health-data-standards 1.0.1 → 2.0.0

data/Gemfile

@@ -4,14 +4,14 @@ gemspec :development_group => :test
 
 group :development do
   gem 'rake'
-  gem 'pry'
-  gem 'pry-nav'
+  gem 'pry', '~> 0.9.10'
+  gem 'pry-nav', '~> 0.2.2'
 
 end
 
 group :test do
-  gem 'factory_girl'
-  gem "tailor"
-  gem "cane"
+  gem 'factory_girl', '~> 4.1.0'
+  gem "tailor", '~> 1.1.2'
+  gem "cane", '~> 2.3.0'
   gem 'simplecov', :require => false
 end

data/lib/health-data-standards.rb

@@ -12,11 +12,13 @@ require_relative 'health-data-standards/ext/string'
 
 require_relative 'health-data-standards/util/hl7_helper'
 require_relative 'health-data-standards/util/code_system_helper'
+require_relative 'health-data-standards/util/qrda_template_helper'
 
 require_relative 'health-data-standards/export/template_helper'
 require_relative 'health-data-standards/export/view_helper'
 require_relative 'health-data-standards/export/rendering_context'
 require_relative 'health-data-standards/export/c32'
+require_relative 'health-data-standards/export/ccda'
 require_relative 'health-data-standards/export/ccr'
 require_relative 'health-data-standards/export/csv'
 require_relative 'health-data-standards/export/html'
@@ -29,6 +31,10 @@ require_relative 'health-data-standards/export/green_c32/export_generator'
 require_relative 'health-data-standards/import/provider_import_utils'
 require_relative 'health-data-standards/import/hdata/metadata_importer'
 
+require_relative 'health-data-standards/models/thing_with_codes'
+require_relative 'health-data-standards/models/result_value'
+require_relative 'health-data-standards/models/coded_result_value'
+require_relative 'health-data-standards/models/physical_quantity_result_value'
 require_relative 'health-data-standards/models/entry'
 require_relative 'health-data-standards/models/allergy'
 require_relative 'health-data-standards/models/encounter'
@@ -39,6 +45,7 @@ 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/functional_status'
 require_relative 'health-data-standards/models/medical_equipment'  
 require_relative 'health-data-standards/models/record'
 require_relative 'health-data-standards/models/personable'
@@ -52,6 +59,7 @@ require_relative 'health-data-standards/models/person'
 require_relative 'health-data-standards/models/organization'
 require_relative 'health-data-standards/models/address'
 require_relative 'health-data-standards/models/telecom'
+require_relative 'health-data-standards/models/facility'
 require_relative 'health-data-standards/models/metadata/base'
 require_relative 'health-data-standards/models/metadata/author'
 require_relative 'health-data-standards/models/metadata/change_info'

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

@@ -0,0 +1,15 @@
+module HealthDataStandards
+  module Export
+    module CCDA
+      include TemplateHelper
+      
+      def export(patient)
+        self.template_format = "ccda"
+        self.template_subdir = "ccda"
+        render(:template => 'show', :locals => {:patient => patient})
+      end
+
+      extend self
+    end
+  end
+end

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

@@ -149,29 +149,33 @@ module HealthDataStandards
       end
       
 
-     def to_result(xml, res, ccr_id )
-       xml.Result do
-         xml.CCRDataObjectID(ccr_id)
-         to_ccr_date(xml, res.as_point_in_time, "Start date")       
-         xml.Source
-         xml.Test do
-           xml.CCRDataObjectID("#{ccr_id}TestResult")
-           xml.Description do
+      def to_result(xml, res, ccr_id )
+        xml.Result do
+          xml.CCRDataObjectID(ccr_id)
+          to_ccr_date(xml, res.as_point_in_time, "Start date")       
+          xml.Source
+          xml.Test do
+            xml.CCRDataObjectID("#{ccr_id}TestResult")
+            xml.Description do
               xml.Text(res.description)
               code_section(xml, res.codes)
-          end
+            end
 
-           xml.Source
-           xml.TestResult do
-             xml.Value(res.value["scalar"])
-             xml.Units do
-               xml.Unit(res.value["units"])
-             end          
-           end
-        end
-       end
-       
-     end
+            xml.Source
+            xml.TestResult do
+              rv = res.values.first
+              if rv.present? && rv.respond_to?(:scalar)
+                xml.Value(rv.scalar)
+                xml.Unit do
+                  xml.Unit(rv.units)
+                end
+              else
+                
+              end
+            end
+          end
+        end     
+      end
      
       # Builds the XML snippet for the medications section inside the CCR standard
       #

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

@@ -3,19 +3,15 @@ module HealthDataStandards
     module HTML
       include TemplateHelper
 
-       def export(patient)
+      def export(patient)
         self.template_format = "html"
+        self.template_subdir = "html"
         render(:template => 'show', :locals => {:patient => patient})
       end
 
       extend self
-
-
-     
-
-
-
-
+      
+      
     end
   end
 end

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

@@ -2,9 +2,14 @@ module HealthDataStandards
   module Export
     module TemplateHelper
       attr_accessor :template_format
+      attr_accessor :template_subdir
 
       def template_root
-        File.join(File.dirname(__FILE__), '..', '..', '..', 'templates')
+        if @template_subdir
+          return File.join(File.dirname(__FILE__), '..', '..', '..', 'templates', @template_subdir)
+        else
+          return File.join(File.dirname(__FILE__), '..', '..', '..', 'templates')
+        end
       end
 
       def template(template_name)
@@ -27,6 +32,7 @@ module HealthDataStandards
         locals ||= {}
         rendering_context = RenderingContext.new(locals)
         rendering_context.template_format = self.template_format
+        rendering_context.template_subdir = self.template_subdir
         eruby = Erubis::EscapedEruby.new(erb)
         eruby.result(rendering_context.my_binding)
       end

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

@@ -27,11 +27,11 @@ module HealthDataStandards
       
       def gc32_effective_time(entry)
         if entry.time
-          "<effectiveTime value=\"#{Time.at(entry.time)}\" />"
+          "<effectiveTime value=\"#{Time.at(entry.time).to_formatted_s(:number)}\" />"
         elsif entry.start_time || entry.end_time
           time = "<effectiveTime>"
-          time += "<start value=\"#{Time.at(entry.start_time)}\" />"  if entry.start_time
-          time += "<end value=\"#{Time.at(entry.end_time)}\" />" if entry.end_time
+          time += "<start value=\"#{Time.at(entry.start_time).to_formatted_s(:number)}\" />"  if entry.start_time
+          time += "<end value=\"#{Time.at(entry.end_time).to_formatted_s(:number)}\" />" if entry.end_time
           time += "</effectiveTime>"
         else
           "<effectiveTime />"
@@ -61,7 +61,11 @@ module HealthDataStandards
       
       def quantity_display(value, tag_name="value")
         return unless value
-        "<#{tag_name} value=\"#{value['value']}\" units=\"#{value['unit']}\" />"
+        if value.respond_to?(:scalar)
+          "<#{tag_name} value=\"#{value.scalar}\" units=\"#{value.units}\" />"
+        else
+          "<#{tag_name} value=\"#{value['value']}\" units=\"#{value['unit']}\" />"
+        end
       end
 
       def time_if_not_nil(*args)
@@ -79,6 +83,22 @@ module HealthDataStandards
       def is_bool?(str)
         return ["true","false"].include? (str || "").downcase
       end
+      
+      def decode_qrda_section(section, oid)
+        if oid
+          HealthDataStandards::Util::QRDATemplateHelper.definition_for_template_id(oid)['definition'].pluralize.to_sym
+        else
+          section
+        end
+      end
+      def decode_qrda_status(status, oid)
+        if oid
+          HealthDataStandards::Util::QRDATemplateHelper.definition_for_template_id(oid)['status']
+        else
+          status
+        end
+      end
+      
     end
   end
 end

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

@@ -29,8 +29,9 @@ module HealthDataStandards
             extract_codes(entry_element, allergy)
             extract_dates(entry_element, allergy)
             extract_description(entry_element, allergy, id_map)
+            extract_negation(entry_element, allergy)
             
-            allergy.status = extract_status(entry_element, allergy)
+            extract_status(entry_element, allergy)
             allergy.type = extract_code(entry_element, @type_xpath)
             allergy.reaction = extract_code(entry_element, @reaction_xpath)
             allergy.severity = extract_code(entry_element, @severity_xpath)

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

@@ -22,7 +22,8 @@ module HealthDataStandards
                        end
             
             entry = importer.create_entry(goal_element, id_map={})
-            
+            extract_negation(goal_element, entry)
+
             
             
             if @check_for_usable

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

@@ -7,10 +7,11 @@ module HealthDataStandards
           @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.103']/cda:entry/cda:act/cda:entryRelationship/cda:observation"
           @code_xpath = "./cda:value"
           @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.50']/cda:value"
-          @priority_xpath = "./cda:priorityCode"
+          @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"
           @cod_xpath = "./cda:entryRelationship[@typeCode='CAUS']/cda:observation/cda:code[@code='419620001']"
+          @priority_xpath = "../cda:sequenceNumber"
         end
         
         def create_entries(doc, id_map = {})
@@ -24,10 +25,12 @@ module HealthDataStandards
             extract_codes(entry_element, condition)
             extract_dates(entry_element, condition)
             extract_status(entry_element, condition)
-            extract_priority(entry_element, condition)
+            extract_ordinality(entry_element, condition)
             extract_description(entry_element, condition, id_map)
             extract_cause_of_death(entry_element, condition) if @cod_xpath
             extract_type(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|
@@ -43,10 +46,28 @@ module HealthDataStandards
 
         private
 
+        def extract_ordinality(parent_element, entry)
+          ordinality_element = parent_element.at_xpath(@ordinality_xpath)
+          if ordinality_element
+            entry.ordinality_code = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
+            case ordinality_element['code']
+            when '8319008'
+              entry.ordinality = :principal
+            end
+          end
+        end
+
         def extract_cause_of_death(entry_element, condition)
           cod = entry_element.at_xpath(@cod_xpath)
           condition.cause_of_death = cod.present?
         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
 
         def extract_type(entry_element, condition)
           code_element = entry_element.at_xpath('./cda:code')

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

@@ -7,7 +7,6 @@ module HealthDataStandards
         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"
-          @status_xpath = "./cda:statusCode"
           @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
           @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:act"
           @check_for_usable = true               # Pilot tools will set this to false
@@ -42,6 +41,7 @@ module HealthDataStandards
           extract_performer(entry_element, encounter)
           extract_facility(entry_element, encounter)
           extract_reason(entry_element, encounter, id_map)
+          extract_negation(entry_element, encounter)
           extract_admission(entry_element, encounter)
           encounter
         end
@@ -56,10 +56,11 @@ module HealthDataStandards
         def extract_facility(parent_element, encounter)
           participant_element = parent_element.at_xpath("./cda:participant[@typeCode='LOC']/cda:participantRole[@classCode='SDLOC']")
           if (participant_element)
-            org = Organization.new(name: participant_element.at_xpath("./cda:playingEntity/cda:name").try(:text))
-            org.addresses = participant_element.xpath("./cda:addr").try(:map) {|ae| import_address(ae)}
-            org.telecoms = participant_element.xpath("./cda:telecom").try(:map) {|te| import_telecom(te)}
-            encounter.facility = org
+            facility = Facility.new(name: participant_element.at_xpath("./cda:playingEntity/cda:name").try(:text))
+            facility.addresses = participant_element.xpath("./cda:addr").try(:map) {|ae| import_address(ae)}
+            facility.telecoms = participant_element.xpath("./cda:telecom").try(:map) {|te| import_telecom(te)}
+            facility.code = extract_code(participant_element, './cda:code')
+            encounter.facility = facility
           end
         end
     

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

@@ -7,7 +7,6 @@ module HealthDataStandards
           @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.117']/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]"
-          @refusal_reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code"
           @check_for_usable = true               # Pilot tools will set this to false
         end
 
@@ -25,7 +24,7 @@ module HealthDataStandards
             extract_codes(entry_element, immunization)
             extract_dates(entry_element, immunization)
             extract_description(entry_element, immunization, id_map)
-            extract_refusal(entry_element, immunization)
+            extract_negation(entry_element, immunization)
             extract_performer(entry_element, immunization)
             if @check_for_usable
               immunization_list << immunization if immunization.usable?
@@ -37,19 +36,6 @@ module HealthDataStandards
         end
     
         private
-        def extract_refusal(parent_element, immunization)
-          negation_indicator = parent_element['negationInd']
-          unless negation_indicator.nil?
-            immunization.refusal_ind = negation_indicator.eql?('true')
-            if immunization.refusal_ind
-              refusal_reason_element = parent_element.at_xpath(@refusal_reason_xpath)
-              if refusal_reason_element
-                immunization.refusal_reason = {'code' => refusal_reason_element['code'],
-                                               'codeSystem' => 'HL7 No Immunization Reason'}
-              end
-            end
-          end
-        end
     
         def extract_performer(parent_element, immunization)
           performer_element = parent_element.at_xpath("./cda:performer")

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

@@ -50,6 +50,7 @@ module HealthDataStandards
           extract_order_information(entry_element, medication)
           
           extract_fulfillment_history(entry_element, medication)
+          extract_negation(entry_element, medication)
           
           medication
         end

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

@@ -97,9 +97,22 @@ module HealthDataStandards
           c32_patient = Record.new
           get_demographics(c32_patient, doc)
           create_c32_hash(c32_patient, doc)
+          check_for_cause_of_death(c32_patient)
           
           c32_patient
         end
+        
+        # Checks the conditions to see if any of them have a cause of death set. If they do,
+        # it will set the expired field on the Record. This is done here rather than replacing
+        # the expried method on Record because other formats may actully tell you whether
+        # a patient is dead or not.
+        # @param [Record] c32_patient to check the conditions on and set the expired
+        #               property if applicable
+        def check_for_cause_of_death(c32_patient)
+          if c32_patient.conditions.any? {|condition| condition.cause_of_death }
+            c32_patient.expired = true
+          end
+        end
 
         # Create a simple representation of the patient from a HITSP C32
         # @param [Record] record Mongoid model to append the Entry objects to

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

@@ -41,6 +41,7 @@ module HealthDataStandards
           extract_description(entry_element, procedure, id_map)
           extract_performer(entry_element, procedure)
           extract_site(entry_element, procedure)
+          extract_negation(entry_element, procedure)
           procedure
         end
 

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

@@ -54,7 +54,7 @@ module HealthDataStandards
         end
         
         def find_or_create_provider(provider_hash)
-          provider = Provider.first(conditions: {npi: provider_hash[:npi]}) if provider_hash[:npi]
+          provider = Provider.where(npi: provider_hash[:npi]).first if provider_hash[:npi]
           provider ||= Provider.create(provider_hash)
         end
       

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

@@ -36,6 +36,7 @@ module HealthDataStandards
           extract_value(entry_element, result)
           extract_description(entry_element, result, id_map)
           extract_interpretation(entry_element, result)
+          extract_negation(entry_element, result)
           result
         end
     

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

@@ -67,9 +67,6 @@ module HealthDataStandards
           if @status_xpath
             extract_status(entry_element, entry)
           end
-          if @priority_xpath
-              extract_priority(entry_element, entry)
-            end
           if @description_xpath
             extract_description(entry_element, entry, id_map)
           end
@@ -81,28 +78,10 @@ module HealthDataStandards
         def extract_status(parent_element, entry)
           status_element = parent_element.at_xpath(@status_xpath)
           if status_element
-            case status_element['code']
-            when '55561003'
-              entry.status = :active
-            when '73425007'
-              entry.status = :inactive
-            when '413322009'      
-              entry.status = :resolved
-            end
-          end
-        end
-
-        def extract_priority(parent_element, entry)
-          priority_element = parent_element.at_xpath(@priority_xpath)
-          if priority_element
-            case priority_element['code']
-            when '8319008'
-              entry.ordinality = :principal
-            end
+            entry.status_code = {CodeSystemHelper.code_system_for(status_element['codeSystem']) => [status_element['code']]}
           end
         end
 
-
         def extract_description(parent_element, entry, id_map)
           code_elements = parent_element.xpath(@description_xpath)
           code_elements.each do |code_element|
@@ -195,6 +174,22 @@ module HealthDataStandards
           tele
         end
 
+        def extract_negation(parent_element, entry)
+          negation_indicator = parent_element['negationInd']
+          unless negation_indicator.nil?
+            entry.negation_ind = negation_indicator.eql?('true')
+            if entry.negation_ind
+              negation_reason_element = parent_element.at_xpath("./cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code")
+              if negation_reason_element
+                code_system_oid = negation_reason_element['codeSystem']
+                code = negation_reason_element['code']
+                code_system = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system_oid)
+                entry.negation_reason = {'code' => code, 'codeSystem' => code_system}
+              end
+            end
+          end
+        end
+    
         def extract_code(parent_element, code_xpath, code_system=nil)
           code_element = parent_element.at_xpath(code_xpath)
           code_hash = nil