health-data-standards 4.0.4 → 4.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/Rakefile

@@ -1,6 +1,5 @@
 require 'rake/testtask'
 require 'cane/rake_task'
-require "simplecov"
 
 import 'lib/tasks/hqmf.rake'
 

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

@@ -34,7 +34,8 @@ module HealthDataStandards
         '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
         '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
         '2.16.840.1.113883.6.13' => 'CDT',
-        '2.16.840.1.113883.18.2' => 'AdministrativeSex'
+        '2.16.840.1.113883.18.2' => 'AdministrativeSex',
+        '2.16.840.1.113883.5.1' => 'AdministrativeGender'
       }
       
       CODE_SYSTEM_ALIASES = {
@@ -73,4 +74,3 @@ module HealthDataStandards
     end
   end
 end
-

data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb

@@ -32,24 +32,17 @@ module HQMF2
     # Returns the population descriptions and criteria found in this document
     def extract_populations_and_criteria
       has_observation = extract_observations
-      document_populations = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection',
-                                        HQMF2::Document::NAMESPACES)
-      # Sort the populations based on the id/extension, since the populations may be out of order; there doesn't seem to
-      # be any other way that order is indicated in the HQMF
-      document_populations = document_populations.sort_by do |pop|
-        pop.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES).try(:value)
-      end
+      document_populations = get_document_populations
       number_of_populations = document_populations.length
       document_populations.each_with_index do |population_def, population_index|
         population = {}
         handle_base_populations(population_def, population)
 
-        id_def = population_def.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES)
-        population['id'] = id_def ? id_def.value : "Population#{population_index}"
-        title_def = population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
-        population['title'] = title_def ? title_def.value : "Population #{population_index}"
+        id_def = get_id_def(population_def)
+        add_id_to_population(population_def, id_def, population, population_index)
+        add_title_to_population(population_def, population)
+        add_observ_to_population(has_observation, population)
 
-        population['OBSERV'] = 'OBSERV' if has_observation
         @populations << population
         handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
       end
@@ -59,6 +52,37 @@ module HQMF2
       [@populations, @population_criteria]
     end
 
+    def get_document_populations
+      document_populations = @doc.xpath('cda:QualityMeasureDocument/cda:component/cda:populationCriteriaSection',
+                                        HQMF2::Document::NAMESPACES)
+      # Sort the populations based on the id/extension, since the populations may be out of order; there doesn't seem to
+      # be any other way that order is indicated in the HQMF
+      document_populations = document_populations.sort_by do |pop|
+        pop.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES).try(:value)
+      end
+    end
+
+    def get_id_def(population_def)
+      population_def.at_xpath('cda:id/@extension', HQMF2::Document::NAMESPACES)
+    end
+
+    def get_title_def(population_def)
+      title_def = population_def.at_xpath('cda:title/@value', HQMF2::Document::NAMESPACES)
+    end
+
+    def add_id_to_population(population_def, id_def, population, population_index)
+      population['id'] = id_def ? id_def.value : "Population#{population_index}"
+    end
+
+    def add_title_to_population(population_def, population)
+      title_def = get_title_def(population_def)
+      population['title'] = title_def ? title_def.value : "Population #{population_index}"
+    end
+
+    def add_observ_to_population(has_observation, population)
+      population['OBSERV'] = 'OBSERV' if has_observation
+    end
+
     # Extracts the measure observations, will return true if one exists
     def extract_observations
       has_observation = false

data/lib/hqmf-parser/cql/document_helpers/doc_population_helper.rb

@@ -120,5 +120,45 @@ module HQMF2CQL
       end
     end
 
+    # Returns the population descriptions and criteria found in this document
+    def extract_populations_and_criteria
+      has_observation = extract_observations
+      document_populations = get_document_populations
+      number_of_populations = document_populations.length
+      document_populations.each_with_index do |population_def, population_index|
+        population = {}
+        handle_base_populations(population_def, population)
+
+        id_def = get_id_def(population_def)
+        add_id_to_population(population_def, id_def, population, population_index)
+        add_title_to_population(population_def, population)
+        add_observ_to_population(has_observation, population)
+
+        add_supplemental_data_elements_to_population(population_def, population)
+
+        @populations << population
+        handle_stratifications(population_def, number_of_populations, population, id_def, population_index)
+      end
+
+      # Push in the stratification populations after the unstratified populations
+      @populations.concat(@stratifications)
+      [@populations, @population_criteria]
+    end
+
+    def add_supplemental_data_elements_to_population(population_def, population)
+      begin
+        supplemental_data_elements_def = population_def.xpath('cda:component/cql-ext:supplementalDataElement')
+      rescue Nokogiri::XML::XPath::SyntaxError
+        # Older fixtures without SDEs don't have the cql-ext namespace
+        return
+      end
+
+      supplemental_data_elements = []
+      supplemental_data_elements_def.each do |sde_def|
+        cql_definition_name = sde_def.at_xpath('cda:precondition/cda:criteriaReference/cda:id').attribute('extension').to_s.match(/"([^"]*)"/)[1]
+        supplemental_data_elements << cql_definition_name
+      end
+      population['supplemental_data_elements'] = supplemental_data_elements
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 4.0.4
+  version: 4.0.5
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-05-03 00:00:00.000000000 Z
+date: 2018-05-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -883,7 +883,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.12
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: A library for generating and consuming various healthcare related formats.