health-data-standards 3.6.1 → 3.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 59b91fc289603c22a9152c776bebee15f193f70e
-  data.tar.gz: cde5d51f408a2eb237bd1ed632a2383936bc5631
+  metadata.gz: 8ef5b18109b56fc92d3ed2097aee343760bf477c
+  data.tar.gz: '008f520093afb25e312ecbed501c3bfdf4cb2761'
 SHA512:
-  metadata.gz: 031ae5473fe9cdb09819c2ee91ca3570fc7e2aa06e720abc3e61cd34bc96b8f32a03279f715eb3ecbd292ff935cdded1fef4b6399dcbcd10e1f9627192c8705a
-  data.tar.gz: 9df5f732d24fc1f85232e13debff907f2afb82d41850301d865279b3a185bd984cc0806b1673005e4a0fd16705b3d96b2080921c4dadcd4bb3ecf3443c0268b1
+  metadata.gz: 3632559346961e5110f26aae8949d7a3d85cdeb937379e11850cbc40dcde4ec3d5bfc14f5aa010c1fd6f403d734efba052fd5bfafb4992001cdd0f30313b4c39
+  data.tar.gz: c211b9f4922b81411fbce83bf193c22a003a12561a86bef90b9c022c54531776f7ad3072e9aca165c4320a6f8c3a5f9887fc59ffa690fb5e029b46d2dc5ff155

data/Gemfile

@@ -2,10 +2,13 @@ source "https://rubygems.org"
 
 gemspec :development_group => :test
 
+group :development, :test do
+  gem 'bundler-audit'
+end
+
 group :development do
   gem 'rake'
-  gem 'pry', '~> 0.9.10'
-  gem 'pry-nav', '~> 0.2.2', platforms: [:ruby_21, :ruby_22]
+  gem 'byebug', '~> 6.0.2',  platforms: [:ruby_20, :ruby_21, :ruby_22]
 end
 
 group :test do
@@ -19,4 +22,6 @@ group :test do
   gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
 
+  gem 'simplexml_parser', :git => 'https://github.com/projecttacoma/simplexml_parser.git', :branch => 'master'
+
 end

data/Rakefile

@@ -7,7 +7,8 @@ import 'lib/tasks/hqmf.rake'
 Rake::TestTask.new(:test_unit) do |t|
   t.libs << "test"
   t.test_files = FileList['test/**/*_test.rb']
-  t.verbose = true
+  t.verbose = false
+  t.warning = false
 end
 
 

data/lib/health-data-standards.rb

@@ -16,6 +16,7 @@ require_relative 'health-data-standards/ext/symbol'
 require_relative 'health-data-standards/ext/string'
 require_relative 'health-data-standards/ext/node'
 
+require_relative 'health-data-standards/util/nlm_helper'
 require_relative 'health-data-standards/util/hl7_helper'
 require_relative 'health-data-standards/util/code_system_helper'
 require_relative 'health-data-standards/util/hqmf_template_helper'
@@ -28,6 +29,7 @@ require_relative 'health-data-standards/export/c32'
 require_relative 'health-data-standards/export/ccda'
 require_relative 'health-data-standards/export/csv'
 require_relative 'health-data-standards/export/hdata/metadata'
+require_relative 'health-data-standards/export/exceptions'
 
 require_relative 'health-data-standards/import/provider_import_utils'
 require_relative 'health-data-standards/import/hdata/metadata_importer'
@@ -42,13 +44,16 @@ require_relative 'health-data-standards/models/entry'
 require_relative 'health-data-standards/models/allergy'
 require_relative 'health-data-standards/models/encounter'
 require_relative 'health-data-standards/models/condition'
+require_relative 'health-data-standards/models/communication'
 require_relative 'health-data-standards/models/immunization'
 require_relative 'health-data-standards/models/fulfillment_history'
 require_relative 'health-data-standards/models/order_information'
 require_relative 'health-data-standards/models/medication'
 require_relative 'health-data-standards/models/procedure'
 require_relative 'health-data-standards/models/lab_result'
+require_relative 'health-data-standards/models/family_history'
 require_relative 'health-data-standards/models/functional_status'
+require_relative 'health-data-standards/models/care_experience'
 require_relative 'health-data-standards/models/medical_equipment'
 require_relative 'health-data-standards/models/record'
 require_relative 'health-data-standards/models/personable'
@@ -71,6 +76,11 @@ require_relative 'health-data-standards/models/metadata/author'
 require_relative 'health-data-standards/models/metadata/change_info'
 require_relative 'health-data-standards/models/metadata/link_info'
 require_relative 'health-data-standards/models/metadata/pedigree'
+require_relative 'health-data-standards/models/provider_preference'
+require_relative 'health-data-standards/models/patient_preference'
+require_relative 'health-data-standards/models/care_goal'
+require_relative 'health-data-standards/models/encounter_principal_diagnosis'
+require_relative 'health-data-standards/models/assessment'
 
 require_relative 'health-data-standards/models/qrda/id'
 require_relative 'health-data-standards/models/qrda/device'
@@ -111,6 +121,7 @@ require_relative 'health-data-standards/import/cda/medication_importer'
 require_relative 'health-data-standards/import/cda/procedure_importer'
 require_relative 'health-data-standards/import/cda/result_importer'
 require_relative 'health-data-standards/import/cda/vital_sign_importer'
+require_relative 'health-data-standards/import/cda/communication_importer'
 
 require_relative 'health-data-standards/import/c32/condition_importer'
 require_relative 'health-data-standards/import/c32/immunization_importer'
@@ -131,18 +142,24 @@ require_relative 'health-data-standards/import/ccda/care_goal_importer'
 require_relative 'health-data-standards/import/ccda/medical_equipment_importer'
 require_relative 'health-data-standards/import/ccda/insurance_provider_importer'
 
+require_relative 'health-data-standards/import/cat1/device_order_importer'
 require_relative 'health-data-standards/import/cat1/gestational_age_importer'
 require_relative 'health-data-standards/import/cat1/procedure_intolerance_importer'
 require_relative 'health-data-standards/import/cat1/procedure_performed_importer'
 require_relative 'health-data-standards/import/cat1/procedure_order_importer'
 require_relative 'health-data-standards/import/cat1/diagnosis_active_importer'
+require_relative 'health-data-standards/import/cat1/diagnosis_importer'
 require_relative 'health-data-standards/import/cat1/diagnosis_inactive_importer'
 require_relative 'health-data-standards/import/cat1/patient_importer'
 require_relative 'health-data-standards/import/cat1/lab_order_importer'
+require_relative 'health-data-standards/import/cat1/immunization_administered_importer'
 require_relative 'health-data-standards/import/cat1/medication_active_importer'
 require_relative 'health-data-standards/import/cat1/medication_dispensed_importer'
+require_relative 'health-data-standards/import/cat1/medication_dispensed_act_importer'
 require_relative 'health-data-standards/import/cat1/encounter_order_importer'
+require_relative 'health-data-standards/import/cat1/encounter_order_act_importer'
 require_relative 'health-data-standards/import/cat1/encounter_performed_importer'
+require_relative 'health-data-standards/import/cat1/encounter_performed_act_importer'
 require_relative 'health-data-standards/import/cat1/diagnostic_study_order_importer'
 require_relative 'health-data-standards/import/cat1/tobacco_use_importer'
 require_relative 'health-data-standards/import/cat1/entry_package'
@@ -150,7 +167,11 @@ require_relative 'health-data-standards/import/cat1/lab_result_importer'
 require_relative 'health-data-standards/import/cat1/ecog_status_importer'
 require_relative 'health-data-standards/import/cat1/symptom_active_importer'
 require_relative 'health-data-standards/import/cat1/insurance_provider_importer'
-require_relative 'health-data-standards/import/cat1/procedure_importer'
+require_relative 'health-data-standards/import/cat1/clinical_trial_participant_importer'
+require_relative 'health-data-standards/import/cat1/transfer_from_importer.rb'
+require_relative 'health-data-standards/import/cat1/transfer_to_importer.rb'
+require_relative 'health-data-standards/import/cat1/transfer_from_act_importer.rb'
+require_relative 'health-data-standards/import/cat1/transfer_to_act_importer.rb'
 
 require_relative 'health-data-standards/import/bundle/importer'
 

data/lib/health-data-standards/export/cat_1.rb

@@ -1,18 +1,37 @@
 module HealthDataStandards
   module Export
     class Cat1
-      def initialize
-        template_helper = HealthDataStandards::Export::TemplateHelper.new('cat1', 'cat1')
+      
+      def initialize(qrda_version = nil)
+        template_helper = HealthDataStandards::Export::TemplateHelper.new('cat1', 'cat1', nil, qrda_version)
         @rendering_context = HealthDataStandards::Export::RenderingContext.new
         @rendering_context.template_helper = template_helper
         @rendering_context.extensions = [HealthDataStandards::Export::Helper::Cat1ViewHelper]
       end
 
+
       @@vs_map = nil
-      def export(patient, measures, start_date, end_date, header=nil, r2_compatibility=false)
-        @rendering_context.render(:template => 'show', :locals => {:patient => patient, :measures => measures,
-						:start_date => start_date, :end_date => end_date, :header => header,
-						:r2_compatibility => r2_compatibility})
+
+      @@most_recent_qrda_version = 'r4'
+      @@valid_qrda_versions = ['r4', 'r3_1', 'r3', 'r2']
+
+      #default qrda_version should default to latest version
+      def export(patient, measures, start_date, end_date, header=nil, qrda_version='r4', cms_compatibility=false)
+        qrda_version = qrda_version.nil? ? @@most_recent_qrda_version : qrda_version
+
+        if (!@@valid_qrda_versions.include? qrda_version)
+          raise "Unknown QRDA version provided"
+        end
+
+        qrda_template = 'show'
+        r2_compatibility = false
+
+        if qrda_version == 'r2'
+          r2_compatibility = true
+        end
+        @rendering_context.render(:template => qrda_template, :locals => {:patient => patient, :measures => measures,
+						:start_date => start_date, :end_date => end_date, :header => header, :qrda_version => qrda_version,
+						:r2_compatibility => r2_compatibility, :cms_compatibility => cms_compatibility})
       end
     end
   end

data/lib/health-data-standards/export/cat_1_r2.rb

@@ -3,8 +3,14 @@
 module HealthDataStandards
   module Export
     class Cat1R2 < Cat1
-      def export(patient, measures, start_date, end_date, header=nil, r2_compatibiliy=true)
-        super(patient, measures, start_date, end_date, header, r2_compatibiliy)
+      
+      def initialize
+        super("r2")
+      end
+      
+      def export(patient, measures, start_date, end_date, header=nil, qrda_version=nil, cms_compatibility=false)
+      	# QRDA version is always 'r2'
+        super(patient, measures, start_date, end_date, header, 'r2', cms_compatibility)
       end
     end
   end

data/lib/health-data-standards/export/cat_3.rb

@@ -1,23 +1,24 @@
 module HealthDataStandards
   module Export
     class Cat3
-      def initialize
-        template_helper = HealthDataStandards::Export::TemplateHelper.new('cat3', 'cat3')
+      def initialize(qrda_version = nil)
+        template_helper = HealthDataStandards::Export::TemplateHelper.new('cat3', 'cat3', nil, qrda_version)
         @rendering_context = HealthDataStandards::Export::RenderingContext.new
         @rendering_context.template_helper = template_helper
-        @cat1_renderer = HealthDataStandards::Export::RenderingContext.new
-        @cat1_renderer.template_helper = HealthDataStandards::Export::TemplateHelper.new('cat1', 'cat1')
       end
 
-      def export(measures, header, effective_date, start_date, end_date, filter=nil,test_id=nil)
+      @@most_recent_qrda_version = 'r2_1'
+      @@valid_qrda_versions = ['r1', 'r1_1', 'r2', 'r2_1']
+
+      def export(measures, header, effective_date, start_date, end_date, qrda3_version=nil, filter=nil,test_id=nil)
         results = {}
         measures.each do |measure|
           results[measure['hqmf_id']] = HealthDataStandards::CQM::QueryCache.aggregate_measure(measure['hqmf_id'], effective_date, filter, test_id)
         end
         @rendering_context.render(:template => 'show', 
                                   :locals => {:measures => measures, :start_date => start_date, 
-                                              :end_date => end_date, :cat1_renderer => @cat1_renderer,
-                                              :results => results,
+                                              :end_date => end_date,
+                                              :results => results, :qrda3_version => qrda3_version,
                                               :header=>header})
       end
     end

data/lib/health-data-standards/export/exceptions.rb

@@ -0,0 +1,13 @@
+module HealthDataStandards
+  module Export
+    class PatientExportDataCriteriaException < Exception
+      attr_reader :patient, :data_criteria, :entries
+      def initialize(string, patient, data_criteria, entries)
+        @patient = patient
+        @data_criteria = data_criteria
+        @entries = entries
+        super(string)
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/helper/cat1_view_helper.rb

@@ -4,27 +4,33 @@ module HealthDataStandards
       module Cat1ViewHelper
         include HealthDataStandards::Export::Helper::ScoopedViewHelper
 
-        def render_data_criteria(dc, entries)
+        def render_data_criteria(dc, entries, r2_compatibility, qrda_version = nil)
           html_array = entries.map do |entry|
               bundle_id = entry.record ? entry.record["bundle_id"] : nil
               vs_map = (value_set_map(bundle_id) || {})[dc['value_set_oid']]
-              render(:partial => HealthDataStandards::Export::QRDA::EntryTemplateResolver.partial_for(dc['data_criteria_oid'], dc['value_set_oid']), :locals => {:entry => entry,
+              render(:partial => HealthDataStandards::Export::QRDA::EntryTemplateResolver.partial_for(dc['data_criteria_oid'], dc['value_set_oid'], qrda_version), :locals => {:entry => entry,
                                                                                                                                    :data_criteria => dc['data_criteria'],
                                                                                                                                    :value_set_oid => dc['value_set_oid'],
-                                                                                                                                   :value_set_map => vs_map,
+                                                                                                                                   :filtered_vs_map => vs_map,
                                                                                                                                    :result_oids => dc["result_oids"],
-                                                                                                                                   :field_oids => dc["field_oids"]})
+                                                                                                                                   :field_oids => dc["field_oids"],
+                                                                                                                                   :r2_compatibility => r2_compatibility,
+                                                                                                                                   :bundle_id => bundle_id})
           end
           html_array.join("\n")
         end
 
-        def render_patient_data(patient, measures)
+        def render_patient_data(patient, measures, r2_compatibility, qrda_version = nil)
           HealthDataStandards.logger.warn("Generating CAT I for #{patient.first} #{patient.last}")
-          udcs = unique_data_criteria(measures)
-
+          udcs = unique_data_criteria(measures, r2_compatibility)
           data_criteria_html = udcs.map do |udc|
-            entries = entries_for_data_criteria(udc['data_criteria'], patient)
-            render_data_criteria(udc, entries)          
+            # If there's an error exporting particular criteria, re-raise an error that includes useful debugging info
+            begin
+              entries = entries_for_data_criteria(udc['data_criteria'], patient)
+              render_data_criteria(udc, entries, r2_compatibility, qrda_version)
+            rescue => e
+              raise HealthDataStandards::Export::PatientExportDataCriteriaException.new(e.message, patient, udc['data_criteria'], entries)
+            end
           end
           data_criteria_html.compact.join("\n")
         end
@@ -46,7 +52,7 @@ module HealthDataStandards
           valueset_oids.each do |vs_oid|
             oid_list = (vs_map[vs_oid] || [])
             oid_map = Hash[oid_list.collect{|x| [x["set"],x["values"]]}]
-            if (oid_map[code_system] || []).index code
+            if (oid_map[code_system] || []).include? code
               return vs_oid
             end
           end
@@ -56,4 +62,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

data/lib/health-data-standards/export/helper/html_view_helper.rb

@@ -6,7 +6,9 @@ module HealthDataStandards
 
         def decode_hqmf_section(section, oid)
           if oid
-            HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['definition'].pluralize.to_sym
+	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+	    definition['definition'].pluralize.to_sym
           else
             section
           end
@@ -14,7 +16,9 @@ module HealthDataStandards
 
         def decode_hqmf_status(status, oid)
           if oid
-            HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['status']
+	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+	    definition['status']
           else
             status
           end
@@ -22,12 +26,14 @@ module HealthDataStandards
 
         def decode_hqmf_description(description, oid)
           if oid
-            definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['definition']
-            status = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)['status']
+	    definition = HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid)
+	    definition ||= HealthDataStandards::Util::HQMFTemplateHelper.definition_for_template_id(oid, 'r2')
+	    definition_text = definition['definition']
+	    status_text = definition['status']
             unless status.blank?
-              "#{definition.titleize}, #{status.titleize}".to_sym  
+	      "#{definition_text.titleize}, #{status_text.titleize}".to_sym
             else
-              "#{definition.titleize}".to_sym
+	      "#{definition_text.titleize}".to_sym
             end
           else
             description
@@ -36,4 +42,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

data/lib/health-data-standards/export/helper/scooped_view_helper.rb

@@ -20,17 +20,32 @@ module HealthDataStandards
         # Given a set of measures, find the data criteria/value set pairs that are unique across all of them
         # Returns an Array of Hashes. Hashes will have a three key/value pairs. One for the data criteria oid,
         # one for the value set oid and one for the data criteria itself
-        def unique_data_criteria(measures)
+        def unique_data_criteria(measures, r2_compatibility)
           all_data_criteria = measures.map {|measure| measure.all_data_criteria}.flatten
           mapped_data_criteria = {}
+
           all_data_criteria.each do |data_criteria|
             data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                               (data_criteria.status || ""),
                                                                               data_criteria.negation)
+          data_criteria_oid ||= HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
+                                                                                (data_criteria.status || ""),
+                                                                                data_criteria.negation, "r2")
+
+            # change a transfer to an encounter since we pull back and write encounters
+            if r2_compatibility
+              if ['2.16.840.1.113883.3.560.1.71', '2.16.840.1.113883.3.560.1.72'].include? data_criteria_oid
+                data_criteria_oid = '2.16.840.1.113883.3.560.1.79'
+              end
+            end
             value_set_oid = data_criteria.code_list_id
+            if data_criteria_oid == '2.16.840.1.113883.3.560.1.71'
+              value_set_oid = data_criteria.field_values['TRANSFER_FROM'].code_list_id
+            elsif data_criteria_oid == '2.16.840.1.113883.3.560.1.72'
+              value_set_oid = data_criteria.field_values['TRANSFER_TO'].code_list_id
+            end
             dc = {'data_criteria_oid' => data_criteria_oid, 'value_set_oid' => value_set_oid}
             mapping = mapped_data_criteria[dc] ||= {'result_oids' => [], 'field_oids' =>{}, 'data_criteria' => data_criteria}
-
             if data_criteria.field_values
               data_criteria.field_values.each_pair do |field,descr|
                 if descr && descr.type == "CD"
@@ -38,7 +53,9 @@ module HealthDataStandards
                 end
               end
             end
-
+            if data_criteria.negation
+              (mapping['field_oids']["REASON"] ||= []) << data_criteria.negation_code_list_id
+            end
             if data_criteria.value && data_criteria.value.type == "CD"
               mapping["result_oids"] << data_criteria.value.code_list_id
             end
@@ -56,6 +73,10 @@ module HealthDataStandards
             data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                                         data_criteria.status || '',
                                                                                         data_criteria.negation)
+            data_criteria_oid ||= HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
+                                                                                        data_criteria.status || '',
+                                                                                        data_criteria.negation, "r2")
+
             if entry.respond_to?(:oid) && (entry.oid == data_criteria_oid)
               codes = *(value_set_map(entry.record["bundle_id"])[data_criteria_info['value_set_oid']] || [])
               if codes.empty?
@@ -73,39 +94,50 @@ module HealthDataStandards
 
         # Find all of the entries on a patient that match the given data criteria
         def entries_for_data_criteria(data_criteria, patient)
+
           data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                                       data_criteria.status || '',
                                                                                        data_criteria.negation)
-          HealthDataStandards.logger.warn("Looking for dc [#{data_criteria_oid}]")
+          is_hqmfr2 = true unless data_criteria_oid
+          data_criteria_oid ||= HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
+                                                                                      data_criteria.status || '',
+                                                                                      data_criteria.negation, "r2")
+          HealthDataStandards.logger.debug("Looking for dc [#{data_criteria_oid}]")
           filtered_entries = []
           entries = []
+
           case data_criteria_oid
           when '2.16.840.1.113883.3.560.1.404'
             filtered_entries = handle_patient_expired(patient)
-          when '2.16.840.1.113883.3.560.1.401'
-            filtered_entries = handle_clinical_trial_participant(patient)
           when '2.16.840.1.113883.3.560.1.405'
             filtered_entries = handle_payer_information(patient)
           else
             entries.concat patient.entries_for_oid(data_criteria_oid)
 
-              case data_criteria_oid
-              when '2.16.840.1.113883.3.560.1.5'
-                #special case handling for Lab Test: Performed being implicitly available through a Lab Test: Result
-                entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.12')
-              when '2.16.840.1.113883.3.560.1.12'
-                entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.5')
-              when '2.16.840.1.113883.3.560.1.6'
-                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.63')
-              when  '2.16.840.1.113883.3.560.1.63'
-                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.6')
-              when '2.16.840.1.113883.3.560.1.3'
-                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.11')
-              when  '2.16.840.1.113883.3.560.1.11'
-                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.3')
+            case data_criteria_oid
+            when '2.16.840.1.113883.3.560.1.5'
+              #special case handling for Lab Test: Performed being implicitly available through a Lab Test: Result
+              entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.12')
+            when '2.16.840.1.113883.3.560.1.12'
+              entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.5')
+            when '2.16.840.1.113883.3.560.1.6'
+               entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.63')
+            when  '2.16.840.1.113883.3.560.1.63'
+               entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.6')
+            when '2.16.840.1.113883.3.560.1.3'
+               entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.11')
+            when  '2.16.840.1.113883.3.560.1.11'
+               entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.3')
+            when '2.16.840.1.113883.3.560.1.71', '2.16.840.1.113883.3.560.1.72'
+              # transfers
+              entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.79')
+              if (data_criteria.field_values)
+                code_list_id = data_criteria.field_values['TRANSFER_FROM'].try(:code_list_id) || data_criteria.field_values['TRANSFER_TO'].try(:code_list_id)
+                codes = (value_set_map(patient["bundle_id"])[code_list_id] || [])
               end
+            end
 
-            codes = (value_set_map(patient["bundle_id"])[data_criteria.code_list_id] || [])
+            codes ||= (value_set_map(patient["bundle_id"])[data_criteria.code_list_id] || [])
             if codes.empty?
               HealthDataStandards.logger.warn("No codes for #{data_criteria.code_list_id}")
             end
@@ -114,16 +146,27 @@ module HealthDataStandards
               # This special case is for when the code list is a reason
               if data_criteria.code_list_id =~ /2\.16\.840\.1\.113883\.3\.526\.3\.100[7-9]/
                 entry.negation_reason.present? && codes.first['values'].include?(entry.negation_reason['code'])
+              elsif data_criteria_oid == '2.16.840.1.113883.3.560.1.71'
+                if (entry.transferFrom)
+                  entry.transferFrom.codes[entry.transferFrom.code_system] = [entry.transferFrom.code]
+                  tfc = entry.transferFrom.codes_in_code_set(codes).values.first
+                  tfc && !tfc.empty?
+                end
+              elsif data_criteria_oid == '2.16.840.1.113883.3.560.1.72'
+                if (entry.transferTo)
+                  entry.transferTo.codes[entry.transferTo.code_system] = [entry.transferTo.code]
+                  ttc = entry.transferTo.codes_in_code_set(codes).values.first
+                  ttc && !ttc.empty?
+                end
               else
-                # The !! hack makes sure that negation_ind is a boolean
-                entry.is_in_code_set?(codes) && !!entry.negation_ind == data_criteria.negation
+                # The !! hack makes sure that negation_ind is a boolean. negations use the same hqmf templates in r2
+                entry.is_in_code_set?(codes) && (is_hqmfr2 || !!entry.negation_ind == data_criteria.negation)
               end
             end
           end
           if filtered_entries.empty?
             HealthDataStandards.logger.debug("No entries for #{data_criteria.title}")
           end
-
           filtered_entries
         end
 
@@ -137,7 +180,7 @@ module HealthDataStandards
 
         def handle_patient_expired(patient)
           if patient.expired
-            [OpenStruct.new(start_date: patient.deathdate, id: UUID.generate)]
+            [OpenStruct.new(start_time: patient.deathdate, id: UUID.generate)]
           else
             []
           end