quality-measure-engine 2.3.0 → 2.4.0

data/lib/qme/map/map_reduce_builder.rb

@@ -11,9 +11,10 @@ module QME
       # Utility class used to supply a binding to Erb
       class Context < OpenStruct
         # Create a new context
-        # @param [Hash] vars a hash of parameter names (String) and values (Object). Each entry is added as an accessor of the new Context
+        # @param [Hash] vars a hash of parameter names (String) and values (Object). Each 
+        # entry is added as an accessor of the new Context
         def initialize(db, vars)
-          super(vars)
+          super(Context.add_defaults(vars))
           @db = db
         end
       
@@ -23,6 +24,17 @@ module QME
           binding
         end
         
+        # Add default parameter values if not specified
+        def self.add_defaults(vars)
+          if !vars.has_key?('enable_logging')
+            vars['enable_logging'] = false
+          end
+          if !vars.has_key?('enable_rationale')
+            vars['enable_rationale'] = false
+          end
+          vars
+        end
+        
         # Inserts any library code into the measure JS. JS library code is loaded from
         # three locations: the js directory of the quality-measure-engine project, the
         # js sub-directory of the current directory (e.g. measures/js), and the bundles

data/lib/qme/map/map_reduce_executor.rb

@@ -7,7 +7,10 @@ module QME
     class Executor
 
       include DatabaseAccess
-
+      SUPPLEMENTAL_DATA_ELEMENTS = {QME::QualityReport::RACE => "$value.race.code",
+                                    QME::QualityReport::ETHNICITY => "$value.ethnicity.code",
+                                    QME::QualityReport::SEX => "$value.gender",
+                                    QME::QualityReport::PAYER => "$value.payer"}
       # Create a new Executor for a specific measure, effective date and patient population.
       # @param [String] measure_id the measure identifier
       # @param [String] sub_id the measure sub-identifier or null if the measure is single numerator
@@ -64,6 +67,44 @@ module QME
         pipeline
       end
 
+
+      #Calculate all of the supoplemental data elements 
+      def calculate_supplemental_data_elements
+
+        match = {'value.measure_id' => @measure_id, 
+                 'value.sub_id'           => @sub_id,
+                 'value.effective_date'   => @parameter_values['effective_date'],
+                 'value.test_id'          => @parameter_values['test_id'],
+                 'value.manual_exclusion' => {'$in' => [nil, false]}}    
+       
+        keys = @measure_def["population_ids"].keys - [QME::QualityReport::OBSERVATION, "stratification"]
+        supplemental_data = Hash[*keys.map{|k| [k,{QME::QualityReport::RACE => {},
+                                                   QME::QualityReport::ETHNICITY => {},
+                                                   QME::QualityReport::SEX => {},
+                                                   QME::QualityReport::PAYER => {}}]}.flatten]
+                                                 
+        keys.each do |pop_id|
+          _match = match.clone
+          _match["value.#{pop_id}"] = {"$gt" => 0}
+          SUPPLEMENTAL_DATA_ELEMENTS.each_pair do |supp_element,location|
+            group1 = {"$group" => { "_id" => { "id" => "$_id", "val" => location}}} 
+            group2 = {"$group" => {"_id" => "$_id.val", "val" =>{"$sum" => 1} }}
+            pipeline = [{"$match" =>_match},group1,group2]
+            aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => pipeline)
+
+            v = {}
+            (aggregate["result"] || []).each  do |entry| 
+              code  = entry["_id"].nil? ? "UNK" : entry["_id"]
+              v[code] = entry["val"]
+            end
+            supplemental_data[pop_id] ||= {}
+            supplemental_data[pop_id][supp_element] = v
+           end
+        end
+        supplemental_data
+      end
+
+
       # Examines the patient_cache collection and generates a total of all groups
       # for the measure. The totals are placed in a document in the query_cache
       # collection.
@@ -104,6 +145,7 @@ module QME
         result.reject! {|k, v| k == '_id'} # get rid of the group id the Mongo forced us to use
         # result['exclusions'] += get_db['patient_cache'].find(base_query.merge({'value.manual_exclusion'=>true})).count
         result.merge!(execution_time: (Time.now.to_i - @parameter_values['start_time'].to_i)) if @parameter_values['start_time']
+        result[:supplemental_data] = self.calculate_supplemental_data_elements
         get_db()["query_cache"].insert(result)
         get_db().command({:getLastError => 1}) # make sure last insert finished before we continue
         result

data/lib/qme/quality_report.rb

@@ -18,6 +18,12 @@ module QME
     ANTINUMERATOR = 'antinumerator'
     CONSIDERED = 'considered'
 
+    RACE = 'RACE'
+    ETHNICITY = 'ETHNICITY'
+    SEX ='SEX'
+    POSTAL_CODE = 'POSTAL_CODE'
+    PAYER   = 'PAYER'
+
     # Gets rid of all calculated QualityReports by dropping the patient_cache
     # and query_cache collections
     def self.destroy_all
@@ -144,11 +150,14 @@ module QME
       filters.each {|key, value| value.sort_by! {|v| (v.is_a? Hash) ? "#{v}" : v} if value.is_a? Array} unless filters.nil?
     end
     
-    def patient_result
+    def patient_result(patient_id = nil)
       cache = get_db()["patient_cache"]
       query = {'value.measure_id' => @measure_id, 'value.sub_id' => @sub_id, 
                'value.effective_date' => @parameter_values['effective_date'],
                'value.test_id' => @parameter_values['test_id']}
+      if patient_id
+        query['value.medical_record_id'] = patient_id
+      end
       cache.find(query).first()
     end
     

data/lib/qme/version.rb

@@ -1,3 +1,3 @@
 module QME
-  VERSION = "2.3.0"
+  VERSION = "2.4.0"
 end

data/lib/quality-measure-engine.rb

@@ -8,13 +8,14 @@ require 'rubyXL'
 require "qme/version"
 require 'qme/database_access'
 require 'qme/quality_measure'
+require 'qme/quality_report'
 
 require 'qme/map/map_reduce_builder'
 require 'qme/map/map_reduce_executor'
 require 'qme/map/measure_calculation_job'
 require 'qme/map/cv_aggregator'
 
-require 'qme/quality_report'
+
 
 require 'qme/bundle/eh_measure_sheet'
 require 'qme/bundle/eh_patient_importer'

data/test/fixtures/records/jane_jones_numerator.json

@@ -2,6 +2,9 @@
     "_id": "507ec2077042f9362c00001b",
     "birthdate": 946715400,
     "medical_record_number": "12345",
+     "ethnicity" : { "code" : "2186-5",
+      "name" : "Not Hispanic or Latino",
+      "codeSystem" : "CDC Race" },
     "conditions": [
         {
             "codes": {

data/test/fixtures/records/jill_jones_denominator.json

@@ -2,6 +2,12 @@
     "_id": "507ec1407042f9362c000017",
     "birthdate": 946715400,
     "medical_record_number" : "1236",
+    "race" : { "code" : "1002-5",
+      "name" : "American Indian or Alaska Native",
+      "codeSystem" : "CDC Race" },
+     "ethnicity" : { "code" : "2186-5",
+      "name" : "Not Hispanic or Latino",
+      "codeSystem" : "CDC Race" },
     "conditions": [
         {
             "codes": {

data/test/unit/qme/map/map_reduce_builder_test.rb

@@ -35,5 +35,14 @@ class MapReduceBuilderTest < MiniTest::Unit::TestCase
     binding = context.get_binding
     assert_equal 10, eval("a",binding)
     assert_equal 20, eval("b",binding)
+    assert_equal false, eval("enable_logging",binding)
+    vars = {'enable_logging'=>true}
+    context = QME::MapReduce::Builder::Context.new(get_db(), vars)
+    binding = context.get_binding
+    assert_equal true, eval("enable_logging",binding)
+    vars = {'enable_logging'=>false}
+    context = QME::MapReduce::Builder::Context.new(get_db(), vars)
+    binding = context.get_binding
+    assert_equal false, eval("enable_logging",binding)
   end
 end

data/test/unit/qme/map/map_reduce_executor_test.rb

@@ -18,6 +18,7 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
                                             'effective_date' => Time.gm(2011, 1, 15).to_i)
                                             
     executor.map_records_into_measure_groups
+    
 
     assert_equal 4, get_db['patient_cache'].find().count
     assert_equal 3, get_db['patient_cache'].find("value.#{QME::QualityReport::POPULATION}" => 1).count
@@ -26,6 +27,44 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
     assert_equal 1, get_db['patient_cache'].find("value.#{QME::QualityReport::NUMERATOR}" => 1).count
   end
 
+
+ def test_calculate_supplemental_data_elements
+    executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
+                                            'effective_date' => Time.gm(2011, 1, 15).to_i)
+                                            
+    executor.map_records_into_measure_groups
+    executor.count_records_in_measure_groups
+    assert_equal 1, get_db['query_cache'].find().count
+    doc = get_db['query_cache'].find().first
+    suppl = doc["supplemental_data"]
+    assert !suppl.empty?, "should contain supplemental data entries"
+    ipp = {QME::QualityReport::RACE =>{"UNK"=>2, "1002-5"=>1},
+     QME::QualityReport::ETHNICITY => {"UNK"=>1, "2186-5"=>2},
+     QME::QualityReport::PAYER => {"UNK"=>3},
+     QME::QualityReport::SEX => {"F"=>2,"M"=>1}
+     }
+
+     denom = {QME::QualityReport::RACE =>{"UNK"=>1, "1002-5"=>1},
+     QME::QualityReport::ETHNICITY => { "2186-5"=>2},
+     QME::QualityReport::PAYER => {"UNK"=>2},
+     QME::QualityReport::SEX => {"F"=>2}
+     }
+
+     numer = {QME::QualityReport::RACE =>{"UNK"=>1},
+     QME::QualityReport::ETHNICITY => {"2186-5"=>1},
+     QME::QualityReport::PAYER => {"UNK"=>1},
+     QME::QualityReport::SEX => {"F"=>1}
+     }
+
+     
+
+    assert_equal ipp, suppl[QME::QualityReport::POPULATION]
+    assert_equal denom, suppl[QME::QualityReport::DENOMINATOR]
+    assert_equal numer, suppl[QME::QualityReport::NUMERATOR]
+
+   
+  end
+
   def test_count_records_in_measure_groups
     executor = QME::MapReduce::Executor.new("2E679CD2-3FEC-4A75-A75A-61403E5EFEE8", nil,
                                             'effective_date' => Time.gm(2011, 1, 15).to_i)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 2.3.0
+  version: 2.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-02-27 00:00:00.000000000 Z
+date: 2013-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: moped
@@ -232,7 +232,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: This library can run JavaScript based clinical quality measures on a repository
@@ -264,4 +264,3 @@ test_files:
 - test/unit/qme/map/measure_calculation_job_test.rb
 - test/unit/qme/quality_measure_test.rb
 - test/unit/qme/quality_report_test.rb
-has_rdoc: