health-data-standards 3.6.1 → 3.7.0

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

@@ -9,14 +9,19 @@ module HealthDataStandards
         @code_map = nil
       end
 
-      def export(patient, measures=[])
-        @code_map ||= self.build_code_map
+      # For environments where value sets are scoped, say by measure, they can be passed in
+      def export(patient, measures=[], scoped_value_sets = nil)
+        if scoped_value_sets
+          @code_map = self.build_code_map(scoped_value_sets) # Don't cache if value sets are passed in
+        else
+          @code_map ||= self.build_code_map
+        end
         @rendering_context.render(:template => 'show', :locals => {:patient => patient, :code_map => @code_map, :measures => measures})
       end
       
-      def build_code_map
+      def build_code_map(scoped_value_sets = nil)
         super_code_map = {}
-        val_set_array = HealthDataStandards::SVS::ValueSet.all.to_a
+        val_set_array = (scoped_value_sets || HealthDataStandards::SVS::ValueSet.all).to_a
         val_set_array.each do |valset| 
           valset.concepts.each do |concept|
             super_code_map[concept.code_system_name] ||= {}

data/lib/health-data-standards/export/qrda/entry_template_resolver.rb

@@ -5,7 +5,7 @@ module HealthDataStandards
         def hqmf_qrda_oid_map
           if @hqmf_qrda_oid_map.blank?
             template_id_file = File.expand_path('../hqmf-qrda-oids.json', __FILE__)
-            @hqmf_qrda_oid_map = JSON.parse(File.read(template_id_file))  
+            @hqmf_qrda_oid_map = JSON.parse(File.read(template_id_file))
           end
           @hqmf_qrda_oid_map
         end
@@ -14,36 +14,54 @@ module HealthDataStandards
           hqmf_qrda_oid_map.any? {|map_tuple| map_tuple['qrda_oid'] == oid}
         end
 
-        def qrda_oid_for_hqmf_oid(hqmf_oid, vs_oid = nil)
+        def qrda_oid_for_hqmf_oid(hqmf_oid, vs_oid = nil, qrda_version = nil)
 
           if (vs_oid && hqmf_oid == '2.16.840.1.113883.3.560.1.1001')
-            qrda_oid_for_hqmf_patient_characteristic(vs_oid)
+            qrda_oid_for_hqmf_patient_characteristic(vs_oid, qrda_version)
           else
             oid_tuple = hqmf_qrda_oid_map.find {|map_tuple| map_tuple['hqmf_oid'] == hqmf_oid }
             if oid_tuple.nil?
-              puts "no qrda oid for #{hqmf_oid}"
+              if hqmf_oid.nil?
+                raise "This may be due to a discrepency between QDM 4.2 and QRDA R3. "\
+                      "Expected cases for this error include: "\
+                      "Diagnosis, Family History, Symptom, Immunization data types, "\
+                      "and Encounter Performed attributes for Diagnosis and Principal Diagnosis."
+              else
+                raise "No QRDA template available for OID #{hqmf_oid}: #{__FILE__} line #{__LINE__}"
+              end
             end
-            oid_tuple['qrda_oid']
+            "#{oid_tuple['qrda_oid']}"
           end
 
         end
 
         # given a value set oid for a patient characteristic, return the qrda oid for the correct characteristic
-        def qrda_oid_for_hqmf_patient_characteristic(vs_oid)
+        def qrda_oid_for_hqmf_patient_characteristic(vs_oid, qrda_version = nil)
           # This is a special case. This HQMF OID maps to more than one QRDA OID.
           # So we need to try to figure out what template we should use based on the
           # content of the entry
-          if vs_oid == '2.16.840.1.113883.3.526.3.1279'
+          case vs_oid
+          when '2.16.840.1.113883.3.526.3.1279'
             # Patient Characteristic Observation Assertion template for
             # Patient Characteristic: ECOG Performance Status-Poor
             '2.16.840.1.113883.10.20.24.3.103'
-          elsif ["2.16.840.1.113883.3.117.1.7.1.402" , "2.16.840.1.113883.3.117.1.7.1.403" , "2.16.840.1.113883.3.117.1.7.1.287" ,"2.16.840.1.113883.3.117.1.7.1.307"].index(vs_oid)
+          when '2.16.840.1.113883.3.117.1.7.1.402', '2.16.840.1.113883.3.117.1.7.1.403',
+               '2.16.840.1.113883.3.117.1.7.1.287', '2.16.840.1.113883.3.117.1.7.1.307'
             # Patient Charasteristic Gestational Age
             '2.16.840.1.113883.10.20.24.3.101'
-          elsif vs_oid == "2.16.840.1.113883.3.526.3.1189" || vs_oid == "2.16.840.1.113883.3.526.3.1170" || vs_oid == '2.16.840.1.113883.3.600.2390'
+          when '2.16.840.1.113883.3.526.3.1189', '2.16.840.1.113883.3.526.3.1170', '2.16.840.1.113883.3.600.2390'
             # Patient Characteristic Tobacco User/Non-User
-            '2.16.840.1.113883.10.20.22.4.85'
+            case qrda_version
+            when 'r3_1', 'r3'
+              '2.16.840.1.113883.10.20.24.3.103'
+            else
+              '2.16.840.1.113883.10.20.22.4.85'
+            end
+          else
+            # return generic pc observation template for anything not specificly mapped to its own template
+            '2.16.840.1.113883.10.20.24.3.103'
           end
+
         end
 
         alias :partial_for :qrda_oid_for_hqmf_oid
@@ -52,4 +70,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

data/lib/health-data-standards/export/qrda/hqmf-qrda-oids.json

@@ -1,5 +1,5 @@
 [
-  {
+  { 
     "hqmf_name": "Care Goal",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.9",
     "qrda_name": "Care Goal",
@@ -101,6 +101,12 @@
     "qrda_name": "Diagnostic Study Order",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.17"
   },
+  {
+    "hqmf_name": "Diagnostic Study, Order not done",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.140",
+    "qrda_name": "Diagnostic Study Order",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.17"
+  },
   {
     "hqmf_name": "Diagnostic Study, Performed",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.3",
@@ -109,7 +115,7 @@
   },
   {
     "hqmf_name": "Diagnostic Study, Recommended",
-    "hqmf_oid": "2.16.840.1.113883.3.560.1.40",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.24",
     "qrda_name": "Diagnostic Study Recommended",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.19"
   },
@@ -179,6 +185,24 @@
     "qrda_name": "Functional Status Result",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.28"
   },
+  {
+    "hqmf_name": "Immunization Administered",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.112",
+    "qrda_name": "Immunization Administered",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.140"
+  },
+  {
+    "hqmf_name": "Immunization, Allergy",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.114",
+    "qrda_name": "Medication Allergy",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.44"
+  },
+  {
+    "hqmf_name": "Immunization, Intolerance",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.115",
+    "qrda_name": "Medication Intolerance",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.46"
+  },
   {
     "hqmf_name": "Incision Datetime (attribute)",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.1007",
@@ -203,6 +227,12 @@
     "qrda_name": "Intervention Order",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.31"
   },
+  {
+    "hqmf_name": "Intervention, Order not done",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.145",
+    "qrda_name": "Intervention Order",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.31"
+  },
   {
     "hqmf_name": "Intervention, Performed",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.46",
@@ -239,6 +269,12 @@
     "qrda_name": "Laboratory Test Order",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.37"
   },
+  {
+    "hqmf_name": "Laboratory Test, Order not done",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.150",
+    "qrda_name": "Laboratory Test Order",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.37"
+  },
   {
     "hqmf_name": "Laboratory Test, Performed",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.5",
@@ -330,19 +366,25 @@
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.55"
   },
   {
-    "hqmf_name": "Patient Charactersitic, ECOG Performance Status Poor",
+    "hqmf_name": "Patient Characteristic, ECOG Performance Status Poor",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.1001",
     "qrda_name": "Patient Characteristic Observation Assertion",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.103"
   },
   {
-    "hqmf_name": "Patient Charactersitic, Estimated Date of Conception",
+    "hqmf_name": "Patient Characteristic, Clinical Trial Participant",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.6",
+    "qrda_name": "Patient Characteristic Clinical Trial Participant",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.51"
+  },
+  {
+    "hqmf_name": "Patient Characteristic, Estimated Date of Conception",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.1001",
     "qrda_name": "Patient Characteristic Estimated Date of Conception",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.102"
   },
   {
-    "hqmf_name": "Patient Charactersitic, Tobacco user and Non-User",
+    "hqmf_name": "Patient Characteristic, Tobacco user and Non-User",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.1001",
     "qrda_name": "Tobacco Use",
     "qrda_oid": "2.16.840.1.113883.10.20.22.4.85"
@@ -557,6 +599,12 @@
     "qrda_name": "Diagnostic Study Performed",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.18"
   },
+  {
+    "hqmf_name": "Discharge Medication, not Performed",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.200",
+    "qrda_name": "Discharge Medication - Active Medication",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.105"
+  },
   {
     "hqmf_name": "Procedure, not Performed",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.106",
@@ -593,6 +641,12 @@
     "qrda_name": "Device Applied",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.7"
   },
+  {
+    "hqmf_name": "Device, Order not done",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.137",
+    "qrda_name": "Device Order",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.9"
+  },
   {
     "hqmf_name": "Procedure, Order not done",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.162",
@@ -634,5 +688,35 @@
     "hqmf_oid": "2.16.840.1.113883.3.560.1.157",
     "qrda_name": "Physical Exam Performed",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.59"
+  },
+  {
+    "hqmf_name": "Diagnosis",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.110",
+    "qrda_name": "Diagnosis",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.135"
+  },
+  {
+    "hqmf_name": "Family History",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.111",
+    "qrda_name": "Family History",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.12"
+  },
+  {
+    "hqmf_name": "Symptom",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.116",
+    "qrda_name": "Symptom",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.136"
+  },
+  {
+    "hqmf_name": "Assessment, Performed",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.117",
+    "qrda_name": "Assessment Performed",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.144"
+  },
+  {
+    "hqmf_name": "Assessment, Recommended",
+    "hqmf_oid": "2.16.840.1.113883.10.20.28.3.118",
+    "qrda_name": "Assessment Recommended",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.145"
   }
 ]

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

@@ -52,9 +52,9 @@ module HealthDataStandards
               rendering_context.extend(extension)
             end
           end
-            erb.result(rendering_context.my_binding)
+          erb.result(rendering_context.my_binding)
         end.join
       end
     end
   end
-end
+end

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

@@ -10,10 +10,11 @@ module HealthDataStandards
     #                      provide a different directory if you want to use this class
     #                      outside of the HDS gem
     class TemplateHelper
-      def initialize(template_format, template_subdir = nil, template_directory = nil)
+      def initialize(template_format, template_subdir = nil, template_directory = nil, qrda_version = nil)
         @template_format = template_format
         @template_directory = template_directory
         @template_subdir = template_subdir
+        @qrda_version = qrda_version
         @template_cache = {}
       end
 
@@ -42,8 +43,12 @@ module HealthDataStandards
       protected 
 
       def cache_template(template_name)
+        subdir = @qrda_version
+        
         entry = @template_cache[template_name] || {mtime:-1, erb:nil}
-        filename = File.join(template_root, "#{template_name}.#{@template_format}.erb")
+        template_dir = template_root
+        template_dir = File.join(template_root, subdir) if subdir
+        filename = File.join(template_dir, "#{template_name}.#{@template_format}.erb")
         mtime = File.mtime(filename).to_i
         if mtime > entry[:mtime]
           src = File.read(filename)

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

@@ -5,9 +5,40 @@ module HealthDataStandards
         options['tag_name'] ||= 'code'
         options['attribute'] ||= :codes
         options['exclude_null_flavor'] ||= false
+        # allowing wild card matching of any code system for generic templates
+        # valueset filtering should filter out a decent code
+        # TODO: Can we add nil? logic to the function?  Make it so that we don't have to include the preferred_code_sets['*'] if we want all?
+        pcs = if options['preferred_code_sets'] && options['preferred_code_sets'].index("*")
+          # all of the code_systems that we know about
+          HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEMS.values | HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEM_ALIASES.keys
+        else
+          options['preferred_code_sets']
+        end
+        create_code_string(entry, entry.preferred_code(pcs, options['attribute'], options['value_set_map']), options)
+      end
+
+      def create_code_string(entry, preferred_code, options={})
+        
+        code_string = create_code_display_string(entry, preferred_code, options)
+        
+        unless entry['negationInd'] == true
+          code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>" if entry.respond_to?(:description)
+
+          code_string += create_laterality_code_string(entry, options) if options["laterality"]
+          
+          code_string += create_translations_code_string(entry, options) if options["attribute"] == :codes && entry.respond_to?(:translation_codes)
+          
+          code_string += "</#{options['tag_name']}>"
+        end
+
+        code_string
+      end
+
+      def create_code_display_string(entry, preferred_code, options={})
         code_string = nil
-        preferred_code = entry.preferred_code(options['preferred_code_sets'], options['attribute'], options['value_set_map'])
-        if preferred_code
+        if entry['negationInd'] == true
+          code_string = "<#{options['tag_name']} nullFlavor=\"NA\" #{options['extra_content']}/>"
+        elsif 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
@@ -15,20 +46,23 @@ module HealthDataStandards
           code_string += "nullFlavor=\"UNK\" " unless options["exclude_null_flavor"]
           code_string += "#{options['extra_content']}>"
         end
-        
-        
-        
-        if options["attribute"] == :codes && entry.respond_to?(:translation_codes)
-          code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>" if entry.respond_to?(:description)
-          entry.translation_codes(options['preferred_code_sets'], options['value_set_map']).each do |translation|
-            code_string += "<translation code=\"#{translation['code']}\" codeSystem=\"#{HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(translation['code_set'])}\"/>\n"
-          end
+        code_string
+      end
+
+      def create_laterality_code_string(entry, options={})
+        code_string = "\n<!-- QDM Attribute: Laterality -->\n<qualifier>\n<name code='182353008' codeSystem='2.16.840.1.113883.6.96' displayName='Side' />\n"
+        code_string += "<value xsi:type='CD' code='#{options['laterality']['code']}' displayName='#{options['laterality']['title']}' sdtc:valueSet='#{oid_for_code(entry.laterality,field_oids['LATERALITY'])}'
+                       codeSystem='#{HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(options['laterality']['code_system'])}'/>\n</qualifier>\n"
+      end
+
+      def create_translations_code_string(entry, options={})
+        code_string = ''
+        entry.translation_codes(options['preferred_code_sets'], options['value_set_map']).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)
         case entry.status.to_s.downcase
         when 'active'
@@ -43,7 +77,7 @@ module HealthDataStandards
       def fulfillment_quantity(codes, fulfillmentHistory, dose)
         if (codes["RxNorm"].present?)
           doses = (fulfillmentHistory.quantity_dispensed['value'].to_f / dose['value'].to_f ).to_i
-          return "value='#{doses}'"
+          return "value='#{doses}' unit='1'"
         else
           return "value='#{fulfillmentHistory.quantity_dispensed['value']}' unit='#{fulfillmentHistory.quantity_dispensed['unit']}'"
         end
@@ -58,10 +92,36 @@ module HealthDataStandards
       end
 
       def dose_quantity(codes, dose)
-        if (codes["RxNorm"].present?)
-          return "value='1'"
+        if (codes["RxNorm"].present? || codes["CVX"].present?)
+          if dose['unit'].present?
+            return "value='1' unit='#{ucum_for_dose_quantity(dose['unit'])}'"
+          else
+            return "value='1'"
+          end
+        else
+          return "value='#{dose['scalar']}' unit='#{dose['units']}'"
+        end
+      end
+
+      def ucum_for_dose_quantity(unit)
+        case unit
+        when 'capsule(s)'
+          '{Capsule}'
+        when 'tablet(s)'
+          '{tbl}'
         else
-          return "value=#{dose['value']} unit=#{dose['unit']}" 
+          unit
+        end
+      end
+
+      def ucum_for_dose_quantity(unit)
+        case unit
+        when 'capsule(s)'
+          '{Capsule}'
+        when 'tablet(s)'
+          '{tbl}'
+        else
+          unit
         end
       end
 
@@ -92,30 +152,12 @@ module HealthDataStandards
 
         if (codes.is_a? Hash)
           clean_hash = {}
-          
+
           if codes['codeSystem']
-            if codes['title']
-              clean_hash[codes['codeSystem']] = codes['code'] + " (#{codes['title']})"
-            else
-              clean_hash[codes['codeSystem']] = codes['code']
-            end
+            clean_hash[codes['codeSystem']] = clean_hash_code_system(codes)
           elsif codes['_id']
             codes.keys.reject {|key| ['_id'].include? key}.each do |hashkey|
-              value = codes[hashkey]
-              if value.nil?
-                clean_hash[hashkey.titleize] = 'none'
-              elsif value.is_a? Hash
-                hash_result = convert_field_to_hash(hashkey, value)
-                if hash_result.is_a? Hash
-                  clean_hash[hashkey.titleize] = hash_result.map {|key, value| "#{key}: #{value}"}.join(' ')
-                else
-                  clean_hash[hashkey.titleize] = hash_result
-                end
-              elsif value.is_a? Array
-                clean_hash[hashkey.titleize] = value.join(', ')
-              else
-                clean_hash[hashkey.titleize] = convert_field_to_hash(hashkey, value)
-              end
+              clean_hash[hashkey.titleize] = clean_hash_id(codes, hashkey)
             end
           elsif codes['scalar']
             return "#{codes['scalar']} #{codes['units']}"
@@ -139,7 +181,33 @@ module HealthDataStandards
         end
       end
       
+      def clean_hash_code_system(codes)
+        if codes['title']
+          return codes['code'] + " (#{codes['title']})"
+        else
+          return codes['code']
+        end
+      end
+      
+      def clean_hash_id(codes, hashkey)
+        value = codes[hashkey]
+        if value.nil?
+          return 'none'
+        elsif value.is_a? Hash
+          hash_result = convert_field_to_hash(hashkey, value)
+          if hash_result.is_a? Hash
+            return hash_result.map {|key, value| "#{key}: #{value}"}.join(' ')
+          else
+            return hash_result
+          end
+        elsif value.is_a? Array
+          return value.join(', ')
+        else
+          return convert_field_to_hash(hashkey, value)
+        end
+      end
+      
       
     end
   end
-end
+end