health-data-standards 3.4.4 → 3.4.5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 2a1f0fe2ae72b74f35d8db365da80e3d0654a915
+  metadata.gz: 68d3be05b049b75724e22b58c9a19635903b9409
+  data.tar.gz: 42ae8b42651d913d9122a4591a6e6789b381ffaa
 SHA512:
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+  data.tar.gz: 5c500ccd6d7687fdcdfc211b1fbf4d9a47bc8148ff9737f302e5c710dcdf042082312aceeb7f5f55583aa964b619ecd0d0f81fed1bdccdf31db7d3a256de1976

data/README.md

@@ -25,11 +25,19 @@ Please try to follow the [GitHub Coding Style Guides](https://github.com/stylegu
 Change Log
 ==========
 
-3.4.4
+3.4.5 - Not yet released
+
+* Performance improvents in all exports through template caching
+* QRDA Cat I export now exports the record's actual address if present
+* QRDA Cat I export - Bug fix - previously patients with a race but no ethnicity would cause exceptions
+* QRDA Cat I import - performance improvements through more efficient XPath expressions
+
+3.4.4 - March 25, 2014
 
 * Updating the Measure model to deal with continuous variable and NQF and CMS ids through Measure.categories
 * Bug fix - Filters were not properly handled by the QueryCache
 * Bug fix - Fixed the order of populations in HQMF::PopulationCriteria::ALL_POPULATION_CODES so that DENEX is after denominator
+* When importing measure bundles, you can now exclude patients and calculation results
 
 3.4.3 - March 6, 2014
 

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

@@ -52,9 +52,7 @@ module HealthDataStandards
               rendering_context.extend(extension)
             end
           end
-            eruby = Erubis::EscapedEruby.new(erb) # TODO: cache these
-            eruby.filename=  @template_helper.template_file((params[:template] || params[:partial]), params[:partial]).path
-            eruby.result(rendering_context.my_binding)
+            erb.result(rendering_context.my_binding)
         end.join
       end
     end

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

@@ -14,6 +14,7 @@ module HealthDataStandards
         @template_format = template_format
         @template_directory = template_directory
         @template_subdir = template_subdir
+        @template_cache = {}
       end
 
       def template_root
@@ -29,20 +30,31 @@ module HealthDataStandards
       # Returns the raw ERb for the template_name provided. This method will look in
       # template_directory/template_subdir/template_name.template_format.erb
       def template(template_name)
-        File.read(File.join(template_root, "#{template_name}.#{@template_format}.erb"))
+        cache_template(template_name)
       end
 
       # Basically the same template, but prepends an underscore to the template name
       # to mimic the Rails convention for template fragments
       def partial(partial_name)
-        template("_#{partial_name}")
+        cache_template("_#{partial_name}")
       end
 
-      def template_file(file,partial=false)
-        file = partial ? "_#{file}" : file
-        File.new(File.join(template_root, "#{file}.#{@template_format}.erb"))
-      end
+      protected 
 
+      def cache_template(template_name)
+        entry = @template_cache[template_name] || {mtime:-1, erb:nil}
+        filename = File.join(template_root, "#{template_name}.#{@template_format}.erb")
+        mtime = File.mtime(filename).to_i
+        if mtime > entry[:mtime]
+          src = File.read(filename)
+          erb = Erubis::EscapedEruby.new(src)
+          erb.filename=filename
+          entry[:mtime]=mtime
+          entry[:erb] = erb
+          @template_cache[template_name]=entry
+        end
+        entry[:erb]
+      end
     end
   end
 end

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class DiagnosisActiveImporter < CDA::ConditionImporter
 
         def initialize
-          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.11']"))
+          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.11']"))
           @status_xpath = nil # We'll hardcode this to active in create entry because this is from the 
                               # diagnosis active template
           @severity_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.8']/cda:value"                    

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class DiagnosisInactiveImporter < CDA::ConditionImporter
 
         def initialize
-          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.13']"))
+          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.13']"))
           @status_xpath = nil # We'll hardcode this to inactive in create entry because this is from the 
                               # diagnosis active template
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class DiagnosticStudyOrderImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.17']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.17']"))
           super(entry_finder)
           @entry_class = Procedure
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class EcogStatusImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.103']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.103']"))
           super(entry_finder)
           @code_xpath = './cda:value'
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class EncounterOrderImporter < CDA::EncounterImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']"))
           super(entry_finder)
         end
 

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class EncounterPerformedImporter < CDA::EncounterImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']"))
           super(entry_finder)
           @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation"
         end

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class GestationalAgeImporter < CDA::SectionImporter
 
         def initialize
-          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.101']"))
+          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.101']"))
 
         end
 

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class InsuranceProviderImporter < CDA::SectionImporter
       
         def initialize
-          super(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.55']"))
+          super(CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.55']"))
           @check_for_usable = false # needs to be this way becase InsuranceProvider does not respond
                                     # to usable?
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class LabOrderImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.37']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.37']"))
           super(entry_finder)
           @entry_class = LabResult
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class LabResultImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.40']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.40']"))
           super(entry_finder)
           @entry_class = LabResult
         end

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       class MedicationActiveImporter < CDA::MedicationImporter
 
         def initialize
-          super(CDA::EntryFinder.new("//cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.41']"))
+          super(CDA::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.41']"))
         end
 
         def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class MedicationDispensedImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:supply[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.45']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:supply[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.45']"))
           super(entry_finder)
           @code_xpath = "./cda:product/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
           @entry_class = Medication

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

@@ -13,53 +13,53 @@ module HealthDataStandards
         def initialize
           # This differs from other HDS patient importers in that sections can have multiple importers
           @section_importers = {}
-          @section_importers[:care_goals] = [generate_importer(CDA::SectionImporter, "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.1']", '2.16.840.1.113883.3.560.1.9')] #care goal
+          @section_importers[:care_goals] = [generate_importer(CDA::SectionImporter, "./cda:entry/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.1']", '2.16.840.1.113883.3.560.1.9')] #care goal
           
           @section_importers[:conditions] = [generate_importer(GestationalAgeImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
                                              generate_importer(EcogStatusImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
                                              generate_importer(SymptomActiveImporter, nil, '2.16.840.1.113883.3.560.1.69', 'active'),
                                              generate_importer(DiagnosisActiveImporter, nil, '2.16.840.1.113883.3.560.1.2', 'active'),
-                                             generate_importer(CDA::ConditionImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']", '2.16.840.1.113883.3.560.1.404'), # patient characteristic age
-                                             generate_importer(CDA::ConditionImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.14']", '2.16.840.1.113883.3.560.1.24', 'resolved'), #diagnosis resolved
+                                             generate_importer(CDA::ConditionImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']", '2.16.840.1.113883.3.560.1.404'), # patient characteristic age
+                                             generate_importer(CDA::ConditionImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.14']", '2.16.840.1.113883.3.560.1.24', 'resolved'), #diagnosis resolved
                                              generate_importer(DiagnosisInactiveImporter, nil, '2.16.840.1.113883.3.560.1.23', 'inactive')] #diagnosis inactive
   
           
-          @section_importers[:medications] = [generate_importer(CDA::MedicationImporter, "//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.105']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.41']", '2.16.840.1.113883.3.560.1.199', 'discharge'), #discharge medication active
+          @section_importers[:medications] = [generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.105']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.41']", '2.16.840.1.113883.3.560.1.199', 'discharge'), #discharge medication active
                                               generate_importer(MedicationActiveImporter, nil, '2.16.840.1.113883.3.560.1.13', 'active'), #medication active
-                                              generate_importer(CDA::MedicationImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16']", '2.16.840.1.113883.3.560.1.14', 'administered'), #medication administered
-                                              generate_importer(CDA::MedicationImporter, "//cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']", '2.16.840.1.113883.3.560.1.17', 'ordered'), #medication order TODO: ADD NEGATON REASON HANDLING SOMEHOW
+                                              generate_importer(CDA::MedicationImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16']", '2.16.840.1.113883.3.560.1.14', 'administered'), #medication administered
+                                              generate_importer(CDA::MedicationImporter, "./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']", '2.16.840.1.113883.3.560.1.17', 'ordered'), #medication order TODO: ADD NEGATON REASON HANDLING SOMEHOW
                                               generate_importer(MedicationDispensedImporter, nil, '2.16.840.1.113883.3.560.1.8', 'dispensed')]
 
-          @section_importers[:procedures] = [generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']", '2.16.840.1.113883.3.560.1.57', 'performed'), #physical exam performed
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.131'), #comm from provider to patient
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']", '2.16.840.1.113883.3.560.1.45', 'ordered'), #intervention ordered
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']", '2.16.840.1.113883.3.560.1.46', 'performed'), #intervention performed
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']", '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
-                                             generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']", '2.16.840.1.113883.3.560.1.30'), #comm from patient to provider
+          @section_importers[:procedures] = [generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']", '2.16.840.1.113883.3.560.1.57', 'performed'), #physical exam performed
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.131'), #comm from provider to patient
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']", '2.16.840.1.113883.3.560.1.45', 'ordered'), #intervention ordered
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']", '2.16.840.1.113883.3.560.1.46', 'performed'), #intervention performed
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']", '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']", '2.16.840.1.113883.3.560.1.30'), #comm from patient to provider
                                              generate_importer(ProcedureOrderImporter, nil, '2.16.840.1.113883.3.560.1.62', 'ordered'),
-                                             generate_importer(ProcedurePerformedImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
-                                             generate_importer(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
-                                             generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'), #risk category assessment
-                                             generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
+                                             generate_importer(ProcedurePerformedImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'), #risk category assessment
+                                             generate_importer(CDA::ProcedureImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
                                              generate_importer(DiagnosticStudyOrderImporter, nil, '2.16.840.1.113883.3.560.1.40', 'ordered')]
 
           @section_importers[:allergies] = [generate_importer(ProcedureIntoleranceImporter, nil, '2.16.840.1.113883.3.560.1.61'),
-                                            generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.46']", '2.16.840.1.113883.3.560.1.67'), #medication intolerance
-                                            generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.43']", '2.16.840.1.113883.3.560.1.7'), #medication adverse effect
-                                            generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.44']", '2.16.840.1.113883.3.560.1.1')] #medication allergy
+                                            generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.46']", '2.16.840.1.113883.3.560.1.67'), #medication intolerance
+                                            generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.43']", '2.16.840.1.113883.3.560.1.7'), #medication adverse effect
+                                            generate_importer(CDA::AllergyImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.44']", '2.16.840.1.113883.3.560.1.1')] #medication allergy
 
-          @section_importers[:medical_equipment] = [generate_importer(CDA::MedicalEquipmentImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']", '2.16.840.1.113883.3.560.1.110', 'applied')]
+          @section_importers[:medical_equipment] = [generate_importer(CDA::MedicalEquipmentImporter, "./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']", '2.16.840.1.113883.3.560.1.110', 'applied')]
 
           @section_importers[:results] = [generate_importer(LabOrderImporter, nil, '2.16.840.1.113883.3.560.1.50', 'ordered'), #lab ordered
-                                          generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']", '2.16.840.1.113883.3.560.1.5', 'performed'), #lab performed
-                                          generate_importer(CDA::ResultImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
-                                          generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.57']", '2.16.840.1.113883.3.560.1.18'), #physical exam finding
-                                          generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result    
-                                          generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.20']", '2.16.840.1.113883.3.560.1.111'), #diagnostic study result not done
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']", '2.16.840.1.113883.3.560.1.5', 'performed'), #lab performed
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.57']", '2.16.840.1.113883.3.560.1.18'), #physical exam finding
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result    
+                                          generate_importer(CDA::ResultImporter, "./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.20']", '2.16.840.1.113883.3.560.1.111'), #diagnostic study result not done
                                           generate_importer(LabResultImporter, nil, '2.16.840.1.113883.3.560.1.12')] #lab result
 
-          @section_importers[:encounters] = [generate_importer(EncounterPerformedImporter, "//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']", '2.16.840.1.113883.3.560.1.79', 'performed'), #encounter performed
+          @section_importers[:encounters] = [generate_importer(EncounterPerformedImporter, "./cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']", '2.16.840.1.113883.3.560.1.79', 'performed'), #encounter performed
                                              generate_importer(EncounterOrderImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered')]
 
           @section_importers[:social_history] = [generate_importer(TobaccoUseImporter, nil, '2.16.840.1.113883.3.560.1.1001', 'completed')]
@@ -79,22 +79,24 @@ module HealthDataStandards
         end
 
         def import_sections(record, doc)
+
+          context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
           nrh = CDA::NarrativeReferenceHandler.new
           nrh.build_id_map(doc)
           @section_importers.each do |section, entry_packages|
             entry_packages.each do |entry_package|
-              record.send(section) << entry_package.package_entries(doc, nrh)
+              record.send(section) << entry_package.package_entries(context, nrh)
             end
           end
         end
 
         def get_clinical_trial_participant(record, doc)
-          entry_elements = doc.xpath("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.51']")
+          entry_elements = doc.xpath("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.51']")
           record.clinicalTrialParticipant = true unless entry_elements.blank?
         end
 
         def get_patient_expired(record, doc)
-          entry_elements = doc.xpath("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
+          entry_elements = doc.xpath("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
           record.expired = true unless entry_elements.empty?
         end
 

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

@@ -4,7 +4,7 @@ module HealthDataStandards
       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']"))
+          super(CDA::EntryFinder.new("./cda:entry/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

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

@@ -2,7 +2,7 @@ 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']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.63']"))
           super(entry_finder)
           @entry_class = Procedure
         end

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class ProcedurePerformedImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
           super(entry_finder)
           @entry_class = Procedure
           @ordinality_xpath = "./cda:priorityCode"

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

@@ -2,7 +2,7 @@ module HealthDataStandards
   module Import
     module Cat1
       class SymptomActiveImporter < CDA::SectionImporter
-        def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.76']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.76']"))
           super(entry_finder)
           @code_xpath = './cda:value'
         end

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

@@ -2,7 +2,7 @@ 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']"))
+        def initialize(entry_finder=CDA::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.85']"))
           super(entry_finder)
           @entry_class = Entry
         end

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

@@ -1,10 +1,10 @@
 module ProviderImportUtils
-  
+
   def extract_provider(performer, element_name="assignedEntity")
     provider_data = extract_provider_data(performer, false, "./cda:#{element_name}")
     find_or_create_provider(provider_data)
   end
-  
+
   def find_or_create_provider(provider_hash)
     provider = Provider.by_npi(provider_hash[:npi]).first if provider_hash[:npi] && !provider_hash[:npi].empty?
     unless provider
@@ -12,8 +12,6 @@ module ProviderImportUtils
         provider = Provider.create(provider_hash)
         provider.npi = provider_hash[:npi]
       else
-        provider ||= Provider.resolve_provider(provider_hash) if Provider.respond_to? :resolve_provider
-
         ident_roots = provider_hash[:cda_identifiers].map {|ident| ident.root}
         ident_extensions = provider_hash[:cda_identifiers].map {|ident| ident.extension}
         unless ident_roots.size == 0
@@ -24,10 +22,11 @@ module ProviderImportUtils
                             :family_name=> provider_hash[:family_name],
                             :specialty => provider_hash[:specialty]}
         provider ||= Provider.where(provider_query).first
+        provider ||= Provider.resolve_provider(provider_hash)
         provider ||= Provider.create(provider_hash)
       end
     end
-    provider 
+    provider
   end
 
   # Returns nil if result is an empty string, block allows text munging of result if there is one
@@ -39,5 +38,5 @@ module ProviderImportUtils
       result.content
     end
   end
-  
-end
+
+end

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

@@ -7,9 +7,9 @@ class Provider
 
   field :specialty   , type: String
   field :phone       , type: String
-  
+
   validates_uniqueness_of :npi, allow_blank: true
-  
+
   embeds_one :organization
   embeds_many :cda_identifiers, class_name: "CDAIdentifier", as: :cda_identifiable
 
@@ -42,21 +42,21 @@ class Provider
   def records(effective_date=nil)
     Record.by_provider(self, effective_date)
   end
-  
+
   # validate the NPI, should be 10 or 15 digits total with the final digit being a
   # checksum using the Luhn algorithm with additional special handling as described in
-  # https://www.cms.gov/NationalProvIdentStand/Downloads/NPIcheckdigit.pdf 
+  # https://www.cms.gov/NationalProvIdentStand/Downloads/NPIcheckdigit.pdf
   def self.valid_npi?(npi)
     return false unless npi
     return false if npi.length != 10 and npi.length != 15
     return false if npi.gsub(/\d/, '').length > 0 # npi must be all digits
     return false if npi.length == 15 and (npi =~ /^80840/)==nil # 15 digit npi must start with 80840
-  
+
     # checksum is always calculated as if 80840 prefix is present
     if npi.length==10
       npi = '80840'+npi
     end
-  
+
     return luhn_checksum(npi[0,14])==npi[14]
   end
 
@@ -72,17 +72,19 @@ class Provider
       end
     end
     sum = (9*sum)%10
-  
+
     return sum.to_s
   end
 
-  #this is intentially left blank. When using the ProviderImporter class this method will be called
-  # if a parsed provider can not be found in the database if the parsed provider does not have an 
-  # npi number associated with it.  This allows applications to handle this how they see fit by redefining
-  # this method.  If this method call return nil an attempt will be made to discover the Provider by name 
-  # matching and if that fails a Provider will be created in the db based on the information in the parsed
-  #  hase
+  # When using the ProviderImporter class this method will be called if a parsed
+  # provider can not be found in the database if the parsed provider does not
+  # have an npi number associated with it.  This allows applications to handle
+  # this how they see fit by redefining this method.  The default implementation
+  # is to return an orphan parent (the singular provider without an NPI) if one
+  # exists.  If this method call return nil an attempt will be made to discover
+  # the Provider by name matching and if that fails a Provider will be created
+  # in the db based on the information in the parsed hash.
   def self.resolve_provider(provider_hash)
-
+    Provider.where(:npi => nil).first
   end
-end
+end

data/templates/cat1/_record_target.cat1.erb

@@ -2,18 +2,30 @@
     <patientRole>
       <!-- id root="Cypress" extension="<%= patient.id %>"/ -->
       <!-- Fake Medicare HIC number -->
-      <% 
+      <%
       # get the pateint id , treate it as a hex number, turn it to a string and strip the last 9 characters off of it
         hic = patient.id.to_s.hex.to_s
         hic = hic.slice(hic.length-9,9)
       %>
       <id extension="<%= hic %>A" root="2.16.840.1.113883.4.572"/>
       <addr use="HP">
-        <streetAddressLine>202 Burlington Rd.</streetAddressLine>
-        <city>Bedford</city>
-        <state>MA</state>
-        <postalCode>01730</postalCode>
-        <country>US</country>
+        <% if patient.addresses.present?
+            patient.addresses.each do |address| -%>
+            <% address.street.each do |street| -%>
+              <streetAddressLine><%= street %></streetAddressLine>
+            <% end %>
+            <city><%= address.city %></city>
+            <state><%= address.state %></state>
+            <postalCode><%= address.zip %></postalCode>
+            <country><%= address.country %></country>
+          <% end -%>
+        <% else -%>
+          <streetAddressLine>202 Burlington Rd.</streetAddressLine>
+          <city>Bedford</city>
+          <state>MA</state>
+          <postalCode>01730</postalCode>
+          <country>US</country>
+        <% end -%>
       </addr>
       <telecom use="WP" value="tel:+1-781-271-3000"/>
       <patient>
@@ -26,11 +38,11 @@
         <% if (patient.race) %>
           <raceCode code="<%= patient.race['code'] %>" <% if patient.race['name']%>displayName="<%= patient.race['name'] %>"<% end %> codeSystemName="CDC Race and Ethnicity" codeSystem="2.16.840.1.113883.6.238"/>
         <% end %>
-        <% if (patient.race) %>
+        <% if (patient.ethnicity) %>
           <ethnicGroupCode code="<%= patient.ethnicity['code'] %>" <% if patient.ethnicity['name']%>displayName="<%= patient.ethnicity['name'] %>"<% end %> codeSystemName="CDC Race and Ethnicity" codeSystem="2.16.840.1.113883.6.238"/>
         <% end %>
         <%
-          languages = patient.languages 
+          languages = patient.languages
           languages = ["eng"] if languages.nil? or languages.empty?
           languages.each do |language|%>
           <languageCommunication>
@@ -41,4 +53,4 @@
         <% end %>
       </patient>
     </patientRole>
-  </recordTarget>
+  </recordTarget>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 3.4.4
+  version: 3.4.5
 platform: ruby
 authors:
 - Andy Gregorowicz
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-25 00:00:00.000000000 Z
+date: 2014-04-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -175,6 +175,10 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- Gemfile
+- README.md
+- Rakefile
+- lib/health-data-standards.rb
 - lib/health-data-standards/export/c32.rb
 - lib/health-data-standards/export/cat_1.rb
 - lib/health-data-standards/export/cat_3.rb
@@ -191,6 +195,7 @@ files:
 - lib/health-data-standards/export/helper/scooped_view_helper.rb
 - lib/health-data-standards/export/html.rb
 - lib/health-data-standards/export/qrda/entry_template_resolver.rb
+- lib/health-data-standards/export/qrda/hqmf-qrda-oids.json
 - lib/health-data-standards/export/rendering_context.rb
 - lib/health-data-standards/export/template_helper.rb
 - lib/health-data-standards/export/view_helper.rb
@@ -325,22 +330,51 @@ files:
 - lib/health-data-standards/models/treating_provider.rb
 - lib/health-data-standards/models/vital_sign.rb
 - lib/health-data-standards/railtie.rb
+- lib/health-data-standards/tasks/bundle.rake
 - lib/health-data-standards/util/code_system_helper.rb
 - lib/health-data-standards/util/hl7_helper.rb
 - lib/health-data-standards/util/hqmf_template_helper.rb
+- lib/health-data-standards/util/hqmf_template_oid_map.json
 - lib/health-data-standards/util/vs_api.rb
-- lib/health-data-standards.rb
+- lib/hqmf-generator/attribute.xml.erb
+- lib/hqmf-generator/characteristic_criteria.xml.erb
+- lib/hqmf-generator/code.xml.erb
+- lib/hqmf-generator/condition_criteria.xml.erb
+- lib/hqmf-generator/derivation.xml.erb
+- lib/hqmf-generator/description.xml.erb
+- lib/hqmf-generator/document.xml.erb
+- lib/hqmf-generator/effective_time.xml.erb
+- lib/hqmf-generator/encounter_criteria.xml.erb
+- lib/hqmf-generator/field.xml.erb
 - lib/hqmf-generator/hqmf-generator.rb
+- lib/hqmf-generator/observation_criteria.xml.erb
+- lib/hqmf-generator/population_criteria.xml.erb
+- lib/hqmf-generator/precondition.xml.erb
+- lib/hqmf-generator/procedure_criteria.xml.erb
+- lib/hqmf-generator/reason.xml.erb
+- lib/hqmf-generator/reference.xml.erb
+- lib/hqmf-generator/source.xml.erb
+- lib/hqmf-generator/specific_occurrence.xml.erb
+- lib/hqmf-generator/subset.xml.erb
+- lib/hqmf-generator/substance_criteria.xml.erb
+- lib/hqmf-generator/supply_criteria.xml.erb
+- lib/hqmf-generator/template_id.xml.erb
+- lib/hqmf-generator/temporal_relationship.xml.erb
+- lib/hqmf-generator/value.xml.erb
+- lib/hqmf-generator/variable_criteria.xml.erb
 - lib/hqmf-model/attribute.rb
+- lib/hqmf-model/data_criteria.json
 - lib/hqmf-model/data_criteria.rb
 - lib/hqmf-model/document.rb
 - lib/hqmf-model/population_criteria.rb
 - lib/hqmf-model/precondition.rb
 - lib/hqmf-model/types.rb
 - lib/hqmf-model/utilities.rb
+- lib/hqmf-parser.rb
 - lib/hqmf-parser/1.0/attribute.rb
 - lib/hqmf-parser/1.0/comparison.rb
 - lib/hqmf-parser/1.0/data_criteria.rb
+- lib/hqmf-parser/1.0/data_criteria_oid_xpath.json
 - lib/hqmf-parser/1.0/document.rb
 - lib/hqmf-parser/1.0/expression.rb
 - lib/hqmf-parser/1.0/observation.rb
@@ -368,7 +402,6 @@ files:
 - lib/hqmf-parser/converter/pass2/comparison_converter.rb
 - lib/hqmf-parser/converter/pass2/operator_converter.rb
 - lib/hqmf-parser/parser.rb
-- lib/hqmf-parser.rb
 - lib/util/counter.rb
 - templates/_author.hdata.erb
 - templates/_pedigree.hdata.erb
@@ -503,39 +536,6 @@ files:
 - templates/html/_section.html.erb
 - templates/html/show.html.erb
 - templates/metadata.hdata.erb
-- lib/health-data-standards/export/qrda/hqmf-qrda-oids.json
-- lib/health-data-standards/util/hqmf_template_oid_map.json
-- lib/hqmf-model/data_criteria.json
-- lib/hqmf-parser/1.0/data_criteria_oid_xpath.json
-- lib/hqmf-generator/attribute.xml.erb
-- lib/hqmf-generator/characteristic_criteria.xml.erb
-- lib/hqmf-generator/code.xml.erb
-- lib/hqmf-generator/condition_criteria.xml.erb
-- lib/hqmf-generator/derivation.xml.erb
-- lib/hqmf-generator/description.xml.erb
-- lib/hqmf-generator/document.xml.erb
-- lib/hqmf-generator/effective_time.xml.erb
-- lib/hqmf-generator/encounter_criteria.xml.erb
-- lib/hqmf-generator/field.xml.erb
-- lib/hqmf-generator/observation_criteria.xml.erb
-- lib/hqmf-generator/population_criteria.xml.erb
-- lib/hqmf-generator/precondition.xml.erb
-- lib/hqmf-generator/procedure_criteria.xml.erb
-- lib/hqmf-generator/reason.xml.erb
-- lib/hqmf-generator/reference.xml.erb
-- lib/hqmf-generator/source.xml.erb
-- lib/hqmf-generator/specific_occurrence.xml.erb
-- lib/hqmf-generator/subset.xml.erb
-- lib/hqmf-generator/substance_criteria.xml.erb
-- lib/hqmf-generator/supply_criteria.xml.erb
-- lib/hqmf-generator/template_id.xml.erb
-- lib/hqmf-generator/temporal_relationship.xml.erb
-- lib/hqmf-generator/value.xml.erb
-- lib/hqmf-generator/variable_criteria.xml.erb
-- lib/health-data-standards/tasks/bundle.rake
-- Gemfile
-- README.md
-- Rakefile
 homepage: https://github.com/projectcypress/health-data-standards
 licenses:
 - APL 2.0
@@ -556,7 +556,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: A library for generating and consuming various healthcare related formats.