qrda-export/helper/code_system_helper.rb

@@ -1,77 +0,0 @@
-module Qrda
-  module Export
-    module Helper
-      # General helpers for working with codes and code systems
-      class CodeSystemHelper
-        CODE_SYSTEMS = {
-          '2.16.840.1.113883.6.1' =>    'LOINC',
-          '2.16.840.1.113883.6.96' =>   'SNOMED-CT',
-          '2.16.840.1.113883.6.12' =>   'CPT',
-          '2.16.840.1.113883.6.88' =>   'RxNorm',
-          '2.16.840.1.113883.6.103' =>  'ICD-9-CM',
-          '2.16.840.1.113883.6.104' =>  'ICD-9-PCS',
-          '2.16.840.1.113883.6.4' =>   'ICD-10-PCS',
-          '2.16.840.1.113883.6.90' =>   'ICD-10-CM',
-          '2.16.840.1.113883.6.14' =>   'HCP',
-          '2.16.840.1.113883.6.285' =>   'HCPCS',
-          '2.16.840.1.113883.5.2' => "HL7 Marital Status",
-          '2.16.840.1.113883.12.292' => 'CVX',
-          '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status',
-          '2.16.840.1.113883.3.26.1.1' => 'NCI Thesaurus',
-          '2.16.840.1.113883.3.88.12.80.20' => 'FDA',
-          "2.16.840.1.113883.4.9" => "UNII",
-          "2.16.840.1.113883.6.69" => "NDC",
-          '2.16.840.1.113883.5.14' => 'HL7 ActStatus',
-          '2.16.840.1.113883.6.259' => 'HL7 Healthcare Service Location',
-          '2.16.840.1.113883.12.112' => 'DischargeDisposition',
-          '2.16.840.1.113883.5.4' => 'HL7 Act Code',
-          '2.16.840.1.113883.1.11.18877' => 'HL7 Relationship Code',
-          '2.16.840.1.113883.6.238' => 'CDC Race',
-          '2.16.840.1.113883.6.177' => 'NLM MeSH',
-          '2.16.840.1.113883.5.1076' => "Religious Affiliation",
-          '2.16.840.1.113883.1.11.19717' => "HL7 ActNoImmunicationReason",
-          '2.16.840.1.113883.3.88.12.80.33' => "NUBC",
-          '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
-          '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
-          '2.16.840.1.113883.6.13' => 'CDT',
-          '2.16.840.1.113883.18.2' => 'AdministrativeSex'
-        }
-        
-        CODE_SYSTEM_ALIASES = {
-          'FDA SPL' => 'NCI Thesaurus',
-          'HSLOC' => 'HL7 Healthcare Service Location',
-          'SOP' => "Source of Payment Typology"
-        }
-        
-        # Some old OID are still around in data, this hash maps retired OID values to 
-        # the new value
-        OID_ALIASES = {
-          '2.16.840.1.113883.6.59' => '2.16.840.1.113883.12.292' # CVX
-        }
-        
-        # Returns the name of a code system given an oid
-        # @param [String] oid of a code system
-        # @return [String] the name of the code system as described in the measure definition JSON
-        def self.code_system_for(oid)
-          oid = OID_ALIASES[oid] if OID_ALIASES[oid]
-          CODE_SYSTEMS[oid] || "Unknown"
-        end
-        
-        # Returns the oid for a code system given a codesystem name
-        # @param [String] the name of the code system
-        # @return [String] the oid of the code system
-        def self.oid_for_code_system(code_system)
-          code_system = CODE_SYSTEM_ALIASES[code_system] if CODE_SYSTEM_ALIASES[code_system]
-          CODE_SYSTEMS.invert[code_system]
-        end
-        
-        # Returns the whole map of OIDs to code systems
-        # @terurn [Hash] oids as keys, code system names as values
-        def self.code_systems
-          CODE_SYSTEMS
-        end
-      end
-    end
-  end
-end
-

data/lib/qrda-export/helper/date_helper.rb

@@ -1,89 +0,0 @@
-module Qrda
-  module Export
-    module Helper
-      module DateHelper
-        def value_or_null_flavor(time)
-          # this is a bit of a hack for a defineded undefined date
-          if time && DateTime.parse(time).year < 3000
-            "value='#{DateTime.parse(time).utc.to_formatted_s(:number)}'"
-          else
-            "nullFlavor='UNK'"
-          end
-        end
-
-        def performance_period_start
-          @performance_period_start.to_formatted_s(:number)
-        end
-
-        def performance_period_end
-          @performance_period_end.to_formatted_s(:number)
-        end
-
-        def current_time
-          Time.now.utc.to_formatted_s(:number)
-        end
-
-        def author_time
-          "<time #{value_or_null_flavor(self['authorDatetime'])}/>"
-        end
-
-        def author_effective_time
-          "<effectiveTime #{value_or_null_flavor(self['authorDatetime'])}/>"
-        end
-
-        def expired_date_time
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['expiredDatetime'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def prevalence_period
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['prevalencePeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['prevalencePeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def relevant_period
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['relevantPeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def relevant_period_as_value
-          "<effectiveTime #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"
-        end
-
-        def insurance_provider_period
-          start_time = self['start_time'] ? DateTime.strptime(self['start_time'].to_s, '%s').to_s : nil
-          end_time = self['end_time'] ? DateTime.strptime(self['end_time'].to_s, '%s').to_s : nil
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(start_time)}/>"\
-          "<high #{value_or_null_flavor(end_time)}/>"\
-          "</effectiveTime>"
-        end
-
-        def medication_duration_effective_time
-          "<effectiveTime xsi:type=\"IVL_TS\">"\
-          "<low #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['relevantPeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def facility_period
-          "<low #{value_or_null_flavor(self['locationPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['locationPeriod']['high'])}/>"
-        end
-
-        def incision_datetime
-          "<effectiveTime #{value_or_null_flavor(self['incisionDatetime'])}/>"
-        end
-
-        def completed_prevalence_period
-          self['prevalencePeriod']['high'] ? true : false
-        end
-      end
-    end
-  end
-end

data/lib/qrda-import/base-importers/demographics_importer.rb

@@ -1,49 +0,0 @@
-module QRDA
-  module Cat1
-    module DemographicsImporter
-      def get_demographics(patient, doc)
-        patient_role_element = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole')
-        patient_element = patient_role_element.at_xpath('./cda:patient')
-        patient.givenNames = [patient_element.at_xpath('cda:name/cda:given').text]
-        patient.familyName = patient_element.at_xpath('cda:name/cda:family').text
-        patient.birthDatetime = Time.parse(patient_element.at_xpath('cda:birthTime')['value']).utc
-        pcbd = QDM::PatientCharacteristicBirthdate.new
-        pcbd.birthDatetime = patient.birthDatetime
-        pcbd.dataElementCodes = [{ code: '21112-8', codeSystem: 'LOINC' }]
-        patient.dataElements << pcbd
-
-        pcs = QDM::PatientCharacteristicSex.new
-        code_element = patient_element.at_xpath('cda:administrativeGenderCode')
-        pcs.dataElementCodes = [code_if_present(code_element)]
-        patient.dataElements << pcs
-
-        pcr = QDM::PatientCharacteristicRace.new
-        code_element = patient_element.at_xpath('cda:raceCode')
-        pcr.dataElementCodes = [code_if_present(code_element)]
-        patient.dataElements << pcr
-
-        pce = QDM::PatientCharacteristicEthnicity.new
-        code_element = patient_element.at_xpath('cda:ethnicGroupCode')
-        pce.dataElementCodes = [code_if_present(code_element)]
-        patient.dataElements << pce
-
-        provider_element = doc.xpath("//cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.55']")
-
-        # If a provider element isn't in the record, return wiihout adding one.
-        return if provider_element.blank?
-        provider_code = provider_element.first.at_xpath('cda:value')['code']
-        ip = {}
-        ip['financial_responsibility_type'] = { 'code' => 'SELF', 'codeSystem' => 'HL7 Relationship Code' }
-        ip['codes'] = { 'SOP' => [provider_code] }
-        patient.extendedData = {}
-        patient.extendedData['insurance_providers'] = JSON.generate([ip])
-      end
-
-      def code_if_present(code_element)
-        return unless code_element && code_element['codeSystem'] && code_element['code']
-
-        QDM::Code.new(code_element['code'], HQMF::Util::CodeSystemHelper.code_system_for(code_element['codeSystem']))
-      end
-    end
-  end
-end

data/lib/qrda-import/base-importers/medication_importer.rb

@@ -1,23 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationImporter < SectionImporter
-  
-      def initialize(entry_finder = nil)
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
-        @relevant_period_xpath = "./cda:effectiveTime"
-        @author_datetime_xpath = "./cda:author/cda:time"
-        @dosage_xpath = "./cda:doseQuantity"
-        @route_xpath = "./cda:routeCode"
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication = super
-        medication.dosage = extract_scalar(entry_element, @dosage_xpath)
-        medication.route = code_if_present(entry_element.at_xpath(@route_xpath))
-        medication
-      end
-    end
-  end
-end

data/lib/qrda-import/base-importers/section_importer.rb

@@ -1,203 +0,0 @@
-module QRDA
-  module Cat1
-    class SectionImporter
-      attr_accessor :check_for_usable, :status_xpath, :code_xpath
-
-      def initialize(entry_finder)
-        @entry_finder = entry_finder
-        @code_xpath = "./cda:code"
-        @entry_id_map = {}
-        @check_for_usable = true
-        @entry_class = QDM::DataElement
-      end
-
-      # Traverses an HL7 CDA document passed in and creates an Array of Entry
-      # objects based on what it finds
-      # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
-      #        will have the "cda" namespace registered to "urn:hl7-org:v3"
-      #        measure definition
-      # @return [Array] will be a list of Entry objects
-      def create_entries(doc, nrh = NarrativeReferenceHandler.new)
-        entry_list = []
-        @entry_id_map = {}
-        entry_elements = @entry_finder.entries(doc)
-        entry_elements.each do |entry_element|
-          entry = create_entry(entry_element, nrh)
-          if @check_for_usable
-            entry_list << entry if usable_entry?(entry)
-          else
-            entry_list << entry
-          end
-        end
-        [entry_list, @entry_id_map]
-      end
-
-      def usable_entry?(entry)
-        entry.dataElementCodes.present?
-      end
-
-      def create_entry(entry_element, _nrh = NarrativeReferenceHandler.new)
-        entry = @entry_class.new
-        entry_qrda_id = extract_id(entry_element, @id_xpath)
-        # Create a hash to map all of entry.ids to the same QRDA ids. This will be used to merge QRDA entries
-        # that represent the same event. 
-        @entry_id_map["#{entry_qrda_id.value}_#{entry_qrda_id.namingSystem}"] ||= []
-        @entry_id_map["#{entry_qrda_id.value}_#{entry_qrda_id.namingSystem}"] << entry.id
-        entry.dataElementCodes = extract_codes(entry_element, @code_xpath)
-        extract_dates(entry_element, entry)
-        if @result_xpath
-          entry.result = extract_result_values(entry_element)
-        end
-        extract_negation(entry_element, entry)
-        entry
-      end
-
-      private
-
-      def extract_id(parent_element, id_xpath)
-        id_element = parent_element.at_xpath(id_xpath)
-        return unless id_element
-        # If an extension is not included, use the root as the value.  Other wise use the extension
-        value = id_element['extension'] || id_element['root']
-        identifier = QDM::Id.new(value: value, namingSystem: id_element['root'])
-        identifier
-      end
-
-      def extract_codes(coded_element, code_xpath)
-        code_list = []
-        code_elements = coded_element.xpath(code_xpath)
-        code_elements.each do |code_element|
-          code_list << code_if_present(code_element)
-          translations = code_element.xpath('cda:translation')
-          translations.each do |translation|
-            code_list << code_if_present(translation)
-          end
-        end
-        code_list.compact
-      end
-
-      def code_if_present(code_element)
-        return unless code_element && code_element['codeSystem'] && code_element['code']
-        QDM::Code.new(code_element['code'], HQMF::Util::CodeSystemHelper.code_system_for(code_element['codeSystem']))
-      end
-
-      def extract_dates(parent_element, entry)
-        entry.authorDatetime = extract_time(parent_element, @author_datetime_xpath) if @author_datetime_xpath
-        entry.relevantPeriod = extract_interval(parent_element, @relevant_period_xpath) if @relevant_period_xpath
-        entry.prevalencePeriod = extract_interval(parent_element, @prevalence_period_xpath) if @prevalence_period_xpath
-      end
-
-      def extract_interval(parent_element, interval_xpath)
-        if parent_element.at_xpath("#{interval_xpath}/@value")
-          low_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
-          high_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
-        end
-        if parent_element.at_xpath("#{interval_xpath}/cda:low")
-          low_time = if parent_element.at_xpath("#{interval_xpath}/cda:low")['value']
-                       DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:low")['value'])
-                     end
-        end
-        if parent_element.at_xpath("#{interval_xpath}/cda:high")
-          high_time = if parent_element.at_xpath("#{interval_xpath}/cda:high")['value']
-                        DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:high")['value'])
-                      end
-        end
-        if parent_element.at_xpath("#{interval_xpath}/cda:center")
-          low_time = Time.parse(parent_element.at_xpath("#{interval_xpath}/cda:center")['value'])
-          high_time = Time.parse(parent_element.at_xpath("#{interval_xpath}/cda:center")['value'])
-        end
-        QDM::Interval.new(low_time, high_time).shift_dates(0)
-      end
-
-      def extract_time(parent_element, datetime_xpath)
-        DateTime.parse(parent_element.at_xpath(datetime_xpath)['value']) if parent_element.at_xpath("#{datetime_xpath}/@value")
-      end
-
-      def extract_result_values(parent_element)
-        result = []
-        parent_element.xpath(@result_xpath).each do |elem|
-          result << extract_result_value(elem)
-        end
-        result.size > 1 ? result : result.first 
-      end
-
-      def extract_result_value(value_element)
-        return unless value_element && !value_element['nullFlavor']
-        value = value_element['value']
-        if value.present?
-          return value.strip.to_f if (value_element['unit'] == "1" || value_element['unit'].nil?)
-          return QDM::Quantity.new(value.strip.to_f, value_element['unit'])
-        elsif value_element['code'].present?
-          return code_if_present(value_element)
-        end
-      end
-
-      def extract_reason(parent_element)
-        return unless @reason_xpath
-        reason_element = parent_element.xpath(@reason_xpath)
-        negation_indicator = parent_element['negationInd']
-        # Return and do not set reason attribute if the entry is negated
-        return nil if negation_indicator.eql?('true')
-        
-        reason_element.blank? ? nil : code_if_present(reason_element.first) 
-      end
-
-      def extract_negation(parent_element, entry)
-        negation_element = parent_element.xpath("./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value")
-        negation_indicator = parent_element['negationInd']
-        # Return and do not set negationRationale attribute if the entry is not negated
-        return unless negation_indicator.eql?('true') 
-        
-        entry.negationRationale = code_if_present(negation_element.first) unless negation_element.blank?
-        extract_negated_code(parent_element, entry)
-      end
-
-      def extract_negated_code(parent_element, entry)
-        code_elements = parent_element.xpath(@code_xpath)
-        code_elements.each do |code_element|
-          if code_element['nullFlavor'] == 'NA' && code_element['sdtc:valueSet']
-            entry.dataElementCodes = [{ code: code_element['sdtc:valueSet'], codeSystem: 'NA_VALUESET' }]
-          end
-        end
-      end
-
-      def extract_scalar(parent_element, scalar_xpath)
-        scalar_element = parent_element.at_xpath(scalar_xpath)
-        return unless scalar_element
-        QDM::Quantity.new(scalar_element['value'].to_f, scalar_element['unit'])
-      end
-
-      def extract_components(parent_element)
-        component_elements = parent_element.xpath(@components_xpath)
-        components = []
-        component_elements&.each do |component_element|
-          component = QDM::Component.new
-          component.code = code_if_present(component_element.at_xpath('./cda:code'))
-          component.result = extract_result_value(component_element.at_xpath('./cda:value'))
-          components << component
-        end
-        components
-      end
-
-      def extract_facility(parent_element, entry)
-        facility_element = parent_element.at_xpath(@facility_xpath)
-        return unless facility_element
-        facility = QDM::FacilityLocation.new
-        participant_element = facility_element.at_xpath("./cda:participantRole[@classCode='SDLOC']/cda:code")
-        facility.code = code_if_present(participant_element)
-        facility.locationPeriod = extract_interval(facility_element, './cda:time')
-        entry.facilityLocations = [facility]
-      end
-
-      def extract_related_to(parent_element)
-        related_to_elements = parent_element.xpath(@related_to_xpath)
-        related_ids = []
-        related_to_elements.each do |related_to_element|
-          related_ids << extract_id(related_to_element, './sdtc:id')
-        end
-        related_ids
-      end
-
-    end
-  end
-end

data/lib/qrda-import/cda_identifier.rb

@@ -1,19 +0,0 @@
-require 'mongoid'
-
-class CDAIdentifier
-  include Mongoid::Document
-  include Mongoid::Attributes::Dynamic
-
-  field :root, type: String
-  field :extension, type: String
-  embedded_in :cda_identifiable, polymorphic: true
-
-  def ==(other)
-    return unless other.respond_to?(:root) && other.respond_to?(:extension)
-    root == other.root && extension == other.extension
-  end
-
-  def hash
-    "#{root}#{extension}".hash
-  end
-end