health-data-standards 3.6.1 → 3.7.0

data/lib/health-data-standards/import/cat1/procedure_order_importer.rb

@@ -11,8 +11,8 @@ module HealthDataStandards
           procedure = super
           procedure.status_code = {'HL7 ActStatus' => ['ordered']}
           extract_performer(entry_element, procedure)
-          extract_site(entry_element, procedure)
-          extract_negation(entry_element, procedure)
+          extract_anatomical_target(entry_element, procedure)
+          extract_reason_or_negation(entry_element, procedure)
           procedure
         end
 
@@ -29,8 +29,8 @@ module HealthDataStandards
           procedure.performer = import_actor(performer_element) if performer_element
         end
 
-        def extract_site(parent_element, procedure)
-          procedure.site = extract_code(parent_element, "./cda:targetSiteCode")
+        def extract_anatomical_target(parent_element, procedure)
+          procedure.anatomical_target = extract_code(parent_element, "./cda:targetSiteCode")
         end
       end
     end

data/lib/health-data-standards/import/cat1/procedure_performed_importer.rb

@@ -5,6 +5,7 @@ module HealthDataStandards
         def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
           super(entry_finder)
           @incision_xpath ="./cda:entryRelationship/cda:procedure[./cda:templateId[@root='2.16.840.1.113883.10.20.24.3.89']]/cda:effectiveTime"
+          @ordinality_xpath = "./cda:priorityCode | ./cda:entryRelationship/cda:observation[./cda:code[@code='260870009']]/cda:value"
         end
 
         def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)

data/lib/health-data-standards/import/cat1/transfer_from_act_importer.rb

@@ -0,0 +1,18 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class TransferFromActImporter < TransferFromImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("./cda:entry/cda:act[./cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.141']/cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.81']"))
+        end
+
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          encounter = super
+          extract_reason_or_negation(entry_element.parent.parent, encounter)
+          encounter
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cat1/transfer_from_importer.rb

@@ -0,0 +1,24 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class TransferFromImporter < CDA::EncounterImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.81']"))
+          super(entry_finder)
+          @time_xpath = ""
+          @entry_class = Encounter
+        end
+        
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          encounter = super
+          transfer_time = HL7Helper.timestamp_to_integer(entry_element.at_xpath("./cda:participant/cda:time/cda:low")['value'])
+          encounter[:start_time] = transfer_time
+          encounter[:end_time] = transfer_time
+          transfer_from_element = entry_element.at_xpath("./cda:participant[@typeCode='ORG']")
+          extract_transfer(transfer_from_element, encounter)
+          encounter
+        end
+
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cat1/transfer_to_act_importer.rb

@@ -0,0 +1,18 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class TransferToActImporter < TransferToImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("./cda:entry/cda:act[./cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.142']/cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.82']"))
+        end
+
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          encounter = super
+          extract_reason_or_negation(entry_element.parent.parent, encounter)
+          encounter
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cat1/transfer_to_importer.rb

@@ -0,0 +1,23 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class TransferToImporter < CDA::EncounterImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.82']"))
+          super(entry_finder)
+          @entry_class = Encounter
+        end
+        
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          encounter = super
+          transfer_to_element = entry_element.at_xpath("./cda:participant[@typeCode='DST']")
+          extract_transfer(transfer_to_element, encounter)
+          transfer_time = HL7Helper.timestamp_to_integer(entry_element.at_xpath("./cda:participant/cda:time/cda:low")['value'])
+          encounter[:start_time] = transfer_time
+          encounter[:end_time] = transfer_time
+          encounter
+        end
+        
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cda/allergy_importer.rb

@@ -16,7 +16,7 @@ module HealthDataStandards
     
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           allergy = super
-          extract_negation(entry_element, allergy)
+          extract_reason_or_negation(entry_element, allergy)
           allergy.type = extract_code(entry_element, @type_xpath)
           allergy.reaction = extract_code(entry_element, @reaction_xpath)
           allergy.severity = extract_code(entry_element, @severity_xpath)

data/lib/health-data-standards/import/cda/communication_importer.rb

@@ -0,0 +1,55 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class CommunicationImporter < SectionImporter
+
+        #scoped to not look in the plan of care section so planned procedures do not end up mixed with
+        #past procedures
+        def initialize(entry_finder=EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2'] | ./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3'] | ./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']"))
+          super(entry_finder)
+          @entry_class = Communication
+          @template_xpath = "./cda:templateId/@root"
+          @reference_xpath = "./sdtc:inFulfillmentOf1"
+        end
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          communication = super
+          communication.direction = find_communication_direction(entry_element)
+          extract_reason_or_negation(entry_element, communication)
+          extract_references(entry_element, communication)
+          communication
+        end
+
+        private
+
+        def find_communication_direction(entry_element)
+          case entry_element.at_xpath(@template_xpath).value
+          when "2.16.840.1.113883.10.20.24.3.3"
+            return "communication_from_provider_to_patient"
+          when "2.16.840.1.113883.10.20.24.3.2"
+            return "communication_from_patient_to_provider"
+          when "2.16.840.1.113883.10.20.24.3.4"
+            return "communication_from_provider_to_provider"
+          end
+        end
+
+        def extract_references(parent_element, entry)
+          parent_element.xpath(@reference_xpath).each do |ref_xml|
+            ref = Reference.new
+            ref.type = case ref_xml.at_xpath("./@typeCode").value
+            when "FLFS"
+              "fulfills"
+            end
+            ref.referenced_type = case ref_xml.at_xpath("./sdtc:actReference/@classCode").value
+            when "ACT"
+              "Procedure"
+            end
+            id_element = ref_xml.at_xpath("./sdtc:actReference/sdtc:id")
+            ref.referenced_id = id_element['extension']
+            entry.references << ref
+          end
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/cda/condition_importer.rb

@@ -20,7 +20,7 @@ module HealthDataStandards
           condition = super
 
           extract_ordinality(entry_element, condition)
-          extract_negation(entry_element, condition)
+          extract_reason_or_negation(entry_element, condition)
           extract_priority(entry_element, condition)
 
           if @provider_xpath
@@ -47,6 +47,22 @@ module HealthDataStandards
             condition.priority = priority_element['value'].to_i
           end
         end
+
+        def extract_severity(entry_element,condition)
+          severity = entry_element.at_xpath(@severity_xpath)
+          if(severity)
+            condition.severity = { 'code_system' => CodeSystemHelper.code_system_for(severity['codeSystem']), 'code' => severity['code'] }
+          end
+        end
+
+        def extract_laterality(entry_element,condition)
+          laterality = entry_element.at_xpath(@laterality_xpath)
+          if laterality
+            # kept to be backward compatible
+            condition.laterality = { 'code_system' => CodeSystemHelper.code_system_for(laterality['codeSystem']), 'code' => laterality['code'] }
+            condition.anatomical_location = { 'code_system' => CodeSystemHelper.code_system_for(laterality['codeSystem']), 'code' => laterality['code'] }
+          end
+        end
       end
     end
   end

data/lib/health-data-standards/import/cda/encounter_importer.rb

@@ -15,10 +15,15 @@ module HealthDataStandards
           extract_performer(entry_element, encounter)
           extract_facility(entry_element, encounter)
           extract_reason(entry_element, encounter, nrh)
-          extract_negation(entry_element, encounter)
+          extract_reason_or_negation(entry_element, encounter)
           extract_admission(entry_element, encounter)
           extract_discharge_disposition(entry_element, encounter)
-          extract_transfers(entry_element, encounter)
+          transfer_elements = entry_element.xpath("./cda:participant[@typeCode='ORG' or 'DST']")
+          if transfer_elements
+            transfer_elements.each do |transfer_element|
+              extract_transfer(transfer_element, encounter)
+            end
+          end
           encounter
         end
     
@@ -62,26 +67,23 @@ module HealthDataStandards
           encounter.discharge_disposition = extract_code(parent_element, "./sdtc:dischargeDispositionCode")
         end
 
-        def extract_transfers(parent_element, encounter)
-          transfer_from_element = parent_element.at_xpath("./cda:participant[@typeCode='ORG']")
-          if (transfer_from_element)
-            transfer_from = Transfer.new(time: transfer_from_element.at_xpath("./cda:time")['value'])
-            transfer_from_subelement = transfer_from_element.at_xpath("./cda:participantRole[@classCode='LOCE']")
-            raw_tf_code = extract_code(transfer_from_subelement, './cda:code')
-            code_hash = {CodeSystemHelper.code_system_for(raw_tf_code["codeSystemOid"]) => [raw_tf_code["code"]]}
-            transfer_from.codes = code_hash
-            encounter.transfer_from = transfer_from
-          end
+        def extract_transfer(transfer_element, encounter)
+          transfer_from, transfer_to = transfer_from_or_to(transfer_element)
+          return unless transfer_to || transfer_from
+          transfer = Transfer.new
+          extract_dates(transfer_element, transfer, 'time')
+          raw_code = extract_code(transfer_element.at_xpath("./cda:participantRole[@classCode='LOCE']"), './cda:code')
+          code_hash = {CodeSystemHelper.code_system_for(raw_code["codeSystemOid"]) => [raw_code["code"]]}
+          transfer['code_system'] = code_hash.keys.first
+          transfer['code'] = code_hash[code_hash.keys.first].first
+          encounter.transfer_from = transfer if transfer_from
+          encounter.transfer_to = transfer if transfer_to
+        end
 
-          transfer_to_element = parent_element.at_xpath("./cda:participant[@typeCode='DST']")
-          if (transfer_to_element)
-            transfer_to = Transfer.new(time: transfer_to_element.at_xpath("./cda:time")['value'])
-            transfer_to_subelement = transfer_to_element.at_xpath("./cda:participantRole[@classCode='LOCE']")
-            raw_tt_code = extract_code(transfer_to_subelement, './cda:code')
-            code_hash = {CodeSystemHelper.code_system_for(raw_tt_code["codeSystemOid"]) => [raw_tt_code["code"]]}
-            transfer_to.codes = code_hash
-            encounter.transfer_to = transfer_to
-          end
+        def transfer_from_or_to(transfer_element)
+          transfer_from = true if transfer_element['typeCode'] && transfer_element['typeCode'] == 'ORG'
+          transfer_to = true if transfer_element['typeCode'] && transfer_element['typeCode'] == 'DST'
+          [transfer_from, transfer_to]
         end
       end
     end

data/lib/health-data-standards/import/cda/medical_equipment_importer.rb

@@ -14,6 +14,7 @@ module HealthDataStandards
           extract_manufacturer(entry_element, medical_equipment)
           extract_anatomical_structure(entry_element, medical_equipment)
           extract_removal_time(entry_element, medical_equipment)
+          extract_reason_or_negation(entry_element, medical_equipment)
           medical_equipment
         end
 

data/lib/health-data-standards/import/cda/medication_importer.rb

@@ -29,8 +29,8 @@ module HealthDataStandards
 
           medication.route = extract_code(entry_element, "./cda:routeCode")
           medication.dose = extract_scalar(entry_element, "./cda:doseQuantity")
-          medication.site = extract_code(entry_element, "./cda:approachSiteCode", 'SNOMED-CT')
-
+          medication.anatomical_approach = extract_code(entry_element, "./cda:approachSiteCode", 'SNOMED-CT')
+          
           extract_dose_restriction(entry_element, medication)
 
           medication.product_form = extract_code(entry_element, "./cda:administrationUnitCode", 'NCI Thesaurus')
@@ -39,16 +39,26 @@ module HealthDataStandards
           medication.indication = extract_code(entry_element, @indication_xpath, 'SNOMED-CT')
           medication.vehicle = extract_code(entry_element, @vehicle_xpath, 'SNOMED-CT')
 
+          medication.allowed_administrations = extract_scalar(entry_element, "./cda:repeatNumber").value unless extract_scalar(entry_element, "./cda:repeatNumber").nil?
+
           extract_order_information(entry_element, medication)
 
           extract_fulfillment_history(entry_element, medication)
-          extract_negation(entry_element, medication)
+          extract_reason_or_negation(entry_element, medication)
 
           medication
         end
 
         private
 
+        def extract_reason_or_negation(parent_element, medication)
+          if parent_element.parent.name == "entryRelationship"
+            super(parent_element.parent.parent, medication, parent_element)
+          else
+            super(parent_element, medication)
+          end
+        end
+
         def extract_fulfillment_history(parent_element, medication)
           fhs = parent_element.xpath("./cda:entryRelationship/cda:supply[@moodCode='EVN']")
           if fhs
@@ -113,4 +123,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

data/lib/health-data-standards/import/cda/procedure_importer.rb

@@ -16,8 +16,8 @@ module HealthDataStandards
           procedure = super
           extract_ordinality(entry_element, procedure)
           extract_performer(entry_element, procedure)
-          extract_site(entry_element, procedure)
-          extract_negation(entry_element, procedure)
+          extract_anatomical_target(entry_element, procedure)
+          extract_reason_or_negation(entry_element, procedure)
           extract_scalar(entry_element, procedure)
           procedure
         end
@@ -36,8 +36,8 @@ module HealthDataStandards
           procedure.performer = import_actor(performer_element) if performer_element
         end
 
-        def extract_site(parent_element, procedure)
-          procedure.site = extract_code(parent_element, "./cda:targetSiteCode")
+        def extract_anatomical_target(parent_element, procedure)
+          procedure.anatomical_target = extract_code(parent_element, "./cda:targetSiteCode")
         end
 
         def extract_scalar(parent_element, procedure)

data/lib/health-data-standards/import/cda/result_importer.rb

@@ -11,7 +11,7 @@ module HealthDataStandards
           result = super
           extract_interpretation(entry_element, result)
           extract_reference_range(entry_element, result)
-          extract_negation(entry_element, result)
+          extract_reason_or_negation(entry_element, result)
           extract_reason_description(entry_element, result, nrh)
           result
         end

data/lib/health-data-standards/import/cda/section_importer.rb

@@ -20,7 +20,7 @@ module HealthDataStandards
         end
 
         # Traverses an HL7 CDA document passed in and creates an Array of Entry
-        # objects based on what it finds                          
+        # 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
@@ -47,7 +47,7 @@ module HealthDataStandards
           if @value_xpath
             extract_values(entry_element, entry)
           end
-          entry.description = entry_element.at_xpath("./cda:text").try("text")
+          extract_description(entry_element, entry, nrh)
           if @status_xpath
             extract_status(entry_element, entry)
           end
@@ -56,6 +56,18 @@ module HealthDataStandards
 
         private
 
+        def extract_description(parent_element, entry, nrh)
+          orig_text_ref_element = parent_element.at_xpath(@description_xpath)
+          desc_ref_element = parent_element.at_xpath("./cda:text/cda:reference")
+          if orig_text_ref_element && orig_text_ref_element['value']
+            entry.description = nrh.lookup_tag(orig_text_ref_element['value'])
+          elsif desc_ref_element && desc_ref_element['value']
+            entry.description = nrh.lookup_tag(desc_ref_element['value'])
+          else
+            entry.description = parent_element.at_xpath("./cda:text").try("text")
+          end
+        end
+
         def extract_status(parent_element, entry)
           status_element = parent_element.at_xpath(@status_xpath)
           if status_element
@@ -120,7 +132,7 @@ module HealthDataStandards
         end
 
         def extract_value(parent_element, value_element, entry)
-          if value_element
+          if value_element && !value_element['nullFlavor']
             value = value_element['value']
             if value.present?
               unit = value_element['unit']
@@ -135,14 +147,14 @@ module HealthDataStandards
               unit = value_element['unit']
               entry.set_value(value.strip, unit)
             end
-            
+
           end
         end
-        
+
         def import_actor(actor_element)
           return ProviderImporter.instance.extract_provider(actor_element)
         end
-        
+
         def import_organization(organization_element)
           return OrganizationImporter.instance.extract_organization(organization_element)
         end
@@ -157,26 +169,55 @@ module HealthDataStandards
             person.family_name = name_element.at_xpath("./cda:family").try(:text)
           end
           person.addresses = person_element.xpath("./cda:addr").map { |addr| import_address(addr) }
-          person.telecoms = person_element.xpath("./cda:telecom").map { |tele| import_telecom(tele) } 
+          person.telecoms = person_element.xpath("./cda:telecom").map { |tele| import_telecom(tele) }
           return person
         end
 
-        def extract_negation(parent_element, entry)
+        # 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.at_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")
           negation_indicator = parent_element['negationInd']
-          unless negation_indicator.nil?
+          if reason_element
+            code_system_oid = reason_element['codeSystem']
+            code = reason_element['code']
+            code_system = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system_oid)
             entry.negation_ind = negation_indicator.eql?('true')
             if entry.negation_ind
-              negation_reason_element = parent_element.at_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")
-              if negation_reason_element
-                code_system_oid = negation_reason_element['codeSystem']
-                code = negation_reason_element['code']
-                code_system = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system_oid)
-                entry.negation_reason = {'code' => code, 'code_system' => code_system, 'codeSystem' => code_system}
-              end
+              entry.negation_reason = {'code' => code, 'code_system' => code_system, 'codeSystem' => code_system}
+            else
+              entry.reason = {'code' => code, 'code_system' => code_system, 'codeSystem' => code_system}
+            end
+          elsif negation_indicator
+            entry.negation_ind = negation_indicator.eql?('true')
+          end
+          extract_negated_code(coded_parent_element, entry)
+        end
+
+        def extract_negated_code(coded_parent_element, entry)
+          code_elements = coded_parent_element.xpath(@code_xpath)
+          code_elements.each do |code_element|
+            if code_element['nullFlavor'] == 'NA' && code_element['sdtc:valueSet']
+              # choose code from valueset
+              valueset = HealthDataStandards::SVS::ValueSet.where(oid: code_element['sdtc:valueSet'], bundle_id: get_bundle_id(coded_parent_element))
+              entry.add_code(valueset.first.concepts.first['code'], valueset.first.concepts.first['code_system_name'])
+              # A "code" is added to indicate the Non-Applicable valueset.
+              entry.add_code(code_element['sdtc:valueSet'], 'NA_VALUESET')
             end
           end
         end
-    
+
+        def get_bundle_id(parent_element)
+          while parent_element.name != 'document'
+            parent_element = parent_element.parent
+          end
+          # first measure id specified in the document
+          measure_id = parent_element.xpath("cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section/cda:entry/cda:organizer[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.98']/cda:reference/cda:externalDocument/cda:id[@root='2.16.840.1.113883.4.738']/@extension").first.value.upcase
+          # bundle of the first measure id 
+          HealthDataStandards::CQM::Measure.where(hqmf_id: measure_id).first['bundle_id']
+        end
+
         def extract_code(parent_element, code_xpath, code_system=nil)
           code_element = parent_element.at_xpath(code_xpath)
           code_hash = nil
@@ -205,4 +246,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end