cqm-parsers 0.2.3 → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: 9485682c59342822202fe6a253ce7bbcbb67b92a428fa04558a093d0995d9765
-  data.tar.gz: e68e467aa5d71626f960a79df31e08569b35cc7faa8c6c35ca893532818e60ae
+SHA1:
+  metadata.gz: 5ae0c0edc66dbccfb1f7bff982ed28472220b223
+  data.tar.gz: a244b962a1ba17b061ac9fbacdb1ce27ef3d9ae0
 SHA512:
-  metadata.gz: 1bc35e9ea6bfadd995d234619315ef036f2f3cfc61e4a3dc8bc35f20bb7f48efe798049642061019fd4351861b906a16989dc54a451dfe32c3bcd56778e72937
-  data.tar.gz: 5fe9cbb48856d6585c433bf33727129d985afd25a71df22f688aab9289904466ac0defbdd7779c9c2fba422c2607d601f4b1519f605970d2bc74ad334e5beea6
+  metadata.gz: aa00da03f1b87750f4dd0fdaa9a60b67616afba80c41f741a35b74b2a2e989b738220d28c5cbfab6ed9087f3b71da829c9a0c3da50e276588ea648d2490853dc
+  data.tar.gz: 29f3149e4f031808f4e956c9d29584ae1acc9cc60b6798192fd4a880fdf41fad302d6da47a0cf1add996a42fccb802e3f5d844a4421d85bc97ca1ba8beb39f45

data/lib/qrda-export/catI-r5/qrda_templates/device_ordered.mustache

@@ -22,10 +22,10 @@
             </playingDevice>
           </participantRole>
         </participant>
-        {{#negationRationale}}
-        {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </supply>
     </entryRelationship>
+    {{#negationRationale}}
+    {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/encounter_ordered.mustache

@@ -15,10 +15,10 @@
         {{#authorDatetime}}
         {{> qrda_templates/template_partials/_author}}
         {{/authorDatetime}}
-        {{#negationRationale}}
-        {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </encounter>
     </entryRelationship>
+    {{#negationRationale}}
+    {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/medication_discharge.mustache

@@ -46,10 +46,10 @@
         {{#authorDatetime}}
         {{> qrda_templates/template_partials/_author_participation}}
         {{/authorDatetime}}
-        {{#negationRationale}}
-        {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}} 
       </substanceAdministration>
     </entryRelationship>
+    {{#negationRationale}}
+    {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}} 
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/medication_dispensed.mustache

@@ -30,10 +30,10 @@
         {{#authorDatetime}}
         {{> qrda_templates/template_partials/_author}}
         {{/authorDatetime}}
-        {{#negationRationale}}
-        {{> qrda_templates/template_partials/_reason}}
-        {{/negationRationale}}
       </supply>
     </entryRelationship>
+    {{#negationRationale}}
+    {{> qrda_templates/template_partials/_reason}}
+    {{/negationRationale}}
   </act>
 </entry>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_medication_details.mustache

@@ -6,6 +6,6 @@
 {{/negated}}
 {{^negated}}
 {{#dosage}}
-	<doseQuantity value="{{value}}" unit="{{unit}}"/>
+	<doseQuantity value="{{value_as_float}}"/>
 {{/dosage}}
 {{/negated}}

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

@@ -123,6 +123,10 @@ module Qrda
           translation_list
         end
 
+        def value_as_float
+          self['value'].to_f
+        end
+
         def result_value
           return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless self['result']
           result_string = if self['result'].is_a? Array

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

@@ -38,14 +38,17 @@ module QRDA
 
       def create_entry(entry_element, _nrh = NarrativeReferenceHandler.new)
         entry = @entry_class.new
-        @entry_id_map[extract_id(entry_element, @id_xpath).value] ||= []
-        @entry_id_map[extract_id(entry_element, @id_xpath).value] << entry.id
+        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_reason_or_negation(entry_element, entry)
+        extract_negation(entry_element, entry)
         entry
       end
 
@@ -55,7 +58,7 @@ module QRDA
         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['extension'] : id_element['root']
+        value = id_element['extension'] || id_element['root']
         identifier = QDM::Id.new(value: value, namingSystem: id_element['root'])
         identifier
       end
@@ -90,13 +93,13 @@ module QRDA
           high_time = DateTime.parse(parent_element.at_xpath(interval_xpath)['value'])
         end
         if parent_element.at_xpath("#{interval_xpath}/cda:low")
-          low_time = DateTime.parse(parent_element.at_xpath("#{interval_xpath}/cda:low")['value'])
+          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'])
-                      else
-                        DateTime.new(9999,1,1)
                       end
         end
         if parent_element.at_xpath("#{interval_xpath}/cda:center")
@@ -122,31 +125,35 @@ module QRDA
         return unless value_element && !value_element['nullFlavor']
         value = value_element['value']
         if value.present?
-          return value.strip.to_i if (value_element['unit'] == "1" || value_element['unit'].nil?)
-          return QDM::Quantity.new(value.strip.to_i, value_element['unit'])
+          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
 
-      # extracts the reason or negation data. if an element is negated and the code has a null flavor, a random code is assigned for calculation
-      # coded_parent_element is the 'parent' element when the coded is nested (e.g., medication order)
-      def extract_reason_or_negation(parent_element, entry, coded_parent_element = nil)
-        coded_parent_element ||= parent_element
-        reason_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 | .//cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code")
+      def extract_reason(parent_element)
+        return unless @reason_xpath
+        reason_element = parent_element.xpath(@reason_xpath)
         negation_indicator = parent_element['negationInd']
-        unless reason_element.blank?
-          if negation_indicator.eql?('true')
-            entry.negationRationale = code_if_present(reason_element.first)
-          else
-            entry.reason = code_if_present(reason_element.first) unless @entry_does_not_have_reason
-          end
-        end
-        extract_negated_code(coded_parent_element, entry)
+        # 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(coded_parent_element, entry)
-        code_elements = coded_parent_element.xpath(@code_xpath)
+      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' }]
@@ -157,7 +164,7 @@ module QRDA
       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_i, scalar_element['unit'])
+        QDM::Quantity.new(scalar_element['value'].to_f, scalar_element['unit'])
       end
 
       def extract_components(parent_element)

data/lib/qrda-import/data-element-importers/assessment_performed_importer.rb

@@ -9,6 +9,7 @@ module QRDA
         @result_xpath = "./cda:value"
         @method_xpath = './cda:methodCode'
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::AssessmentPerformed
       end
 
@@ -16,6 +17,7 @@ module QRDA
         assessment_performed = super
         assessment_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         assessment_performed.components = extract_components(entry_element)
+        assessment_performed.reason = extract_reason(entry_element)
         assessment_performed
       end
 

data/lib/qrda-import/data-element-importers/device_applied_importer.rb

@@ -9,6 +9,7 @@ module QRDA
         @relevant_period_xpath = "./cda:effectiveTime"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @anatomical_approach_site_xpath = "./cda:approachSiteCode"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::DeviceApplied
       end
 
@@ -16,6 +17,7 @@ module QRDA
         device_applied = super
         device_applied.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         device_applied.anatomicalApproachSite = code_if_present(entry_element.at_xpath(@anatomical_approach_site_xpath))
+        device_applied.reason = extract_reason(entry_element)
         device_applied
       end
 

data/lib/qrda-import/data-element-importers/device_order_importer.rb

@@ -6,11 +6,13 @@ module QRDA
         @id_xpath = './cda:entryRelationship/cda:supply/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.9']/cda:participant/cda:participantRole/cda:playingDevice/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.9']/cda:author/cda:time"
+        @reason_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.9']/cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::DeviceOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         device_order = super
+        device_order.reason = extract_reason(entry_element)
         device_order
       end
 

data/lib/qrda-import/data-element-importers/diagnostic_study_order_importer.rb

@@ -7,12 +7,14 @@ module QRDA
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @method_xpath = './cda:methodCode'
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::DiagnosticStudyOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         diagnostic_study_order = super
         diagnostic_study_order.method = code_if_present(entry_element.at_xpath(@method_xpath))
+        diagnostic_study_order.reason = extract_reason(entry_element)
         diagnostic_study_order
       end
 

data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb

@@ -13,6 +13,7 @@ module QRDA
         @method_xpath = './cda:methodCode'
         @facility_location_xpath = "./cda:participant[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.100']/cda:participantRole[@classCode='SDLOC']/cda:code"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::DiagnosticStudyPerformed
       end
 
@@ -23,6 +24,7 @@ module QRDA
         diagnostic_study_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         diagnostic_study_performed.facilityLocation = code_if_present(entry_element.at_xpath(@facility_location_xpath))
         diagnostic_study_performed.components = extract_components(entry_element)
+        diagnostic_study_performed.reason = extract_reason(entry_element)
         diagnostic_study_performed
       end
 

data/lib/qrda-import/data-element-importers/encounter_order_importer.rb

@@ -7,12 +7,14 @@ module QRDA
         @code_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:code"
         @author_datetime_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:author/cda:time"
         @facility_location_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:participant[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.100']/cda:participantRole[@classCode='SDLOC']/cda:code"
+        @reason_xpath = "./cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']/cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::EncounterOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         encounter_order = super
         encounter_order.facilityLocation = code_if_present(entry_element.at_xpath(@facility_location_xpath))
+        encounter_order.reason = extract_reason(entry_element)
         encounter_order
       end
 

data/lib/qrda-import/data-element-importers/immunization_administered_importer.rb

@@ -5,11 +5,13 @@ module QRDA
         super(entry_finder)
         @relevant_period_xpath = nil
         @author_datetime_xpath = "./cda:effectiveTime"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::ImmunizationAdministered
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         immunization_administered = super
+        immunization_administered.reason = extract_reason(entry_element)
         immunization_administered
       end
 

data/lib/qrda-import/data-element-importers/intervention_order_importer.rb

@@ -6,11 +6,13 @@ module QRDA
         @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::InterventionOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         intervention_order = super
+        intervention_order.reason = extract_reason(entry_element)
         intervention_order
       end
 

data/lib/qrda-import/data-element-importers/intervention_performed_importer.rb

@@ -9,12 +9,14 @@ module QRDA
         @author_datetime_xpath = "./cda:author/cda:time"
         @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
         @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.93']/cda:value"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::InterventionPerformed
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         intervention_performed = super
         intervention_performed.status = code_if_present(entry_element.at_xpath(@status_xpath))
+        intervention_performed.reason = extract_reason(entry_element)
         intervention_performed
       end
 

data/lib/qrda-import/data-element-importers/laboratory_test_order_importer.rb

@@ -7,12 +7,14 @@ module QRDA
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"
         @method_xpath = './cda:methodCode'
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::LaboratoryTestOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         laboratory_test_order = super
         laboratory_test_order.method = code_if_present(entry_element.at_xpath(@method_xpath))
+        laboratory_test_order.reason = extract_reason(entry_element)
         laboratory_test_order
       end
 

data/lib/qrda-import/data-element-importers/laboratory_test_performed_importer.rb

@@ -12,6 +12,7 @@ module QRDA
         @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:value"
         @result_datetime_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:effectiveTime"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::LaboratoryTestPerformed
       end
 
@@ -21,6 +22,7 @@ module QRDA
         laboratory_test_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         laboratory_test_performed.resultDatetime = extract_time(entry_element, @result_datetime_xpath)
         laboratory_test_performed.components = extract_components(entry_element)
+        laboratory_test_performed.reason = extract_reason(entry_element)
         laboratory_test_performed
       end
 

data/lib/qrda-import/data-element-importers/medication_administered_importer.rb

@@ -4,11 +4,13 @@ module QRDA
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']"))
         super(entry_finder)
         @route_xpath = "./cda:routeCode"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::MedicationAdministered
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         medication_administered = super
+        medication_administered.reason = extract_reason(entry_element)
         medication_administered
       end
 

data/lib/qrda-import/data-element-importers/medication_order_importer.rb

@@ -3,11 +3,13 @@ module QRDA
     class MedicationOrderImporter < MedicationImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']"))
         super(entry_finder)
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::MedicationOrder
       end
 
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         medication_order = super
+        medication_order.reason = extract_reason(entry_element)
         medication_order
       end
 

data/lib/qrda-import/data-element-importers/physical_exam_performed_importer.rb

@@ -11,6 +11,7 @@ module QRDA
         @result_xpath = "./cda:value"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::PhysicalExamPerformed
       end
 
@@ -19,6 +20,7 @@ module QRDA
         physical_exam_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
         physical_exam_performed.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         physical_exam_performed.components = extract_components(entry_element)
+        physical_exam_performed.reason = extract_reason(entry_element)
         physical_exam_performed
       end
 

data/lib/qrda-import/data-element-importers/procedure_order_importer.rb

@@ -10,6 +10,7 @@ module QRDA
         @anatomical_approach_site_xpath = "./cda:approachSiteCode"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
         @ordinality_xpath = "./cda:priorityCode"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::ProcedureOrder
       end
 
@@ -19,6 +20,7 @@ module QRDA
         procedure_order.anatomicalApproachSite = code_if_present(entry_element.at_xpath(@anatomical_approach_site_xpath))
         procedure_order.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
         procedure_order.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
+        procedure_order.reason = extract_reason(entry_element)
         procedure_order
       end
 

data/lib/qrda-import/data-element-importers/procedure_performed_importer.rb

@@ -15,6 +15,7 @@ module QRDA
         @ordinality_xpath = "./cda:priorityCode"
         @incision_datetime_xpath = "./cda:entryRelationship/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.89']/cda:effectiveTime"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
+        @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::ProcedurePerformed
       end
 
@@ -27,6 +28,7 @@ module QRDA
         procedure_performed.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
         procedure_performed.incisionDatetime = extract_time(entry_element, @incision_datetime_xpath)
         procedure_performed.components = extract_components(entry_element)
+        procedure_performed.reason = extract_reason(entry_element)
         procedure_performed
       end
 

data/lib/qrda-import/data-element-importers/substance_administered_importer.rb

@@ -1,9 +1,9 @@
 module QRDA
   module Cat1
-    class SubstanceAdministeredImporter < MedicationAdministeredImporter
+    class SubstanceAdministeredImporter < MedicationImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']"))
         super(entry_finder)
-        @entry_does_not_have_reason = true
+        @route_xpath = "./cda:routeCode"
         @entry_class = QDM::SubstanceAdministered
       end
 

data/lib/qrda-import/patient_importer.rb

@@ -92,7 +92,7 @@ module QRDA
           next unless data_element.respond_to?(:relatedTo) && data_element.relatedTo
           relations_to_add = []
           data_element.relatedTo.each do |related_to|
-            relations_to_add << entry_id_map[related_to.value]
+            relations_to_add << entry_id_map["#{related_to.value}_#{related_to.namingSystem}"]
           end
           data_element.relatedTo.destroy
           relations_to_add.each do |relation_to_add|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-parsers
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-30 00:00:00.000000000 Z
+date: 2019-09-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mustache
@@ -411,7 +411,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.9
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: A library for parsing HQMF documents.