quality-measure-engine 3.1.2 → 3.2.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 54f1d94d1b3c43ee810b625b40c6082208812a30
+  data.tar.gz: 3c5283e6e770e9b7e278c4fe99cdf62a5929cdf4
+SHA512:
+  metadata.gz: 58370f38f783d1ea5e014cf812611faf2cc0f7884a09664c4e2d4c27100e84931f870bb4d4af5dff87811ddfa5492177e5451ac3380aaedec806bdd5952f367b
+  data.tar.gz: 38a9fd3db563f81e183d7862aa8c80698c1fca4285f715dc93e20aee609f55887453dcadb289b77fe9320a6849f89a9d19259d7620579e357f2cd0c593f7b5cc

data/.travis.yml

@@ -1,8 +1,15 @@
 language: ruby
 rvm:
-  - 1.9.3
-  - 2.0.0
-  - 2.1.1
+  - 2.3.5
+sudo: false
+dist: precise
+addons:
+  apt:
+    sources:
+      - sourceline: 'deb http://repo.mongodb.org/apt/ubuntu precise/mongodb-org/3.4 multiverse'
+        key_url: 'http://keyserver.ubuntu.com/pks/lookup?op=get&fingerprint=on&search=0x9ECBEC467F0CEB10'
+    packages:
+      - mongodb-org-server=3.4.5
 script: bundle exec rake test
 services:
   - mongodb
@@ -12,7 +19,7 @@ notifications:
       - healthcare-ci@googlegroups.com
     on_failure: change
 
-branches: 
+branches:
   only:
     - master
-    - mongoid_refactor
+    - bump_mongoid

data/Gemfile

@@ -3,7 +3,6 @@ source 'https://rubygems.org'
 # Specify your gem's dependencies in quality-measure-engine.gemspec
 gemspec
 
-gem 'pry'
-gem 'pry-nav'
-gem 'pry-rescue'
-gem 'pry-stack_explorer'
+group :development, :test do
+  gem "byebug"
+end

data/Gemfile.lock

@@ -1,144 +1,124 @@
 PATH
   remote: .
   specs:
-    quality-measure-engine (3.1.2)
-      delayed_job_mongoid (~> 2.1.0)
-      mongoid (~> 4.0.0)
-      moped (~> 2.0.0)
-      rubyzip (~> 0.9.9)
+    quality-measure-engine (3.2.0)
+      delayed_job_mongoid (~> 2.2)
+      mongoid (~> 5.0)
+      rubyzip (~> 1.0)
+      zip-zip (~> 0.3)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    actionmailer (4.1.5)
-      actionpack (= 4.1.5)
-      actionview (= 4.1.5)
-      mail (~> 2.5.4)
-    actionpack (4.1.5)
-      actionview (= 4.1.5)
-      activesupport (= 4.1.5)
+    actionmailer (4.1.15)
+      actionpack (= 4.1.15)
+      actionview (= 4.1.15)
+      mail (~> 2.5, >= 2.5.4)
+    actionpack (4.1.15)
+      actionview (= 4.1.15)
+      activesupport (= 4.1.15)
       rack (~> 1.5.2)
       rack-test (~> 0.6.2)
-    actionview (4.1.5)
-      activesupport (= 4.1.5)
+    actionview (4.1.15)
+      activesupport (= 4.1.15)
       builder (~> 3.1)
       erubis (~> 2.7.0)
-    activemodel (4.1.5)
-      activesupport (= 4.1.5)
+    activemodel (4.1.15)
+      activesupport (= 4.1.15)
       builder (~> 3.1)
-    activerecord (4.1.5)
-      activemodel (= 4.1.5)
-      activesupport (= 4.1.5)
+    activerecord (4.1.15)
+      activemodel (= 4.1.15)
+      activesupport (= 4.1.15)
       arel (~> 5.0.0)
-    activesupport (4.1.5)
+    activesupport (4.1.15)
       i18n (~> 0.6, >= 0.6.9)
       json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
       thread_safe (~> 0.1)
       tzinfo (~> 1.1)
     arel (5.0.1.20140414130214)
-    binding_of_caller (0.7.2)
-      debug_inspector (>= 0.0.1)
-    bson (2.3.0)
+    bson (4.2.2)
     builder (3.2.2)
-    coderay (1.1.0)
-    connection_pool (2.0.0)
-    debug_inspector (0.0.2)
-    delayed_job (4.0.3)
-      activesupport (>= 3.0, < 4.2)
-    delayed_job_mongoid (2.1.0)
+    byebug (5.0.0)
+      columnize (= 0.9.0)
+    columnize (0.9.0)
+    concurrent-ruby (1.0.5)
+    delayed_job (4.1.3)
+      activesupport (>= 3.0, < 5.2)
+    delayed_job_mongoid (2.2.0)
       delayed_job (>= 3.0, < 5)
-      mongoid (>= 3.0, < 5)
+      mongoid (>= 3.0, < 6)
+      mongoid-compatibility
     docile (1.1.5)
     erubis (2.7.0)
-    hike (1.2.3)
-    i18n (0.6.11)
-    interception (0.5)
-    json (1.8.1)
-    mail (2.5.4)
-      mime-types (~> 1.16)
-      treetop (~> 1.4.8)
-    method_source (0.8.2)
-    mime-types (1.25.1)
-    minitest (5.4.0)
-    mongoid (4.0.0)
+    i18n (0.7.0)
+    json (1.8.3)
+    mail (2.6.4)
+      mime-types (>= 1.16, < 4)
+    mime-types (3.0)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2016.0221)
+    minitest (5.4.3)
+    mongo (2.4.3)
+      bson (>= 4.2.1, < 5.0.0)
+    mongoid (5.0.2)
       activemodel (~> 4.0)
-      moped (~> 2.0.0)
+      mongo (~> 2.1)
       origin (~> 2.1)
       tzinfo (>= 0.3.37)
-    moped (2.0.0)
-      bson (~> 2.2)
-      connection_pool (~> 2.0)
-      optionable (~> 0.2.0)
+    mongoid-compatibility (0.5.0)
+      activesupport
+      mongoid (>= 2.0)
     multi_json (1.10.1)
-    optionable (0.2.0)
-    origin (2.1.1)
-    polyglot (0.3.5)
-    pry (0.10.1)
-      coderay (~> 1.1.0)
-      method_source (~> 0.8.1)
-      slop (~> 3.4)
-    pry-nav (0.2.4)
-      pry (>= 0.9.10, < 0.11.0)
-    pry-rescue (1.4.1)
-      interception (>= 0.5)
-      pry
-    pry-stack_explorer (0.4.9.1)
-      binding_of_caller (>= 0.7)
-      pry (>= 0.9.11)
-    rack (1.5.2)
-    rack-test (0.6.2)
+    origin (2.3.1)
+    rack (1.5.5)
+    rack-test (0.6.3)
       rack (>= 1.0)
-    rails (4.1.5)
-      actionmailer (= 4.1.5)
-      actionpack (= 4.1.5)
-      actionview (= 4.1.5)
-      activemodel (= 4.1.5)
-      activerecord (= 4.1.5)
-      activesupport (= 4.1.5)
+    rails (4.1.15)
+      actionmailer (= 4.1.15)
+      actionpack (= 4.1.15)
+      actionview (= 4.1.15)
+      activemodel (= 4.1.15)
+      activerecord (= 4.1.15)
+      activesupport (= 4.1.15)
       bundler (>= 1.3.0, < 2.0)
-      railties (= 4.1.5)
+      railties (= 4.1.15)
       sprockets-rails (~> 2.0)
-    railties (4.1.5)
-      actionpack (= 4.1.5)
-      activesupport (= 4.1.5)
+    railties (4.1.15)
+      actionpack (= 4.1.15)
+      activesupport (= 4.1.15)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (10.3.2)
-    rubyzip (0.9.9)
+    rake (11.1.2)
+    rubyzip (1.2.1)
     simplecov (0.9.0)
       docile (~> 1.1.0)
       multi_json
       simplecov-html (~> 0.8.0)
     simplecov-html (0.8.0)
-    slop (3.6.0)
-    sprockets (2.12.1)
-      hike (~> 1.2)
-      multi_json (~> 1.0)
-      rack (~> 1.0)
-      tilt (~> 1.1, != 1.3.0)
-    sprockets-rails (2.1.3)
+    sprockets (3.6.0)
+      concurrent-ruby (~> 1.0)
+      rack (> 1, < 3)
+    sprockets-rails (2.3.3)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
-      sprockets (~> 2.8)
+      sprockets (>= 2.8, < 4.0)
     thor (0.19.1)
-    thread_safe (0.3.4)
-    tilt (1.4.1)
-    treetop (1.4.15)
-      polyglot
-      polyglot (>= 0.3.1)
+    thread_safe (0.3.5)
     tzinfo (1.2.2)
       thread_safe (~> 0.1)
+    zip-zip (0.3)
+      rubyzip (>= 1.0.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  minitest (~> 5.4.0)
-  pry
-  pry-nav
-  pry-rescue
-  pry-stack_explorer
+  byebug
+  minitest (~> 5.4)
   quality-measure-engine!
-  rails (~> 4.1.5)
-  simplecov (~> 0.9.0)
+  rails (~> 4.1)
+  simplecov (~> 0.9)
+
+BUNDLED WITH
+   1.15.4

data/LICENSE

@@ -0,0 +1,201 @@
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+                           Version 2.0, January 2004
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data/lib/qme/database_access.rb

@@ -4,7 +4,7 @@ module QME
     # JavaScript environment
     # @return [Moped::Session]
     def get_db
-      Mongoid.default_session
+      Mongoid.default_client
     end
   end
 end

data/lib/qme/map/map_reduce_executor.rb

@@ -51,10 +51,13 @@ module QME
           if (filters['genders'] && filters['genders'].size > 0)
             match['value.gender'] = {'$in' => filters['genders']}
           end
+          if (filters['patients'] && filters['patients'].size > 0)
+            match['value.patient_id'] = {'$in' => filters['patients']}
+          end
           if (filters['providers'] && filters['providers'].size > 0)
             providers = filters['providers'].map { |pv| {'providers' => BSON::ObjectId.from_string(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
@@ -87,19 +90,23 @@ module QME
         supplemental_data = Hash[*keys.map{|k| [k,{QME::QualityReport::RACE => {},
                                                    QME::QualityReport::ETHNICITY => {},
                                                    QME::QualityReport::SEX => {},
-                                                   QME::QualityReport::PAYER => {}}]}.flatten]
-
+                                                   QME::QualityReport::PAYER => {}}]}.flatten]                                      
         keys.each do |pop_id|
-          _match = match.clone
+          pline = build_query
+
+          _match = pline[0]["$match"]
           _match["value.#{pop_id}"] = {"$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)
+            pipeline = pline.clone
+            pipeline << group1
+            pipeline << group2
 
+            aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => pipeline)
+            aggregate_document = aggregate.documents[0]
             v = {}
-            (aggregate["result"] || []).each  do |entry|
+            (aggregate_document["result"] || []).each  do |entry|
               code  = entry["_id"].nil? ? "UNK" : entry["_id"]
               v[code] = entry["val"]
             end
@@ -127,14 +134,16 @@ module QME
           QME::QualityReport::EXCLUSIONS => {"$sum" => "$value.#{QME::QualityReport::EXCLUSIONS}"},
           QME::QualityReport::EXCEPTIONS => {"$sum" => "$value.#{QME::QualityReport::EXCEPTIONS}"},
           QME::QualityReport::MSRPOPL => {"$sum" => "$value.#{QME::QualityReport::MSRPOPL}"},
+          QME::QualityReport::MSRPOPLEX => {"$sum" => "$value.#{QME::QualityReport::MSRPOPLEX}"},
           QME::QualityReport::CONSIDERED => {"$sum" => 1}
         }}
 
         aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => pipeline)
-        if aggregate['ok'] != 1
+        aggregate_document = aggregate.documents[0]
+        if !aggregate.successful?
           raise RuntimeError, "Aggregation Failed"
-        elsif aggregate['result'].size !=1
-           aggregate['result'] =[{"defaults" => true,
+        elsif aggregate_document['result'].size !=1
+           aggregate_document['result'] =[{"defaults" => true,
                                  QME::QualityReport::POPULATION => 0,
                                  QME::QualityReport::DENOMINATOR => 0,
                                  QME::QualityReport::NUMERATOR =>0,
@@ -142,6 +151,7 @@ module QME
                                  QME::QualityReport::EXCLUSIONS => 0,
                                  QME::QualityReport::EXCEPTIONS => 0,
                                  QME::QualityReport::MSRPOPL => 0,
+                                 QME::QualityReport::MSRPOPLEX => 0,
                                  QME::QualityReport::CONSIDERED => 0}]
         end
 
@@ -155,7 +165,7 @@ module QME
           result[QME::QualityReport::OBSERVATION] = aggregated_value
         end
 
-        agg_result = aggregate['result'].first
+        agg_result = aggregate_document['result'].first
         agg_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
         agg_result.merge!(execution_time: (Time.now.to_i - @parameter_values['start_time'].to_i)) if @parameter_values['start_time']
@@ -179,11 +189,12 @@ module QME
         cv_pipeline << {'$group' => {'_id' => '$value.values', 'count' => {'$sum' => 1}}}
 
         aggregate = get_db.command(:aggregate => 'patient_cache', :pipeline => cv_pipeline)
+        aggregate_document = aggregate.documents[0]
 
-        raise RuntimeError, "Aggregation Failed" if aggregate['ok'] != 1
+        raise RuntimeError, "Aggregation Failed" if aggregate_document['ok'] != 1
 
         frequencies = {}
-        aggregate['result'].each do |freq_count_pair|
+        aggregate_document['result'].each do |freq_count_pair|
           frequencies[freq_count_pair['_id']] = freq_count_pair['count']
         end
         QME::MapReduce::CVAggregator.send(@measure_def.aggregator.parameterize, frequencies)
@@ -224,15 +235,17 @@ module QME
       # result is returned directly.
       def get_patient_result(patient_id)
         measure = Builder.new(get_db(), @measure_def, @parameter_values)
-        result = get_db().command(:mapreduce => 'records',
+        operation = get_db().command(:mapreduce => 'records',
                                   :map => measure.map_function,
                                   :reduce => "function(key, values){return values;}",
                                   :out => {:inline => true},
-                                  :raw => 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']
+
+        raise operation.documents[0]['err'] if !operation.successful?
+        return nil if operation.documents[0]['results'].empty?
+        operation.documents[0]['results'][0]['value']
       end
 
 

data/lib/qme/quality_report.rb

@@ -47,6 +47,7 @@ module QME
     EXCLUSIONS = 'DENEX'
     EXCEPTIONS = 'DENEXCEP'
     MSRPOPL = 'MSRPOPL'
+    MSRPOPLEX = 'MSRPOPLEX'
     OBSERVATION = 'OBSERV'
     ANTINUMERATOR = 'antinumerator'
     CONSIDERED = 'considered'
@@ -100,13 +101,13 @@ module QME
     end
 
     def self.queue_staged_rollups(measure_id,sub_id,effective_date)
-     query = Mongoid.default_session["rollup_buffer"].find({measure_id: measure_id, sub_id: sub_id, effective_date: effective_date})
+     query = Mongoid.default_client["rollup_buffer"].find({measure_id: measure_id, sub_id: sub_id, effective_date: effective_date})
      query.each do |options|
         if QME::QualityReport.where("_id" => options["quality_report_id"]).count == 1
            QME::QualityReport.enque_job(options,:rollup)
         end
      end
-     query.remove_all
+     query.delete_many
     end
 
     # Determines whether the quality report has been calculated for the given
@@ -149,7 +150,7 @@ module QME
           self.status["state"] = "stagged"
           self.save
           options.merge!( {measure_id: self.measure_id, sub_id: self.sub_id, effective_date: self.effective_date })
-          Mongoid.default_session["rollup_buffer"].insert(options)
+          Mongoid.default_client["rollup_buffer"].insert_one(options)
         else
           # queue the job for calculation
           QME::QualityReport.enque_job(options,:calculation)

data/lib/qme/version.rb

@@ -1,3 +1,3 @@
 module QME
-  VERSION = "3.1.2"
+  VERSION = "3.2.0"
 end

data/lib/quality-measure-engine.rb

@@ -1,6 +1,5 @@
 require "bundler/setup"
 
-require 'moped'
 require 'delayed_job_mongoid'
 require 'zip/zip'
 

data/quality-measure-engine.gemspec

@@ -6,23 +6,24 @@ require 'qme/version'
 Gem::Specification.new do |gem|
   gem.name          = "quality-measure-engine"
   gem.version       = QME::VERSION
-  gem.authors       = ["Marc Hadley", "Andy Gregorowicz", "Rob Dingwell", "Adam Goldstein", "Andre Quina"]
-  gem.email         = ["talk@projectpophealth.org"]
+  gem.authors       = ["The MITRE Corporation"]
+  gem.email         = ["tacoma-list@lists.mitre.org"]
   gem.description   = %q{A library for running clinical quality measures}
   gem.summary       = %q{This library can run JavaScript based clinical quality measures on a repository of patients stored in MongoDB}
-  gem.homepage      = "http://www.projectpophealth.org"
+  gem.homepage      = "https://github.com/projectcypress/quality-measure-engine"
+  gem.license = 'Apache-2.0'
 
   gem.files         = `git ls-files`.split($/)
   gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
   gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
   gem.require_paths = ["lib"]
 
-  gem.add_dependency 'moped', '~> 2.0.0'
-  gem.add_dependency 'mongoid', '~> 4.0.0'
-  gem.add_dependency 'rubyzip', '~> 0.9.9'
-  gem.add_dependency 'delayed_job_mongoid', '~> 2.1.0'
+  gem.add_dependency 'mongoid', '~> 5.0'
+  gem.add_dependency 'rubyzip', '~> 1.0'
+  gem.add_dependency 'zip-zip', "~> 0.3"
+  gem.add_dependency 'delayed_job_mongoid', '~> 2.2'
 
-  gem.add_development_dependency "minitest", "~> 5.4.0"
-  gem.add_development_dependency "simplecov", "~> 0.9.0"
-  gem.add_development_dependency "rails", "~> 4.1.5"
+  gem.add_development_dependency "minitest", "~> 5.4"
+  gem.add_development_dependency "simplecov", "~> 0.9"
+  gem.add_development_dependency "rails", "~> 4.1"
 end

data/test/mongoid.yml

@@ -1,5 +1,5 @@
 test:
-  sessions:
+  clients:
     default:
       database: test
       hosts:

data/test/test_helper.rb

@@ -1,39 +1,71 @@
 require 'simplecov_setup'
 require 'minitest/autorun'
 require 'quality-measure-engine'
-require 'pry-nav'
 
+Mongo::Logger.logger.level = Logger::WARN
 Mongoid.load!(File.join(File.dirname(__FILE__),"mongoid.yml"), :test)
 
 class MiniTest::Unit::TestCase
 
   def load_system_js
-    Mongoid.default_session['system.js'].find.remove_all
+    Mongoid.default_client['system.js'].delete_many({})
     Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', "library_functions", '*.js')).each do |json_fixture_file|
       name = File.basename(json_fixture_file,".*")
       fn = "function () {\n #{File.read(json_fixture_file)} \n }"
-      Mongoid.default_session['system.js'].find('_id' => name).upsert(
+      Mongoid.default_client['system.js'].update_one({
+          "_id" => name},
         {
           "_id" => name,
           "value" => BSON::Code.new(fn)
-        }
+        },{upsert: true}
       )
     end
 
   end
 
-  # Add more helper methods to be used by all tests here...
 
-  def collection_fixtures(db, collection, *id_attributes)
-    db[collection].drop
-    Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', collection, '*.json')).each do |json_fixture_file|
-      #puts "Loading #{json_fixture_file}"
-      fixture_json = JSON.parse(File.read(json_fixture_file))
-      id_attributes.each do |attr|
-        fixture_json[attr] = BSON::ObjectId.from_string(fixture_json[attr])
+  def value_or_bson(v)
+    if v.is_a? Hash
+      if v['$oid']
+        BSON::ObjectId.from_string(v['$oid'])
+      else
+        map_bson_ids(v)
       end
+    else
+      v
+    end
+  end
+
+  def map_array(arr)
+    ret = []
+    arr.each do |v|
+      ret << value_or_bson(v)
+    end
+    ret
+  end
 
-      db[collection].insert(fixture_json)
+  def map_bson_ids(json)
+    json.each_pair do |k, v|
+      if v.is_a? Hash
+        json[k] = value_or_bson(v)
+      elsif v.is_a? Array
+        json[k] = map_array(v)
+      elsif k == 'create_at' || k == 'updated_at'
+        json[k] = Time.at.local(v).in_time_zone
+      end
+    end
+    json
+  end
+
+  def collection_fixtures(*collections)
+    collections.each do |collection|
+      get_db()[collection].drop
+      Dir.glob(File.join(File.dirname(__FILE__), 'fixtures', collection, '*.json')).each do |json_fixture_file|
+        fixture_json = JSON.parse(File.read(json_fixture_file), max_nesting: 250)
+        fixture_json['_id'] = BSON::ObjectId.from_string(fixture_json['_id']) if fixture_json['_id']
+        map_bson_ids(fixture_json)
+        Mongoid.default_client[collection].insert_one(fixture_json)
+      end
     end
   end
-end
+end

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

@@ -4,7 +4,7 @@ class MapReduceBuilderTest < MiniTest::Unit::TestCase
   include QME::DatabaseAccess
 
   def setup
-    collection_fixtures(get_db(), 'measures')
+    collection_fixtures('measures')
     @measure_json = QME::QualityMeasure.where({"nqf_id" => '0043'}).first
      load_system_js
   end

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

@@ -7,9 +7,9 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
 
     get_db['query_cache'].drop()
     get_db['patient_cache'].drop()
-    collection_fixtures(get_db(), 'measures')
-    collection_fixtures(get_db(), 'records', '_id')
-    collection_fixtures(get_db(), 'bundles')
+    collection_fixtures('measures')
+    collection_fixtures('records')
+    collection_fixtures('bundles')
     options = {'measure_id' => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8",
                'effective_date' => Time.gm(2011, 1, 15).to_i}
     @quality_report =QME::QualityReport.find_or_create_by(options)
@@ -117,7 +117,7 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
   def test_get_patient_result_with_bundle_id
     measure_id = "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8"
     bundle_id = get_db()['bundles'].find.first
-    get_db()['measures'].find('id' => measure_id).update(:$set => {'bundle_id' => bundle_id})
+    get_db()['measures'].update_many({'id' => measure_id}, {:$set => {'bundle_id' => bundle_id}})
     executor = QME::MapReduce::Executor.new(measure_id, nil,
                                             'effective_date' => Time.gm(2011, 1, 15).to_i, 'bundle_id' => bundle_id)
     result = executor.get_patient_result("12345")
@@ -125,4 +125,4 @@ class MapReduceExecutorTest < MiniTest::Unit::TestCase
     assert result[QME::QualityReport::NUMERATOR]
   end
 
-end
+end

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

@@ -6,9 +6,9 @@ class MapCalculationJobTest < MiniTest::Unit::TestCase
   def setup
     get_db['query_cache'].drop()
     get_db['patient_cache'].drop()
-    collection_fixtures(get_db(), 'measures')
-    collection_fixtures(get_db(), 'records', '_id')
-    collection_fixtures(get_db(), 'bundles')
+    collection_fixtures('measures')
+    collection_fixtures('records')
+    collection_fixtures('bundles')
     load_system_js
 
     Delayed::Worker.delay_jobs = false
@@ -21,4 +21,4 @@ class MapCalculationJobTest < MiniTest::Unit::TestCase
     job = Delayed::Job.enqueue(QME::MapReduce::MeasureCalculationJob.new({'quality_report_id' => qr.id,"oid_dictionary"=>{}}))
     assert job
   end
-end
+end

data/test/unit/qme/quality_measure_test.rb

@@ -4,8 +4,8 @@ class QualityMeasureTest < MiniTest::Unit::TestCase
   include QME::DatabaseAccess
   def setup
 
-    collection_fixtures(get_db(), 'measures')
-    collection_fixtures(get_db(), 'bundles')
+    collection_fixtures('measures')
+    collection_fixtures('bundles')
     load_system_js
   end
 
@@ -14,4 +14,4 @@ class QualityMeasureTest < MiniTest::Unit::TestCase
     assert_equal 5, all_measures.size
     assert all_measures.where({"hqmf_id" => "2E679CD2-3FEC-4A75-A75A-61403E5EFEE8"}).first
   end
-end
+end

data/test/unit/qme/quality_report_test.rb

@@ -5,50 +5,51 @@ class QualityReportTest < MiniTest::Unit::TestCase
 
   def setup
     load_system_js
-    collection_fixtures(get_db(), 'bundles')
-    collection_fixtures(get_db(), 'records')
-    collection_fixtures(get_db(), 'measures')
+    collection_fixtures('bundles')
+    collection_fixtures('records')
+    collection_fixtures('measures')
+
     get_db()['query_cache'].drop()
     get_db()['patient_cache'].drop()
-    get_db()['query_cache'].insert(
-      "measure_id" => "test2",
-      "sub_id" =>  "b",
-      "status" =>{"state" => "completed"},
-      "initialPopulation" => 4,
-      "result" => {
-      QME::QualityReport::NUMERATOR => 1,
-      QME::QualityReport::DENOMINATOR => 2,
-      QME::QualityReport::EXCLUSIONS => 1},
-      "effective_date" => Time.gm(2010, 9, 19).to_i
+    get_db()['query_cache'].insert_one({
+          "measure_id" => "test2",
+          "sub_id" =>  "b",
+          "status" =>{"state" => "completed"},
+          "initialPopulation" => 4,
+          "result" => {
+          QME::QualityReport::NUMERATOR => 1,
+          QME::QualityReport::DENOMINATOR => 2,
+          QME::QualityReport::EXCLUSIONS => 1},
+          "effective_date" => Time.gm(2010, 9, 19).to_i}
     )
-    get_db()['patient_cache'].insert(
-      "value" => {
-        QME::QualityReport::POPULATION => 0,
-        QME::QualityReport::DENOMINATOR => 0,
-        QME::QualityReport::NUMERATOR => 0,
-        QME::QualityReport::EXCLUSIONS => 0,
-        QME::QualityReport::ANTINUMERATOR => 0,
-        "medical_record_id" => "0616911582",
-        "first" => "Mary",
-        "last" => "Edwards",
-        "gender" => "F",
-        "birthdate" => Time.gm(1940, 9, 19).to_i,
-        "test_id" => nil,
-        "provider_performances" => nil,
-        "race" => {
-          "code" => "2106-3",
-          "code_set" => "CDC-RE"
-        },
-        "ethnicity" => {
-          "code" => "2135-2",
-          "code_set" => "CDC-RE"
-        },
-        "measure_id" => "test2",
-        "sub_id" =>  "b",
-        "effective_date" => Time.gm(2010, 9, 19).to_i
-      }
+    get_db()['patient_cache'].insert_one({
+          "value" => {
+            QME::QualityReport::POPULATION => 0,
+            QME::QualityReport::DENOMINATOR => 0,
+            QME::QualityReport::NUMERATOR => 0,
+            QME::QualityReport::EXCLUSIONS => 0,
+            QME::QualityReport::ANTINUMERATOR => 0,
+            "medical_record_id" => "0616911582",
+            "first" => "Mary",
+            "last" => "Edwards",
+            "gender" => "F",
+            "birthdate" => Time.gm(1940, 9, 19).to_i,
+            "test_id" => nil,
+            "provider_performances" => nil,
+            "race" => {
+              "code" => "2106-3",
+              "code_set" => "CDC-RE"
+            },
+            "ethnicity" => {
+              "code" => "2135-2",
+              "code_set" => "CDC-RE"
+            },
+            "measure_id" => "test2",
+            "sub_id" =>  "b",
+            "effective_date" => Time.gm(2010, 9, 19).to_i
+          }}
     )
-    collection_fixtures(get_db(), 'delayed_backend_mongoid_jobs', '_id')
+    collection_fixtures('delayed_backend_mongoid_jobs')
   end
 
   def test_calculated
@@ -86,6 +87,7 @@ class QualityReportTest < MiniTest::Unit::TestCase
   def test_status
     status = QME::MapReduce::MeasureCalculationJob.status('not really a job id')
     assert_equal :complete, status
+
     status = QME::MapReduce::MeasureCalculationJob.status("508aeff07042f9f88900000d")
     assert_equal :queued, status
   end
@@ -95,7 +97,7 @@ class QualityReportTest < MiniTest::Unit::TestCase
     assert Delayed::Worker.delay_jobs
     Delayed::Job.destroy_all
     QME::QualityReport.destroy_all
-    Mongoid.default_session["rollup_buffer"].find({}).remove_all
+    Mongoid.default_client["rollup_buffer"].delete_many({})
     qr = QME::QualityReport.find_or_create('2E679CD2-3FEC-4A75-A75A-61403E5EFEE8', nil, "effective_date" => Time.gm(2011, 9, 19).to_i)
     qr2 = QME::QualityReport.find_or_create('2E679CD2-3FEC-4A75-A75A-61403E5EFEE8', nil, {"effective_date" => Time.gm(2011, 9, 19).to_i,:filters=>{"providers"=>["a"]}})
     assert !qr.calculated?
@@ -112,9 +114,9 @@ class QualityReportTest < MiniTest::Unit::TestCase
     assert qr.calculation_queued_or_running?
     assert qr2.calculation_queued_or_running?
 
-    assert_equal 0, Mongoid.default_session["rollup_buffer"].find({}).count
+    assert_equal 0, Mongoid.default_client["rollup_buffer"].count({})
     qr2.calculate({"oid_dictionary"=>{}},true)
-    assert_equal 1, Mongoid.default_session["rollup_buffer"].find({}).count
+    assert_equal 1, Mongoid.default_client["rollup_buffer"].count({})
 
 
     assert_equal 1, Delayed::Job.count()
@@ -127,6 +129,6 @@ class QualityReportTest < MiniTest::Unit::TestCase
     job = Delayed::Job.where({}).first
     assert_equal "rollup", job.queue
 
-    assert_equal 0, Mongoid.default_session["rollup_buffer"].find({}).count
+    assert_equal 0, Mongoid.default_client["rollup_buffer"].count({})
   end
 end

metadata

@@ -1,135 +1,116 @@
 --- !ruby/object:Gem::Specification
 name: quality-measure-engine
 version: !ruby/object:Gem::Version
-  version: 3.1.2
-  prerelease: 
+  version: 3.2.0
 platform: ruby
 authors:
-- Marc Hadley
-- Andy Gregorowicz
-- Rob Dingwell
-- Adam Goldstein
-- Andre Quina
+- The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-13 00:00:00.000000000 Z
+date: 2017-11-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: moped
+  name: mongoid
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: '5.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: '5.0'
 - !ruby/object:Gem::Dependency
-  name: mongoid
+  name: rubyzip
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: '1.0'
 - !ruby/object:Gem::Dependency
-  name: rubyzip
+  name: zip-zip
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: '0.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: '0.3'
 - !ruby/object:Gem::Dependency
   name: delayed_job_mongoid
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '2.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: '2.2'
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.4.0
+        version: '5.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.4.0
+        version: '5.4'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: '0.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: '0.9'
 - !ruby/object:Gem::Dependency
   name: rails
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.1.5
+        version: '4.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.1.5
+        version: '4.1'
 description: A library for running clinical quality measures
 email:
-- talk@projectpophealth.org
+- tacoma-list@lists.mitre.org
 executables: []
 extensions: []
 extra_rdoc_files: []
@@ -138,7 +119,7 @@ files:
 - ".travis.yml"
 - Gemfile
 - Gemfile.lock
-- LICENSE.txt
+- LICENSE
 - README.md
 - Rakefile
 - lib/qme/database_access.rb
@@ -180,29 +161,29 @@ files:
 - test/unit/qme/map/measure_calculation_job_test.rb
 - test/unit/qme/quality_measure_test.rb
 - test/unit/qme/quality_report_test.rb
-homepage: http://www.projectpophealth.org
-licenses: []
+homepage: https://github.com/projectcypress/quality-measure-engine
+licenses:
+- Apache-2.0
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.6.12
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: This library can run JavaScript based clinical quality measures on a repository
   of patients stored in MongoDB
 test_files:

data/LICENSE.txt

@@ -1,13 +0,0 @@
-Copyright (c) 2012 The MITRE Corporation
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-   http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.