health-data-standards 2.2.1 → 3.0.3

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

@@ -0,0 +1,24 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class MedicalEquipmentImporter < SectionImporter
+        def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.128']/cda:entry/cda:supply"))
+          super(entry_finder)
+          @code_xpath = "./cda:participant/cda:participantRole/cda:playingDevice/cda:code"
+          @entry_class = MedicalEquipment
+        end
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          medical_equipment = super
+          extract_manufacturer(entry_element, medical_equipment)
+          medical_equipment
+        end
+
+        def extract_manufacturer(entry_element, entry)
+          manufacturer = entry_element.at_xpath("./cda:participant/cda:participantRole/cda:scopingEntity/cda:desc").try(:inner_text)
+          entry.manufacturer = manufacturer.strip if manufacturer
+        end
+      end
+    end
+  end
+end

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

@@ -1,6 +1,6 @@
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       
       # TODO: Coded Product Name, Free Text Product Name, Coded Brand Name and Free Text Brand name need to be pulled out separatelty
       #       This would mean overriding extract_codes
@@ -11,23 +11,19 @@ module HealthDataStandards
       #       dose indicator is not implemented.
       # TODO: Fill Status is not implemented. Couldn't figure out which entryRelationship it should be nested in
       class MedicationImporter < SectionImporter
-
-        def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.112']/cda:entry/cda:substanceAdministration"
+        def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.112']/cda:entry/cda:substanceAdministration"))
+          super(entry_finder)
           @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]"
           @type_of_med_xpath = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.8.1']/cda:code"
           @indication_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.28']/cda:code"
           @vehicle_xpath = "cda:participant/cda:participantRole[cda:code/@code='412307009' and cda:code/@codeSystem='2.16.840.1.113883.6.96']/cda:playingEntity/cda:code"
           @fill_number_xpath = "./cda:entryRelationship[@typeCode='COMP']/cda:sequenceNumber/@value"
-          @check_for_usable = true               # Pilot tools will set this to false
+          @entry_class = Medication
         end
-        
-        def create_entry(entry_element, id_map={})
-          medication = Medication.new
-          extract_codes(entry_element, medication)
-          extract_dates(entry_element, medication)
-          extract_description(entry_element, medication, id_map)
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          medication = super
           
           if medication.description.present?
             medication.free_text = medication.description
@@ -56,7 +52,7 @@ module HealthDataStandards
         end
 
         private
-    
+
         def extract_fulfillment_history(parent_element, medication)
           fhs = parent_element.xpath("./cda:entryRelationship/cda:supply[@moodCode='EVN']")
           if fhs
@@ -82,7 +78,10 @@ module HealthDataStandards
           if order_elements
             order_elements.each do |order_element|
               order_information = OrderInformation.new
-          
+              actor_element = order_element.at_xpath('./cda:author')
+              if actor_element
+                order_information.provider = ProviderImporter.instance.extract_provider(actor_element, "assignedAuthor")
+              end
               order_information.order_number = order_element.at_xpath('./cda:id').try(:[], 'root')
               order_information.fills = order_element.at_xpath('./cda:repeatNumber').try(:[], 'value').try(:to_i)
               order_information.quantity_ordered = extract_scalar(order_element, "./cda:quantity")
@@ -115,8 +114,7 @@ module HealthDataStandards
             medication.dose_restriction = dr
           end
         end
-
       end
     end
   end
-end
+end

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

@@ -0,0 +1,35 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class NarrativeReferenceHandler
+        def initialize
+          @id_map = {}
+        end
+
+        def build_id_map(doc)
+          path = "//*[@ID]"
+          ids = doc.xpath(path)
+          ids.each do |id|
+            tag = id['ID']
+            value = id.content
+            @id_map[tag] = value
+          end
+        end
+
+        # @param [String] tag      
+        # @return [String] text description of tag
+        def lookup_tag(tag)
+          value = @id_map[tag]
+          # Not sure why, but sometimes the reference is #<Reference> and the ID value is <Reference>, and 
+          # sometimes it is #<Reference>.  We look for both.
+          if !value and tag[0] == '#'  
+           tag = tag[1,tag.length]
+           value = @id_map[tag]
+          end
+
+          value
+        end
+      end
+    end
+  end
+end

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

@@ -1,6 +1,6 @@
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       class OrganizationImporter < SectionImporter
         include Singleton
         

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

@@ -0,0 +1,35 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class ProcedureImporter < 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:section[cda:templateId/@root!='2.16.840.1.113883.3.88.11.83.124']//cda:procedure"))
+          super(entry_finder)
+          @entry_class = Procedure
+        end
+        
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          procedure = super
+          extract_performer(entry_element, procedure)
+          extract_site(entry_element, procedure)
+          extract_negation(entry_element, procedure)
+          procedure
+        end
+
+        private
+
+        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/{c32 → cda}/provider_importer.rb

@@ -3,7 +3,7 @@ require "date"
 
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       class ProviderImporter < SectionImporter
         
         
@@ -28,9 +28,10 @@ module HealthDataStandards
 
         private
       
-        def extract_provider_data(performer, use_dates=true)
+        def extract_provider_data(performer, use_dates=true, entity_path="./cda:assignedEntity")
           provider = {}
-          entity = performer.xpath("./cda:assignedEntity")
+          entity = performer.xpath(entity_path)
+          
           name = entity.xpath("./cda:assignedPerson/cda:name")
           provider[:title]        = extract_data(name, "./cda:prefix")
           provider[:given_name]   = extract_data(name, "./cda:given[1]")
@@ -52,11 +53,6 @@ module HealthDataStandards
           provider[:npi] = npi if Provider.valid_npi?(npi)
           provider
         end
-        
-        def find_or_create_provider(provider_hash)
-          provider = Provider.where(npi: provider_hash[:npi]).first if provider_hash[:npi]
-          provider ||= Provider.create(provider_hash)
-        end
       
         def extract_date(subject,query)
           date = extract_data(subject,query)

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

@@ -0,0 +1,31 @@
+module HealthDataStandards
+  module Import
+    module CDA
+      class ResultImporter < SectionImporter
+        def initialize(entry_finder=EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15.1'] | //cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15']"))
+          super(entry_finder)
+          @entry_class = LabResult
+        end
+        
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          result = super
+          extract_value(entry_element, result)
+          extract_interpretation(entry_element, result)
+          extract_negation(entry_element, result)
+          result
+        end
+    
+        private
+        def extract_interpretation(parent_element, result)
+          interpretation_element = parent_element.at_xpath("./cda:interpretationCode")
+          if interpretation_element
+            code = interpretation_element['code']
+            code_system = CodeSystemHelper.code_system_for(interpretation_element['codeSystem'])
+            result.interpretation = {'code' => code, 'codeSystem' => code_system}
+          end
+        end
+    
+      end
+    end
+  end
+end

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

@@ -1,56 +1,33 @@
 module HealthDataStandards
   module Import
-    module C32
-      # Class that can be used to create an importer for a section of a HITSP C32 document. It usually
-      # operates by selecting all CDA entries in a section and then creates entries for them.
+    module CDA
       class SectionImporter
-        include HealthDataStandards::Import::C32::LocatableImportUtils
+        attr_accessor :check_for_usable, :status_xpath, :code_xpath
+
         include HealthDataStandards::Util
-        
-        attr_accessor :check_for_usable
-        # Creates a new SectionImporter
-        # @param [Hash] id_map A hash of all ID tags to values for the enclosing document.  Used to look up descriptions.
-        # @param [String] entry_xpath An XPath expression that can be used to find the desired entries
-        # @param [String] code_xpath XPath expression to find the code element as a child of the desired CDA entry.
-        #        Defaults to "./cda:code"
-        # @param [String] status_xpath XPath expression to find the status element as a child of the desired CDA
-        #        entry. Defaults to nil. If not provided, a status will not be checked for since it is not applicable
-        #        to all enrty types
-        def initialize(entry_xpath, code_xpath="./cda:code", status_xpath=nil,priority_xpath=nil, description_xpath="./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] ")
-          @entry_xpath = entry_xpath
-          @code_xpath = code_xpath
-          @status_xpath = status_xpath
-          @priority_xpath = priority_xpath
-          @description_xpath = description_xpath
-          @check_for_usable = true               # Pilot tools will set this to false
+        include LocatableImportUtils
+
+        def initialize(entry_finder)
+          @entry_finder = entry_finder
+          @code_xpath = "./cda:code"
+          @status_xpath = nil
+          @priority_xpath = nil
+          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
+          @check_for_usable = true
+          @entry_class = Entry
         end
 
-        # @param [String] tag
-        # @param [Hash] id_map A map of ids to all tagged text in the narrative portion of a document
-        # @return [String] text description of tag
-        def lookup_tag(tag, id_map)
-           value = id_map[tag]
-           # Not sure why, but sometimes the reference is #<Reference> and the ID value is <Reference>, and 
-           # sometimes it is #<Reference>.  We look for both.
-           if !value and tag[0] == '#'  
-             tag = tag[1,tag.length]
-             value = id_map[tag]
-           end
-
-           value
-         end
-
-        # Traverses that HITSP C32 document passed in using XPath and creates an Array of Entry
+        # Traverses an HL7 CDA document passed in 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 = {})
+        def create_entries(doc, nrh = NarrativeReferenceHandler.new)
           entry_list = []
-          entry_elements = doc.xpath(@entry_xpath)
+          entry_elements = @entry_finder.entries(doc)
           entry_elements.each do |entry_element|
-            entry = create_entry(entry_element, id_map)
+            entry = create_entry(entry_element, nrh)
             if @check_for_usable
               entry_list << entry if entry.usable?
             else
@@ -59,17 +36,18 @@ module HealthDataStandards
           end
           entry_list
         end
-        
-        def create_entry(entry_element, id_map={})
-          entry = Entry.new
+
+        def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+          entry = @entry_class.new
           extract_codes(entry_element, entry)
           extract_dates(entry_element, entry)
           extract_value(entry_element, entry)
+          entry.free_text = entry_element.at_xpath("./cda:text").try("text")
           if @status_xpath
             extract_status(entry_element, entry)
           end
           if @description_xpath
-            extract_description(entry_element, entry, id_map)
+            extract_description(entry_element, entry, nrh)
           end
           entry
         end
@@ -83,11 +61,11 @@ module HealthDataStandards
           end
         end
 
-        def extract_description(parent_element, entry, id_map)
+        def extract_description(parent_element, entry, nrh)
           code_elements = parent_element.xpath(@description_xpath)
           code_elements.each do |code_element|
             tag = code_element['value']
-            entry.description = lookup_tag(tag, id_map)
+            entry.description = nrh.lookup_tag(tag)
           end
         end
 
@@ -198,8 +176,8 @@ module HealthDataStandards
             nil
           end
         end
+
       end
     end
   end
-end
-
+end

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

@@ -1,10 +1,9 @@
 module HealthDataStandards
   module Import
-    module C32
+    module CDA
       class VitalSignImporter < ResultImporter
         def initialize
-          super
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.14']"
+          super(EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.14']"))
         end
       end
     end

data/lib/health-data-standards/import/green_c32/section_importer.rb

@@ -89,7 +89,7 @@ module HealthDataStandards
           
           return {} unless node_value
           
-          {"scalar" => node_value, "unit" => node_units}
+          {"scalar" => node_value, "units" => node_units}
         end
         
         def extract_value(element, entry)
@@ -111,14 +111,15 @@ module HealthDataStandards
         
         def extract_organization(organization_element)
           org_id = extract_node_text(organization_element.xpath("./gc32:id"))
-          organization = org_id ? Organization.find_or_create_by(id: org_id) : Organization.new
-          if organization.new_record?
-          else
+          organization = org_id ? Organization.find(org_id) : Organization.new
+          organization ||= Organization.new
+          # if organization.new_record?
+          # else
             organization.name = extract_node_text(organization_element.xpath("./gc32:name"))
             organization.addresses = organization_element.xpath("./gc32:address").map { |addr| extract_address(addr)  }
             organization.telecoms = organization_element.xpath("./gc32:telecom").map { |tele| extract_telecom(tele) }
-            organization.save!
-          end
+            # organization.save!
+          # end
           
           return organization
         end
@@ -142,6 +143,7 @@ module HealthDataStandards
         def extract_address(address_element)
           return unless address_element
           address = Address.new
+          address.use = address_element['use']
           address.street = address_element.xpath("./gc32:street").map { |st| extract_node_text(st)  }
           address.city = extract_node_text(address_element.xpath("./gc32:city"))
           address.state = extract_node_text(address_element.xpath("./gc32:state"))

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

@@ -1,7 +1,7 @@
 module ProviderImportUtils
   
-  def extract_provider(performer)
-    provider_data = extract_provider_data(performer, false)
+  def extract_provider(performer, element_name="assignedEntity")
+    provider_data = extract_provider_data(performer, false, "./cda:#{element_name}")
     find_or_create_provider(provider_data)
   end
   

data/lib/health-data-standards/models/address.rb

@@ -1,7 +1,7 @@
 class Address
   include Mongoid::Document
   
-  field :street, type: Array
+  field :street, type: Array, default: []
   field :city, type: String
   field :state, type: String
   field :zip, type: String

data/lib/health-data-standards/models/condition.rb

@@ -1,10 +1,11 @@
 class Condition < Entry
-  field :type,                type: String
-  field :causeOfDeath,        type: Boolean
-  field :priority,            type: Integer
-  field :name,                type: String
-  field :ordinality,          type: Hash
-  field :severity,            type: Hash # Currently unsupported by any importers
+  field :type,          type: String
+  field :causeOfDeath,  type: Boolean
+  field :time_of_death, type: Integer
+  field :priority,      type: Integer
+  field :name,          type: String
+  field :ordinality,    type: Hash
+  field :severity,      type: Hash # Currently unsupported by any importers
 
   embeds_many :treating_provider,  class_name: "Provider"