health-data-standards 3.6.1 → 3.7.0

data/lib/health-data-standards/import/bulk_record_importer.rb

@@ -27,7 +27,8 @@ module HealthDataStandards
             end
             next if entry.directory?
             data = zipfile.read(entry.name)
-	    self.import_file(entry.name,data,failed_dir)
+	          status = self.import_file(entry.name,data,failed_dir)
+            raise StandardError, status[:message] if status.is_a?(Hash) && status[:status] === 'error'
           end
         end
 
@@ -48,7 +49,7 @@ module HealthDataStandards
       rescue
         FileUtils.mkdir_p(failed_dir)
         FileUtils.cp(file,File.join(failed_dir,File.basename(file)))
-        File.open(File.join(failed_dir,"#{file}.error")) do |f|
+        File.open(File.join(failed_dir,"#{file}.error"), 'w') do |f|
           f.puts($!.message)
           f.puts($!.backtrace)
         end
@@ -73,6 +74,7 @@ module HealthDataStandards
             f.puts($!.message)
             f.puts($!.backtrace)
           end
+          raise $!
         end
       end
 
@@ -89,7 +91,7 @@ module HealthDataStandards
       end
 
       def self.import(xml_data, provider_map = {})
-        doc = Nokogiri::XML(xml_data)
+        doc = xml_data.kind_of?(Nokogiri::XML::Document) ? xml_data : Nokogiri::XML(xml_data)
 
         providers = []
         root_element_name = doc.root.name
@@ -126,8 +128,9 @@ module HealthDataStandards
             record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))
           end
         end
-        record.save
-
+        if record.save
+          return record
+        end
       end
     end
   end

data/lib/health-data-standards/import/bundle/importer.rb

@@ -62,7 +62,13 @@ module HealthDataStandards
 
           end
 
-          bundle
+          return bundle
+        ensure
+          # If the bundle is nil or the bundle has never been saved then do not set done_importing or run save.
+          if bundle && bundle.created_at
+            bundle.done_importing = true
+            bundle.save
+          end
         end
 
 
@@ -72,11 +78,12 @@ module HealthDataStandards
         # @param [String] fn The body of the function being saved.
         def self.save_system_js_fn(name, fn)
           fn = "function () {\n #{fn} \n }"
-          Mongoid.default_session['system.js'].find('_id' => name).upsert(
-            {
-              "_id" => name,
-              "value" => BSON::Code.new(fn)
-            }
+          Mongoid.default_client['system.js'].replace_one({
+                "_id" => name},
+                    {
+                      "_id" => name,
+                      "value" => BSON::Code.new(fn)
+              },{upsert: true}
           )
         end
 
@@ -110,14 +117,14 @@ module HealthDataStandards
             measure = source_measure.clone
             measure_ids << measure['id']
             measure['bundle_id'] = bundle.id
-            Mongoid.default_session["measures"].insert(measure)
+            Mongoid.default_client["measures"].insert_one(measure)
 
             if update_measures
-              Mongoid.default_session["measures"].where({hqmf_id: measure["hqmf_id"], sub_id: measure["sub_id"]}).each do |m|
+              Mongoid.default_client["measures"].find({hqmf_id: measure["hqmf_id"], sub_id: measure["sub_id"]}).each do |m|
                 b = HealthDataStandards::CQM::Bundle.find(m["bundle_id"])
                 if b.version < bundle.version
                   m.merge!(source_measure)
-                  Mongoid.default_session["measures"].where({"_id" => m["_id"]}).update(m)
+                  Mongoid.default_client["measures"].update_one({"_id" => m["_id"]},m)
                 end
               end
             end
@@ -175,14 +182,14 @@ module HealthDataStandards
 
         def self.compare_dates(entry, start_date, end_date)
           if entry.start_time * 1000 ==  start_date
-            if entry.end_time == nil 
+            if entry.end_time == nil
               if end_date == nil
                 return true
-              else 
+              else
                 return false
               end
             else entry.end_time * 1000 == end_date
-              return true   
+              return true
             end
           end
           return false
@@ -205,7 +212,7 @@ module HealthDataStandards
           entries.each_with_index do |entry, index|
             vs = HealthDataStandards::SVS::ValueSet.new(unpack_json(entry))
             vs['bundle_id'] = bundle.id
-            HealthDataStandards::SVS::ValueSet.collection.insert(vs.as_document)
+            HealthDataStandards::SVS::ValueSet.collection.insert_one(vs.as_document)
             report_progress('Value Sets', (index*100/entries.length)) if index%10 == 0
           end
           puts "\rLoading: Value Sets Complete          "
@@ -233,7 +240,7 @@ module HealthDataStandards
                 end
               end
               document['bundle_id'] = bundle.id
-              Mongoid.default_session[collection].insert(document)
+              Mongoid.default_client[collection].insert_one(document)
             end
           end
           puts "\rLoading: Results Complete          "

data/lib/health-data-standards/import/c32/care_goal_importer.rb

@@ -18,7 +18,7 @@ module HealthDataStandards
                        end
             
           entry = importer.create_entry(goal_element, nrh)
-          extract_negation(goal_element, entry)
+          extract_reason_or_negation(goal_element, entry)
 
           entry
         end

data/lib/health-data-standards/import/c32/immunization_importer.rb

@@ -12,7 +12,7 @@ module HealthDataStandards
 
         def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
           immunization = super
-          extract_negation(entry_element, immunization)
+          extract_reason_or_negation(entry_element, immunization)
           extract_performer(entry_element, immunization)
           immunization
         end

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

@@ -0,0 +1,20 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class ClinicalTrialParticipantImporter < CDA::ConditionImporter
+
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.51']"))
+          super(entry_finder)
+          @code_xpath = './cda:value'
+        end
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          entry = super
+          entry.description ||= 'Patient Characteristic Clinical Trial Participant'
+          entry
+        end
+
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class DeviceOrderImporter < CDA::MedicalEquipmentImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.130']/cda:entryRelationship/cda:supply[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.9']"))
+        end
+
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          medical_equipment = super
+          # the negation is at the level of the encapsulating Device Order Act Template (parent.parent)
+          extract_reason_or_negation(entry_element.parent.parent, medical_equipment, entry_element)
+          medical_equipment
+        end
+
+      end
+    end
+  end
+end

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

@@ -3,25 +3,20 @@ module HealthDataStandards
     module Cat1
       class DiagnosisActiveImporter < CDA::ConditionImporter
 
-        def initialize
-          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.11']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.11']"))
+          super(entry_finder)
           @status_xpath = nil # We'll hardcode this to active in create entry because this is from the 
                               # diagnosis active template
           @severity_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.8']/cda:value"                    
+          @laterality_xpath = "./cda:value/cda:qualifier[cda:name/@code='182353008']/cda:value"
         end
 
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           condition = super(entry_element,nrh)
           extract_severity(entry_element,condition)
+          extract_laterality(entry_element,condition)
           condition
         end
-
-        def extract_severity(entry_element,condition)
-          severity = entry_element.at_xpath(@severity_xpath)
-          if(severity)
-            condition.severity = {CodeSystemHelper.code_system_for(severity['codeSystem']) => [severity['code']]}
-          end
-        end
       end
     end
   end

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

@@ -0,0 +1,15 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class DiagnosisImporter < DiagnosisActiveImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.135']"))
+          @status_xpath = nil # We'll hardcode this to active in create entry because this is from the 
+                              # diagnosis active template
+          @laterality_xpath = "./cda:targetSiteCode"
+        end
+      end
+    end
+  end
+end

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class DiagnosisInactiveImporter < CDA::ConditionImporter
 
         def initialize
-          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.13']"))
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.13']"))
           @status_xpath = nil # We'll hardcode this to inactive in create entry because this is from the 
                               # diagnosis active template
         end

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

@@ -7,6 +7,12 @@ module HealthDataStandards
           @entry_class = Procedure
         end
 
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          procedure = super
+          extract_reason_or_negation(entry_element, procedure)
+          procedure
+        end
+
         private
 
         def extract_dates(parent_element, entry, element_name="author")

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

@@ -0,0 +1,19 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class EncounterOrderActImporter < EncounterOrderImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("./cda:entry/cda:act[./cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.132']/cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']"))
+        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/encounter_performed_act_importer.rb

@@ -0,0 +1,19 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class EncounterPerformedActImporter < EncounterPerformedImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("./cda:entry/cda:act[./cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.133']/cda:entryRelationship/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']"))
+        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/encounter_performed_importer.rb

@@ -5,17 +5,33 @@ module HealthDataStandards
         def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']"))
           super(entry_finder)
           @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation"
+          @principal_diagnosis_xpath = "./cda:entryRelationship/cda:observation[cda:code/@code='8319008']"
+          @diagnosis_xpath = "./cda:entryRelationship/cda:act/cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.4']"
         end
 
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           encounter = super
           extract_admit_time(entry_element, encounter)
           extract_reason(entry_element, encounter, nrh)
+          encounter.principal_diagnosis = extract_diagnosis(entry_element, @principal_diagnosis_xpath)
+          encounter.diagnosis = extract_diagnosis(entry_element, @diagnosis_xpath)
           encounter
         end
 
         private
 
+        def extract_diagnosis(parent_element, xpath)
+          diagnosis_element = parent_element.at_xpath(xpath)
+          if(diagnosis_element)
+            diagnosis = Entry.new
+            extract_workaround_codes(diagnosis_element, diagnosis)
+            diagnosis.codes[diagnosis['code_system']] ||= []
+            diagnosis.codes[diagnosis['code_system']] << diagnosis['code']
+            return diagnosis
+          end
+          nil
+        end
+
         def extract_reason(parent_element, encounter, nrh)
           reason_element = parent_element.at_xpath(@reason_xpath)
           if reason_element

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

@@ -0,0 +1,14 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class ImmunizationAdministeredImporter < CDA::MedicationImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:act/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.52']"))
+          super(entry_finder)
+          #@code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
+          #@entry_class = Medication
+        end
+
+      end
+    end
+  end
+end

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

@@ -0,0 +1,18 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class MedicationDispensedActImporter < MedicationDispensedImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("./cda:entry/cda:act[./cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.139']/cda:entryRelationship/cda:supply[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.45']"))
+        end
+
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          medication = super
+          extract_reason_or_negation(entry_element.parent.parent, medication)
+          medication
+        end
+      end
+    end
+  end
+end

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

@@ -13,30 +13,34 @@ module HealthDataStandards
         def initialize
           # This differs from other HDS patient importers in that sections can have multiple importers
           @section_importers = {}
+          @section_importers[:assessments] = [generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.144']", '2.16.840.1.113883.10.20.28.3.117')] #assessment performed
           @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:entry/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(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='2.16.840.1.113883.10.20.24.3.41']", '2.16.840.1.113883.3.560.1.199', 'discharge'), #discharge medication active
+          @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(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 = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.131'), #comm from provider to patient
                                              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(Cat1::ProcedureImporter, nil, '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
-                                             generate_importer(CDA::ProcedureImporter, "./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(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'),
@@ -50,7 +54,9 @@ module HealthDataStandards
                                             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')]
+          @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', 'ordered')]
 
           @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
@@ -61,7 +67,14 @@ module HealthDataStandards
                                           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(EncounterOrderImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered')]
+                                             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')]
 
@@ -73,9 +86,9 @@ module HealthDataStandards
           record = Record.new
           HealthDataStandards::Import::C32::PatientImporter.instance.get_demographics(record, doc)
           import_sections(record, doc)
-          get_clinical_trial_participant(record, doc)
           get_patient_expired(record, doc)
           record.dedup_record!
+          normalize_references(record)
           record
         end
 
@@ -91,14 +104,28 @@ module HealthDataStandards
           end
         end
 
-        def get_clinical_trial_participant(record, doc)
-          entry_elements = doc.xpath("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.51']")
-          record.clinicalTrialParticipant = true unless entry_elements.blank?
+        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 get_patient_expired(record, doc)
-          entry_elements = doc.xpath("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
-          record.expired = true unless entry_elements.empty?
+        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