health-data-standards 3.4.6 → 3.5.0

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

@@ -1,4 +1,5 @@
 class ResultValue
   include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
   embedded_in :entry
 end

data/lib/health-data-standards/models/svs/concept.rb

@@ -4,6 +4,7 @@ module HealthDataStandards
     class Concept
 	
     	include Mongoid::Document
+      include Mongoid::Attributes::Dynamic
     	field :code, type: String
     	field :code_system_name, type: String
     	field :code_system_version, type: String

data/lib/health-data-standards/models/svs/value_set.rb

@@ -3,6 +3,7 @@ module HealthDataStandards
     class ValueSet
 
       include Mongoid::Document
+      include Mongoid::Attributes::Dynamic
       field :oid, type: String
       field :display_name, type: String
       field :version, type: String

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

@@ -1,5 +1,6 @@
 class Telecom
   include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
   
   field :use, type: String
   field :value, type: String

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

@@ -1,5 +1,6 @@
 class Transfer
   include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
   include ThingWithCodes
 
   field :time, type: Integer 

data/lib/health-data-standards/tasks/bundle.rake

@@ -6,7 +6,7 @@ namespace :bundle do
 
   desc 'Activate/Inactivate a measure bundle'
   task :activate,[:version,:active] => [:environment] do |task, args|
-    bundle = Bundle.where({version: args.version})
+    bundle = HealthDataStandards::CQM::Bundle.where({version: args.version})
     if bundle.count == 0
       puts "Cannot find bundle with version number #{args.version}"
       return
@@ -23,7 +23,7 @@ namespace :bundle do
 
   desc 'List bundles'
   task :list  => [:environment] do
-     Bundle.where({}).each do |b|
+     HealthDataStandards::CQM::Bundle.where({}).each do |b|
       puts "Bundle #{b.title} - #{b.version}  active: #{b.active}"
      end
   end
@@ -49,7 +49,7 @@ namespace :bundle do
 
     if (args.create_indexes != 'false')
       ::Rails.application.eager_load!
-      ::Rails::Mongoid.create_indexes
+      ::Mongoid::Tasks::Database.create_indexes
     end
 
     puts "Successfully imported bundle at: #{args.bundle_path}"

data/lib/health-data-standards/util/vs_api.rb

@@ -12,10 +12,10 @@ module HealthDataStandards
 				@password = password
 			end
 
-
-			def get_valueset(oid, effective_date=nil, &block)
+			def get_valueset(oid, effective_date=nil, include_draft=false, &block)
 				params = {id: oid, ticket: get_ticket}
 				params[:effectiveDate] = effective_date if effective_date
+				params[:includeDraft] = 'yes' if include_draft
 				vs = RestClient.get api_url, {:params=>params}
 				yield oid,vs if block_given?
 				vs

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

@@ -1,11 +1,9 @@
-	<subjectOf>
-		<measureAttribute>
-			<id root="2.16.840.1.113883.3.100.1" extension="<%= attribute.id %>"/>
-			<code code="<%= attribute.code %>">
-				<displayName value="<%= attribute.name %>"/>
-			</code>
-			<%- if attribute.value -%>
-			<value xsi:type="ED" value="<%= attribute.value %>"/>
-			<%- end -%>
-		</measureAttribute>
-	</subjectOf>
+  <subjectOf>
+    <measureAttribute classCode="OBS" moodCode="EVN">
+      <%- if attribute.id_obj -%>
+      <id root="2.16.840.1.113883.3.100.1" <%="extension=\"#{attribute.id_obj.extension}\"" if attribute.id_obj.extension %>"/>
+      <%- end -%>
+      <%= xml_for_value(attribute.code_obj, 'code', false) %>
+      <%= xml_for_value(attribute.value_obj, 'value') %>
+    </measureAttribute>
+  </subjectOf>

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

@@ -1,9 +1,8 @@
       <entry typeCode="DRIV">
+        <%= xml_for_local_variable(criteria) %>
         <observationCriteria moodCode="EVN" classCode="OBS">
           <%= xml_for_template(criteria, is_source_data_criteria) %>
-          <id>
-            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
-          </id>
+          <id root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
           <%= xml_for_code(criteria) %>
           <%= xml_for_description(criteria) %>
           <%= xml_for_effective_time(criteria) %>
@@ -11,11 +10,12 @@
           <%= xml_for_value(criteria.value) %>
           <%- end -%>
           <definition>
-            <observationReference moodCode="EVN" classCode="OBS">
+            <criteriaReference moodCode="EVN" classCode="OBS">
               <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
-            </observationReference>
+            </criteriaReference>
           </definition>
           <%= xml_for_temporal_references(criteria) %>
           <%= xml_for_fields(criteria) %>
+          <%= xml_for_subsets(criteria) %>
         </observationCriteria>
       </entry>

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

@@ -4,10 +4,14 @@
           <%- code_system_oid = oid_for_name(code_system_name) -%>
           <<%= name %> codeSystemName="<%= code_system_name %>" codeSystem="<%= code_system_oid %>"
             code="<%= code %>">
-            <displayName value="<%= criteria.title %>"/>
+            <%- if criteria.title -%>
+              <displayName value="<%=ERB::Util::h criteria.title %>"/>
+            <%- end -%>
           </<%= name %>>
           <%- elsif criteria.code_list_id -%>
           <<%= name %><%= " xsi:type=\"CD\"" if include_type %> valueSet="<%= criteria.code_list_id %>">
-            <displayName value="<%= criteria.title %>"/>
+            <%- if criteria.title -%>
+              <displayName value="<%=ERB::Util::h criteria.title %>"/>
+            <%- end -%>
           </<%= name %>>
           <%- end -%>

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

@@ -1,18 +1,17 @@
       <entry typeCode="DRIV">
+        <%= xml_for_local_variable(criteria) %>
         <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>
+          <id root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
           <%= xml_for_description(criteria) %>
           <%= "<statusCode code=\"#{criteria.status}\"/>" if criteria.status %>
           <%= xml_for_effective_time(criteria) %>
           <%= xml_for_reason(criteria) %>
           <%= xml_for_code(criteria, 'value') %>
           <definition>
-            <observationReference moodCode="EVN" classCode="OBS">
+            <criteriaReference moodCode="EVN" classCode="OBS">
               <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
-            </observationReference>
+            </criteriaReference>
           </definition>
           <%= xml_for_temporal_references(criteria) %>
           <%= xml_for_fields(criteria) %>

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

@@ -1,6 +1,6 @@
-          <excerpt typeCode="XCRPT">
-            <subsetCode code="<%= criteria.derivation_operator %>"/>
-            <%- criteria.children_criteria.each do |child_id| -%>
-            <%= xml_for_reference_id(child_id) %>
-            <%- end -%>
-          </excerpt>
+          <%- criteria.children_criteria.each do |child_id| -%>
+            <outboundRelationship typeCode="COMP">
+              <conjunctionCode code="<%= criteria.derivation_operator == 'UNION' ? 'OR' : 'AND' %>"/>
+              <%= xml_for_reference_id(child_id) %>
+            </outboundRelationship>
+          <%- end -%>

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

@@ -1 +1 @@
-          <text value="<%= text %>"/>
+          <text value="<%=ERB::Util::h text %>"/>

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

@@ -1,13 +1,17 @@
 <?xml version="1.0" encoding="utf-8"?>
 <QualityMeasureDocument xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <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" />
+  </templateId>
   <id root="2.16.840.1.113883.3.100.1" extension="<%= doc.hqmf_id %>" />
   <code code="57024-2" codeSystem="2.16.840.1.113883.6.1"/>
-  <title value="<%= doc.title %>"/>
-  <text value="<%= doc.description %>"/>
+  <title value="<%=ERB::Util::h doc.title %>"/>
+  <text value="<%=ERB::Util::h doc.description %>"/>
   <statusCode code="completed" />
   <setId root="2.16.840.1.113883.3.100.1" extension="<%= doc.hqmf_set_id %>" />
   <versionNumber value="<%= doc.hqmf_version_number %>"/>
-  <author typeCode="AUT" contextControlCode="OP">
+  <author typeCode="AUT">
     <responsibleParty classCode="ASSIGNED" />
   </author>
   <custodian typeCode="CST">
@@ -18,9 +22,18 @@
       <code code="MSRTP" codeSystem="2.16.840.1.113883.3.560">
         <displayName value="Measurement period"/>
       </code>
-      <value>
-        <low value="<%= doc.measure_period.low.value %>" />
-        <high value="<%= doc.measure_period.high.value %>" />
+      <value xsi:type="PIVL_TS">
+        <phase lowClosed="true" highClosed="true">
+            <%- if doc.measure_period.low != nil -%>
+                <low value="<%= doc.measure_period.low.value %>" />
+            <%- end -%>
+            <%- if doc.measure_period.high != nil -%>
+                <high value="<%= doc.measure_period.high.value %>" />
+            <%- end -%>
+            <%- if doc.measure_period.width != nil -%>
+                <width xsi:type="PQ" value="<%= doc.measure_period.width.value %>" unit="a" />
+            <%- end -%>
+        </phase>
       </value>
     </measurePeriod>
   </controlVariable>
@@ -29,9 +42,12 @@
   <%- end -%>
   <component>
     <dataCriteriaSection>
+      <templateId>
+        <item root="2.16.840.1.113883.10.20.28.2.2" />
+      </templateId>
       <code code="57025-9" codeSystem="2.16.840.1.113883.6.1"/>
       <title value="Data Criteria Section"/>
-      <text>This section describes the data criteria.</text>
+      <text value="This section describes the data criteria."/>
       <%- doc.all_data_criteria.each do |data_criteria| -%>
       <%= xml_for_data_criteria(data_criteria, false) %>
       <%- end -%>
@@ -47,17 +63,36 @@
 		  <templateId>
 		    <item root="<%= HQMF::Document::STRATIFIED_POPULATION_TEMPLATE_ID %>" identifierName="<%= HQMF::Document::STRATIFIED_POPULATION_TEMPLATE_TITLE %>" controlInformationRoot="<%= population['stratification'] %>"/>
 		  </templateId>
+      <%- else -%>
+      <templateId>
+        <item root="2.16.840.1.113883.10.20.28.2.1"/>
+      </templateId>
       <%- end -%>
       <id root="2.16.840.1.113883.3.100.1" extension="<%= population['id'] || "Population#{population_index}" %>"/>
       <code code="57026-7" codeSystem="2.16.840.1.113883.6.1"/>
-      <title value="<%= population['title'] %>"/>
-      <text>This section describes the Initial Patient Population,
-        Numerator, Denominator, Denominator Exceptions, and Measure
-        Populations</text>
+      <title value="<%=ERB::Util::h population['title'] %>"/>
+      <text value="This section describes the Initial Patient Population, Numerator, Denominator, Denominator Exceptions, and Measure Populations"/>
       <%- population.keys.each do |criteria_id| -%>
       <%= xml_for_population_criteria(population, criteria_id) %>
       <%- end -%>
     </populationCriteriaSection>
   </component>
+ <%- if doc.is_cv? -%>
+
+   <component>
+    <measureObservationsSection>
+      <templateId>
+        <item root="2.16.840.1.113883.10.20.28.2.4" />
+      </templateId>
+      <code code="57027-5" codeSystem="2.16.840.1.113883.6.1">
+        <displayName value="Measure Observation" />
+      </code>
+      <title value="Measure Observation Section" />
+      <text></text>
+      <%= xml_for_measure_observation_definition(doc) %>
+    </measureObservationsSection>
+  </component>
+
+  <%- end -%>
   <%- end -%>
 </QualityMeasureDocument>

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

@@ -1,17 +1,16 @@
       <entry typeCode="DRIV">
+        <%= xml_for_local_variable(criteria) %>
         <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>
+          <id root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
           <%= xml_for_code(criteria) %>
           <%= xml_for_description(criteria) %>
           <%= xml_for_effective_time(criteria) %>
           <%= xml_for_reason(criteria) %>
           <definition>
-            <encounterReference moodCode="EVN" classCode="ENC">
+            <criteriaReference moodCode="EVN" classCode="ENC">
               <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
-            </encounterReference>
+            </criteriaReference>
           </definition>
           <%= xml_for_temporal_references(criteria) %>
           <%= xml_for_fields(criteria) %>

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

@@ -19,10 +19,22 @@
                 <item root="<%= details[:template_id] %>"/>
               </templateId> 
               <%- end -%>
+              
+              <%- if is_transfer(details[:code]) -%>
+              <title value="<%= details[:code] %>" />
+              <statusCode code="completed" />
+              <%= xml_for_value(value) %>
+              <participation  typeCode="ORG">
+                <role classCode="LOCE">
+                  <code xsi:type="CD" />
+                </role>
+              </participation>
+              <%- else -%>
               <code code="<%= details[:code] %>" codeSystem="<%= details[:code_system] %>" codeSystemName="<%= details[:code_system_name] %>">
-                <displayName value="<%= details[:title] %>"/> 
+                <displayName value="<%=ERB::Util::h details[:title] %>"/> 
               </code>
               <%= xml_for_value(value) %>
+              <%- end -%>
             </observationCriteria>
 <%- end -%>
           </outboundRelationship>

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

@@ -0,0 +1,17 @@
+      <entry typeCode="DRIV">
+        <%= xml_for_local_variable(criteria) %>
+        <grouperCriteria moodCode="EVN" classCode="GROUPER">
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          <%= xml_for_description(criteria) %>
+          <definition>
+            <criteriaReference moodCode="EVN" classCode="GROUPER">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </criteriaReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %> 
+          <%= xml_for_fields(criteria) %>
+          <%= xml_for_derivation(criteria) %>
+          <%= xml_for_subsets(criteria) %>
+        </grouperCriteria>
+      </entry>

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

@@ -23,8 +23,11 @@ module HQMF2
     # 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
@@ -33,6 +36,19 @@ module HQMF2
         binding
       end
       
+      def xml_for_local_variable(criteria)
+        name = @local_var_names[criteria.id]
+        unless name
+          if criteria.specific_occurrence
+            name = "Occurrence#{criteria.specific_occurrence}#{criteria.id}"
+          else
+            name = criteria.id
+          end
+          @local_var_names[criteria.id] = name
+        end
+        HQMF2::Generator.render_template('local_variable', {'name' => name})
+      end
+
       def xml_for_reference_id(id)
         reference = HQMF::Reference.new(id)
         xml_for_reference(reference)
@@ -132,7 +148,11 @@ module HQMF2
         end
         subsets_xml.join()
       end
-      
+
+      def xml_for_precondition_cv(precondition)
+        HQMF2::Generator.render_template('precondition_cv', {'doc' => doc, 'precondition' => precondition})
+      end
+
       def xml_for_precondition(precondition)
         HQMF2::Generator.render_template('precondition', {'doc' => doc, 'precondition' => precondition})
       end
@@ -144,7 +164,7 @@ module HQMF2
       def xml_for_population_criteria(population, criteria_id)
         xml = ''
         population_criteria = doc.population_criteria(population[criteria_id])
-        if population_criteria
+        if population_criteria && population_element_prefix(criteria_id) != "measureObservation"
           xml = HQMF2::Generator.render_template('population_criteria', {'doc' => doc, 'population' => population, 'criteria_id' => criteria_id, 'population_criteria' => population_criteria})
         end
         xml
@@ -159,6 +179,23 @@ module HQMF2
         end
         refs.join
       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)
+        HQMF2::Generator.render_template('measure_observation_definition', {'doc' => doc, 'observation' => observation, "msrpopl" => msrpopl})
+      end
+
+      def expression_for_observation(doc,observation)
+        "NOT IMPLEMENTED"
+      end
+
+      def data_criteria_should_be_grouper?(criteria)
+        return false unless criteria
+        return false unless criteria.definition == 'derived'
+        return true unless criteria.subset_operators
+        criteria.subset_operators.all? {|o| o.supports_grouper_criteria?}
+      end
       
       def oid_for_name(code_system_name)
         HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(code_system_name)
@@ -189,8 +226,14 @@ module HQMF2
           'SBADM'
         when :medication_supply
           'SPLY'
+        when :observation
+           'OBS'
         else
-          'OBS'
+          if data_criteria_should_be_grouper?(referenced_criteria)
+            'GROUPER'
+          else
+            'OBS'
+          end
         end
       end
       
@@ -212,7 +255,15 @@ module HQMF2
           raise "Unknown demographic code [#{characteristic}]"
         end
       end
-      
+   
+      def is_transfer(code)
+        if code == "TRANSFER_TO" || code == "TRANSFER_FROM"
+          true
+        else
+          false
+        end
+      end
+   
       def oid_for_characteristic(characteristic)
         case characteristic
         when :birthtime
@@ -245,6 +296,12 @@ module HQMF2
           'characteristic_criteria'
         when 'variable'
           'variable_criteria'
+        when 'derived'
+          if data_criteria_should_be_grouper?(data_criteria)
+            'grouper_criteria'
+          else
+            'observation_criteria'
+          end
         else
           'observation_criteria'
         end
@@ -266,14 +323,18 @@ module HQMF2
         when :medication_supply
           'supply'
         else
-          'observation'
+          if data_criteria_should_be_grouper?(data_criteria)
+            'grouper'
+          else
+            'observation'
+          end
         end
       end
       
       def population_element_prefix(population_criteria_code)
         case population_criteria_code
         when HQMF::PopulationCriteria::IPP
-          'patientPopulation'
+          'initialPopulation'
         when HQMF::PopulationCriteria::DENOM
           'denominator'
         when HQMF::PopulationCriteria::NUMER
@@ -282,11 +343,17 @@ module HQMF2
           'denominatorException'
         when HQMF::PopulationCriteria::DENEX
           'denominatorExclusion'
-        else
+        when HQMF::PopulationCriteria::MSRPOPL
+          'measurePopulation'  
+        when HQMF::PopulationCriteria::OBSERV
+           'measureObservation'  
+        when HQMF::PopulationCriteria::STRAT
+           'stratifier'  
+        else  
           raise "Unknown population criteria type #{population_criteria_code}"
         end
       end
     end
     
   end
-end
+end