health-data-standards 2.2.1 → 3.0.3

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

@@ -0,0 +1,13 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class ProcedureIntoleranceImporter < CDA::SectionImporter
+
+        def initialize
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.62']/cda:entryRelationship/cda:procedure[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.64']"))
+          @entry_class = Allergy
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,38 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class ProcedureOrderImporter < CDA::SectionImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.63']"))
+          super(entry_finder)
+          @entry_class = Procedure
+        end
+        
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          procedure = super
+          procedure.status_code = {'HL7 ActStatus' => ['ordered']}
+          extract_performer(entry_element, procedure)
+          extract_site(entry_element, procedure)
+          extract_negation(entry_element, procedure)
+          procedure
+        end
+
+        private
+
+        def extract_dates(parent_element, entry, element_name="author")
+          if parent_element.at_xpath("cda:#{element_name}/cda:time/@value")
+            entry.start_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
+          end
+        end
+
+        def extract_performer(parent_element, procedure)
+          performer_element = parent_element.at_xpath("./cda:performer")
+          procedure.performer = import_actor(performer_element) if performer_element
+        end
+
+        def extract_site(parent_element, procedure)
+          procedure.site = extract_code(parent_element, "./cda:targetSiteCode")
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,19 @@
+module HealthDataStandards
+  module Import
+    module Cat1
+      class TobaccoUseImporter < CDA::SectionImporter
+        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.85']"))
+          super(entry_finder)
+          @entry_class = Entry
+        end
+        
+        def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
+          history = super
+          codehash = extract_code(entry_element, "./cda:value")
+          history.add_code(codehash['code'], CodeSystemHelper.code_system_for(codehash['codeSystemOid']))
+          history
+        end
+      end
+    end
+  end
+end

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

@@ -1,19 +1,13 @@
 module HealthDataStandards
   module Import
     module CCDA
-      class AllergyImporter < C32::AllergyImporter
-        
-        
+      class AllergyImporter < CDA::AllergyImporter        
         def initialize
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.7']"
-          @code_xpath = "./cda:participant/cda:participantRole/cda:playingEntity/cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
-          @type_xpath = "./cda:code"
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.7']"))
           @reaction_xpath = "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.9']/cda:value"
           @severity_xpath = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.8']/cda:value"
           @status_xpath   = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.28']/cda:value"
         end
-        
       end
     end
   end

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class CareGoalImporter < C32::CareGoalImporter
 
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.10']/cda:entry/cda:*"
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.10']/cda:entry/cda:*"))
         end
         
       end

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

@@ -4,10 +4,9 @@ module HealthDataStandards
       class ConditionImporter < C32::ConditionImporter
         
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.5' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.5.1']/cda:entry/cda:act/cda:entryRelationship/cda:observation"
+          super
+          @entry_finder = CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.5' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.5.1']/cda:entry/cda:act/cda:entryRelationship/cda:observation")
           @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.6']/cda:value"
-          @description_xpath = "./cda:text/cda:reference[@value]"
-          @code_xpath = "./cda:value"
           
           #optional
           #health status

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

@@ -2,13 +2,10 @@ module HealthDataStandards
   module Import
     module CCDA
       # TODO Extract Discharge Disposition
-      class EncounterImporter < C32::EncounterImporter
+      class EncounterImporter < CDA::EncounterImporter
     
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.22' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.22.1']/cda:entry/cda:encounter"
-          @code_xpath = "./cda:code"
-          @status_xpath = "./cda:statusCode"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.22' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.22.1']/cda:entry/cda:encounter"))
           @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation"
         end
         

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

@@ -4,9 +4,7 @@ module HealthDataStandards
       class ImmunizationImporter < C32::ImmunizationImporter
 
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.2' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.2.1']/cda:entry/cda:substanceAdministration"
-          @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
-          @description_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code/cda:originalText/cda:reference[@value]"
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.2' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.2.1']/cda:entry/cda:substanceAdministration"))
           @refusal_reason_xpath = "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.9']/cda:value"
         end
         

data/lib/health-data-standards/import/ccda/insurance_provider_importer.rb

@@ -4,7 +4,7 @@ module HealthDataStandards
       class InsuranceProviderImporter < C32::InsuranceProviderImporter
         
         def initialize
-          @entry_xpath = "//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.61']"
+          super(CDA::EntryFinder.new("//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.61']"))
         end
         
       end

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

@@ -1,12 +1,10 @@
 module HealthDataStandards
   module Import
     module CCDA
-      class MedicalEquipmentImporter < C32::MedicalEquipmentImporter
+      class MedicalEquipmentImporter < CDA::MedicalEquipmentImporter
         
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.23']/cda:entry/cda:supply"
-          @code_xpath = "./cda:participant/cda:participantRole/cda:playingDevice/cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.23']/cda:entry/cda:supply"))
         end
   
       end

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

@@ -2,12 +2,10 @@ module HealthDataStandards
   module Import
     module CCDA
       
-      class MedicationImporter < C32::MedicationImporter
+      class MedicationImporter < CDA::MedicationImporter
 
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.1' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.1.1']/cda:entry/cda:substanceAdministration"
-          @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
-          @description_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code/cda:originalText/cda:reference[@value]"
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.1' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.1.1']/cda:entry/cda:substanceAdministration"))
           @indication_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.19']/cda:code"
           @vehicle_xpath = "./cda:participant/cda:participantRole[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.24']/cda:playingEntity/cda:code"
           @fill_number_xpath = './cda:repeatNumber'

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

@@ -11,7 +11,7 @@ module HealthDataStandards
           @section_importers[:vital_signs] = VitalSignImporter.new
           @section_importers[:medications] = MedicationImporter.new
           @section_importers[:conditions] = ConditionImporter.new
-          @section_importers[:social_history] = C32::SectionImporter.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.38' or cda:templateId/@root='2.16.840.1.113883.10.20.15.3.8']")
+          @section_importers[:social_history] = CDA::SectionImporter.new(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.38' or cda:templateId/@root='2.16.840.1.113883.10.20.15.3.8']"))
           @section_importers[:care_goals] = CareGoalImporter.new
           @section_importers[:medical_equipment] = MedicalEquipmentImporter.new
           @section_importers[:allergies] = AllergyImporter.new

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

@@ -1,14 +1,10 @@
 module HealthDataStandards
   module Import
     module CCDA
-      class ProcedureImporter < C32::ProcedureImporter
+      class ProcedureImporter < CDA::ProcedureImporter
 
         def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.7' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.7.1']/cda:entry/cda:*"
-          @code_xpath = "./cda:code"
-          @status_xpath = "./cda:statusCode"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
-          @check_for_usable = true               # Pilot tools will set this to false
+          super(CDA::EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.10.20.22.2.7' or cda:templateId/@root='2.16.840.1.113883.10.20.22.2.7.1']/cda:entry/cda:*"))
         end
 
       end

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

@@ -1,12 +1,9 @@
 module HealthDataStandards
   module Import
     module CCDA
-      class ResultImporter < C32::ResultImporter
+      class ResultImporter < CDA::ResultImporter
         def initialize
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.2']"
-          @code_xpath = "./cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
-          @check_for_usable = true  
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.2']"))
         end
       end
     end

data/lib/health-data-standards/import/ccda/vital_sign_importer.rb

@@ -1,10 +1,9 @@
 module HealthDataStandards
   module Import
     module CCDA
-      class VitalSignImporter < C32::VitalSignImporter
+      class VitalSignImporter < CDA::ResultImporter
         def initialize
-          super
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.27']"
+          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.27']"))
         end
       end
     end

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

@@ -0,0 +1,32 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class AllergyImporter < SectionImporter
+    
+        def initialize(entry_finder=EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.18']"))
+          @entry_finder = entry_finder
+          @code_xpath = "./cda:participant/cda:participantRole/cda:playingEntity/cda:code"
+          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
+          @type_xpath = "./cda:code"
+          @free_text_xpath= "./cda:participant/cda:participantRole/cda:playingEntity/cda:name"
+          @reaction_xpath = "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.54']/cda:value"
+          @severity_xpath = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.55']/cda:value"
+          @status_xpath   = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.39']/cda:value"
+          @entry_class = Allergy
+        end
+    
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          allergy = super
+          allergy.free_text = entry_element.at_xpath(@free_text_xpath).try(:text)
+          extract_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)
+
+          allergy
+        end
+        
+      end
+    end
+  end
+end

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

@@ -0,0 +1,51 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class ConditionImporter < SectionImporter
+        
+        def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.103']/cda:entry/cda:act/cda:entryRelationship/cda:observation"))
+          @entry_finder = entry_finder
+          @code_xpath = "./cda:value"
+          @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.50']/cda:value"
+          @ordinality_xpath = "./cda:priorityCode"
+          @description_xpath = "./cda:text/cda:reference[@value]"
+          @provider_xpath = "./cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:performer"
+          @priority_xpath = "../cda:sequenceNumber"
+          @entry_class = Condition
+        end
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          condition = super
+
+          extract_ordinality(entry_element, condition)
+          extract_negation(entry_element, condition)
+          extract_priority(entry_element, condition)
+
+          if @provider_xpath
+            entry_element.xpath(@provider_xpath).each do |provider_element|
+              condition.treating_provider << import_actor(provider_element)
+            end
+          end
+
+          condition
+        end
+
+        private
+
+        def extract_ordinality(parent_element, entry)
+          ordinality_element = parent_element.at_xpath(@ordinality_xpath)
+          if ordinality_element
+            entry.ordinality = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
+          end
+        end
+
+        def extract_priority(entry_element, condition)
+          priority_element = entry_element.at_xpath(@priority_xpath)
+          if priority_element
+            condition.priority = priority_element['value'].to_i
+          end
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/{c32 → cda}/encounter_importer.rb

@@ -1,46 +1,20 @@
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       # TODO Extract Discharge Disposition
       class EncounterImporter < SectionImporter
     
-        def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.127']/cda:entry/cda:encounter"
-          @code_xpath = "./cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
+        def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.127']/cda:entry/cda:encounter"))
+          super(entry_finder)
           @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:act"
-          @check_for_usable = true               # Pilot tools will set this to false
-          @id_map = {}
-        end
-    
-        # Traverses that HITSP C32 document passed in using XPath and creates an Array of Entry
-        # 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
-        # @return [Array] will be a list of Entry objects
-        def create_entries(doc,id_map = {})
-          encounter_list = []
-          entry_elements = doc.xpath(@entry_xpath)
-          entry_elements.each do |entry_element|
-            encounter = create_entry(entry_element, id_map={})
-            if @check_for_usable
-              encounter_list << encounter if encounter.usable?
-            else
-              encounter_list << encounter
-            end
-          end
-          encounter_list
+          @entry_class = Encounter
         end
         
-        def create_entry(entry_element, id_map={})
-          encounter = Encounter.new
-          extract_codes(entry_element, encounter)
-          extract_dates(entry_element, encounter)
-          extract_description(entry_element, encounter, id_map)
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          encounter = super
           extract_performer(entry_element, encounter)
           extract_facility(entry_element, encounter)
-          extract_reason(entry_element, encounter, id_map)
+          extract_reason(entry_element, encounter, nrh)
           extract_negation(entry_element, encounter)
           extract_admission(entry_element, encounter)
           encounter
@@ -65,12 +39,12 @@ module HealthDataStandards
           end
         end
     
-        def extract_reason(parent_element, encounter, id_map)
+        def extract_reason(parent_element, encounter, nrh)
           reason_element = parent_element.at_xpath(@reason_xpath)
           if reason_element
             reason = Entry.new
             extract_codes(reason_element, reason)
-            extract_description(reason_element, reason, id_map)
+            extract_description(reason_element, reason, nrh)
             extract_status(reason_element, reason)
             extract_dates(reason_element, reason)
             encounter.reason = reason

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

@@ -0,0 +1,22 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class EntryFinder
+        def initialize(entry_xpath)
+          @entry_xpath = entry_xpath
+        end
+
+        def entries(doc)
+          entry_elements = doc.xpath(@entry_xpath)
+          if block_given?
+            entry_elements.each do |entry_element|
+              yield entry_element
+            end
+          else
+            entry_elements
+          end
+        end
+      end
+    end
+  end
+end

data/lib/health-data-standards/import/{c32 → cda}/locatable_import_utils.rb

@@ -1,6 +1,6 @@
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       # Helpers for importing C32 addresses and telecoms
       module LocatableImportUtils
         def import_address(address_element)
@@ -23,5 +23,4 @@ module HealthDataStandards
       end
     end
   end
-end
-    
+end