health-data-standards 0.3.0 → 0.5.0

data/Gemfile

@@ -2,5 +2,8 @@ source "http://rubygems.org"
 
 gemspec :development_group => :test
 
-gem 'rake'
-gem 'pry'
+group :development do
+  gem 'rake'
+  gem 'pry'
+  gem 'cover_me'
+end

data/Rakefile

@@ -1,7 +1,12 @@
 require 'rake/testtask'
 
-Rake::TestTask.new do |t|
+Rake::TestTask.new(:test_unit) do |t|
   t.libs << "test"
   t.test_files = FileList['test/**/*_test.rb']
   t.verbose = true
+end
+
+task :test => [:test_unit] do
+  require 'cover_me'
+  CoverMe.complete!
 end

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.5.0

data/lib/health-data-standards.rb

@@ -2,9 +2,16 @@ require 'erubis'
 require 'active_support'
 require 'mongoid'
 require 'uuid'
-require 'quality-measure-engine'
 require 'builder'
 require 'csv'
+require 'nokogiri'
+
+# Freedom patches
+require_relative 'health-data-standards/ext/symbol'
+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/export/template_helper'
 require_relative 'health-data-standards/export/view_helper'
@@ -14,4 +21,22 @@ require_relative 'health-data-standards/export/ccr'
 require_relative 'health-data-standards/export/csv'
 
 require_relative 'health-data-standards/models/entry'
-require_relative 'health-data-standards/models/record'
+require_relative 'health-data-standards/models/allergy'
+require_relative 'health-data-standards/models/encounter'
+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/record'
+
+require_relative 'health-data-standards/import/c32/section_importer'
+require_relative 'health-data-standards/import/c32/allergy_importer'
+require_relative 'health-data-standards/import/c32/encounter_importer'
+require_relative 'health-data-standards/import/c32/immunization_importer'
+require_relative 'health-data-standards/import/c32/medication_importer'
+require_relative 'health-data-standards/import/c32/procedure_importer'
+require_relative 'health-data-standards/import/c32/result_importer'
+require_relative 'health-data-standards/import/c32/vital_sign_importer'
+require_relative 'health-data-standards/import/c32/patient_importer'

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

@@ -1,23 +1,22 @@
 module HealthDataStandards
   module Export
     module ViewHelper
-      def code_display(entry, tag_name='code', extra_content=nil)
-        if entry.single_code_value?
-          code = entry.codes.first[1].first
-          code_system_oid = QME::Importer::CodeSystemHelper.oid_for_code_system(entry.codes.first[0])
-          "<#{tag_name} code=\"#{code}\" codeSystem=\"#{code_system_oid}\" #{extra_content}><originalText>#{ERB::Util.html_escape entry.description}</originalText></#{tag_name}>"
+      def code_display(entry, options={})
+        options['tag_name'] ||= 'code'
+        code_string = nil
+        preferred_code = entry.preferred_code(options['preferred_code_sets'])
+        if preferred_code
+          code_system_oid = HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(preferred_code['code_set'])
+          code_string = "<#{options['tag_name']} code=\"#{preferred_code['code']}\" codeSystem=\"#{code_system_oid}\" #{options['extra_content']}>"
         else
-          all_codes = []
-          entry.codes.each_pair {|key, values| values.each {|v| all_codes << {:set => key, :value => v}}}
-          first_code = all_codes.first
-          code_string = "<#{tag_name} code=\"#{first_code[:value]}\" codeSystem=\"#{QME::Importer::CodeSystemHelper.oid_for_code_system(first_code[:set])}\">\n"
-          code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>\n"
-          all_codes[1..-1].each do |cv|
-            code_string += "<translation code=\"#{cv[:value]}\" codeSystem=\"#{QME::Importer::CodeSystemHelper.oid_for_code_system(cv[:set])}\"/>\n"
-          end
-          code_string += "</#{tag_name}>"
-          code_string
+          code_string = "<#{options['tag_name']} nullFlavor=\"UNK\" #{options['extra_content']}>"
         end
+        code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>"
+        entry.translation_codes(options['preferred_code_sets']).each do |translation|
+          code_string += "<translation code=\"#{translation['code']}\" codeSystem=\"#{HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(translation['code_set'])}\"/>\n"
+        end
+        code_string += "</#{options['tag_name']}>"
+        code_string
       end
       
       def status_code_for(entry)
@@ -29,7 +28,7 @@ module HealthDataStandards
         when 'resolved'
           '413322009'
         end
-      end      
+      end
     end
   end
 end

data/lib/health-data-standards/ext/string.rb

@@ -0,0 +1,5 @@
+class String
+  def to_boolean
+    ['1', 'true', 't'].include?(self.downcase)
+  end
+end

data/lib/health-data-standards/ext/symbol.rb

@@ -0,0 +1,8 @@
+class Symbol
+  # Will take the current symbol and append an "=" to the end of it.
+  # So :bacon will become :bacon=. It is assumed that this would be
+  # passed to Object#send to set the value of something
+  def to_setter
+    (self.to_s + '=').to_sym
+  end
+end

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

@@ -0,0 +1,42 @@
+module HealthDataStandards
+  module Import
+    module C32
+      class AllergyImporter < SectionImporter
+    
+        def initialize
+          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.18']"
+          @code_xpath = "./cda:participant/cda:participantRole/cda:playingEntity/cda:code"
+          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
+          @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 = {})
+          @id_map = id_map
+          allergy_list = []
+          entry_elements = doc.xpath(@entry_xpath)
+          entry_elements.each do |entry_element|
+            allergy = Allergy.new
+            extract_codes(entry_element, allergy)
+            extract_dates(entry_element, allergy)
+            extract_description(entry_element, allergy, id_map)
+
+            allergy.reaction = extract_code(entry_element, 
+              "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.54']/cda:value")
+
+            allergy.severity = extract_code(entry_element, 
+              "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.54']/cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.55']/cda:value")
+
+            allergy_list << allergy
+          end
+          allergy_list
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,80 @@
+module HealthDataStandards
+  module Import
+    module C32
+      # 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"
+          @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
+          @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 = Encounter.new
+            extract_codes(entry_element, encounter)
+            extract_dates(entry_element, encounter)
+            extract_description(entry_element, encounter, id_map)
+            if @check_for_usable
+              encounter_list << encounter if encounter.usable?
+            else
+              encounter_list << encounter
+            end
+            extract_performer(entry_element, encounter)
+            extract_facility(entry_element, encounter)
+            extract_reason(entry_element, encounter, id_map)
+            extract_admission(entry_element, encounter)
+          end
+          encounter_list
+        end
+    
+        private
+    
+        def extract_performer(parent_element, encounter)
+          performer_element = parent_element.at_xpath("./cda:performer")
+          encounter.performer = import_actor(performer_element) if performer_element
+        end
+
+        def extract_facility(parent_element, encounter)
+          participant_element = parent_element.at_xpath("./cda:participant[@typeCode='LOC']/cda:participantRole[@classCode='SDLOC']")
+          encounter.facility = {}
+          if (participant_element)
+            encounter.facility['organizationName'] = participant_element.at_xpath("./cda:playingEntity/cda:name").try(:text)
+            addresses = participant_element.xpath("./cda:addr").try(:map) {|ae| import_address(ae)}
+            encounter.facility['addresses'] = addresses
+            telecoms = participant_element.xpath("./cda:telecom").try(:map) {|te| import_telecom(te)}
+            encounter.facility['telcoms'] = telecoms
+          end
+        end
+    
+        def extract_reason(parent_element, encounter, id_map)
+          reason_element = parent_element.at_xpath("./cda:entryRelationship[@typeCode='RSON']/cda:act")
+          if reason_element
+            reason = Entry.new
+            extract_codes(reason_element, reason)
+            extract_description(reason_element, reason, id_map)
+            extract_status(reason_element, reason)
+            extract_dates(reason_element, reason)
+            encounter.reason = reason
+          end
+        end
+    
+        def extract_admission(parent_element, encounter)
+          encounter.admit_type = extract_code(parent_element, "./cda:priorityCode")
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,61 @@
+module HealthDataStandards
+  module Import
+    module C32
+      class ImmunizationImporter < SectionImporter
+
+        def initialize
+          @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_resason_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
+
+        # 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 = {})
+          immunization_list = []
+          entry_elements = doc.xpath(@entry_xpath)
+          entry_elements.each do |entry_element|
+            immunization = Immunization.new
+            extract_codes(entry_element, immunization)
+            extract_dates(entry_element, immunization)
+            extract_description(entry_element, immunization, id_map)
+            extract_refusal(entry_element, immunization)
+            extract_performer(entry_element, immunization)
+            if @check_for_usable
+              immunization_list << immunization if immunization.usable?
+            else
+              immunization_list << immunization
+            end
+          end
+          immunization_list
+        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_resason_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")
+          immunization.performer = import_actor(performer_element) if performer_element
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,138 @@
+module HealthDataStandards
+  module Import
+    module C32
+      
+      # 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
+      # TODO: Patient Instructions needs to be implemented. Will likely be a reference to the narrative section
+      # TODO: Couldn't find an example medication reaction. Isn't clear to me how it should be implemented from the specs, so
+      #       reaction is not implemented.
+      # TODO: Couldn't find an example dose indicator. Isn't clear to me how it should be implemented from the specs, so
+      #       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"
+          @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]"
+
+          @check_for_usable = true               # Pilot tools will set this to false
+        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 = {})
+          medication_list = []
+          entry_elements = doc.xpath(@entry_xpath)
+          entry_elements.each do |entry_element|
+            medication = Medication.new
+            extract_codes(entry_element, medication)
+            extract_dates(entry_element, medication)
+            extract_description(entry_element, medication, id_map)
+
+            if medication.description.present?
+              medication.free_text_sig = medication.description
+            end
+
+            extract_administration_timing(entry_element, medication)
+
+            medication.route = extract_code(entry_element, "./cda:routeCode")
+            medication.dose = extract_scalar(entry_element, "./cda:doseQuantity")
+            medication.site = extract_code(entry_element, "./cda:approachSiteCode", 'SNOMED-CT')
+
+            extract_dose_restriction(entry_element, medication)
+        
+            medication.product_form = extract_code(entry_element, "./cda:administrationUnitCode", 'NCI Thesaurus')
+            medication.delivery_method = extract_code(entry_element, "./cda:code", 'SNOMED-CT')
+            medication.type_of_medication = extract_code(entry_element,
+                "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.8.1']/cda:code", 'SNOMED-CT')
+            medication.indication = extract_code(entry_element,
+                "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.28']/cda:code", 'SNOMED-CT')
+            medication.vehicle = extract_code(entry_element,
+                    "cda:participant/cda:participantRole[cda:code/@code='412307009' and cda:code/@codeSystem='2.16.840.1.113883.6.96']/cda:playingEntity/cda:code", 'SNOMED-CT')
+
+            extract_order_information(entry_element, medication)
+        
+            extract_fulfillment_history(entry_element, medication)
+
+            if @check_for_usable
+              medication_list << medication if medication.usable?
+            else
+              medication_list << medication_list
+            end
+          end
+          medication_list
+        end
+
+        private
+    
+        def extract_fulfillment_history(parent_element, medication)
+          fhs = parent_element.xpath("./cda:entryRelationship/cda:supply[@moodCode='EVN']")
+          if fhs
+            fhs.each do |fh_element|
+              fulfillment_history = FulfillmentHistory.new
+              fulfillment_history.prescription_number = fh_element.at_xpath('./cda:id').try(:[], 'root')
+              actor_element = fh_element.at_xpath('./cda:performer')
+              if actor_element
+                fulfillment_history.provider = import_actor(actor_element)
+                addr_element = actor_element.at_xpath("./cda:assignedEntity/cda:addr")
+                if addr_element
+                  fulfillment_history.dispensing_pharmacy_location = import_address(addr_element)
+                end
+              end
+              hl7_timestamp = fh_element.at_xpath('./cda:effectiveTime').try(:[], 'value')
+              fulfillment_history.dispense_date = HL7Helper.timestamp_to_integer(hl7_timestamp) if hl7_timestamp
+              fulfillment_history.quantity_dispensed = extract_scalar(fh_element, "./cda:quantity")
+              fulfillment_history.fill_number = fh_element.at_xpath("./cda:entryRelationship[@typeCode='COMP']/cda:sequenceNumber").try(:[], 'value').to_i
+              medication.fulfillmentHistory << fulfillment_history
+            end
+          end
+        end
+    
+        def extract_order_information(parent_element, medication)
+          order_elements = parent_element.xpath("./cda:entryRelationship[@typeCode='REFR']/cda:supply[@moodCode='INT']")
+          if order_elements
+            order_elements.each do |order_element|
+              order_information = OrderInformation.new
+          
+              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")
+          
+              medication.orderInformation << order_information
+            end
+          end
+        end
+
+        def extract_administration_timing(parent_element, medication)
+          administration_timing_element = parent_element.at_xpath("./cda:effectiveTime[2]")
+          if administration_timing_element
+            at = {}
+            if administration_timing_element['institutionSpecified']
+              at['institutionSpecified'] = administration_timing_element['institutionSpecified'].to_boolean
+            end
+            at['period'] = extract_scalar(administration_timing_element, "./cda:period")
+            if at.present?
+              medication.administration_timing = at
+            end
+          end
+        end
+
+        def extract_dose_restriction(parent_element, medication)
+          dre = parent_element.at_xpath("./cda:maxDoseQuantity")
+          if dre
+            dr = {}
+            dr['numerator'] = extract_scalar(dre, "./cda:numerator")
+            dr['denominator'] = extract_scalar(dre, "./cda:denominator")
+            medication.dose_restriction = dr
+          end
+        end
+      end
+    end
+  end
+end