cqm-parsers 0.1.0

data/lib/hqmf-parser/parser.rb

@@ -0,0 +1,100 @@
+module HQMF
+  class Parser
+
+    HQMF_VERSION_1 = "1.0"
+    HQMF_VERSION_2 = "2.0"
+
+    # HQMF v2 Parser for measures that use QDM for measure logic
+    class V2Parser
+      def initialize
+      end
+
+      def parse(xml_contents, codes=nil)
+        HQMF::Counter.instance.reset()
+        HQMF2::Document.new(xml_contents).to_model
+      end
+
+      def parse_fields(xml_contents)
+        result = {}
+        doc = HQMF2::Document.parse(xml_contents)
+        type = doc.at_xpath('/cda:QualityMeasureDocument/cda:code/@code').value
+        if type == '57024-2'
+          id = doc.at_xpath('cda:QualityMeasureDocument/cda:id/@extension', HQMF2::Document::NAMESPACES).value.upcase
+          set_id = doc.at_xpath('cda:QualityMeasureDocument/cda:setId/@extension').value.upcase
+          version_number = doc.at_xpath('cda:QualityMeasureDocument/cda:versionNumber/@value').value.to_i
+          title = doc.at_xpath('cda:QualityMeasureDocument/cda:title/@value').inner_text
+          description = doc.at_xpath('cda:QualityMeasureDocument/cda:text/@value').inner_text
+          result=  {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
+        end
+        result
+      end
+
+      def version
+        HQMF_VERSION_2
+      end
+
+      def self.valid?(xml_contents)
+         doc = HQMF2::Document.parse(xml_contents)
+        !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_HD000001UV02']").nil?
+      end
+
+    end
+
+    # HQMF v2 Parser for measures that use CQL for measure logic
+    class V2CQLParser < V2Parser
+
+      def parse(xml_contents, codes=nil)
+        HQMF::Counter.instance.reset()
+        HQMF2CQL::Document.new(xml_contents).to_model
+      end
+
+      def self.valid?(xml_contents)
+        doc = HQMF2::Document.parse(xml_contents)
+        hqmf2 = !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_HD000001UV02']").nil?
+        cql = !doc.at_xpath("/cda:QualityMeasureDocument/cda:relatedDocument/cda:expressionDocument/cda:text[@mediaType='application/cql']").nil?
+        if !cql
+          # The media type changed for MAT version 5.3
+          cql = !doc.at_xpath("/cda:QualityMeasureDocument/cda:relatedDocument/cda:expressionDocument/cda:text[@mediaType='text/cql']").nil?
+        end
+        hqmf2 && cql
+      end
+
+    end
+
+    # HQMF v1 Parser for measures that use QDM for measure logic
+    class V1Parser
+
+      def parse(xml_contents, codes=nil)
+        HQMF::Counter.instance.reset()
+        HQMF::DocumentConverter.convert(HQMF1::Document.new(xml_contents).to_json, codes)
+      end
+
+      def version
+        HQMF_VERSION_1
+      end
+
+      def parse_fields(xml_contents)
+        doc = HQMF1::Document.parse(xml_contents)
+        type = doc.at_xpath('//cda:code/@code').value
+        result = {}
+        if type == '57024-2'
+          id = doc.at_xpath('//cda:id/@root').value.upcase
+          set_id = doc.at_xpath('//cda:setId/@root').value.upcase
+          version_number = doc.at_xpath('//cda:versionNumber/@value').value.to_i
+          title = doc.at_xpath('cda:QualityMeasureDocument/cda:title').inner_text
+          description = doc.at_xpath('cda:QualityMeasureDocument/cda:text').inner_text
+          result = {'id' => id, 'set_id' => set_id, 'version' => version_number, 'title' => title, 'description' => description}
+        end
+        result
+      end
+
+      def self.valid?(xml_contents)
+        doc = HQMF1::Document.parse(xml_contents)
+        !doc.at_xpath("/cda:QualityMeasureDocument/cda:typeId[@root='2.16.840.1.113883.1.3' and @extension='POQM_HD000001']").nil?
+      end
+
+    end
+
+  end
+
+end

data/lib/qrda-export/catI-r5/qrda1_r5.rb

@@ -0,0 +1,125 @@
+require 'mustache'
+class Qrda1R5 < Mustache
+  include Qrda::Export::Helper::DateHelper
+  include Qrda::Export::Helper::Cat1ViewHelper
+
+  self.template_path = __dir__
+
+  def initialize(patient, measures, options = {})
+    @patient = patient
+    @measures = measures
+    @provider = options[:provider]
+    @performance_period_start = options[:start_time]
+    @performance_period_end = options[:end_time]
+    @submission_program = options[:submission_program]
+    @insurance_provider = JSON.parse(@patient.extendedData.insurance_providers) if @patient.extendedData && @patient.extendedData['insurance_providers']
+  end
+
+  def adverse_event
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.120').to_json)
+  end
+
+  def allergy_intolerance
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.119').to_json)
+  end
+
+  def assessment_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.117').to_json)
+  end
+
+  def communication_from_patient_to_provider
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.30').to_json)
+  end
+
+  def communication_from_provider_to_patient
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.31','2.16.840.1.113883.3.560.1.131'] }).to_json)
+  end
+
+  def communication_from_provider_to_provider
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.29','2.16.840.1.113883.3.560.1.129'] }).to_json)
+  end
+
+  def diagnosis
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.110').to_json)
+  end
+
+  def device_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.37','2.16.840.1.113883.3.560.1.137'] }).to_json)
+  end
+
+  def device_applied
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.10','2.16.840.1.113883.3.560.1.110'] }).to_json)
+  end
+
+  def diagnostic_study_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.40','2.16.840.1.113883.3.560.1.140'] }).to_json)
+  end
+
+  def diagnostic_study_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.103','2.16.840.1.113883.3.560.1.3'] }).to_json)
+  end
+
+  def encounter_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.83').to_json)
+  end
+
+  def encounter_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.79').to_json)
+  end
+
+  def immunization_aministered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.10.20.28.3.112'] }).to_json)
+  end
+
+  def intervention_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.45','2.16.840.1.113883.3.560.1.145'] }).to_json)
+  end
+
+  def intervention_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.46','2.16.840.1.113883.3.560.1.146'] }).to_json)
+  end
+
+  def lab_test_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.5').to_json)
+  end
+
+  def lab_test_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.50','2.16.840.1.113883.3.560.1.150'] }).to_json)
+  end
+
+  def medication_active
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.13').to_json)
+  end
+
+  def medication_administered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.14','2.16.840.1.113883.3.560.1.64','2.16.840.1.113883.3.560.1.114'] }).to_json)
+  end
+
+  def medication_discharge
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.199','2.16.840.1.113883.3.560.1.200'] }).to_json)
+  end
+
+  def medication_dispensed
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.8').to_json)
+  end
+
+  def medication_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.78','2.16.840.1.113883.3.560.1.17'] }).to_json)
+  end
+
+  def patient_characteristic_expired
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.57').to_json)
+  end
+  
+  def physical_exam_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.57','2.16.840.1.113883.3.560.1.157'] }).to_json)
+  end
+
+  def procedure_ordered
+    JSON.parse(@patient.dataElements.where(hqmfOid: '2.16.840.1.113883.3.560.1.62').to_json)
+  end
+
+  def procedure_performed
+    JSON.parse(@patient.dataElements.where(hqmfOid: { '$in' => ['2.16.840.1.113883.3.560.1.6','2.16.840.1.113883.3.560.1.106'] }).to_json)
+  end
+end

data/lib/qrda-export/helper/cat_1_view_helper.rb

@@ -0,0 +1,142 @@
+module Qrda
+  module Export
+    module Helper
+      module Cat1ViewHelper
+        def random_id
+          UUID.generate
+        end
+
+        def as_id
+          self['$oid']
+        end
+
+        def object_id
+          self[:_id]['$oid']
+        end
+
+        def submission_program
+          @submission_program
+        end
+
+        def provider
+          JSON.parse(@provider.to_json) if @provider
+        end
+
+        def provider_addresses
+          @provider['addresses']
+        end
+
+        def provider_street
+          self['street'].join('')
+        end
+
+        def provider_npi
+          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.6' }.compact.first
+        end
+
+        def provider_tin
+          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.2' }.compact.first
+        end
+
+        def provider_ccn
+          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.336' }.compact.first
+        end
+
+        def provider_type_code
+          @provider['specialty']
+        end
+
+        def mrn
+          @patient.extendedData['medical_record_number']
+        end
+
+        def given_name
+          @patient.givenNames.join(' ')
+        end
+
+        def family_name
+          @patient.familyName
+        end
+
+        def birthdate
+          @patient.birthDatetime.to_formatted_s(:number)
+        end
+
+        def gender
+          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.55').first.dataElementCodes.first['code']
+        end
+
+        def race
+          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.59').first.dataElementCodes.first['code']
+        end
+
+        def ethnic_group
+          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.56').first.dataElementCodes.first['code']
+        end
+
+        def insurance_provider
+          @insurance_provider
+        end
+
+        def insurance_provider_code_and_code_system
+          "code=\"#{self['codes'].values.first[0]}\" codeSystem=\"#{code_system_oid(self['codes'].keys.first)}\" codeSystemName=\"#{self['codes'].keys.first}\""
+        end
+
+        def measures
+          @measures.only(:hqmf_id, :hqmf_set_id, :description).as_json
+        end
+
+        def negation_ind
+          self[:negationRationale].nil? ? "" : "negationInd=\"true\""
+        end
+
+        def negated
+          self[:negationRationale].nil? ? false : true
+        end
+
+        def multiple_codes?
+          self[:dataElementCodes].size > 1
+        end
+
+        def code_system_oid(name)
+          Qrda::Export::Helper::CodeSystemHelper.oid_for_code_system(name)
+        end
+
+        def code_and_codesystem
+          "code=\"#{self['code']}\" codeSystem=\"#{code_system_oid(self['codeSystem'])}\" codeSystemName=\"#{self['codeSystem']}\""
+        end
+
+        def primary_code_and_codesystem
+          "code=\"#{self[:dataElementCodes][0]['code']}\" codeSystem=\"#{code_system_oid(self[:dataElementCodes][0]['codeSystem'])}\" codeSystemName=\"#{self[:dataElementCodes][0]['codeSystem']}\""
+        end
+
+        def translation_codes_and_codesystem_list
+          translation_list = ""
+          self[:dataElementCodes].each_with_index do |_dec, index|
+            next if index.zero?
+            translation_list += "<translation code=\"#{self[:dataElementCodes][index]['code']}\" codeSystem=\"#{code_system_oid(self[:dataElementCodes][index]['codeSystem'])}\" codeSystemName=\"#{self[:dataElementCodes][index]['codeSystem']}\"/>"
+          end
+          translation_list
+        end
+
+        def result_value
+          return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless self['result']
+          result_string = if self['result'].is_a? Array
+                            result_value_as_string(self['result'][0])
+                          elsif self['result'].is_a? Hash
+                            result_value_as_string(self['result'])
+                          elsif !self['result'].nil?
+                            "<value xsi:type=\"PQ\" value=\"#{self['result']}\" unit=\"1\"/>"
+                          end
+          result_string
+        end
+
+        def result_value_as_string(result)
+          return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless result
+          return "<value xsi:type=\"CD\" code=\"#{result['code']}\" codeSystem=\"#{code_system_oid(result['codeSystem'])}\" codeSystemName=\"#{result['codeSystem']}\"/>" if result['code']
+          return "<value xsi:type=\"PQ\" value=\"#{result['value']}\" unit=\"#{result['unit']}\"/>" if result['unit']
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,77 @@
+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

@@ -0,0 +1,81 @@
+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 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 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