quality-measure-engine 3.0.1 → 3.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: deaefc5e9b3fdf34cc27f3e132bc62c1019f995b
+  metadata.gz: 35e476899eb214e4601ce6d61c96bbb2e9dbbd7a
+  data.tar.gz: f4d5ac3ac53c4e6fcbd39d4237799443274368a0
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quality-measure-engine (3.0.1)
+    quality-measure-engine (3.0.2)
       delayed_job_mongoid (~> 2.0.0)
       mongoid (~> 3.1.4)
       moped (~> 1.5.1)

data/lib/qme/map/map_reduce_executor.rb

@@ -19,13 +19,13 @@ module QME
 
         @measure_id = measure_id
         @sub_id =sub_id
-        
+
         @parameter_values = parameter_values
         q_filter = {hqmf_id: @measure_id,sub_id: @sub_id}
         if @parameter_values.keys.index("bundle_id")
           q_filter["bundle_id"] == @parameter_values['bundle_id']
           @bundle_id = @parameter_values['bundle_id']
-        end  
+        end
         @measure_def = QualityMeasure.where(q_filter).first
       end
 
@@ -34,8 +34,8 @@ module QME
 
         filters = @parameter_values["filters"]
 
-        
-        match = {'value.measure_id' => @measure_id, 
+
+        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'],
@@ -53,8 +53,8 @@ module QME
           end
           if (filters['providers'] && filters['providers'].size > 0)
             providers = filters['providers'].map { |pv| {'providers' => Moped::BSON::ObjectId(pv) } }
-            pipeline.concat [{'$project' => {'value' => 1, 'providers' => "$value.provider_performances.provider_id"}}, 
-                             {'$unwind' => '$providers'}, 
+            pipeline.concat [{'$project' => {'value' => 1, 'providers' => "$value.provider_performances.provider_id"}},
+                             {'$unwind' => '$providers'},
                              {'$match' => {'$or' => providers}},
                              {'$group' => {"_id" => "$_id", "value" => {"$first" => "$value"}}}]
           end
@@ -74,32 +74,32 @@ module QME
       end
 
 
-      #Calculate all of the supoplemental data elements 
+      #Calculate all of the supoplemental data elements
       def calculate_supplemental_data_elements
 
-        match = {'value.measure_id' => @measure_id, 
+        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' => {'$in' => [nil, false]}}    
-       
+                 'value.manual_exclusion' => {'$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" => "$_id", "val" => location}}} 
+            group1 = {"$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| 
+            (aggregate["result"] || []).each  do |entry|
               code  = entry["_id"].nil? ? "UNK" : entry["_id"]
               v[code] = entry["val"]
             end
@@ -119,8 +119,8 @@ module QME
         pipeline = build_query
 
         pipeline << {'$group' => {
-          "_id" => "$value.measure_id", # we don't really need this, but Mongo requires that we group 
-          QME::QualityReport::POPULATION => {"$sum" => "$value.#{QME::QualityReport::POPULATION}"}, 
+          "_id" => "$value.measure_id", # we don't really need this, but Mongo requires that we group
+          QME::QualityReport::POPULATION => {"$sum" => "$value.#{QME::QualityReport::POPULATION}"},
           QME::QualityReport::DENOMINATOR => {"$sum" => "$value.#{QME::QualityReport::DENOMINATOR}"},
           QME::QualityReport::NUMERATOR => {"$sum" => "$value.#{QME::QualityReport::NUMERATOR}"},
           QME::QualityReport::ANTINUMERATOR => {"$sum" => "$value.#{QME::QualityReport::ANTINUMERATOR}"},
@@ -135,7 +135,7 @@ module QME
           raise RuntimeError, "Aggregation Failed"
         elsif aggregate['result'].size !=1
            aggregate['result'] =[{"defaults" => true,
-                                 QME::QualityReport::POPULATION => 0, 
+                                 QME::QualityReport::POPULATION => 0,
                                  QME::QualityReport::DENOMINATOR => 0,
                                  QME::QualityReport::NUMERATOR =>0,
                                  QME::QualityReport::ANTINUMERATOR => 0,
@@ -151,7 +151,7 @@ module QME
 
 
         if @measure_def.continuous_variable
-          aggregated_value = calculate_cv_aggregation 
+          aggregated_value = calculate_cv_aggregation
           result[QME::QualityReport::OBSERVATION] = aggregated_value
         end
 
@@ -167,8 +167,8 @@ module QME
 
       end
 
-      # This method calculates the aggregated value for a CV measure.  It extracts all 
-      # the values for patients in the MSRPOPL and uses the aggregator to combine those 
+      # This method calculates the aggregated value for a CV measure.  It extracts all
+      # the values for patients in the MSRPOPL and uses the aggregator to combine those
       # values into an aggregated value.  The currently supported aggregators are:
       #   MEDIAN
       #   MEAN
@@ -193,17 +193,17 @@ module QME
       # This method runs the MapReduce job for the measure which will create documents
       # in the patient_cache collection. These documents will state the measure groups
       # that the record belongs to, such as numerator, etc.
-      def map_records_into_measure_groups
+      def map_records_into_measure_groups(prefilter={})
         measure = Builder.new(get_db(), @measure_def, @parameter_values)
         get_db().command(:mapreduce => 'records',
                          :map => measure.map_function,
                          :reduce => "function(key, values){return values;}",
-                         :out => {:reduce => 'patient_cache', :sharded => true}, 
+                         :out => {:reduce => 'patient_cache', :sharded => true},
                          :finalize => measure.finalize_function,
-                         :query => {:test_id => @parameter_values['test_id']})
+                         :query => prefilter)
         QME::ManualExclusion.apply_manual_exclusions(@measure_id,@sub_id)
       end
-      
+
       # This method runs the MapReduce job for the measure and a specific patient.
       # This will create a document in the patient_cache collection. This document
       # will state the measure groups that the record belongs to, such as numerator, etc.
@@ -212,13 +212,13 @@ module QME
         get_db().command(:mapreduce => 'records',
                          :map => measure.map_function,
                          :reduce => "function(key, values){return values;}",
-                         :out => {:reduce => 'patient_cache', :sharded => true}, 
+                         :out => {:reduce => 'patient_cache', :sharded => true},
                          :finalize => measure.finalize_function,
                          :query => {:medical_record_number => patient_id, :test_id => @parameter_values["test_id"]})
         QME::ManualExclusion.apply_manual_exclusions(@measure_id,@sub_id)
 
       end
-      
+
       # This method runs the MapReduce job for the measure and a specific patient.
       # This will *not* create a document in the patient_cache collection, instead the
       # result is returned directly.
@@ -227,14 +227,14 @@ module QME
         result = get_db().command(:mapreduce => 'records',
                                   :map => measure.map_function,
                                   :reduce => "function(key, values){return values;}",
-                                  :out => {:inline => true}, 
-                                  :raw => true, 
+                                  :out => {:inline => true},
+                                  :raw => true,
                                   :query => {:medical_record_number => patient_id, :test_id => @parameter_values["test_id"]})
 
         raise result['err'] if result['ok']!=1
         result['results'][0]['value']
       end
-      
+
 
     end
   end

data/lib/qme/map/measure_calculation_job.rb

@@ -4,7 +4,7 @@ module QME
     #
     #     Delayed::Job.enqueue QME::MapRedude::MeasureCalculationJob.new(quality_report, :effective_date => 1291352400, :test_id => xyzzy)
     #
-    # MeasureCalculationJob will check to see if a measure has been calculated before running the calculation. It will do this by 
+    # MeasureCalculationJob will check to see if a measure has been calculated before running the calculation. It will do this by
     # checking the status of the quality report that this calculation job was created with.
     #
     # When a measure needs calculation, the job will create a QME::MapReduce::Executor and interact with it to calculate
@@ -17,21 +17,21 @@ module QME
         @options = options
         @options.merge! @quality_report.attributes
       end
-      
+
       def perform
 
         if !@quality_report.calculated?
           map = QME::MapReduce::Executor.new(@quality_report.measure_id,@quality_report.sub_id, @options.merge('start_time' => Time.now.to_i))
           if !@quality_report.patients_cached?
             tick('Starting MapReduce')
-            map.map_records_into_measure_groups
+            map.map_records_into_measure_groups(@options['prefilter'])
             tick('MapReduce complete')
           end
-          
+
           tick('Calculating group totals')
           result = map.count_records_in_measure_groups
           @quality_report.result=result
-          # backwards compatibility with previous q cahce users.  Should be reomved going foward 
+          # backwards compatibility with previous q cahce users.  Should be reomved going foward
           # and provide a means to update existing results to the newer format
           result.attributes.each_pair do |k,v|
             unless k.to_s == "_id"
@@ -58,7 +58,7 @@ module QME
       end
 
       def enqueue(job)
-        @quality_report.status = {"state" => "queued", "log" => ["Queued at #{Time.now}"], "job_id" => job.id} 
+        @quality_report.status = {"state" => "queued", "log" => ["Queued at #{Time.now}"], "job_id" => job.id}
         @quality_report.save
       end
 
@@ -96,10 +96,10 @@ module QME
             :failed
           else
             :running
-          end            
+          end
         end
       end
     end
     end
   end
-end
+end

data/lib/qme/version.rb

@@ -1,3 +1,3 @@
 module QME
-  VERSION = "3.0.1"
+  VERSION = "3.0.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.0.2
 platform: ruby
 authors:
 - Marc Hadley
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-04 00:00:00.000000000 Z
+date: 2014-05-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: moped