health-data-standards 2.2.1 → 3.0.3

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

@@ -0,0 +1,4 @@
+          <effectiveTime xsi:type="IVL_TS">
+            <%= xml_for_value(effective_time.low, 'low', false) if effective_time.low -%>
+            <%= xml_for_value(effective_time.high, 'high', false) if effective_time.high -%>
+          </effectiveTime>

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

@@ -0,0 +1,21 @@
+      <entry typeCode="DRIV">
+        <encounterCriteria moodCode="EVN" classCode="ENC"<%= " actionNegationInd='true'" if criteria.negation %>>
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id>
+            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          </id>
+          <%= xml_for_code(criteria) %>
+          <%= xml_for_description(criteria) %>
+          <%= xml_for_effective_time(criteria) %>
+          <%= xml_for_reason(criteria) %>
+          <definition>
+            <encounterReference moodCode="EVN" classCode="ENC">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </encounterReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %>
+          <%= xml_for_fields(criteria) %>
+          <%= xml_for_derivation(criteria) %>
+          <%= xml_for_subsets(criteria) %>
+        </encounterCriteria>
+      </entry>

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

@@ -0,0 +1,28 @@
+          <outboundRelationship typeCode="SUBJ">
+<%- if details[:code] == 'SDLOC' -%>
+            <encounterCriteria classCode="ENC" moodCode="EVN">
+              <%- if details[:templateId] -%>
+              <templateId>
+                <item root="<%= details[:template_id] %>"/>
+              </templateId> 
+              <%- end -%>
+              <participation typeCode="LOC">
+                <role classCode="SDLOC">
+                  <%= xml_for_value(value, 'code') %>
+                </role>
+              </participation>
+            </encounterCriteria>
+<%- else -%>
+            <observationCriteria classCode="OBS" moodCode="EVN">
+              <%- if details[:templateId] -%>
+              <templateId>
+                <item root="<%= details[:template_id] %>"/>
+              </templateId> 
+              <%- end -%>
+              <code code="<%= details[:code] %>" codeSystem="<%= details[:code_system] %>" codeSystemName="<%= details[:code_system_name] %>">
+                <displayName value="<%= details[:title] %>"/> 
+              </code>
+              <%= xml_for_value(value) %>
+            </observationCriteria>
+<%- end -%>
+          </outboundRelationship>

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

@@ -0,0 +1,292 @@
+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)        
+    end
+  
+    # Class to serialize HQMF::Document as HQMF V2 XML
+    class ModelProcessor
+      # Convert the supplied model instance to XML
+      # @param [HQMF::Document] doc the model instance
+      # @return [String] the serialized XML as a String
+      def self.to_hqmf(doc)
+        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)
+      end
+      
+      # Get a binding that contains all the instance variables
+      # @return [Binding]
+      def get_binding
+        binding
+      end
+      
+      def xml_for_reference_id(id)
+        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|
+            details = HQMF::DataCriteria::FIELDS[key]
+            details[:code_system_name] = HealthDataStandards::Util::CodeSystemHelper.code_system_for(details[:code_system])
+            fields << HQMF2::Generator.render_template('field', {'details' => details, 'value' => value})
+          end
+        end
+        if criteria.specific_occurrence
+          fields << HQMF2::Generator.render_template('specific_occurrence', {'source_criteria_id' => criteria.source_data_criteria, 'type' => criteria.specific_occurrence_const, 'id' => criteria.specific_occurrence})
+        elsif criteria.source_data_criteria
+          fields << HQMF2::Generator.render_template('source', {'source_criteria_id' => criteria.source_data_criteria})
+        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
+          xml = HQMF2::Generator.render_template('derivation', {'doc' => doc, 'criteria' => data_criteria})
+        end
+        xml
+      end
+      
+      def xml_for_effective_time(data_criteria)
+        xml = ''
+        if data_criteria.effective_time
+          xml = HQMF2::Generator.render_template('effective_time', {'doc' => doc, 'effective_time' => data_criteria.effective_time})
+        end
+        xml
+      end
+      
+      def xml_for_reason(data_criteria)
+        xml = ''
+        if data_criteria.negation && data_criteria.negation_code_list_id
+          xml = HQMF2::Generator.render_template('reason', {'doc' => doc, 'code_list_id' => data_criteria.negation_code_list_id})
+        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)
+        if template_id
+          templates << {:id => template_id, :title => HQMF::DataCriteria.title_for_template_id(template_id)}
+        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
+        # they are only used for negating specific occurrences
+        if is_source_data_criteria
+          templates << {:id => HQMF::DataCriteria::SOURCE_DATA_CRITERIA_TEMPLATE_ID, :title => HQMF::DataCriteria::SOURCE_DATA_CRITERIA_TEMPLATE_TITLE}
+        end
+        if templates.length > 0
+          xml = HQMF2::Generator.render_template('template_id', {'templates' => templates})
+        end
+        xml
+      end
+      
+      def xml_for_description(data_criteria)
+        xml = ''
+        if data_criteria.description
+          xml = HQMF2::Generator.render_template('description', {'text' => data_criteria.description})
+        end
+        xml
+      end
+      
+      def xml_for_subsets(data_criteria)
+        subsets_xml = []
+        if data_criteria.subset_operators
+          subsets_xml = data_criteria.subset_operators.collect do |operator|
+            HQMF2::Generator.render_template('subset', {'doc' => doc, 'subset' => operator, 'criteria' => data_criteria})
+          end
+        end
+        subsets_xml.join()
+      end
+      
+      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])
+        if population_criteria
+          xml = HQMF2::Generator.render_template('population_criteria', {'doc' => doc, 'population' => population, 'criteria_id' => criteria_id, 'population_criteria' => population_criteria})
+        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})
+          end
+        end
+        refs.join
+      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
+        if referenced_criteria
+          type = referenced_criteria.type
+        elsif id=="MeasurePeriod"
+          type = :observation
+        end
+        if !type
+          raise "No data criteria with ID: #{id}"
+        end
+        case type
+        when :encounters
+          'ENC'
+        when :procedures
+          'PROC'
+        when :medications, :allMedications
+          'SBADM'
+        when :medication_supply
+          'SPLY'
+        else
+          'OBS'
+        end
+      end
+      
+      def code_for_characteristic(characteristic)
+        case characteristic
+        when :birthtime
+          '21112-8'
+        when :age
+          '424144002'
+        when :gender
+          '263495000'
+        when :languages
+          '102902016'
+        when :maritalStatus
+          '125680007'
+        when :race
+          '103579009'
+        else
+          raise "Unknown demographic code [#{characteristic}]"
+        end
+      end
+      
+      def oid_for_characteristic(characteristic)
+        case characteristic
+        when :birthtime
+          '2.16.840.1.113883.6.1'
+        else
+          '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' 
+          '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?
+            'procedure_criteria'
+          else
+            'observation_criteria'
+          end
+        when 'medication'
+          case data_criteria.status
+          when 'dispensed', 'ordered'
+            'supply_criteria'
+          else # active or administered
+            'substance_criteria'
+          end
+        when 'patient_characteristic', 'patient_characteristic_birthdate', 'patient_characteristic_clinical_trial_participant', 'patient_characteristic_expired', 'patient_characteristic_gender', 'patient_characteristic_age', 'patient_characteristic_languages', 'patient_characteristic_marital_status', 'patient_characteristic_race'
+          'characteristic_criteria'
+        when 'variable'
+          'variable_criteria'
+        else
+          'observation_criteria'
+        end
+      end
+
+      def section_name(data_criteria)
+        data_criteria.definition.to_s
+      end
+
+      def element_name_prefix(data_criteria)
+        type = data_criteria ? data_criteria.type : :observation
+        case type
+        when :encounters
+          'encounter'
+        when :procedures
+          'procedure'
+        when :medications, :allMedications
+          'substanceAdministration'
+        when :medication_supply
+          'supply'
+        else
+          'observation'
+        end
+      end
+      
+      def population_element_prefix(population_criteria_code)
+        case population_criteria_code
+        when HQMF::PopulationCriteria::IPP
+          'patientPopulation'
+        when HQMF::PopulationCriteria::DENOM
+          'denominator'
+        when HQMF::PopulationCriteria::NUMER
+          'numerator'
+        when HQMF::PopulationCriteria::DENEXCEP
+          'denominatorException'
+        when HQMF::PopulationCriteria::DENEX
+          'denominatorExclusion'
+        else
+          raise "Unknown population criteria type #{population_criteria_code}"
+        end
+      end
+    end
+    
+  end
+end

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

@@ -0,0 +1,25 @@
+      <entry typeCode="DRIV">
+        <observationCriteria moodCode="EVN" classCode="OBS"<%= " actionNegationInd='true'" if criteria.negation %>>
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id>
+            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          </id>
+          <%= xml_for_code(criteria) %>
+          <%= xml_for_description(criteria) %>
+          <%= "<statusCode code=\"#{criteria.status}\"/>" if criteria.status %>
+          <%= xml_for_effective_time(criteria) %>
+          <%= xml_for_reason(criteria) %>
+          <%- if criteria.value -%>
+          <%= xml_for_value(criteria.value) %>
+          <%- end -%>
+          <definition>
+            <observationReference moodCode="EVN" classCode="OBS">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </observationReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %>
+          <%= xml_for_fields(criteria) %>
+          <%= xml_for_derivation(criteria) %>
+          <%= xml_for_subsets(criteria) %>
+        </observationCriteria>
+      </entry>

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

@@ -0,0 +1,23 @@
+      <component typeCode="COMP">
+        <<%= population_element_prefix(criteria_id) %>Criteria  classCode="OBS" moodCode="EVN">
+          <id root="c75181d0-73eb-11de-8a39-0800200c9a66"
+            extension="<%= population_criteria.hqmf_id %>"/>
+          <code codeSystem="2.16.840.1.113883.5.1063"
+              codeSystemName="HL7 Observation Value"
+              code="<%= population_criteria.type %>">
+            <displayName value="<%= population_criteria.title %>"/>
+          </code>
+          <isCriterionInd value="true"/>
+          <%- if population_criteria.preconditions.present? && population_criteria.preconditions.length > 0 -%>
+            <%- population_criteria.preconditions.each do |precondition| -%>
+          <%= xml_for_precondition(precondition) %>
+            <%- end -%>
+          <%- else -%>
+          <precondition typeCode="PRCN" nullFlavor="NA">
+            <allTrue>
+              <id/>
+            </allTrue>
+          </precondition>
+          <%- end -%>
+        </<%= population_element_prefix(criteria_id) %>Criteria>
+      </component>

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

@@ -0,0 +1,14 @@
+<precondition typeCode="PRCN">
+  <%- if precondition.conjunction? -%>
+  <<%= precondition.conjunction_code_with_negation %>>
+    <id/>
+    <%- precondition.preconditions.each do |child| -%>
+    <%= xml_for_precondition(child) %>
+    <%- end -%>
+  </<%= precondition.conjunction_code_with_negation %>>
+  <%- else -%>
+    <<%= reference_element_name(precondition.reference.id) %>Reference moodCode="EVN" classCode="<%= reference_type_name(precondition.reference.id) %>">
+      <id root="2.16.840.1.113883.3.100.1" extension="<%= precondition.reference.id %>"/>
+    </<%= reference_element_name(precondition.reference.id) %>Reference>
+  <%- end -%>
+</precondition>

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

@@ -0,0 +1,22 @@
+      <entry typeCode="DRIV">
+        <procedureCriteria moodCode="EVN" classCode="PROC"<%= " actionNegationInd='true'" if criteria.negation %>>
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id>
+            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          </id>
+          <%= xml_for_code(criteria) %>
+          <%= xml_for_description(criteria) %>
+          <%= "<statusCode code=\"#{criteria.status}\"/>" if criteria.status %>
+          <%= xml_for_effective_time(criteria) %>
+          <%= xml_for_reason(criteria) %>
+          <definition>
+            <procedureReference moodCode="EVN" classCode="PROC">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </procedureReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %>
+          <%= xml_for_fields(criteria) %>
+          <%= xml_for_derivation(criteria) %>
+          <%= xml_for_subsets(criteria) %>
+        </procedureCriteria>
+      </entry>

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

@@ -0,0 +1,3 @@
+          <reasonCode>
+            <item valueSet="<%= code_list_id %>"/>
+          </reasonCode>

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

@@ -0,0 +1,3 @@
+            <<%= reference_element_name(reference.id) %>Reference moodCode="EVN" classCode="<%= reference_type_name(reference.id) %>">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= reference.id %>"/>
+            </<%= reference_element_name(reference.id) %>Reference>