quality-measure-engine 1.0.2 → 1.0.3

data/Gemfile

@@ -4,6 +4,7 @@ gemspec :development_group => :test
 
 gem 'bson_ext', :platforms => :mri
 gem 'rake'
+gem 'pry', :require => true
 
 group :test do
   gem 'cover_me', '>= 1.0.0.rc5', :platforms => :ruby_19

data/VERSION

@@ -1 +1 @@
-1.0.2
+1.0.3

data/js/map_reduce_utils.js

@@ -122,7 +122,9 @@ function() {
                  exclusions: false, antinumerator: false, patient_id: record._id,
                  medical_record_id: record.patient_id,
                  first: record.first, last: record.last, gender: record.gender,
-                 birthdate: record.birthdate, test_id: record.test_id};
+                 birthdate: record.birthdate, test_id: record.test_id,
+                 provider_performances: record.provider_performances,
+                 race: record.race, ethnicity: record.ethnicity};
     if (population()) {
       value.population = true;
       if (denominator()) {

data/lib/qme/ext/string.rb

@@ -0,0 +1,5 @@
+class String
+  def to_boolean
+    ['1', 'true', 't'].include?(self.downcase)
+  end
+end

data/lib/qme/importer/code_system_helper.rb

@@ -12,7 +12,8 @@ module QME
         '2.16.840.1.113883.6.104' =>  'ICD-9-CM',
         '2.16.840.1.113883.6.90' =>   'ICD-10-CM',
         '2.16.840.1.113883.6.14' =>   'HCPCS',
-        '2.16.840.1.113883.6.59' =>   'CVX'
+        '2.16.840.1.113883.6.59' =>   'CVX',
+        '2.16.840.1.113883.6.238' =>   'CDC-RE'
       }
       
       # Returns the name of a code system given an oid
@@ -22,23 +23,18 @@ module QME
         CODE_SYSTEMS[oid] || "Unknown"
       end
       
-      @@oid_map = nil
-      
       # Returns the oid for a code system given a codesystem name
       # @param [String] the name of the code system
       # @return [String] the oid of the code system
-      def self.oid_for_code_system(codesystem)
-        if(!@@oid_map)
-          @@oid_map = {}
-          CODE_SYSTEMS.each_pair do |oid, codesystem|
- #            STDERR.puts "Adding #{oid}, #{codesystem}"
-            @@oid_map[codesystem] = oid
-          end
-        end
-#        STDERR.puts "@@oid_map[#{codesystem}] = #{@@oid_map[codesystem]}"
-        return @@oid_map[codesystem]    
+      def self.oid_for_code_system(code_system)
+        CODE_SYSTEMS.invert[code_system]
       end
       
+      # Returns the whole map of OIDs to code systems
+      # @terurn [Hash] oids as keys, code system names as values
+      def self.code_systems
+        CODE_SYSTEMS
+      end
     end
   end
 end

data/lib/qme/importer/entry.rb

@@ -14,7 +14,10 @@ module QME
         entry = Entry.new
         if event['code']
           entry.add_code(event['code'], event['code_set'])
+        elsif event['codes']
+          entry.instance_eval { @codes = event['codes'] }
         end
+        
         entry.time = event['time']
         if event['value']
           entry.set_value(event['value'], event['unit'])

data/lib/qme/importer/patient_importer.rb

@@ -121,6 +121,8 @@ module QME
         patient_record['gender'] = patient_hash['gender']
         patient_record['patient_id'] = patient_hash['patient_id']
         patient_record['birthdate'] = patient_hash['birthdate']
+        patient_record['race'] = patient_hash['race']
+        patient_record['ethnicity'] = patient_hash['ethnicity']
         patient_record['addresses'] = patient_hash['addresses']
         event_hash = {}
         patient_hash['events'].each do |key, value|
@@ -209,6 +211,10 @@ module QME
         patient['birthdate'] = HL7Helper.timestamp_to_integer(birthdate_in_hl7ts)
         gender_node = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:patient/cda:administrativeGenderCode')
         patient['gender'] = gender_node['code']
+        race_node = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:patient/cda:raceCode')
+        patient['race'] = race_node['code'] if race_node
+        ethnicity_node = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:patient/cda:ethnicGroupCode')
+        patient['ethnicity'] = ethnicity_node['code'] if ethnicity_node
         id_node = doc.at_xpath('/cda:ClinicalDocument/cda:recordTarget/cda:patientRole/cda:id')
         patient['patient_id'] = id_node['extension']
       end

data/lib/qme/importer/property_matcher.rb

@@ -46,6 +46,8 @@ module QME
           if value
             if @property_description['items']['properties']['value']['type'] == 'number'
               value = value.to_f
+            elsif @property_description['items']['properties']['value']['type'] == 'boolean'
+              value = value.to_boolean
             end
             
             matching_values << {'date' => entry.as_point_in_time, 'value' => value}

data/lib/qme/importer/provider_importer.rb

@@ -0,0 +1,94 @@
+require "date"
+require "date/delta"
+
+module QME
+  module Importer
+    class ProviderImporter
+      include Singleton
+      
+      # Extract Healthcare Providers from C32
+      #
+      # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
+      #        will have the "cda" namespace registered to "urn:hl7-org:v3"
+      # @return [Array] an array of providers found in the document
+      def extract_providers(doc)
+        
+        performers = doc.xpath("//cda:documentationOf/cda:serviceEvent/cda:performer")
+        
+        providers = performers.map do |performer|
+          provider = {}
+          entity = performer.xpath(performer, "./cda:assignedEntity")
+          name = entity.xpath("./cda:assignedPerson/cda:name")
+          provider[:title]        = extract_data(name, "./cda:prefix")
+          provider[:given_name]   = extract_data(name, "./cda:given")
+          provider[:family_name]  = extract_data(name, "./cda:family")
+          provider[:phone]        = extract_data(entity, "./cda:telecom/@value") { |text| text.gsub("tel:", "") }
+          provider[:organization] = extract_data(entity, "./cda:representedOrganization/cda:name")
+          provider[:specialty]    = extract_data(entity, "./cda:code/@code")
+          time                    = performer.xpath(performer, "./cda:time")
+          provider[:start]        = extract_date(time, "./cda:low/@value")
+          provider[:end]          = extract_date(time, "./cda:high/@value")
+          # NIST sample C32s use different OID for NPI vs C83, support both
+          npi                     = extract_data(entity, "./cda:id[@root='2.16.840.1.113883.4.6' or @root='2.16.840.1.113883.3.72.5.2']/@extension")
+          if ProviderImporter::valid_npi?(npi)
+            provider[:npi]        = npi
+          else
+            puts "Warning: Invalid NPI (#{npi})"
+          end
+          provider
+        end
+      end
+      
+      private
+      
+      def extract_date(subject,query)
+        date = extract_data(subject,query)
+        date ? Date.parse(date).to_time.to_i : nil
+      end
+      
+      # Returns nil if result is an empty string, block allows text munging of result if there is one
+      def extract_data(subject, query)
+        result = subject.xpath(query).text
+        if result == ""
+          nil
+        elsif block_given?
+          yield(result)
+        else
+          result
+        end
+      end
+      
+      # validate the NPI, should be 10 or 15 digits total with the final digit being a
+      # checksum using the Luhn algorithm with additional special handling as described in
+      # https://www.cms.gov/NationalProvIdentStand/Downloads/NPIcheckdigit.pdf 
+      def self.valid_npi?(npi)
+        return false if npi.length != 10 and npi.length != 15
+        return false if npi.gsub(/\d/, '').length > 0 # npi must be all digits
+        return false if npi.length == 15 and (npi =~ /^80840/)==nil # 15 digit npi must start with 80840
+        
+        # checksum is always calculated as if 80840 prefix is present
+        if npi.length==10
+          npi = '80840'+npi
+        end
+        
+        return luhn_checksum(npi[0,14])==npi[14]
+      end
+      
+      def self.luhn_checksum(num)
+        double = {'0' => 0, '1' => 2, '2' => 4, '3' => 6, '4' => 8, '5' => 1, '6' => 3, '7' => 5, '8' => 7, '9' => 9}
+        sum = 0
+        num.reverse!
+        num.split("").each_with_index do |char, i|
+          if (i%2)==0
+            sum+=double[char]
+          else
+            sum+=char.to_i
+          end
+        end
+        sum = (9*sum)%10
+        
+        return sum.to_s
+      end
+    end
+  end
+end

data/lib/qme/map/map_reduce_executor.rb

@@ -28,15 +28,31 @@ module QME
         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']}
+        
+        query.merge!(filter_parameters)
+        
         result = {:measure_id => @measure_id, :sub_id => @sub_id, 
                   :effective_date => @parameter_values['effective_date'],
-                  :test_id => @parameter_values['test_id']}
-        %w(population denominator numerator antinumerator exclusions).each do |measure_group|
-          patient_cache.find(query.merge("value.#{measure_group}" => true)) do |cursor|
-            result[measure_group] = cursor.count
-          end
-        end
-        get_db.collection("query_cache").save(result)
+                  :test_id => @parameter_values['test_id'], :filters => @parameter_values['filters']}
+        
+        aggregate = patient_cache.group({cond: query, 
+                                           initial: {population: 0, denominator: 0, numerator: 0, antinumerator: 0,  exclusions: 0, considered: 0}, 
+                                           reduce: "function(record,sums) { for (var key in sums) { sums[key] += (record['value'][key] || key == 'considered') ? 1 : 0 } }"}).first
+        
+        aggregate ||= {population: 0, denominator: 0, numerator: 0, antinumerator: 0,  exclusions: 0}
+        aggregate.each {|key, value| aggregate[key] = value.to_i}
+        result.merge!(aggregate)
+        
+# need to time the old way agains the single query to verify that the single query is more performant        
+#        %w(population denominator numerator antinumerator exclusions).each do |measure_group|
+#          patient_cache.find(query.merge("value.#{measure_group}" => true)) do |cursor|
+#            result[measure_group] = cursor.count
+#          end
+#        end
+
+        result.merge!(execution_time: (Time.now.to_i - @parameter_values['start_time'].to_i)) if @parameter_values['start_time']
+
+        get_db.collection("query_cache").save(result, safe: true)
         result
       end
 
@@ -52,6 +68,47 @@ module QME
                            :finalize => measure.finalize_function,
                            :query => {:test_id => @parameter_values['test_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.
+      def map_record_into_measure_groups(patient_id)
+        qm = QualityMeasure.new(@measure_id, @sub_id)
+        measure = Builder.new(get_db, qm.definition, @parameter_values)
+        records = get_db.collection('records')
+        records.map_reduce(measure.map_function, "function(key, values){return values;}",
+                           :out => {:reduce => 'patient_cache'}, 
+                           :finalize => measure.finalize_function,
+                           :query => {:patient_id => patient_id, :test_id => @parameter_values['test_id']})
+      end
+
+      def filter_parameters
+        results = {}
+        conditions = []
+        if(filters = @parameter_values['filters'])
+          if (filters['providers'] && filters['providers'].size > 0)
+            providers = filters['providers'].map {|provider_id| BSON::ObjectId(provider_id) if provider_id }
+            conditions << provider_queries(providers, @parameter_values['effective_date'])
+          end
+          if (filters['races'] && filters['races'].size > 0)
+            conditions << {'value.race.code' => {'$in' => filters['races']}}
+          end
+          if (filters['ethnicities'] && filters['ethnicities'].size > 0)
+            conditions << {'value.ethnicity.code' => {'$in' => filters['ethnicities']}}
+          end
+          if (filters['genders'] && filters['genders'].size > 0)
+            conditions << {'value.gender' => {'$in' => filters['genders']}}
+          end
+        end
+        results.merge!({'$and'=>conditions}) if conditions.length > 0
+        results
+      end
+      def provider_queries(provider_ids, effective_date)
+       {'$or' => [provider_query(provider_ids, effective_date,effective_date), provider_query(provider_ids, nil,effective_date), provider_query(provider_ids, effective_date,nil)]}
+      end
+      def provider_query(provider_ids, start_before, end_after)
+        {'value.provider_performances' => {'$elemMatch' => {'provider_id' => {'$in' => provider_ids}, 'start_date'=> {'$lt'=>start_before}, 'end_date'=> {'$gt'=>end_after} } }}
+      end
     end
   end
 end

data/lib/qme/map/measure_calculation_job.rb

@@ -15,20 +15,34 @@ module QME
     # the report.
     class MeasureCalculationJob < Resque::JobWithStatus
       def perform
+        MeasureCalculationJob.calculate(options)
+      end
+      
+      def self.calculate(options)
         test_id = options['test_id'] ? BSON::ObjectId(options['test_id']) : nil
-        qr = QualityReport.new(options['measure_id'], options['sub_id'], 'effective_date' => options['effective_date'], 'test_id' => test_id)
+        qr = QualityReport.new(options['measure_id'], options['sub_id'], 'effective_date' => options['effective_date'], 'test_id' => test_id, 'filters' => options['filters'])
         if qr.calculated?
-          completed("#{options['measure_id']}#{options['sub_id']} has already been calculated")
+          completed("#{options['measure_id']}#{options['sub_id']} has already been calculated") if respond_to? :completed
         else
-          map = QME::MapReduce::Executor.new(options['measure_id'], options['sub_id'], 'effective_date' => options['effective_date'], 'test_id' => test_id)
-          tick('Starting MapReduce')
-          map.map_records_into_measure_groups
-          tick('MapReduce complete')
-          tick('Calculating group totals')
+          map = QME::MapReduce::Executor.new(options['measure_id'], options['sub_id'], 'effective_date' => options['effective_date'], 'test_id' => test_id, 'filters' => options['filters'], 'start_time' => Time.now.to_i)
+
+          if !qr.patients_cached?
+            tick('Starting MapReduce') if respond_to? :tick
+            map.map_records_into_measure_groups
+            tick('MapReduce complete') if respond_to? :tick
+          end
+          
+          tick('Calculating group totals') if respond_to? :tick
           result = map.count_records_in_measure_groups
-          completed("#{options['measure_id']}#{options['sub_id']}: p#{result['population']}, d#{result['denominator']}, n#{result['numerator']}, e#{result['exclusions']}")
+          completed("#{options['measure_id']}#{options['sub_id']}: p#{result['population']}, d#{result['denominator']}, n#{result['numerator']}, e#{result['exclusions']}") if respond_to? :completed
         end
+        
       end
+      
+#      This can be uncommented and changed to put the jobs on a separate queue.  
+#      def self.queue
+#        :statused
+#      end
     end
   end
 end

data/lib/qme/quality_report.rb

@@ -13,6 +13,37 @@ module QME
       get_db.collection("query_cache").drop
       get_db.collection("patient_cache").drop
     end
+    
+    # Removes the cached results for the patient with the supplied id and
+    # recalculates as necessary
+    def self.update_patient_results(id)
+      determine_connection_information
+      
+      # TODO: need to wait for any outstanding calculations to complete and then prevent
+      # any new ones from starting until we are done.
+
+      # drop any cached measure result calculations for the modified patient
+      get_db.collection("patient_cache").remove('value.medical_record_id' => id)
+      
+      # get a list of cached measure results for a single patient
+      sample_patient = get_db.collection('patient_cache').find_one()
+      if sample_patient
+        cached_results = get_db.collection('patient_cache').find({'value.patient_id' => sample_patient['value']['patient_id']})
+        
+        # for each cached result (a combination of measure_id, sub_id, effective_date and test_id)
+        cached_results.each do |measure|
+          # recalculate patient_cache value for modified patient
+          value = measure['value']
+          map = QME::MapReduce::Executor.new(value['measure_id'], value['sub_id'],
+            'effective_date' => value['effective_date'], 'test_id' => value['test_id'])
+          map.map_record_into_measure_groups(id)
+        end
+      end
+      
+      # remove the query totals so they will be recalculated using the new results for
+      # the modified patient
+      get_db.collection("query_cache").drop
+    end
 
     # Creates a new QualityReport
     # @param [String] measure_id value of the measure's id field
@@ -33,13 +64,25 @@ module QME
     def calculated?
       ! result().nil?
     end
+
+    # Determines whether the patient mapping for the quality report has been
+    # completed
+    def patients_cached?
+      ! patient_result().nil?
+    end
     
     # Kicks off a background job to calculate the measure
     # @return a unique id for the measure calculation job
-    def calculate
-      MapReduce::MeasureCalculationJob.create(:measure_id => @measure_id, :sub_id => @sub_id, 
-                                              :effective_date => @parameter_values['effective_date'], 
-                                              :test_id => @parameter_values['test_id'])
+    def calculate(asynchronous=true)
+      options = {'measure_id' => @measure_id, 'sub_id' => @sub_id, 
+                 'effective_date' => @parameter_values['effective_date'],
+                 'test_id' => @parameter_values['test_id'],
+                 'filters' => QME::QualityReport.normalize_filters(@parameter_values['filters'])}
+      if (asynchronous)
+        MapReduce::MeasureCalculationJob.create(options)
+      else
+        MapReduce::MeasureCalculationJob.calculate(options)
+      end
     end
     
     # Returns the status of a measure calculation job
@@ -57,7 +100,27 @@ module QME
       query = {:measure_id => @measure_id, :sub_id => @sub_id, 
                :effective_date => @parameter_values['effective_date'],
                :test_id => @parameter_values['test_id']}
+      if @parameter_values['filters']
+        query.merge!({filters: QME::QualityReport.normalize_filters(@parameter_values['filters'])})
+      else
+        query.merge!({filters: nil})
+      end
+        
       cache.find_one(query)
     end
+    
+    # make sure all filter id arrays are sorted
+    def self.normalize_filters(filters)
+      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
+      cache = get_db.collection("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']}
+      cache.find_one(query)
+    end
+    
   end
 end

data/lib/qme/randomizer/patient_randomizer.rb

@@ -46,6 +46,40 @@ module QME
         def gender
           @genders[rand(@genders.length)]
         end
+        
+        # Picks a race based on 2010 census estimates
+        # Pacific Islander 0.2%
+        # American Indian 0.9%
+        # Asian 4.8%
+        # Black persons 12.6%
+        # Hispanic 16.3%
+        # White 63.7%
+        def race_and_ethnicity
+          race_percent = rand(999)
+          case race_percent
+          when 0..1
+           # pacific islander
+           {race: '2076-8', ethnicity: '2186-5'}
+          when 2..10
+           # american indian
+           {race: '1002-5', ethnicity: '2186-5'}
+          when 11..58
+           # asian
+           {race: '2028-9', ethnicity: '2186-5'}
+          when 59..184
+           # black
+           {race: '2054-5', ethnicity: '2186-5'}
+          when 185..347
+           # hispanic
+           {race: '2106-3', ethnicity: '2135-2'}
+          when 348..984
+           # white (not hispanic)
+           {race: '2106-3', ethnicity: '2186-5'}
+          when 985..999
+           # other
+            {race: '2131-1', ethnicity: '2186-5'}
+          end
+        end
 
         # Pick a forename at random appropriate for the supplied gender
         # @param [String] gender the gender 'M' or 'F'

data/lib/quality-measure-engine.rb

@@ -2,6 +2,8 @@ require "bundler/setup"
 
 require 'resque/job_with_status'
 
+require_relative 'qme/ext/string'
+
 require_relative 'qme/database_access'
 require_relative 'qme/quality_measure'
 
@@ -24,6 +26,7 @@ require_relative 'qme/importer/hl7_helper'
 
 require_relative 'qme/importer/section_importer'
 require_relative 'qme/importer/generic_importer'
+require_relative 'qme/importer/provider_importer'
 
 require 'json'
 require 'mongo'

metadata

@@ -2,7 +2,7 @@
 name: quality-measure-engine
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 1.0.2
+  version: 1.0.3
 platform: ruby
 authors: 
 - Marc Hadley
@@ -12,7 +12,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-29 00:00:00 -04:00
+date: 2011-12-08 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -157,12 +157,14 @@ extra_rdoc_files: []
 
 files: 
 - lib/qme/database_access.rb
+- lib/qme/ext/string.rb
 - lib/qme/importer/code_system_helper.rb
 - lib/qme/importer/entry.rb
 - lib/qme/importer/generic_importer.rb
 - lib/qme/importer/hl7_helper.rb
 - lib/qme/importer/patient_importer.rb
 - lib/qme/importer/property_matcher.rb
+- lib/qme/importer/provider_importer.rb
 - lib/qme/importer/section_importer.rb
 - lib/qme/map/map_reduce_builder.rb
 - lib/qme/map/map_reduce_executor.rb
@@ -211,7 +213,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.5.0
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: A library for extracting quality measure information from HITSP C32's and ASTM CCR's