health-data-standards 3.6.1 → 3.7.0

data/lib/health-data-standards/validate/reported_result_extractor.rb

@@ -152,7 +152,11 @@ module ReportedResultExtractor
             value = node.at_xpath('cda:value')
             count = get_aggregate_count(node)
             if value.at_xpath("./@nullFlavor")
-             key_hash["UNK"] = count
+             if supp == "PAYER" && value['xsi:type'] == 'CD' && value['nullFlavor'] == 'OTH' && value.at_xpath("cda:translation") && value.at_xpath("cda:translation")['code']
+              key_hash[value.at_xpath("cda:translation")['code']] = count
+             else
+              key_hash["UNK"] = count
+             end
             else
              key_hash[value['code']] = count
             end

data/lib/health-data-standards/validate/schematron_validator.rb

@@ -22,6 +22,12 @@ module HealthDataStandards
         end
 
         def validate(document,data = {})
+          file_errors = document.errors.select { |e| e.fatal? || e.error? }
+          if file_errors
+            file_errors.each do |error|
+              build_error(error, '/', data[:file_name])
+            end
+          end
           errors = get_errors(document).root.xpath("//svrl:failed-assert",NAMESPACE).map do |el|
             build_error(el.xpath('svrl:text',NAMESPACE).text, el['location'], data[:file_name])
           end

data/lib/health-data-standards/validate/validators.rb

@@ -5,14 +5,20 @@ require_relative 'schematron_validator'
 require_relative 'measure_validator'
 require_relative 'data_validator'
 require_relative 'performance_rate_validator'
+require_relative 'qrda_qdm_template_validator'
 
 module HealthDataStandards
   module Validate
 
     CDA_SDTC_SCHEMA = 'resources/schema/infrastructure/cda/CDA_SDTC.xsd'
     QRDA_CAT1_SCHEMATRON = 'resources/schematron/qrda/cat_1_r2/QRDA Category I Release 2.sch'
-    QRDA_CAT1_R3_SCHEMATRON = 'resources/schematron/qrda/cat_1/CDAR2_QRDA_I_R1_D3_2015MAY_Schematron.sch'
+    QRDA_CAT1_R3_SCHEMATRON = 'resources/schematron/qrda/cat_1/HL7_CDAR2_QRDA_Category_I_2_12_16.sch'
+    QRDA_CAT1_R3_1_SCHEMATRON = 'resources/schematron/qrda/cat_1_r3_1/HL7 QRDA Category I STU 3.1.sch'
+    QRDA_CAT1_R4_SCHEMATRON = 'resources/schematron/qrda/cat_1_r4/HL7 QRDA Category I STU 4.sch'
     QRDA_CAT3_SCHEMATRON = 'resources/schematron/qrda/cat_3/QRDA Category III.sch'
+    QRDA_CAT3_1_1SCHEMATRON = 'resources/schematron/qrda/cat_3_r1_1/HL7 QRDA Category III STU 1.1.sch'
+    QRDA_CAT3_2SCHEMATRON = 'resources/schematron/qrda/cat_3_r2/HL7 QRDA Category III STU 2.sch'
+    QRDA_CAT3_21SCHEMATRON = 'resources/schematron/qrda/cat_3_r2_1/HL7 QRDA Category III STU 2.1.sch'
     BASE_DIR = File.expand_path("../../../../", __FILE__)
 
     class Cat1Measure < MeasureValidator
@@ -60,6 +66,24 @@ module HealthDataStandards
 
     end
 
+    class Cat1R31 < Schematron::Validator
+      include Singleton
+
+      def initialize
+        super("QRDA Cat 1 Validator", File.join(BASE_DIR, QRDA_CAT1_R3_1_SCHEMATRON))
+      end
+
+    end
+
+    class Cat1R4 < Schematron::Validator
+      include Singleton
+
+      def initialize
+        super("QRDA Cat 1 Validator", File.join(BASE_DIR, QRDA_CAT1_R4_SCHEMATRON))
+      end
+
+    end
+
     class Cat3 < Schematron::Validator
       include Singleton
 
@@ -68,6 +92,30 @@ module HealthDataStandards
       end
     end
 
+    class Cat3R11 < Schematron::Validator
+      include Singleton
+
+      def initialize
+        super("QRDA Cat 3 Validator", File.join(BASE_DIR, QRDA_CAT3_1_1SCHEMATRON))
+      end
+    end
+
+    class Cat3R2 < Schematron::Validator
+      include Singleton
+
+      def initialize
+        super("QRDA Cat 3 Validator", File.join(BASE_DIR, QRDA_CAT3_2SCHEMATRON))
+      end
+    end
+
+    class Cat3R21 < Schematron::Validator
+      include Singleton
+
+      def initialize
+        super("QRDA Cat 3 Validator", File.join(BASE_DIR, QRDA_CAT3_21SCHEMATRON))
+      end
+    end
+
     class Cat3PerformanceRate < PerformanceRateValidator
       include Singleton
 

data/lib/hqmf-generator/document.xml.erb

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<QualityMeasureDocument xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<QualityMeasureDocument xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:qdm="urn:hhs-qdm:hqmf-r2-extensions:v1">
   <typeId root="2.16.840.1.113883.1.3" extension="POQM_MT000001UV03" />
   <templateId>
     <item root="2.16.840.1.113883.10.20.28.1.1" />
@@ -77,10 +77,12 @@
       <%- end -%>
     </populationCriteriaSection>
   </component>
- <%- if doc.is_cv? -%>
+ 
+  <%- end -%>
+  <%- if doc.is_cv? -%>
 
    <component>
-    <measureObservationsSection>
+    <measureObservationSection>
       <templateId>
         <item root="2.16.840.1.113883.10.20.28.2.4" />
       </templateId>
@@ -90,9 +92,8 @@
       <title value="Measure Observation Section" />
       <text></text>
       <%= xml_for_measure_observation_definition(doc) %>
-    </measureObservationsSection>
+    </measureObservationSection>
   </component>
 
   <%- end -%>
-  <%- end -%>
 </QualityMeasureDocument>

data/lib/hqmf-generator/field.xml.erb

@@ -19,6 +19,7 @@
                 <item root="<%= details[:template_id] %>"/>
               </templateId> 
               <%- end -%>
+              <id root="<%= details[:id] %>"/>
               
               <%- if is_transfer(details[:code]) -%>
               <title value="<%= details[:code] %>" />

data/lib/hqmf-generator/hqmf-generator.rb

@@ -1,14 +1,14 @@
 module HQMF2
   module Generator
-  
+
     def self.render_template(name, params)
       template_path = File.expand_path(File.join('..', "#{name}.xml.erb"), __FILE__)
       template_str = File.read(template_path)
       template = ERB.new(template_str, nil, '-', "_templ#{HQMF::Counter.instance.next}")
       context = ErbContext.new(params)
-      template.result(context.get_binding)        
+      template.result(context.get_binding)
     end
-  
+
     # Class to serialize HQMF::Document as HQMF V2 XML
     class ModelProcessor
       # Convert the supplied model instance to XML
@@ -18,28 +18,28 @@ module HQMF2
         HQMF2::Generator.render_template('document', {'doc' => doc})
       end
     end
-  
+
     # Utility class used to supply a binding to Erb. Contains utility functions used
     # by the erb templates that are used to generate the HQMF document.
     class ErbContext < OpenStruct
-      
+
 
       def initialize(vars)
         super(vars)
         @local_var_names = {}
         @local_var_counter = {}
       end
-      
+
       # Get a binding that contains all the instance variables
       # @return [Binding]
       def get_binding
         binding
       end
-      
+
       def xml_for_local_variable(criteria)
         name = @local_var_names[criteria.id]
         unless name
-          if criteria.specific_occurrence
+          if criteria.specific_occurrence && !criteria.id.starts_with?("Occurrence#{criteria.specific_occurrence}")
             name = "Occurrence#{criteria.specific_occurrence}#{criteria.id}"
           else
             name = criteria.id
@@ -53,22 +53,22 @@ module HQMF2
         reference = HQMF::Reference.new(id)
         xml_for_reference(reference)
       end
-      
+
       def xml_for_reference(reference)
         HQMF2::Generator.render_template('reference', {'doc' => doc, 'reference' => reference})
       end
-      
+
       def xml_for_attribute(attribute)
         HQMF2::Generator.render_template('attribute', {'attribute' => attribute})
       end
-      
+
       def xml_for_fields(criteria)
         fields = []
         if criteria.field_values
           criteria.field_values.each_pair do |key, value|
             if key == "FLFS"
               fields << HQMF2::Generator.render_template('fulfills', {'value' => value})
-            else   
+            else
               details = HQMF::DataCriteria::FIELDS[key]
               details[:code_system_name] = HealthDataStandards::Util::CodeSystemHelper.code_system_for(details[:code_system])
               details[:id] = "#{criteria.id}_#{key}"
@@ -83,15 +83,15 @@ module HQMF2
         end
         fields.join
       end
-      
+
       def xml_for_value(value, element_name='value', include_type=true)
         HQMF2::Generator.render_template('value', {'doc' => doc, 'value' => value, 'name' => element_name, 'include_type' => include_type})
       end
-      
+
       def xml_for_code(criteria, element_name='code', include_type=true)
         HQMF2::Generator.render_template('code', {'doc' => doc, 'criteria' => criteria, 'name' => element_name, 'include_type' => include_type})
       end
-           
+
       def xml_for_derivation(data_criteria)
         xml = ''
         if data_criteria.derivation_operator
@@ -99,7 +99,7 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_effective_time(data_criteria)
         xml = ''
         if data_criteria.effective_time
@@ -107,7 +107,7 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_reason(data_criteria)
         xml = ''
         if data_criteria.negation && data_criteria.negation_code_list_id
@@ -115,14 +115,14 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_template(data_criteria, is_source_data_criteria)
         xml = ''
         templates = []
         # Add a template ID if one is defined for this data criteria
-        template_id = HQMF::DataCriteria.template_id_for_definition(data_criteria.definition, data_criteria.status, data_criteria.negation)
+        template_id = HQMF::DataCriteria.template_id_for_definition(data_criteria.definition, data_criteria.status, false, "r2")
         if template_id
-          templates << {:id => template_id, :title => HQMF::DataCriteria.title_for_template_id(template_id)}
+          templates << {:id => template_id, :title => HQMF::DataCriteria.title_for_template_id(template_id, 'r2')}
         end
         # Add our own template id if this is a source data criteria from HQMF V1. Source
         # data criteria are the 'raw' HQMF V1 data criteria before any restrictions are applied
@@ -135,7 +135,7 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_description(data_criteria)
         xml = ''
         if data_criteria.description
@@ -143,7 +143,7 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_subsets(data_criteria)
         subsets_xml = []
         if data_criteria.subset_operators
@@ -161,11 +161,11 @@ module HQMF2
       def xml_for_precondition(precondition)
         HQMF2::Generator.render_template('precondition', {'doc' => doc, 'precondition' => precondition})
       end
-      
+
       def xml_for_data_criteria(data_criteria, is_source_data_criteria)
         HQMF2::Generator.render_template(data_criteria_template_name(data_criteria), {'doc' => doc, 'criteria' => data_criteria, 'is_source_data_criteria' => is_source_data_criteria})
       end
-      
+
       def xml_for_population_criteria(population, criteria_id)
         xml = ''
         population_criteria = doc.population_criteria(population[criteria_id])
@@ -174,17 +174,45 @@ module HQMF2
         end
         xml
       end
-      
+
       def xml_for_temporal_references(criteria)
         refs = []
         if criteria.temporal_references
           refs = criteria.temporal_references.collect do |reference|
-            HQMF2::Generator.render_template('temporal_relationship', {'doc' => doc, 'relationship' => reference})
+            HQMF2::Generator.render_template('temporal_relationship', {'doc' => doc, 'relationship' => reference, 'criteria' => criteria})
           end
         end
         refs.join
       end
 
+      def xml_for_temporal_relationship_attribute(criteria, relationship)
+        targetCriteria = doc.data_criteria(relationship.reference.id)
+        if (criteria.field_values || targetCriteria.try(:field_values))
+          sourceKeys = (criteria.field_values || {}).keys.select {|key| [:timestamp, :nested_timestamp].include? HQMF::DataCriteria::FIELDS[key][:field_type]}
+          targetKeys = (targetCriteria.try(:field_values) || {}).keys.select {|key| [:timestamp, :nested_timestamp].include? HQMF::DataCriteria::FIELDS[key][:field_type]}
+          if (!sourceKeys.empty? || !targetKeys.empty?)
+            data = {
+              sourceKeys: sourceKeys,
+              targetKeys: targetKeys
+            }
+
+            HQMF2::Generator.render_template('temporal_relationship_attribute', {'doc' => doc, 'criteria' => criteria, 'targetCriteria'=>targetCriteria, 'data'=> data})
+          end
+        end
+
+      end
+
+      def temporal_relationship_attribute_effective_time(field)
+        {facility_arrival: 'low',
+        facility_departure: 'high',
+        discharge_time: 'high',
+        admit_time: 'low',
+        start_date: 'low',
+        end_date: 'high',
+        incision_time: 'low',
+        removal_time: 'high'}[HQMF::DataCriteria::FIELDS[field][:coded_entry_method]]
+      end
+
       def xml_for_measure_observation_definition(doc)
         observation = doc.find_population_by_type(HQMF::PopulationCriteria::OBSERV)
         msrpopl = doc.find_population_by_type( HQMF::PopulationCriteria::MSRPOPL)
@@ -192,7 +220,14 @@ module HQMF2
       end
 
       def expression_for_observation(doc,observation)
-        "NOT IMPLEMENTED"
+        pre = observation.preconditions[0]
+        if pre && pre.reference
+          dc = doc.data_criteria(pre.reference.id)
+          children = dc.children_criteria
+          if children && children.length == 2
+            return "#{children[0]} - #{children[1]}"
+          end
+        end
       end
 
       def data_criteria_should_be_grouper?(criteria)
@@ -201,16 +236,21 @@ module HQMF2
         return true unless criteria.subset_operators
         criteria.subset_operators.all? {|o| o.supports_grouper_criteria?}
       end
-      
+
+      def percision_unit_for_range(relationship)
+        percision_map = {'a'=>'d', 'mo'=>'d', 'wk'=>'d', 'd'=>'d', 'h'=>'min', 'min'=>'min', 's'=>'s'}
+        percision_map[relationship.try(:range).try(:high).try(:unit) || relationship.try(:range).try(:low).try(:unit) || "min"]
+      end
+
       def oid_for_name(code_system_name)
         HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(code_system_name)
       end
-      
+
       def reference_element_name(id)
         referenced_criteria = doc.data_criteria(id)
         element_name_prefix(referenced_criteria)
       end
-      
+
       def reference_type_name(id)
         referenced_criteria = doc.data_criteria(id)
         type = nil
@@ -241,7 +281,7 @@ module HQMF2
           end
         end
       end
-      
+
       def code_for_characteristic(characteristic)
         case characteristic
         when :birthtime
@@ -260,7 +300,7 @@ module HQMF2
           raise "Unknown demographic code [#{characteristic}]"
         end
       end
-   
+
       def is_transfer(code)
         if code == "TRANSFER_TO" || code == "TRANSFER_FROM"
           true
@@ -268,7 +308,7 @@ module HQMF2
           false
         end
       end
-   
+
       def oid_for_characteristic(characteristic)
         case characteristic
         when :birthtime
@@ -277,12 +317,12 @@ module HQMF2
           '2.16.840.1.113883.6.96'
         end
       end
-      
+
       def data_criteria_template_name(data_criteria)
         case data_criteria.definition
         when 'diagnosis', 'diagnosis_family_history'
           'condition_criteria'
-        when 'encounter' 
+        when 'encounter'
           'encounter_criteria'
         when 'procedure', 'risk_category_assessment', 'physical_exam', 'communication_from_patient_to_provider', 'communication_from_provider_to_provider', 'device', 'diagnostic_study', 'intervention'
           if data_criteria.value.nil?
@@ -335,7 +375,7 @@ module HQMF2
           end
         end
       end
-      
+
       def population_element_prefix(population_criteria_code)
         case population_criteria_code
         when HQMF::PopulationCriteria::IPP
@@ -344,21 +384,25 @@ module HQMF2
           'denominator'
         when HQMF::PopulationCriteria::NUMER
           'numerator'
+        when HQMF::PopulationCriteria::NUMEX
+          'numeratorExclusion'
         when HQMF::PopulationCriteria::DENEXCEP
           'denominatorException'
         when HQMF::PopulationCriteria::DENEX
           'denominatorExclusion'
         when HQMF::PopulationCriteria::MSRPOPL
-          'measurePopulation'  
+          'measurePopulation'
+        when HQMF::PopulationCriteria::MSRPOPLEX
+          'measurePopulationExclusion'
         when HQMF::PopulationCriteria::OBSERV
-           'measureObservation'  
+           'measureObservation'
         when HQMF::PopulationCriteria::STRAT
-           'stratifier'  
-        else  
+           'stratifier'
+        else
           raise "Unknown population criteria type #{population_criteria_code}"
         end
       end
     end
-    
+
   end
 end