Merge pull request #3 from dehall/multiversion

Add multiversion support - both dstu2 and stu3 now supported

Gemfile.lock

@@ -2,6 +2,7 @@ PATH
   remote: .
   specs:
     fhir_scorecard (3.0.1)
+      fhir_dstu2_models
       fhir_models (>= 3.0.0)
 
 GEM
@@ -15,12 +16,17 @@ GEM
     coderay (1.1.1)
     date_time_precision (0.8.1)
     docile (1.1.5)
+    fhir_dstu2_models (1.0.2)
+      bcp47 (>= 0.3)
+      date_time_precision (>= 0.8)
+      mime-types (>= 1.16, < 3)
+      nokogiri (>= 1.7)
     fhir_models (3.0.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 1.16, < 3)
       nokogiri (>= 1.6)
-    i18n (0.8.1)
+    i18n (0.8.4)
     json (2.0.3)
     method_source (0.8.2)
     mime-types (2.99.3)
@@ -31,7 +37,7 @@ GEM
       builder
       minitest (>= 5.0)
       ruby-progressbar
-    nokogiri (1.7.1)
+    nokogiri (1.7.2)
       mini_portile2 (~> 2.1.0)
     pry (0.10.4)
       coderay (~> 1.1.0)

fhir_scorecard.gemspec

@@ -12,4 +12,5 @@ Gem::Specification.new do |s|
   s.files = s.files = `git ls-files`.split("\n")
 
   s.add_runtime_dependency 'fhir_models', '>= 3.0.0'
+  s.add_runtime_dependency 'fhir_dstu2_models'
 end

lib/fhir_helper.rb

@@ -0,0 +1,21 @@
+module FHIR
+  # check whether the given object is an instance of any version of the given resource type
+  # if you only care about a single version, don't use this, just use x.is_a?(FHIR::Whatever)
+  def self.is_any_version?(object, resource_type)
+    # resource type should be a string
+    # TODO: maybe expand this to accept a map, ex { dstu2: 'MedicationOrder', stu3: 'MedicationRequest' }
+
+    classnames = ["FHIR::#{resource_type}", "FHIR::DSTU2::#{resource_type}"]
+
+    classnames.any? do |classname|
+      klass = Object.const_defined?(classname) && Object.const_get(classname) # get the class for the name
+      # note that there may not be a class with that name, in which case const_defined => false
+      klass && object.is_a?(klass)
+    end
+  end
+
+  # shorter version for this one class that is used all over the place
+  def self.is_model?(object)
+    object.is_a?(FHIR::Model) || object.is_a?(FHIR::DSTU2::Model)
+  end
+end

lib/fhir_scorecard.rb

@@ -1,13 +1,15 @@
 # Top level include file that brings in all the necessary code
 require 'bundler/setup'
 require 'fhir_models'
+require 'fhir_dstu2_models'
 
 root = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
 
 require File.join(root,'lib','scorecard.rb')
 require File.join(root,'lib','terminology.rb')
 require File.join(root,'lib','implementation_guides.rb')
 require File.join(root,'lib','rubrics.rb')
+require File.join(root,'lib','fhir_helper.rb')
 
 Dir.glob(File.join(root, 'lib','rubrics','**','*.rb')).each do |file|
   require file

lib/rubrics/codes_exist.rb

@@ -45,9 +45,9 @@ def self.check_metadata(fhir_model)
           value = fhir_model.instance_variable_get("@#{field_name}")
           if !value.nil?
             if value.is_a?(Array)
-              value.each{|v| results.merge!(check_metadata(v)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+              value.each{|v| results.merge!(check_metadata(v)){ |k,a,b|a+b} if FHIR.is_model?(v) }
             else # not an Array
-              results.merge!(check_metadata(value)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+              results.merge!(check_metadata(value)){|k,a,b|a+b} if FHIR.is_model?(value)
             end
           end            
         end
@@ -60,9 +60,9 @@ def self.type_okay(type,item)
       when 'code'
         item.is_a?(String)
       when 'Coding'
-        item.is_a?(FHIR::Coding) && !item.code.nil? && !item.system.nil?
+        FHIR.is_any_version?(item, 'Coding') && !item.code.nil? && !item.system.nil?
       when 'CodeableConcept'
-        item.is_a?(FHIR::CodeableConcept) && item.coding.any?{|c| c.is_a?(FHIR::Coding) && !c.code.nil? && !c.system.nil?}
+        FHIR.is_any_version?(item, 'CodeableConcept') && item.coding.any?{ |c| FHIR.is_any_version?(c, 'Coding') && !c.code.nil? && !c.system.nil? }
       else
         false
       end

lib/rubrics/codes_umls.rb

@@ -57,9 +57,9 @@ def self.check_fields(fhir_model)
           end
         elsif !value.nil?
           if value.is_a?(Array)
-            value.each{|v| results.merge!(check_fields(v)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+            value.each{|v| results.merge!(check_fields(v)){|k,a,b|a+b} if FHIR.is_model?(v) }
           else # not an Array
-            results.merge!(check_fields(value)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+            results.merge!(check_fields(value)){|k,a,b|a+b} if FHIR.is_model?(value)
           end
         end
       end

lib/rubrics/codes_umls_preferred_descriptions.rb

@@ -57,9 +57,9 @@ def self.check_fields(fhir_model)
           end
         elsif !value.nil?
           if value.is_a?(Array)
-            value.each{|v| results.merge!(check_fields(v)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+            value.each{|v| results.merge!(check_fields(v)){|k,a,b|a+b} if FHIR.is_model?(v)}
           else # not an Array
-            results.merge!(check_fields(value)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+            results.merge!(check_fields(value)){|k,a,b|a+b} if FHIR.is_model?(value)
           end
         end
       end

lib/rubrics/completeness.rb

@@ -12,14 +12,20 @@ class Completeness < FHIR::Rubrics
       'QuestionnaireResponse','Coverage'
     ]
 
-    MEDICATIONS = [ 'MedicationStatement','MedicationDispense','MedicationAdministration','MedicationRequest' ]
+    COMMON_MEDICATIONS = [ 'MedicationStatement','MedicationDispense','MedicationAdministration']
+
+    DSTU2_MEDICATIONS = COMMON_MEDICATIONS + ['MedicationOrder']
+
+    STU3_MEDICATIONS = COMMON_MEDICATIONS + ['MedicationRequest']
 
     # A Patient Record is not complete without certain required items and medications.
     rubric :completeness do |record|
 
+      curr_version_meds = record.is_a?(FHIR::Model) ? STU3_MEDICATIONS : DSTU2_MEDICATIONS
+
       missing_required = REQUIRED.clone
       missing_expected = EXPECTED.clone
-      missing_meds = MEDICATIONS.clone
+      missing_meds = curr_version_meds.clone
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
@@ -32,7 +38,7 @@ class Completeness < FHIR::Rubrics
 
       # 15 points for required resources
       numerator = (REQUIRED.length.to_f - missing_required.length.to_f)
-      numerator += 1 if (missing_meds.length < MEDICATIONS.length)
+      numerator += 1 if (missing_meds.length < curr_version_meds.length)
       denominator = REQUIRED.length.to_f + 1.0 # add one for medications
       percentage_required = (  numerator / denominator )
       percentage_required = 0.0 if percentage_required.nan?

lib/rubrics/cvx_immunizations.rb

@@ -10,7 +10,7 @@ class CVXImmunizations < FHIR::Rubrics
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::Immunization)
+        if FHIR.is_any_version?(resource, 'Immunization')
             results[:eligible_fields] += 1
             results[:validated_fields] += 1 if cvx?(resource.vaccineCode)        
         end

lib/rubrics/cvx_meds.rb

@@ -10,19 +10,20 @@ class CVXMeds < FHIR::Rubrics
       # Medication.code (CodeableConcept)
       # MedicationAdministration.medicationCodeableConcept / medicationReference
       # MedicationDispense.medicationCodeableConcept / medicationReference
-      # MedicationRequest.medicationCodeableConcept / medicationReference
+      # MedicationRequest.medicationCodeableConcept / medicationReference -- in STU3
+      # MedicationOrder.medicationCodeableConcept / medicationReference -- in DSTU2
       # MedicationStatement.medicationCodeableConcept / medicationReference
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::Medication)
+        if FHIR.is_any_version?(resource, 'Medication')
             results[:eligible_fields] += 1
             results[:validated_fields] += 1 if cvx?(resource.code)        
         elsif (
-            resource.is_a?(FHIR::MedicationRequest) ||
-            resource.is_a?(FHIR::MedicationDispense) ||
-            resource.is_a?(FHIR::MedicationAdministration) ||
-            resource.is_a?(FHIR::MedicationStatement) )
+            resource.is_a?(FHIR::MedicationRequest) || resource.is_a?(FHIR::DSTU2::MedicationOrder) ||
+            FHIR.is_any_version?(resource, 'MedicationDispense') ||
+            FHIR.is_any_version?(resource, 'MedicationAdministration') ||
+            FHIR.is_any_version?(resource, 'MedicationStatement') )
           if resource.medicationCodeableConcept
             results[:eligible_fields] += 1
             results[:validated_fields] += 1 if cvx?(resource.medicationCodeableConcept)
@@ -48,11 +49,11 @@ def self.cvx?(codeableconcept)
     def self.local_cvx_reference?(reference,record,contained)
       if contained && reference.reference && reference.reference.start_with?('#')
         contained.each do |resource|
-          return true if resource.is_a?(FHIR::Medication) && reference.reference[1..-1]==resource.id
+          return true if FHIR.is_any_version?(resource, 'Medication') && reference.reference[1..-1]==resource.id
         end
       end
       record.entry.each do |entry|
-        if entry.resource.is_a?(FHIR::Medication) && reference_matchs?(reference,entry)
+        if FHIR.is_any_version?(entry.resource, 'Medication') && reference_matchs?(reference,entry)
           return true
         end
       end

lib/rubrics/datetimes_iso8601.rb

@@ -45,9 +45,9 @@ def self.check_metadata(fhir_model)
           value = fhir_model.instance_variable_get("@#{field_name}")
           if !value.nil?
             if value.is_a?(Array)
-              value.each{|v| results.merge!(check_metadata(v)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+              value.each{|v| results.merge!(check_metadata(v)){ |k,a,b| a + b } if FHIR.is_model?(v) }
             else # not an Array
-              results.merge!(check_metadata(value)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+              results.merge!(check_metadata(value)){ |k,a,b| a + b } if FHIR.is_model?(value)
             end
           end            
         end

lib/rubrics/labs_loinc.rb

@@ -9,13 +9,13 @@ class LabsLoinc < FHIR::Rubrics
       }
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::DiagnosticReport) || resource.is_a?(FHIR::Observation)
+        if FHIR.is_any_version?(resource, 'DiagnosticReport') || FHIR.is_any_version?(resource, 'Observation')
           results[:eligible_fields] += 1
           if resource.code
             results[:validated_fields] += 1 if resource.code.coding.any?{|x| x.system=='http://loinc.org' && FHIR::Terminology.is_top_lab_code?(x.code)}
           end
         end
-        if resource.is_a?(FHIR::Observation)
+        if FHIR.is_any_version?(resource, 'Observation')
           if resource.component
             resource.component.each do |comp|
               results[:eligible_fields] += 1

lib/rubrics/quantities_ucum.rb

@@ -5,11 +5,13 @@ class QuantitiesUcum < FHIR::Rubrics
       'TestScript','Task','StructureDefinition','SearchParameter','Questionnaire','QuestionnaireResponse','Parameters','OperationDefinition',
       'Group','ExplanationOfBenefit','Contract','Conformance','Claim','ActivityDefinition'
     ]
+    # Note: Task and ActivityDefinition don't exist in DSTU2
 
     CHECK = [
-      'VisionPrescription','SupplyDelivery','Substance','Specimen','Sequence','Observation','NutritionRequest',
-      'MedicationStatement','MedicationRequest','MedicationDispense','MedicationAdministration','Medication','Immunization','CarePlan'
+      'VisionPrescription','SupplyDelivery','Substance','Specimen','Sequence','Observation','NutritionOrder',
+      'MedicationStatement','MedicationRequest','MedicationOrder','MedicationDispense','MedicationAdministration','Medication','Immunization','CarePlan'
     ]
+    # Note: MedicationRequest renamed to MedicationOrder between 2->3; Sequence doesn't exist in DSTU2
 
     # Physical quantities should use UCUM
     rubric :ucum_quantities do |record|

lib/rubrics/references_resolve.rb

@@ -49,9 +49,9 @@ def self.check_metadata(fhir_model,record)
           value = fhir_model.instance_variable_get("@#{field_name}")
           if !value.nil?
             if value.is_a?(Array)
-              value.each{|v| results.merge!(check_metadata(v,record)){|k,a,b|a+b} if v.is_a?(FHIR::Model)}
+              value.each{ |v| results.merge!(check_metadata(v, record)){ |k,a,b| a + b } if FHIR.is_model?(v) }
             else # not an Array
-              results.merge!(check_metadata(value,record)){|k,a,b|a+b} if value.is_a?(FHIR::Model)
+              results.merge!(check_metadata(value, record)){ |k,a,b| a + b } if FHIR.is_model?(value)
             end
           end            
         end

lib/rubrics/rxnorm_meds.rb

@@ -10,19 +10,20 @@ class RxNormMeds < FHIR::Rubrics
       # Medication.code (CodeableConcept)
       # MedicationAdministration.medicationCodeableConcept / medicationReference
       # MedicationDispense.medicationCodeableConcept / medicationReference
-      # MedicationRequest.medicationCodeableConcept / medicationReference
+      # MedicationRequest.medicationCodeableConcept / medicationReference -- in STU3
+      # MedicationOrder.medicationCodeableConcept / medicationReference -- in DSTU2
       # MedicationStatement.medicationCodeableConcept / medicationReference
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::Medication)
+        if FHIR.is_any_version?(resource, 'Medication')
             results[:eligible_fields] += 1
             results[:validated_fields] += 1 if rxnorm?(resource.code)        
         elsif (
-            resource.is_a?(FHIR::MedicationRequest) ||
-            resource.is_a?(FHIR::MedicationDispense) ||
-            resource.is_a?(FHIR::MedicationAdministration) ||
-            resource.is_a?(FHIR::MedicationStatement) )
+            resource.is_a?(FHIR::MedicationRequest) || resource.is_a?(FHIR::DSTU2::MedicationOrder) ||
+            FHIR.is_any_version?(resource, 'MedicationDispense') ||
+            FHIR.is_any_version?(resource, 'MedicationAdministration') ||
+            FHIR.is_any_version?(resource, 'MedicationStatement') )
           if resource.medicationCodeableConcept
             results[:eligible_fields] += 1
             results[:validated_fields] += 1 if rxnorm?(resource.medicationCodeableConcept)
@@ -48,11 +49,11 @@ def self.rxnorm?(codeableconcept)
     def self.local_rxnorm_reference?(reference,record,contained)
       if contained && reference.reference && reference.reference.start_with?('#')
         contained.each do |resource|
-          return true if resource.is_a?(FHIR::Medication) && reference.reference[1..-1]==resource.id
+          return true if FHIR.is_any_version?(resource, 'Medication') && reference.reference[1..-1]==resource.id
         end
       end
       record.entry.each do |entry|
-        if entry.resource.is_a?(FHIR::Medication) && reference_matchs?(reference,entry)
+        if FHIR.is_any_version?(entry.resource, 'Medication') && reference_matchs?(reference,entry)
           return true
         end
       end

lib/rubrics/smoking_status.rb

@@ -17,7 +17,7 @@ class SmokingStatus < FHIR::Rubrics
 
       resources = record.entry.map{|e|e.resource}
       has_smoking_status = resources.any? do |resource|
-        resource.is_a?(FHIR::Observation) && smoking_observation?(resource)
+        FHIR.is_any_version?(resource, 'Observation') && smoking_observation?(resource)
       end
 
       if has_smoking_status

lib/rubrics/snomed_conditions.rb

@@ -10,7 +10,7 @@ class SnomedConditions < FHIR::Rubrics
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::Condition)
+        if FHIR.is_any_version?(resource, 'Condition')
           results[:eligible_fields] += 1
           results[:validated_fields] += 1 if snomed_core?(resource.code)
         end

lib/rubrics/vital_signs.rb

@@ -25,7 +25,7 @@ class VitalSigns < FHIR::Rubrics
 
       resources = record.entry.map{|e|e.resource}
       resources.each do |resource|
-        if resource.is_a?(FHIR::Observation)
+        if FHIR.is_any_version?(resource, 'Observation')
           found_code = get_vital_code(resource.code)
           components = not_found[ found_code ]
           if components.nil?